Shay Tzur

MYH9 has been proposed as a major genetic risk locus for a spectrum of non-diabetic end stage kidney disease (ESKD). We use recently released sequences from the 1000 Genomes Project to identify two western African specific missense mutations (S342G and I384M) in the neighbouring APOL1 gene, and demonstrate that these are more strongly associated with ESKD than previously reported MYH9 variants. We also show that the distribution of these risk variants in African populations is consistent with the pattern of African ancestry ESKD risk previously attributed to the MYH9 gene. Additional associations were also found among other members of the APOL gene family, and we propose that ESKD risk is caused by western African variants in members of the APOL gene family, which evolved to confer protection against pathogens, such as Trypanosoma.

The quest to explain demographic history during the early part of human evolution has been limited because of the scarce paleoanthropological record from the Middle Stone Age. To shed light on the structure of the mitochondrial DNA (mtDNA) phylogeny at the dawn of Homo sapiens, we constructed a matrilineal tree composed of 624 complete mtDNA genomes from sub-Saharan Hg L lineages. We paid particular attention to the Khoi and San (Khoisan) people of South Africa because they are considered to be a unique relic of hunter-gatherer lifestyle and to carry paternal and maternal lineages belonging to the deepest clades known among modern humans. Both the tree phylogeny and coalescence calculations suggest that Khoisan matrilineal ancestry diverged from the rest of the human mtDNA pool 90,000–150,000 years before present (ybp) and that at least five additional, currently extant maternal lineages existed during this period in parallel. Furthermore, we estimate that a minimum of 40 other evolutionarily successful lineages flourished in sub-Saharan Africa during the period of modern human dispersal out of Africa approximately 60,000–70,000 ybp. Only much later, at the beginning of the Late Stone Age, about 40,000 ybp, did introgression of additional lineages occur into the Khoisan mtDNA pool. This process was further accelerated during the recent Bantu expansions. Our results suggest that the early settlement of humans in Africa was already matrilineally structured and involved small, separately evolving isolated populations. The quest to explain demographic history during the early part of human evolution has been limited because of the scarce paleoanthropological record from the Middle Stone Age. To shed light on the structure of the mitochondrial DNA (mtDNA) phylogeny at the dawn of Homo sapiens, we constructed a matrilineal tree composed of 624 complete mtDNA genomes from sub-Saharan Hg L lineages. We paid particular attention to the Khoi and San (Khoisan) people of South Africa because they are considered to be a unique relic of hunter-gatherer lifestyle and to carry paternal and maternal lineages belonging to the deepest clades known among modern humans. Both the tree phylogeny and coalescence calculations suggest that Khoisan matrilineal ancestry diverged from the rest of the human mtDNA pool 90,000–150,000 years before present (ybp) and that at least five additional, currently extant maternal lineages existed during this period in parallel. Furthermore, we estimate that a minimum of 40 other evolutionarily successful lineages flourished in sub-Saharan Africa during the period of modern human dispersal out of Africa approximately 60,000–70,000 ybp. Only much later, at the beginning of the Late Stone Age, about 40,000 ybp, did introgression of additional lineages occur into the Khoisan mtDNA pool. This process was further accelerated during the recent Bantu expansions. Our results suggest that the early settlement of humans in Africa was already matrilineally structured and involved small, separately evolving isolated populations. IntroductionCurrent genetic data support the hypothesis of a predominantly single origin for anatomically modern humans.1Cann R.L. Stoneking M. Wilson A.C. Mitochondrial DNA and human evolution.Nature. 1987; 325: 31-36Crossref PubMed Scopus (1871) Google Scholar, 2Underhill P.A. Kivisild T. Use of Y chromosome and mitochondrial DNA population structure in tracing human migrations.Annu. Rev. Genet. 2007; 41: 539-564Crossref PubMed Scopus (302) Google Scholar The phylogeny of the maternally inherited mitochondrial DNA (mtDNA) has played a pivotal role in this model by anchoring our most recent maternal common ancestor to sub-Saharan Africa and suggesting a single dispersal wave out of that continent which populated the rest of the world much later.3Mellars P. Going east: New genetic and archaeological perspectives on the modern human colonization of Eurasia.Science. 2006; 313: 796-800Crossref PubMed Scopus (362) Google Scholar, 4Macaulay V. Hill C. Achilli A. Rengo C. Clarke D. Meehan W. Blackburn J. Semino O. Scozzari R. Cruciani F. et al.Single, rapid coastal settlement of Asia revealed by analysis of complete mitochondrial genomes.Science. 2005; 308: 1034-1036Crossref PubMed Scopus (561) Google Scholar, 5Torroni A. Achilli A. Macaulay V. Richards M. Bandelt H.J. Harvesting the fruit of the human mtDNA tree.Trends Genet. 2006; 22: 339-345Abstract Full Text Full Text PDF PubMed Scopus (351) Google Scholar However, despite its importance as the cradle of humanity and the main location of anatomically modern humans for most of their existence, the initial Homo sapiens population dynamics and dispersal routes remain poorly understood.6Mellars P. Why did modern human populations disperse from Africa ca. 60,000 years ago? A new model.Proc. Natl. Acad. Sci. USA. 2006; 103: 9381-9386Crossref PubMed Scopus (435) Google Scholar, 7Hawks J. Wang E.T. Cochran G.M. Harpending H.C. Moyzis R.K. Recent acceleration of human adaptive evolution.Proc. Natl. Acad. Sci. USA. 2007; 104: 20753-20758Crossref PubMed Scopus (332) Google Scholar The potential to use present-day genetic patterns to detect the existence, or lack thereof, of matrilineal genetic structure among early Homo sapiens populations in sub-Saharan Africa is therefore of particular interest.The human mtDNA phylogeny can be collapsed into two daughter branches, L0 and L1′2′3′4′5′6 (L1′5),5Torroni A. Achilli A. Macaulay V. Richards M. Bandelt H.J. Harvesting the fruit of the human mtDNA tree.Trends Genet. 2006; 22: 339-345Abstract Full Text Full Text PDF PubMed Scopus (351) Google Scholar located on opposite sides of its root (Figure 1).8Kivisild T. Shen P. Wall D.P. Do B. Sung R. Davis K. Passarino G. Underhill P.A. Scharfe C. Torroni A. et al.The role of selection in the evolution of human mitochondrial genomes.Genetics. 2006; 172: 373-387Crossref PubMed Scopus (359) Google Scholar, 9Mishmar D. Ruiz-Pesini E. Golik P. Macaulay V. Clark A.G. Hosseini S. Brandon M. Easley K. Chen E. Brown M.D. et al.Natural selection shaped regional mtDNA variation in humans.Proc. Natl. Acad. Sci. USA. 2003; 100: 171-176Crossref PubMed Scopus (774) Google Scholar The L1′5 branch is far more widespread and has given rise to almost every mtDNA lineage found today, with two clades on this branch, (L3)M and (L3)N, forming the bulk of worldwide non-African genetic diversity and marking the out-of-Africa dispersal 50,000–65,000 years before present (ybp)4Macaulay V. Hill C. Achilli A. Rengo C. Clarke D. Meehan W. Blackburn J. Semino O. Scozzari R. Cruciani F. et al.Single, rapid coastal settlement of Asia revealed by analysis of complete mitochondrial genomes.Science. 2005; 308: 1034-1036Crossref PubMed Scopus (561) Google Scholar (Figure 1). Current models, predating the recognition of L0 as sister to L1′5,9Mishmar D. Ruiz-Pesini E. Golik P. Macaulay V. Clark A.G. Hosseini S. Brandon M. Easley K. Chen E. Brown M.D. et al.Natural selection shaped regional mtDNA variation in humans.Proc. Natl. Acad. Sci. USA. 2003; 100: 171-176Crossref PubMed Scopus (774) Google Scholar, 10Maca-Meyer N. Gonzalez A.M. Larruga J.M. Flores C. Cabrera V.M. Major genomic mitochondrial lineages delineate early human expansions.BMC Genet. 2001; 2: 13Crossref PubMed Scopus (263) Google Scholar suggest that the contemporary sub-Saharan mtDNA gene pool is the result of an early expansion of modern humans from their homeland, often suggested to be East Africa, to most of the African continent by exclusively L1 Hg clades, before being overwhelmed by a later expansion wave of L2 and L3 clades dated to 60,000–80,000 ybp.11Forster P. Ice Ages and the mitochondrial DNA chronology of human dispersals: A review.Philos. Trans. R. Soc. Lond. B Biol. Sci. 2004; 359: 255-264Crossref PubMed Scopus (221) Google Scholar, 12Watson E. Forster P. Richards M. Bandelt H.J. Mitochondrial footprints of human expansions in Africa.Am. J. Hum. Genet. 1997; 61: 691-704Abstract Full Text PDF PubMed Scopus (297) Google Scholar A more recent geographically restricted enrichment of the African maternal gene pool was shown to have occurred during the early Upper Paleolithic, when populations carrying mtDNA clades M1 and U6 arrived to north and northeast Africa from Eurasia, hardly penetrating the sub-Saharan portion of the continent, except Ethiopia.13Kivisild T. Reidla M. Metspalu E. Rosa A. Brehm A. Pennarun E. Parik J. Geberhiwot T. Usanga E. Villems R. Ethiopian mitochondrial DNA heritage: Tracking gene flow across and around the gate of tears.Am. J. Hum. Genet. 2004; 75: 752-770Abstract Full Text Full Text PDF PubMed Scopus (200) Google Scholar, 14Olivieri A. Achilli A. Pala M. Battaglia V. Fornarino S. Al-Zahery N. Scozzari R. Cruciani F. Behar D.M. Dugoujon J.M. et al.The mtDNA legacy of the Levantine early Upper Palaeolithic in Africa.Science. 2006; 314: 1767-1770Crossref PubMed Scopus (196) Google Scholar Therefore, the current sub-Saharan mtDNA gene pool is overwhelmingly a rich mix of L0 and L1′5 clades, found at varying frequencies throughout the continent.15Salas A. Richards M. De la Fe T. Lareu M.V. Sobrino B. Sanchez-Diz P. Macaulay V. Carracedo A. The making of the African mtDNA landscape.Am. J. Hum. Genet. 2002; 71: 1082-1111Abstract Full Text Full Text PDF PubMed Scopus (386) Google ScholarThis entangled pattern of mtDNA variation gives an initial impression of lack of internal maternal genetic structure within the continent. Alternatively, it might indicate the elimination of such an early structure because of massive demographic shifts within the continent, the most dominant of which was certainly the recent Bantu expansions and spread of agriculturist style of living.15Salas A. Richards M. De la Fe T. Lareu M.V. Sobrino B. Sanchez-Diz P. Macaulay V. Carracedo A. The making of the African mtDNA landscape.Am. J. Hum. Genet. 2002; 71: 1082-1111Abstract Full Text Full Text PDF PubMed Scopus (386) Google Scholar However, some L(xM,N) clades do show significant phylogeographic structure in Africa, such as the localization of L1c1a to central Africa16Quintana-Murci L. Quach H. Harmant C. Luca F. Massonnet B. Patin E. Sica L. Mouguiama-Daouda P. Comas D. Tzur S. et al.Maternal traces of deep common ancestry and asymmetric gene flow between Pygmy hunter-gatherers and Bantu-speaking farmers.Proc. Natl. Acad. Sci. USA. 2008; 105: 1596-1601Crossref PubMed Scopus (138) Google Scholar or the localization of L0d and L0k (previously L1d and L1k) to the Khoisan people,17Chen Y.S. Olckers A. Schurr T.G. Kogelnik A.M. Huoponen K. Wallace D.C. mtDNA variation in the South African Kung and Khwe-and their genetic relationships to other African populations.Am. J. Hum. Genet. 2000; 66: 1362-1383Abstract Full Text Full Text PDF PubMed Scopus (147) Google Scholar, 18Knight A. Underhill P.A. Mortensen H.M. Zhivotovsky L.A. Lin A.A. Henn B.M. Louis D. Ruhlen M. Mountain J.L. African Y chromosome and mtDNA divergence provides insight into the history of click languages.Curr. Biol. 2003; 13: 464-473Abstract Full Text Full Text PDF PubMed Scopus (124) Google Scholar, 19Tishkoff S.A. Gonder M.K. Henn B.M. Mortensen H. Knight A. Gignoux C. Fernandopulle N. Lema G. Nyambo T.B. Ramakrishnan U. et al.History of click-speaking populations of Africa inferred from mtDNA and Y chromosome genetic variation.Mol. Biol. Evol. 2007; 24: 2180-2195Crossref PubMed Scopus (155) Google Scholar, 20Vigilant L. Stoneking M. Harpending H. Hawkes K. Wilson A.C. African populations and the evolution of human mitochondrial DNA.Science. 1991; 253: 1503-1507Crossref PubMed Scopus (951) Google Scholar in which they account for over 60% of the contemporary mtDNA gene pool. Early studies based on mtDNA control region variation have suggested that Khoisan divergence dates to an early stage in the history of modern humans,18Knight A. Underhill P.A. Mortensen H.M. Zhivotovsky L.A. Lin A.A. Henn B.M. Louis D. Ruhlen M. Mountain J.L. African Y chromosome and mtDNA divergence provides insight into the history of click languages.Curr. Biol. 2003; 13: 464-473Abstract Full Text Full Text PDF PubMed Scopus (124) Google Scholar whereas their anthropological and linguistic features show closer affinities to each other than to those of other populations in Africa.21Barnard A. Hunters and Herders of Southern Africa: A Comparative Ethnography of the Khoisan Peoples. Cambridge University Press, New York1992Crossref Google Scholar, 22Guldemann T. Quotative Indexes in African Languages: A Synchronic and Diachronic Survey. Mouton de Gruyter, Berlin2007Google Scholar Their distinctiveness is also supported by phylogenetic studies of the male-specific Y chromosome that indicate that the most basal branch of the Y phylogeny is now common among the Khoisan but is rare or absent in other populations.18Knight A. Underhill P.A. Mortensen H.M. Zhivotovsky L.A. Lin A.A. Henn B.M. Louis D. Ruhlen M. Mountain J.L. African Y chromosome and mtDNA divergence provides insight into the history of click languages.Curr. Biol. 2003; 13: 464-473Abstract Full Text Full Text PDF PubMed Scopus (124) Google ScholarTo better understand the reason for the high prevalence of two basal mtDNA lineages L0d and L0k within Khoisan, and the possible implications that this pattern might have on our understanding of early maternal genetic structure within Homo sapiens populations, we studied, at the level of complete mtDNA sequences, the variation of 624 Hg L(xM,N) mtDNA genomes. Our findings enable the identification of different phylogenetic origins for L0d and L0k lineages versus all other contemporary mtDNA lineages found within the Khoisan and support a demographic model with extensive maternal genetic structure during the early evolutionary history of Homo sapiens. This maternal structure is likely the result of ancient population splits and movements and is not consistent with a homogenous distribution of modern humans throughout sub-Saharan Africa.Material and MethodsSamplingTable S1 available online details the information for each of the 624 samples included in this study. We evaluated all 315 Hg L(xM,N) complete mtDNA sequences reported in the literature.5Torroni A. Achilli A. Macaulay V. Richards M. Bandelt H.J. Harvesting the fruit of the human mtDNA tree.Trends Genet. 2006; 22: 339-345Abstract Full Text Full Text PDF PubMed Scopus (351) Google Scholar, 8Kivisild T. Shen P. Wall D.P. Do B. Sung R. Davis K. Passarino G. Underhill P.A. Scharfe C. Torroni A. et al.The role of selection in the evolution of human mitochondrial genomes.Genetics. 2006; 172: 373-387Crossref PubMed Scopus (359) Google Scholar, 9Mishmar D. Ruiz-Pesini E. Golik P. Macaulay V. Clark A.G. Hosseini S. Brandon M. Easley K. Chen E. Brown M.D. et al.Natural selection shaped regional mtDNA variation in humans.Proc. Natl. Acad. Sci. USA. 2003; 100: 171-176Crossref PubMed Scopus (774) Google Scholar, 10Maca-Meyer N. Gonzalez A.M. Larruga J.M. Flores C. Cabrera V.M. Major genomic mitochondrial lineages delineate early human expansions.BMC Genet. 2001; 2: 13Crossref PubMed Scopus (263) Google Scholar, 16Quintana-Murci L. Quach H. Harmant C. Luca F. Massonnet B. Patin E. Sica L. Mouguiama-Daouda P. Comas D. Tzur S. et al.Maternal traces of deep common ancestry and asymmetric gene flow between Pygmy hunter-gatherers and Bantu-speaking farmers.Proc. Natl. Acad. Sci. USA. 2008; 105: 1596-1601Crossref PubMed Scopus (138) Google Scholar, 23Ingman M. Kaessmann H. Paabo S. Gyllensten U. Mitochondrial genome variation and the origin of modern humans.Nature. 2000; 408: 708-713Crossref PubMed Scopus (1017) Google Scholar, 24Howell N. Elson J.L. Turnbull D.M. Herrnstadt C. African laplogroup L mtDNA sequences show violations of clock-like evolution.Mol. Biol. Evol. 2004; 21: 1843-1854Crossref PubMed Scopus (29) Google Scholar, 25Behar D.M. Metspalu A. Kivisild T. Rosset S. Tzur S. Hadid Y. Yodkovsky G. Rosengarten D. Pereira L. Amorim A. et al.Counting the founders: The matrilineal genetic ancestry of the Jewish Diaspora.PLoS ONE. 2008; (in press)Google Scholar Next, we identified all Hg L(xM,N) samples in all population sample collections available in Haifa (D.M.B.), Family Tree DNA (D.M.B.), Johannesburg (H.S. and H.M.), National Geographic Society (R.S.W. and J.B.S.), Paris (L.Q.M.), Porto (L.P.), Rome (R.S.), and Tartu (E.M. and R.V.) and chose 309 for complete mtDNA sequencing. Samples were chosen to include the widest possible range of Hg L(xM,N) internal variation on the basis of the previously available sequence analysis of the mtDNA control region and are, therefore, biased toward rare variants. In addition, we attempted to focus on branches (e.g., L0d, L0k), populations (e.g., Khoisan), and geographic regions (e.g., Chad) for which the current data were scant. Last, we preferred to sequence variants that the current literature suggested to be rare or anecdotal in any given geographic region (e.g., L0k in the Near East). All samples reported herein were derived from blood, buccal swab, or blood cell samples that were collected with informed consent according to procedures approved by the Institutional Human Subjects Review Committees in their respective locations.Complete mtDNA SequencingDNA was amplified with 18 primers to yield nine overlapping fragments as previously reported.26Taylor R.W. Taylor G.A. Durham S.E. Turnbull D.M. The determination of complete human mitochondrial DNA sequences in single cells: Implications for the study of somatic mitochondrial DNA point mutations.Nucleic Acids Res. 2001; 29 (E74–E74)Crossref Scopus (12) Google Scholar After purification, the nine fragments were sequenced by means of 56 internal primers to obtain the complete mtDNA genome. Sequencing was performed on a 3730xl DNA Analyzer (Applied Biosystems), and the resulting sequences were analyzed with the Sequencher software (Gene Codes Corporation). Mutations were scored relative to the revised Cambridge Reference Sequence (rCRS).27Andrews R.M. Kubacka I. Chinnery P.F. Lightowlers R.N. Turnbull D.M. Howell N. Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA.Nat. Genet. 1999; 23: 147Crossref PubMed Scopus (2521) Google Scholar The 309 Hg L(xM,N) complete mtDNA sequences reported herein have been submitted to GenBank (accession numbers EU092658 – EU092966 ). Sample quality control was assured as follows:1.After the primary polymerase chain reaction (PCR) amplification of the nine fragments, DNA handling and distribution to the 56 sequencing reactions was aided by the Beckman Coulter Biomek FX liquid handler to minimize the chance for human pipetting errors.2.All 56 sequencing reactions of each sample were attempted simultaneously in the same sequencing run and included resequencing of the control region to assure that the correct sample was chosen. Therefore, most observed polymorphisms were determined by at least two sequences. However, in a minority of the cases only one sequence is available because of various technical reasons, usually related to the amount and quality of the DNA available.3.Any fragment that failed the first sequencing attempt or any ambiguous base call was tested by additional and independent PCR and sequencing reactions. In these cases, the first hypervariable segment was again resequenced to assure that the correct sample was chosen.4.Table S1 includes for each sample that needed several genotyping attempts the information regarding fragments26Taylor R.W. Taylor G.A. Durham S.E. Turnbull D.M. The determination of complete human mitochondrial DNA sequences in single cells: Implications for the study of somatic mitochondrial DNA point mutations.Nucleic Acids Res. 2001; 29 (E74–E74)Crossref Scopus (12) Google Scholar that were resequenced to help in the search for DNA handling errors and artificial recombination events.5.All sequences were aligned by the software Sequencher (Gene Codes Corporation), and all positions with a Phred score less than 30 were directly inspected by an operator.28Ewing B. Green P. Base-calling of automated sequencer traces using phred. II. Error probabilities.Genome Res. 1998; 8: 186-194Crossref PubMed Google Scholar, 29Ewing B. Hillier L. Wendl M.C. Green P. Base-calling of automated sequencer traces using phred. I. Accuracy assessment.Genome Res. 1998; 8: 175-185Crossref PubMed Scopus (4846) Google Scholar All positions that differed from the rCRS were recorded electronically to minimize typographic errors.6.Any sample that showed a deviation from the expected evolutionary hierarchy as suggested by the established Hg L(xM,N) phylogeny was highlighted and resequenced when a lab error was suspected.7.Any comments and remarks raised by external investigators after release of the data will be addressed by reobservation of the original sequences for accuracy. After that, any unresolved result will be further examined by resequencing and, if necessary, immediately corrected by publication of an erratum.NomenclatureThe term African Hg L(xM,N) is used to describe all mtDNA Haplogroups but (L3)M and (L3)N. We reserve the term branch to describe the two evolving sides of the root and have labeled them L0 and L1′2′3′4′5′6 (L1′5).5Torroni A. Achilli A. Macaulay V. Richards M. Bandelt H.J. Harvesting the fruit of the human mtDNA tree.Trends Genet. 2006; 22: 339-345Abstract Full Text Full Text PDF PubMed Scopus (351) Google Scholar The two major branches each composed of one to several haplogroups.30Torroni A. Sukernik R.I. Schurr T.G. Starikorskaya Y.B. Cabell M.F. Crawford M.H. Comuzzie A.G. Wallace D.C. mtDNA variation of aboriginal Siberians reveals distinct genetic affinities with Native Americans.Am. J. Hum. Genet. 1993; 53: 591-608PubMed Google Scholar Note that the L0 branch is made of the L0 Hg alone, whereas the L1′5 branch includes haplogroups L1–L6. Haplogroups are composed of clades (e.g., L0d and L0k), which in their turn are composed of lineages, which represent an evolving set of closely related haplotypes. The term haplotype describes the entire combination of substitutions retrieved from the complete sequence in any given sample and therefore indicates the tips of the phylogeny, whether a singleton or not. Numbers 1–16569 refer to the position of the substitution in the rCRS.27Andrews R.M. Kubacka I. Chinnery P.F. Lightowlers R.N. Turnbull D.M. Howell N. Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA.Nat. Genet. 1999; 23: 147Crossref PubMed Scopus (2521) Google Scholar We followed the consensus nomenclature scheme31Richards M.B. Macaulay V.A. Bandelt H.J. Sykes B.C. Phylogeography of mitochondrial DNA in western Europe.Ann. Hum. Genet. 1998; 62: 241-260Crossref PubMed Google Scholar when possible. In many cases, we labeled previously unreported deep branches (e.g., L1c1c), understanding that these designations are meant to facilitate reading and future literature comparison and are prospective candidates of clades to be fully defined in the future, provided common ancestral substitution motifs could be identified in complete mtDNA sequences of other samples. Nomenclature within Hg L(xM,N) has been the subject of some ambiguity because of the relabeling of some of the clades. The clades L0d, L0f, L0k, and L5 were previously labeled L1d, L1f, L1k, and L1e, respectively. We followed the designation in5Torroni A. Achilli A. Macaulay V. Richards M. Bandelt H.J. Harvesting the fruit of the human mtDNA tree.Trends Genet. 2006; 22: 339-345Abstract Full Text Full Text PDF PubMed Scopus (351) Google Scholar, 8Kivisild T. Shen P. Wall D.P. Do B. Sung R. Davis K. Passarino G. Underhill P.A. Scharfe C. Torroni A. et al.The role of selection in the evolution of human mitochondrial genomes.Genetics. 2006; 172: 373-387Crossref PubMed Scopus (359) Google Scholar, 15Salas A. Richards M. De la Fe T. Lareu M.V. Sobrino B. Sanchez-Diz P. Macaulay V. Carracedo A. The making of the African mtDNA landscape.Am. J. Hum. Genet. 2002; 71: 1082-1111Abstract Full Text Full Text PDF PubMed Scopus (386) Google Scholar, 32Salas A. Richards M. Lareu M.V. Scozzari R. Coppa A. Torroni A. Macaulay V. Carracedo A. The African diaspora: Mitochondrial DNA and the Atlantic slave trade.Am. J. Hum. Genet. 2004; 74: 454-465Abstract Full Text Full Text PDF PubMed Scopus (202) Google Scholar for the definitions of the major branches with a single exception. We have eliminated the label L7 coined in5Torroni A. Achilli A. Macaulay V. Richards M. Bandelt H.J. Harvesting the fruit of the human mtDNA tree.Trends Genet. 2006; 22: 339-345Abstract Full Text Full Text PDF PubMed Scopus (351) Google Scholar and revert back to the original label L4a as suggested in13Kivisild T. Reidla M. Metspalu E. Rosa A. Brehm A. Pennarun E. Parik J. Geberhiwot T. Usanga E. Villems R. Ethiopian mitochondrial DNA heritage: Tracking gene flow across and around the gate of tears.Am. J. Hum. Genet. 2004; 75: 752-770Abstract Full Text Full Text PDF PubMed Scopus (200) Google Scholar because of the following: (1) A large number of samples (17) suggest position 16362 to be at the root of both clades, (2) both clades share similar distribution in East Africa and in southern West Eurasia, and (3) coalescence ages and the observed subclade-type architecture appear to be similar. We have not used the label L1c5 suggested by33Batini C. Coia V. Battaggia C. Rocha J. Pilkington M.M. Spedini G. Comas D. Destro-Bisol G. Calafell F. Phylogeography of the human mitochondrial L1c haplogroup: Genetic signatures of the prehistory of Central Africa.Mol. Phylogenet. Evol. 2007; 43: 635-644Crossref PubMed Scopus (51) Google Scholar because our complete mtDNA-based analysis indicates it to be L1c1a1, as suggested by.15Salas A. Richards M. De la Fe T. Lareu M.V. Sobrino B. Sanchez-Diz P. Macaulay V. Carracedo A. The making of the African mtDNA landscape.Am. J. Hum. Genet. 2002; 71: 1082-1111Abstract Full Text Full Text PDF PubMed Scopus (386) Google Scholar To avoid confusion, we have skipped this label and moved from L1c4 to L1c6. We added labeling for previously unlabeled bifurcations if they became relevant for our discussion.The term Khoisan is used in reference to two major ethnic groups of Southern Africa, the Khoi and San, though several other names exist for either one or both of these groups, such as the Khoi, Khoe, Khoi-San, and Khoe-San.African Hg L PhylogenyWe generated a maximum-parsimony tree of 624 complete mtDNA sequences belonging to Hg L(xM,N) (Figure S1). The tree was rooted according to8Kivisild T. Shen P. Wall D.P. Do B. Sung R. Davis K. Passarino G. Underhill P.A. Scharfe C. Torroni A. et al.The role of selection in the evolution of human mitochondrial genomes.Genetics. 2006; 172: 373-387Crossref PubMed Scopus (359) Google Scholar and includes 309 samples reported herein and 315 previously reported samples: 21 sequences from,23Ingman M. Kaessmann H. Paabo S. Gyllensten U. Mitochondrial genome variation and the origin of modern humans.Nature. 2000; 408: 708-713Crossref PubMed Scopus (1017) Google Scholar six from,10Maca-Meyer N. Gonzalez A.M. Larruga J.M. Flores C. Cabrera V.M. Major genomic mitochondrial lineages delineate early human expansions.BMC Genet. 2001; 2: 13Crossref PubMed Scopus (263) Google Scholar five from,34Torroni A. Rengo C. Guida V. Cruciani F. Sellitto D. Coppa A. Calderon F.L. Simionati B. Valle G. Richards M. et al.Do the four clades of the mtDNA haplogroup L2 evolve at different rates?.Am. J. Hum. Genet. 2001; 69: 1348-1356Abstract Full Text Full Text PDF PubMed Scopus (168) Google Scholar ten from,9Mishmar D. Ruiz-Pesini E. Golik P. Macaulay V. Clark A.G. Hosseini S. Brandon M. Easley K. Chen E. Brown M.D. et al.Natural selection shaped regional mtDNA variation in humans.Proc. Natl. Acad. Sci. USA. 2003; 100: 171-176Crossref PubMed Scopus (774) Google Scholar 93 from,24Howell N. Elson J.L. Turnbull D.M. Herrnstadt C. African laplogroup L mtDNA sequences show violations of clock-like evolution.Mol. Biol. Evol. 2004; 21: 1843-1854Crossref PubMed Scopus (29) Google Scholar 126 from,8Kivisild T. Shen P. Wall D.P. Do B. Sung R. Davis K. Passarino G. Underhill P.A. Scharfe C. Torroni A. et al.The role of selection in the evolution of human mitochondrial genomes.Genetics. 2006; 172: 373-387Crossref PubMed Scopus (359) Google Scholar 23 from,5Torroni A. Achilli A. Macaulay V. Richards M. Bandelt H.J. Harvesting the fruit of the human mtDNA tree.Trends Genet. 2006; 22: 339-345Abstract Full Text Full Text PDF PubMed Scopus (351) Google Scholar four from,25Behar D.M. Metspalu A. Kivisild T. Rosset S. Tzur S. Hadid Y. Yodkovsky G. Rosengarten D. Pereira L. Amorim A. et al.Counting the founders: The matrilineal genetic ancestry of the Jewish Diaspora.PLoS ONE. 2008; (in press)Google Scholar and 27 from.16Quintana-Murci L. Quach H. Harmant C. Luca F. Massonnet B. Patin E. Sica L. Mouguiama-Daouda P. Comas D. Tzur S. et al.Maternal traces of deep common ancestry and asymmetric gene flow between Pygmy hunter-gatherers and Bantu-speaking farmers.Proc. Natl. Acad. Sci. USA. 2008; 105: 1596-1601Crossref PubMed Scopus (138) Google Scholar The genotyping information from5Torroni A. Achilli A. Macaulay V. Richards M. Bandelt H.J. Harvesting the fruit of the human mtDNA tree.Trends Genet. 2006; 22: 339-345Abstract Full Text Full Text PDF PubMed Scopus (351) Google Scholar, 34Torroni A. Rengo C. Guida V. Cruciani F. Sellitto D. Coppa A. Calderon F.L. Simionati B. Valle G. Richards M. et al.Do the four clades of the mtDNA haplogroup L2 evolve at different rates?.Am. J. Hum. 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Two groups of populations with completely different lifestyles-the Pygmy hunter-gatherers and the Bantu-speaking farmers-coexist in Central Africa. We investigated the origins of these two groups and the interactions between them, by analyzing mtDNA variation in 1,404 individuals from 20 farming populations and 9 Pygmy populations from Central Africa, with the aim of shedding light on one of the most fascinating cultural transitions in human evolution (the transition from hunting and gathering to agriculture). Our data indicate that this region was colonized gradually, with an initial L1c-rich ancestral population ultimately giving rise to current-day farmers, who display various L1c clades, and to Pygmies, in whom L1c1a is the only surviving clade. Detailed phylogenetic analysis of complete mtDNA sequences for L1c1a showed this clade to be autochthonous to Central Africa, with its most recent branches shared between farmers and Pygmies. Coalescence analyses revealed that these two groups arose through a complex evolutionary process characterized by (i) initial divergence of the ancestors of contemporary Pygmies from an ancestral Central African population no more than approximately 70,000 years ago, (ii) a period of isolation between the two groups, accounting for their phenotypic differences, (iii) long-standing asymmetric maternal gene flow from Pygmies to the ancestors of the farming populations, beginning no more than approximately 40,000 years ago and persisting until a few thousand years ago, and (iv) enrichment of the maternal gene pool of the ancestors of the farming populations by the arrival and/or subsequent demographic expansion of L0a, L2, and L3 carriers.

Both the extent and location of the maternal ancestral deme from which the Ashkenazi Jewry arose remain obscure. Here, using complete sequences of the maternally inherited mitochondrial DNA (mtDNA), we show that close to one-half of Ashkenazi Jews, estimated at 8,000,000 people, can be traced back to only 4 women carrying distinct mtDNAs that are virtually absent in other populations, with the important exception of low frequencies among non-Ashkenazi Jews. We conclude that four founding mtDNAs, likely of Near Eastern ancestry, underwent major expansion(s) in Europe within the past millennium.

Primary ovarian insufficiency (POI) is caused by ovarian follicle depletion or follicle dysfunction. The phenotypic spectrum ranges from absence of pubertal maturation to early menopause. Genes involved in essential steps in chromosome synapsis and recombination during meiosis, such as synaptonemal complex central element 1 (SYCE1), have been shown to cause POI in animal models. We describe for the first time a homozygous mutation in SYCE1 in humans. To identify the genetic cause of POI in an Israeli Arab family with a consanguineous pedigree. A family-based genetic study conducted at a tertiary medical center. Two daughters of consanguineous parents (first cousins) from a 13-member family were diagnosed with POI. Genotyping was performed in the index patients, their parents, and four unaffected siblings. DNA from the affected sisters was subjected to whole-exome sequencing. The genotypes of interest were confirmed and genotypes of the additional family members were determined by Sanger sequencing. Genotyping was also performed in 90 ethnically matched control individuals. A nonsense homozygous mutation (c.613C>T) was identified in the SYCE1 gene in both affected sisters. The parents and three brothers were heterozygous for the mutation, and an unaffected sister did not carry the mutation. The mutation was not identified in the DNA samples from the 90 control subjects. Given the known function of the SYCE1 gene, we suggest that the nonsense mutation identified accounts for the POI phenotype. These results highlight the importance of the synaptonemal complex and meiosis in ovarian function.

With earlier institution of antiretroviral therapy, kidney diseases other than HIV-associated nephropathy (HIVAN) predominate in HIV-infected persons. Outcomes for these diseases are typically worse among those infected with HIV, but the reasons for this are not clear. Here, we examined the role of APOL1 risk variants in predicting renal histopathology and progression to ESRD in 98 HIV-infected African Americans with non-HIVAN kidney disease on biopsy. We used survival analysis to determine time to ESRD associated with APOL1 genotype. Among the 29 patients with two APOL1 risk alleles, the majority (76%) had FSGS and 10% had hypertensive nephrosclerosis. In contrast, among the 54 patients with one APOL1 risk allele, 47% had immune-complex GN as the predominant lesion and only 23% had FSGS. Among the 25 patients with no APOL1 risk allele, 40% had immune-complex GN and 12% had FSGS. In 310 person-years of observation, 29 patients progressed to ESRD. In adjusted analyses, individuals with two APOL1 risk alleles had a nearly three-fold higher risk for ESRD compared with those with one or zero risk alleles (P=0.03). In summary, these data demonstrate an association between APOL1 variants and renal outcomes in non-HIVAN kidney disease, suggesting a possible use for APOL1 genotyping to help guide the care of HIV-infected patients.

MicroRNAs (miRNAs) are post-transcriptional regulators of gene expression. Heterozygous loss-of-function point mutations of miRNA genes are associated with several human congenital disorders1-5, but neomorphic (gain-of-new-function) mutations in miRNAs due to nucleotide substitutions have not been reported. Here we describe a neomorphic seed region mutation in the chondrocyte-specific, super-enhancer-associated MIR140 gene encoding microRNA-140 (miR-140) in a novel autosomal dominant human skeletal dysplasia. Mice with the corresponding single nucleotide substitution show skeletal abnormalities similar to those of the patients but distinct from those of miR-140-null mice6. This mutant miRNA gene yields abundant mutant miR-140-5p expression without miRNA-processing defects. In chondrocytes, the mutation causes widespread derepression of wild-type miR-140-5p targets and repression of mutant miR-140-5p targets, indicating that the mutation produces both loss-of-function and gain-of-function effects. Furthermore, the mutant miR-140-5p seed competes with the conserved RNA-binding protein Ybx1 for overlapping binding sites. This finding may explain the potent target repression and robust in vivo effect by this mutant miRNA even in the absence of evolutionary selection of miRNA-target RNA interactions, which contributes to the strong regulatory effects of conserved miRNAs7,8. Our study presents the first case of a pathogenic gain-of-function miRNA mutation and provides molecular insight into neomorphic actions of emerging and/or mutant miRNAs.

We identified two unrelated consanguineous families with three children affected by the rare association of congenital nephrotic syndrome (CNS) diagnosed in the first days of life, of hypogonadism, and of prenatally detected adrenal calcifications, associated with congenital adrenal insufficiency in one case. Using exome sequencing and targeted Sanger sequencing, two homozygous truncating mutations, c.1513C>T (p.Arg505*) and c.934delC (p.Leu312Phefs*30), were identified in SGPL1-encoding sphingosine-1-phosphate (S1P) lyase 1. SGPL1 catalyzes the irreversible degradation of endogenous and dietary S1P, the final step of sphingolipid catabolism, and of other phosphorylated long-chain bases. S1P is an intracellular and extracellular signaling molecule involved in angiogenesis, vascular maturation, and immunity. The levels of SGPL1 substrates, S1P, and sphingosine were markedly increased in the patients' blood and fibroblasts, as determined by liquid chromatography-tandem mass spectrometry. Vascular alterations were present in a patient's renal biopsy, in line with changes seen in Sgpl1 knockout mice that are compatible with a developmental defect in vascular maturation. In conclusion, loss of SGPL1 function is associated with CNS, adrenal calcifications, and hypogonadism.

The Genographic Project is studying the genetic signatures of ancient human migrations and creating an open-source research database. It allows members of the public to participate in a real-time anthropological genetics study by submitting personal samples for analysis and donating the genetic results to the database. We report our experience from the first 18 months of public participation in the Genographic Project, during which we have created the largest standardized human mitochondrial DNA (mtDNA) database ever collected, comprising 78,590 genotypes. Here, we detail our genotyping and quality assurance protocols including direct sequencing of the mtDNA HVS-I, genotyping of 22 coding-region SNPs, and a series of computational quality checks based on phylogenetic principles. This database is very informative with respect to mtDNA phylogeny and mutational dynamics, and its size allows us to develop a nearest neighbor-based methodology for mtDNA haplogroup prediction based on HVS-I motifs that is superior to classic rule-based approaches. We make available to the scientific community and general public two new resources: a periodically updated database comprising all data donated by participants, and the nearest neighbor haplogroup prediction tool.

The history of the Jewish Diaspora dates back to the Assyrian and Babylonian conquests in the Levant, followed by complex demographic and migratory trajectories over the ensuing millennia which pose a serious challenge to unraveling population genetic patterns. Here we ask whether phylogenetic analysis, based on highly resolved mitochondrial DNA (mtDNA) phylogenies can discern among maternal ancestries of the Diaspora. Accordingly, 1,142 samples from 14 different non-Ashkenazi Jewish communities were analyzed. A list of complete mtDNA sequences was established for all variants present at high frequency in the communities studied, along with high-resolution genotyping of all samples. Unlike the previously reported pattern observed among Ashkenazi Jews, the numerically major portion of the non-Ashkenazi Jews, currently estimated at 5 million people and comprised of the Moroccan, Iraqi, Iranian and Iberian Exile Jewish communities showed no evidence for a narrow founder effect, which did however characterize the smaller and more remote Belmonte, Indian and the two Caucasus communities. The Indian and Ethiopian Jewish sample sets suggested local female introgression, while mtDNAs in all other communities studied belong to a well-characterized West Eurasian pool of maternal lineages. Absence of sub-Saharan African mtDNA lineages among the North African Jewish communities suggests negligible or low level of admixture with females of the host populations among whom the African haplogroup (Hg) L0-L3 sub-clades variants are common. In contrast, the North African and Iberian Exile Jewish communities show influence of putative Iberian admixture as documented by mtDNA Hg HV0 variants. These findings highlight striking differences in the demographic history of the widespread Jewish Diaspora.

Background.The APOL1 G1 and G2 genetic variants make a major contribution to the African ancestry risk for a number of common forms of non-diabetic end-stage kidney disease (ESKD). We sought to clarify the relationship of APOL1 variants with age of dialysis initiation and dialysis vintage (defined by the time between dialysis initiation and sample collection) in African and Hispanic Americans, diabetic and non-diabetic ESKD.

<b><i>Background:</i></b> Continental Africa is facing an epidemic of chronic kidney disease (CKD). APOL1 risk variants have been shown to be strongly associated with an increased risk for non-diabetic kidney disease including HIV nephropathy, primary non-monogenic focal and segmental glomerulosclerosis, and hypertension-attributed nephropathy among African ancestry populations in the USA. The world's highest frequencies of APOL1 risk alleles have been reported in West African nations, overlapping regions with a high incidence of CKD and hypertension. One such region is south-eastern Nigeria, and therefore we sought to quantify the association of APOL1 risk alleles with CKD in this region. <b><i>Methods:</i></b> APOL1 risk variants were genotyped in a case-control sample set consisting of non-diabetic, CKD patients (n = 44) and control individuals (n = 43) from Enugu and Abakaliki, Nigeria. <b><i>Results:</i></b> We found a high frequency of two APOL1 risk alleles in the general population of Igbo people of south-eastern Nigeria (23.3%). The two APOL1 risk allele frequency in the CKD patient group was 66%. Logistic regression analysis under a recessive inheritance model showed a strong and significant association of APOL1 two-risk alleles with CKD, yielding an odds ratio of 6.4 (unadjusted p = 1.2E-4); following correction for age, gender, HIV and BMI, the odds ratio was 4.8 (adjusted p = 5.1E-03). <b><i>Conclusion:</i></b> APOL1 risk variants are common in the Igbo population of south-eastern Nigeria, and are also highly associated with non-diabetic CKD in this area. APOL1 may explain the increased prevalence of CKD in this region.

Recent studies identified MYH9 as a major susceptibility gene for common forms of non-diabetic end-stage kidney disease (ESKD). A set of African ancestry DNA sequence variants comprising the E-1 haplotype, was significantly associated with ESKD. In order to determine whether African ancestry variants are also associated with disease susceptibility in admixed populations with differing genomic backgrounds, we genotyped a total of 1425 African and Hispanic American subjects comprising dialysis patients with diabetic and non-diabetic ESKD and controls, using 42 single nucleotide polymorphisms (SNPs) within the MYH9 gene and 40 genome-wide and 38 chromosome 22 ancestry informative markers. Following ancestry correction, logistic regression demonstrated that three of the E-1 SNPs are also associated with non-diabetic ESKD in the new sample sets of both African and Hispanic Americans, with a stronger association in Hispanic Americans. We also identified MYH9 SNPs that are even more powerfully associated with the disease phenotype than the E-1 SNPs. These newly associated SNPs, could be divided into those comprising a haplotype termed S-1 whose association was significant under a recessive or additive inheritance mode (rs5750248, OR 4.21, P < 0.01, Hispanic Americans, recessive), and those comprising a haplotype termed F-1 whose association was significant under a dominant or additive inheritance mode (rs11912763, OR 4.59, P < 0.01, Hispanic Americans, dominant). These findings strengthen the contention that a sequence variant of MYH9, common in populations with varying degrees of African ancestry admixture, and in strong linkage disequilibrium with the associated SNPs and haplotypes reported herein, strongly predisposes to non-diabetic ESKD.

The origin and history of the Ashkenazi Jewish population have long been of great interest, and advances in high-throughput genetic analysis have recently provided a new approach for investigating these topics. We and others have argued on the basis of genome-wide data that the Ashkenazi Jewish population derives its ancestry from a combination of sources tracing to both Europe and the Middle East. It has been claimed, however, through a reanalysis of some of our data, that a large part of the ancestry of the Ashkenazi population originates with the Khazars, a Turkic-speaking group that lived to the north of the Caucasus region ∼1,000 years ago. Because the Khazar population has left no obvious modern descendants that could enable a clear test for a contribution to Ashkenazi Jewish ancestry, the Khazar hypothesis has been difficult to examine using genetics. Furthermore, because only limited genetic data have been available from the Caucasus region, and because these data have been concentrated in populations that are genetically close to populations from the Middle East, the attribution of any signal of Ashkenazi-Caucasus genetic similarity to Khazar ancestry rather than shared ancestral Middle Eastern ancestry has been problematic. Here, through integration of genotypes from newly collected samples with data from several of our past studies, we have assembled the largest data set available to date for assessment of Ashkenazi Jewish genetic origins. This data set contains genome-wide single-nucleotide polymorphisms in 1,774 samples from 106 Jewish and non-Jewish populations that span the possible regions of potential Ashkenazi ancestry: Europe, the Middle East, and the region historically associated with the Khazar Khaganate. The data set includes 261 samples from 15 populations from the Caucasus region and the region directly to its north, samples that have not previously been included alongside Ashkenazi Jewish samples in genomic studies. Employing a variety of standard techniques for the analysis of population-genetic structure, we found that Ashkenazi Jews share the greatest genetic ancestry with other Jewish populations and, among non-Jewish populations, with groups from Europe and the Middle East. No particular similarity of Ashkenazi Jews to populations from the Caucasus is evident, particularly populations that most closely represent the Khazar region. Thus, analysis of Ashkenazi Jews together with a large sample from the region of the Khazar Khaganate corroborates the earlier results that Ashkenazi Jews derive their ancestry primarily from populations of the Middle East and Europe, that they possess considerable shared ancestry with other Jewish populations, and that there is no indication of a significant genetic contribution either from within or from north of the Caucasus region.

We report genome-wide DNA data for 73 individuals from five archaeological sites across the Bronze and Iron Ages Southern Levant. These individuals, who share the "Canaanite" material culture, can be modeled as descending from two sources: (1) earlier local Neolithic populations and (2) populations related to the Chalcolithic Zagros or the Bronze Age Caucasus. The non-local contribution increased over time, as evinced by three outliers who can be modeled as descendants of recent migrants. We show evidence that different "Canaanite" groups genetically resemble each other more than other populations. We find that Levant-related modern populations typically have substantial ancestry coming from populations related to the Chalcolithic Zagros and the Bronze Age Southern Levant. These groups also harbor ancestry from sources we cannot fully model with the available data, highlighting the critical role of post-Bronze-Age migrations into the region over the past 3,000 years.

Epigenetic integrity is critical for many eukaryotic cellular processes. An important question is how different epigenetic regulators control development and influence disease. Lysine acetyltransferase 8 (KAT8) is critical for acetylation of histone H4 at lysine 16 (H4K16), an evolutionarily conserved epigenetic mark. It is unclear what roles KAT8 plays in cerebral development and human disease. Here, we report that cerebrum-specific knockout mice displayed cerebral hypoplasia in the neocortex and hippocampus, along with improper neural stem and progenitor cell (NSPC) development. Mutant cerebrocortical neuroepithelia exhibited faulty proliferation, aberrant neurogenesis, massive apoptosis, and scant H4K16 propionylation. Mutant NSPCs formed poor neurospheres, and pharmacological KAT8 inhibition abolished neurosphere formation. Moreover, we describe KAT8 variants in 9 patients with intellectual disability, seizures, autism, dysmorphisms, and other anomalies. The variants altered chromobarrel and catalytic domains of KAT8, thereby impairing nucleosomal H4K16 acetylation. Valproate was effective for treating epilepsy in at least 2 of the individuals. This study uncovers a critical role of KAT8 in cerebral and NSPC development, identifies 9 individuals with KAT8 variants, and links deficient H4K16 acylation directly to intellectual disability, epilepsy, and other developmental anomalies.

Susceptibility to end-stage kidney disease (ESKD) among HIV-infected Americans of African ancestral heritage has been attributed to APOL1 genetic variation. We determined the frequency of the APOL1 G1 and G2 risk variants together with the prevalence of HIV-associated nephropathy (HIVAN) among individuals of Ethiopian ancestry to determine whether the kidney disease genetic risk is PanAfrican or restricted to West Africa, and can explain the previously reported low risk of HIVAN among Ethiopians.We studied a cohort of 338 HIV-infected individuals of Ethiopian ancestry treated in one Israeli and one Ethiopian center. We sought clinical evidence for HIVAN (serum creatinine >1.4 mg/dl or proteinuria >30 mg/dl in a spot urine sample). Genetic analyses included the genotyping of the APOL1 G1 and G2 variants, and a panel of 33 genomic ancestry-informative markers. Statistical analysis compared clinical and genetic indices for HIV-infected individuals of Ethiopian ancestry and overall Ethiopians to those reported for HIV-infected African-Americans, overall African-Americans, West Africans and non-Africans.Three (0.8%) of 338 HIV-infected patients of Ethiopian ancestry showed clinical criteria compatible with renal impairment. Two of these 3 patients also have severe poorly controlled diabetes mellitus. The third nondiabetic patient underwent renal biopsy which ruled out HIVAN. This absence of clinically apparent HIVAN was significantly different from that reported for African-Americans. The APOL1 G1 and G2 risk variants were found, respectively, in 0 and 2 (heterozygote state) of the 338 HIV-infected individuals. Global ancestry and the frequencies of the APOL1 G1 and G2 variants are not statistically different from their frequencies in the general Ethiopian population, but are significantly and dramatically lower than those observed among HIV-infected African-Americans, African-Americans and West Africans.The coinciding absence of HIVAN and the APOL1 risk variants among HIV-infected individuals of Ethiopian ancestry support a Western rather than Pan-African ancestry risk for ESKD, and can readily explain the lack of HIVAN among individuals of Ethiopian ancestry.

Sympatric speciation has been controversial since it was first proposed as a mode of speciation. Subterranean blind mole rats (Spalacidae) are considered to speciate allopatrically or peripatrically. Here, we report a possible incipient sympatric adaptive ecological speciation in Spalax galili (2 n = 52). The study microsite (0.04 km 2 ) is sharply subdivided geologically, edaphically, and ecologically into abutting barrier-free ecologies divergent in rock, soil, and vegetation types. The Pleistocene Alma basalt abuts the Cretaceous Senonian Kerem Ben Zimra chalk. Only 28% of 112 plant species were shared between the soils. We examined mitochondrial DNA in the control region and ATP6 in 28 mole rats from basalt and in 14 from chalk habitats. We also sequenced the complete mtDNA (16,423 bp) of four animals, two from each soil type. Remarkably, the frequency of all major haplotype clusters (HC) was highly soil-biased. HCI and HCII are chalk biased. HC-III was abundant in basalt (36%) but absent in chalk; HC-IV was prevalent in basalt (46.5%) but was low (20%) in chalk. Up to 40% of the mtDNA diversity was edaphically dependent, suggesting constrained gene flow. We identified a homologous recombinant mtDNA in the basalt/chalk studied area. Phenotypically significant divergences differentiate the two populations, inhabiting different soils, in adaptive oxygen consumption and in the amount of outside-nest activity. This identification of a possible incipient sympatric adaptive ecological speciation caused by natural selection indirectly refutes the allopatric alternative. Sympatric ecological speciation may be more prevalent in nature because of abundant and sharply abutting divergent ecologies.

Abstract Context: Primary ovarian insufficiency (POI) is caused by ovarian follicle depletion or follicle dysfunction, characterized by amenorrhea with elevated gonadotropin levels. The disorder presents as absence of normal progression of puberty. Objective: To elucidate the cause of ovarian dysfunction in a family with POI. Design: We performed whole-exome sequencing in 2 affected individuals. To evaluate whether DNA double-strand break (DSB) repair activities are altered in biallelic mutation carriers, we applied an enhanced green fluorescent protein-based assay for the detection of specific DSB repair pathways in blood-derived cells. Setting: Diagnoses were made at the Pediatric Endocrine Clinic, Clalit Health Services, Sharon-Shomron District, Israel. Genetic counseling and sample collection were performed at the Pediatric Genetics Unit, Schneider Children’s Medical Center Israel, Petah Tikva, Israel. Patients and Intervention: Two sisters born to consanguineous parents of Israeli Muslim Arab ancestry presented with a lack of normal progression of puberty, high gonadotropin levels, and hypoplastic or absent ovaries on ultrasound. Blood samples for DNA extraction were obtained from all family members. Main Outcome Measure: Exome analysis to elucidate the cause of POI in 2 affected sisters. Results: Analysis revealed a stop-gain homozygous mutation in the SPIDR gene (KIAA0146) c.839G&amp;gt;A, p.W280*. This mutation altered SPIDR activity in homologous recombination, resulting in the accumulation of 53BP1-labeled DSBs postionizing radiation and γH2AX-labeled damage during unperturbed growth. Conclusions: SPIDR is important for ovarian function in humans. A biallelic mutation in this gene may be associated with ovarian dysgenesis in cases of autosomal recessive inheritance.

In the vast majority of pediatric patients with dilated cardiomyopathy, the specific etiology is unknown. Studies on families with dilated cardiomyopathy have exemplified the role of genetic factors in cardiomyopathy etiology. In this study, we applied whole-exome sequencing to members of a non-consanguineous family affected by a previously unreported congenital dilated cardiomyopathy syndrome necessitating early-onset heart transplant. Exome analysis identified compound heterozygous variants in the FLNC gene. Histological analysis of the cardiac muscle demonstrated marked sarcomeric and myofibrillar abnormalities, and immunohistochemical staining demonstrated the presence of Filamin C aggregates in cardiac myocytes. We conclude that biallelic variants in FLNC can cause congenital dilated cardiomyopathy. As the associated clinical features of affected patients are mild, and can be easily overlooked, testing for FLNC should be considered in children presenting with dilated cardiomyopathy.

We describe two siblings born to consanguineous Arab-Muslim parents who presented in early infancy with myoclonic seizures, hypertonia and contractures, arrested head growth, inability to swallow, and bouts of apnea-bradycardia, culminating in cardiac arrest and death. Whole-genome sequencing yielded a c.1173delG mutation in the BRAT1 gene. Three recent reports identified mutations in the same gene in three infants from three Amish sibships, one Mexican neonate and two Japanese siblings with similar clinical manifestations. The authors speculated that the destabilization of the encoded protein may underlie the catastrophic epilepsy and corticobasal neuronal degeneration. We suggest that BRAT1 be added to the growing list of genes that are related to severe early infantile (neonatal) epileptic encephalopathy.

Congenital pancreatic lipase (PNLIP) deficiency is a rare monoenzymatic form of exocrine pancreatic failure characterized by decreased absorption of dietary fat and greasy voluminous stools, but apparent normal development and an overall good state of health. While considered to be an autosomal recessive state affecting a few dozens of individuals world-wide and involving the PNLIP gene, no causative mutations for this phenotype were so far reported. Here, we report the identification of the homozygote missense mutation, Thr221Met [c.662C>T], in two brothers from a consanguineous family of Arab ancestry. The observed genotypes among the family members were concordant with an autosomal recessive mode of inheritance but moreover a clear segregation between the genotype state and the serum PNLIP activity was evident. Based on biophysical computational tools, we suggest the mutation disrupts the protein's stability and impairs its normal function. Although the role of PNLIP is well established, our observations provide genetic evidence that PNLIP mutations are causative for this phenotype.

Previous Y-chromosome studies have demonstrated that Ashkenazi Levites, members of a paternally inherited Jewish priestly caste, display a distinctive founder event within R1a, the most prevalent Y-chromosome haplogroup in Eastern Europe. Here we report the analysis of 16 whole R1 sequences and show that a set of 19 unique nucleotide substitutions defines the Ashkenazi R1a lineage. While our survey of one of these, M582, in 2,834 R1a samples reveals its absence in 922 Eastern Europeans, we show it is present in all sampled R1a Ashkenazi Levites, as well as in 33.8% of other R1a Ashkenazi Jewish males and 5.9% of 303 R1a Near Eastern males, where it shows considerably higher diversity. Moreover, the M582 lineage also occurs at low frequencies in non-Ashkenazi Jewish populations. In contrast to the previously suggested Eastern European origin for Ashkenazi Levites, the current data are indicative of a geographic source of the Levite founder lineage in the Near East and its likely presence among pre-Diaspora Hebrews.

Retinitis pigmentosa (RP), the most common form of inherited retinal degeneration, is associated with different groups of genes, including those encoding proteins involved in centriole and cilium biogenesis. Exome sequencing revealed a homozygous nonsense mutation [c.304_305delGA (p. D102*)] in POC5, encoding the Proteome Of Centriole 5 protein, in a patient with RP, short stature, microcephaly and recurrent glomerulonephritis. The POC5 gene is ubiquitously expressed, and immunohistochemistry revealed a distinct POC5 localization at the photoreceptor connecting cilium. Morpholino-oligonucleotide-induced knockdown of poc5 translation in zebrafish resulted in decreased length of photoreceptor outer segments and a decreased visual motor response, a measurement of retinal function. These phenotypes could be rescued by wild-type human POC5 mRNA. These findings demonstrate that Poc5 is important for normal retinal development and function. Altogether, this study presents POC5 as a novel gene involved autosomal recessively inherited RP, and strengthens the hypothesis that mutations in centriolar proteins are important cause of retinal dystrophies.

Inheritance of apolipoprotein L1 gene (APOL1) renal-risk variants in a recessive pattern strongly associates with non-diabetic end-stage kidney disease (ESKD). Further evidence supports risk modifiers in APOL1-associated nephropathy; some studies demonstrate that heterozygotes possess excess risk for ESKD or show earlier age at ESKD, relative to those with zero risk alleles. Nearby loci are also associated with ESKD in non-African Americans.We assessed the role of the APOL3 null allele rs11089781 on risk of non-diabetic ESKD. Four cohorts containing 2781 ESKD cases and 2474 controls were analyzed.Stratifying by APOL1 risk genotype (recessive) and adjusting for African ancestry identified a significant additive association between rs11089781 and ESKD in each stratum and in a meta-analysis [meta-analysis P = 0.0070; odds ratio (OR) = 1.29]; ORs were consistent across APOL1 risk strata. The biological significance of this association is supported by the finding that the APOL3 gene is co-regulated with APOL1, and that APOL3 protein was able to bind to APOL1 protein.Taken together, the genetic and biological data support the concept that other APOL proteins besides APOL1 may also influence the risk of non-diabetic ESKD.

Herein, we describe two members of one family who presented with recurrent episodes of hepatic failure, cerebellar ataxia, peripheral neuropathy, and short stature. Liver transplantation was considered. Whole-exome sequencing (Trio) revealed a synonymous variant in exon 4 of SCYL1:c.459C>T p. (Gly153Gly), which did not appear to affect the protein sequence. Computational prediction analysis suggested that this modification could alter the SCYL1 mRNA splicing processing to create a premature termination codon. The SCYL1 mRNAs in our patient's lymphocytes were analyzed and aberrant splicing was found. Molecular analysis of family members identified the parents as heterozygous recessive carriers and the proband as well as an affected aunt as homozygous. Evidently, harmless synonymous variants in the SCYL1 gene can damage gene splicing and hence the expression. We confirmed that the pathogenicity of this variant in the SCYL1 gene was associated with spinocerebellar ataxia, autosomal recessive 21 (SCAR21). Other reported cases (accept one) of liver failure found in the SCYL1 variants resolved during childhood, therefore orthotropic liver transplantation was no longer appropriate.

Background Early-onset epileptic encephalopathy (EOEE) is a severe convulsive disorder with a poor developmental prognosis. Although it has been associated with mutations in a number of genes, the fact that there is a large proportion of patients who remain undiagnosed suggests that there are many more still-unknown genetic causes of EOEE. Achieving a genetic diagnosis is important for understanding the biological basis of the disease, with its implications for treatment and family planning. Methods Whole-exome sequencing was performed in a family of Ashkenazi Jewish origin in which a male infant was diagnosed with EOEE. There was no family history of a similar neurologic disease. The patient had extreme hypotonia, neonatal hypothermia, choreiform movements, and vision impairment in addition to the convulsive disorder. Results A de novo heterozygous missense mutation, c.1003A > C, p.Asn335His, was identified in a conserved domain of GABRA2. GABRA2 encodes the α2 subunit of the GABAA receptor. Conclusions In the context of previous reports of an association of de novo mutations in genes encoding different subunits of the GABAA receptor (GABRB1, GABRA1, GABRG2, GABRB3) with autosomal dominant epileptic disorders, we conclude that a de novo mutation in GABRA2 is likely to cause autosomal dominant EOEE accompanied by a movement disorder and vision impairment.

<h2>Summary</h2> Dysregulated transforming growth factor TGF-β signaling underlies the pathogenesis of genetic disorders affecting the connective tissue such as Loeys-Dietz syndrome. Here, we report 12 individuals with bi-allelic loss-of-function variants in <i>IPO8</i> who presented with a syndromic association characterized by cardio-vascular anomalies, joint hyperlaxity, and various degree of dysmorphic features and developmental delay as well as immune dysregulation; the individuals were from nine unrelated families. Importin 8 belongs to the karyopherin family of nuclear transport receptors and was previously shown to mediate TGF-β-dependent SMADs trafficking to the nucleus <i>in vitro</i>. The important <i>in vivo</i> role of IPO8 in pSMAD nuclear translocation was demonstrated by CRISPR/Cas9-mediated inactivation in zebrafish. Consistent with IPO8's role in BMP/TGF-β signaling, <i>ipo8</i>^−/− zebrafish presented mild to severe dorso-ventral patterning defects during early embryonic development. Moreover, <i>ipo8</i>^−/− zebrafish displayed severe cardiovascular and skeletal defects that mirrored the human phenotype. Our work thus provides evidence that IPO8 plays a critical and non-redundant role in TGF-β signaling during development and reinforces the existing link between TGF-β signaling and connective tissue defects.

We describe a Bedouin family with a novel autosomal recessive syndrome characterized by dilated cardiomyopathy and septo-optic dysplasia. Genetic analysis revealed a homozygous missense mutation in TAX1BP3, which encodes a small PDZ domain containing protein implicated in regulation of the Wnt/β-catenin signaling pathway, as the causative mutation. The mutation affects a conserved residue located at the core of TAX1BP3 binding pocket and is predicted to impair the nature of a crucial hydrophobic patch, thereby interrupting the structure and stability of the protein, and its ability to interact with other proteins. TAX1BP3 is highly expressed in heart and brain and consistent with the clinical findings observed in our patients; a knockdown of TAX1BP3 causes elongation defects, enlarged pericard, and enlarged head structures in zebrafish embryos. Thus, we describe a new genetic disorder that expands the monogenic cardiomyopathy disease spectrum and suggests that TAX1BP3 is essential for heart and brain development.

Abstract Context NaPi-IIa, encoded by SLC34A1, is a key phosphate transporter in the mammalian proximal tubule and plays a cardinal role in renal phosphate handling. NaPi-IIa impairment has been linked to various overlapping clinical syndromes, including hypophosphatemic nephrolithiasis with osteoporosis, renal Fanconi syndrome with chronic kidney disease, and, most recently, idiopathic infantile hypercalcemia and nephrocalcinosis. Objectives We studied the molecular basis of idiopathic infantile hypercalcemia with partial proximal tubulopathy in two apparently unrelated patients of Israeli and Turkish descent. Design Genetic analysis in two affected children and their close relatives was performed using whole-exome sequencing, followed by in vitro localization and trafficking analysis of mutant NaPi-IIa. Results Mutation and haplotype analyses in both patients revealed a previously described homozygous loss-of-function inserted duplication (p.I154_V160dup) in NaPi-IIa, which is inherited identical-by-descent from a common ancestor. The shared mutation was originally reported by our team in two adult siblings with renal Fanconi syndrome, hypophosphatemic bone disease, and progressive renal failure who are family members of one of the infants reported herein. In vitro localization assays and biochemical analysis of p.I154_V160dup and of additional NaPi-IIa mutants harboring a trafficking defect indicate aberrant retention at the endoplasmic reticulum in an immature and underglycosylated state, leading to premature proteasomal degradation. Conclusions Our findings expand the phenotypic spectrum of NaPi-IIa disruption, reinforce its link with proximal tubular impairment, enable longitudinal study of the natural history of the disease, and shed light on cellular pathways associated with loss of function and impaired trafficking of NaPi-IIa mutants.

Genetic syndromes involving both brain and eye abnormalities are numerous and include syndromes such as Warburg micro syndrome, Kaufman oculocerebrofacial syndrome, Cerebro-oculo-facio-skeletal syndrome, Kahrizi syndrome and others. Using exome sequencing, we have been able to identify homozygous mutation p.(Tyr39Cys) in MED25 as the cause of a syndrome characterized by eye, brain, cardiac and palatal abnormalities as well as growth retardation, microcephaly and severe intellectual disability in seven patients from four unrelated families, all originating from the same village. The protein encoded by MED25 belongs to Mediator complex or MED complex, which is an evolutionary conserved multi-subunit RNA polymerase II transcriptional regulator complex. The MED25 point mutation is located in the von Willebrand factor type A (MED25 VWA) domain which is responsible for MED25 recruitment into the Mediator complex; co-immunoprecipitation experiment demonstrated that this mutation dramatically impairs MED25 interaction with the Mediator complex in mammalian cells.

Pathogenic variants in the NONO gene have been most recently implicated in X-linked intellectual disability syndrome. This observation has been supported by studies of NONO-deficient mice showing that NONO has an important role in regulating inhibitory synaptic activity. Thus far, the phenotypic spectrum of affected patients remains limited. We applied whole exome sequencing to members of a family in which the proband was presented with a complex phenotype consisting of developmental delay, dysmorphism, and non-compaction cardiomyopathy. Exome analysis identified a novel de novo splice-site variant c.1171+1G>T in exon 11 of NONO gene that is suspected to abolish the donor splicing site. Thus, we propose that the phenotypic spectrum of NONO-related disorder is much broader than described and that pathogenic variants in NONO cause a recognizable phenotype.

The origin and history of the Ashkenazi Jewish population have long been of great interest, and advances in high-throughput genetic analysis have recently provided a new approach for investigating these topics. We and others have argued on the basis of genome-wide data that the Ashkenazi Jewish population derives its ancestry from a combination of sources tracing to both Europe and the Middle East. It has been claimed, however, through a reanalysis of some of our data, that a large part of the ancestry of the Ashkenazi population originates with the Khazars, a Turkic-speaking group that lived to the north of the Caucasus region ~1,000 years ago. Because the Khazar population has left no obvious modern descendants that could enable a clear test for a contribution to Ashkenazi Jewish ancestry, the Khazar hypothesis has been difficult to examine using genetics. Furthermore, because only limited genetic data have been available from the Caucasus region, and because these data have been concentrated in populations that are genetically close to populations from the Middle East, the attribution of any signal of Ashkenazi-Caucasus genetic similarity to Khazar ancestry rather than shared ancestral Middle Eastern ancestry has been problematic. Here, through integration of genotypes from newly collected samples with data from several of our past studies, we have assembled the largest data set available to date for assessment of Ashkenazi Jewish genetic origins. This data set contains genome-wide single-nucleotide polymorphisms in 1,774 samples from 106 Jewish and non-Jewish populations that span the possible regions of potential Ashkenazi ancestry: Europe, the Middle East, and the region historically associated with the Khazar Khaganate. The data set includes 261 samples from 15 populations from the Caucasus region and the region directly to its north, samples that have not previously been included alongside Ashkenazi Jewish samples in genomic studies. Employing a variety of standard techniques for the analysis of population-genetic structure, we found that Ashkenazi Jews share the greatest genetic ancestry with other Jewish populations and, among non-Jewish populations, with groups from Europe and the Middle East. No particular similarity of Ashkenazi Jews to populations from the Caucasus is evident, particularly populations that most closely represent the Khazar region. Thus, analysis of Ashkenazi Jews together with a large sample from the region of the Khazar Khaganate corroborates the earlier results that Ashkenazi Jews derive their ancestry primarily from populations of the Middle East and Europe, that they possess considerable shared ancestry with other Jewish populations, and that there is no indication of a significant genetic contribution either from within or from north of the Caucasus region.

The human WW Domain Containing Oxidoreductase (WWOX) gene was originally described as a tumor suppressor gene. However, recent reports have demonstrated its cardinal role in the pathogenesis of central nervous systems disorders such as epileptic encephalopathy, intellectual disability, and spinocerebellar ataxia. We report on six patients from three unrelated families of full or partial Yemenite Jewish ancestry exhibiting early infantile epileptic encephalopathy and profound developmental delay. Importantly, four patients demonstrated facial dysmorphism. Exome sequencing revealed that four of the patients were homozygous for a novel WWOX c.517-2A > G splice-site variant and two were compound heterozygous for this variant and a novel c.689A > C, p.Gln230Pro missense variant. Complementary DNA sequencing demonstrated that the WWOX c.517-2A > G splice-site variant causes skipping of exon six. A carrier rate of 1:177 was found among Yemenite Jews. We provide the first detailed description of patients harboring a splice-site variant in the WWOX gene and propose that the clinical synopsis of WWOX related epileptic encephalopathy should be broadened to include facial dysmorphism. The increased frequency of the c.517-2A > G splice-site variant among Yemenite Jews coupled with the severity of the phenotype makes it a candidate for inclusion in expanded preconception screening programs.

Approximately 300,000 men around the globe self-identify as Ashkenazi Levites, of whom two thirds were previously shown to descend from a single male. The paucity of whole Y-chromosome sequences precluded conclusive identification of this ancestor's age, geographic origin and migration patterns. Here, we report the variation of 486 Y-chromosomes within the Ashkenazi and non-Ashkenazi Levite R1a clade, other Ashkenazi Jewish paternal lineages, as well as non-Levite Jewish and non-Jewish R1a samples. Cumulatively, the emerging profile is of a Middle Eastern ancestor, self-affiliating as Levite, and carrying the highly resolved R1a-Y2619 lineage, which was likely a minor haplogroup among the Hebrews. A star-like phylogeny, coalescing similarly to other Ashkenazi paternal lineages, ~1,743 ybp, suggests it to be one of the Ashkenazi paternal founders; to have expanded as part of the overall Ashkenazi demographic expansion, without special relation to the Levite affiliation; and to have subsequently spread to non-Ashkenazi Levites.

Concealing coloration in rodents is well established. However, only a few studies examined how soil color, pelage color, hair-melanin content, and genetics (i.e., the causal chain) synergize to configure it. This study investigates the causal chain of dorsal coloration in Israeli subterranean blind mole rats, Spalax ehrenbergi.We examined pelage coloration of 128 adult animals from 11 populations belonging to four species of Spalax ehrenbergi superspecies (Spalax galili, Spalax golani, Spalax carmeli, and Spalax judaei) and the corresponding coloration of soil samples from the collection sites using a digital colorimeter. Additionally, we quantified hair-melanin contents of 67 animals using HPLC and sequenced the MC1R gene in 68 individuals from all four mole rat species.Due to high variability of soil colors, the correlation between soil and pelage color coordinates was weak and significant only between soil hue and pelage lightness. Multiple stepwise forward regression revealed that soil lightness was significantly associated with all pelage color variables. Pelage color lightness among the four species increased with the higher southward aridity in accordance to Gloger's rule (darker in humid habitats and lighter in arid habitats). Darker and lighter pelage colors are associated with darker basalt and terra rossa, and lighter rendzina soils, respectively. Despite soil lightness varying significantly, pelage lightness and eumelanin converged among populations living in similar soil types. Partial sequencing of the MC1R gene identified three allelic variants, two of which were predominant in northern species (S. galili and S. golani), and the third was exclusive to southern species (S. carmeli and S. judaei), which might have caused the differences found in pheomelanin/eumelanin ratio.Darker dorsal pelage in darker basalt and terra rossa soils in the north and lighter pelage in rendzina and loess soils in the south reflect the combined results of crypsis and thermoregulatory function following Gloger's rule.

Chronic granulomatous disease (CGD) is a rare congenital immune deficiency caused by mutations in any of the five genes encoding NADPH oxidase subunits. One of these genes is NCF1, encoding the p47(phox) protein. A group of 39 patients, 14 of whom are of Kavkazi Jewish descent, was investigated for a founder effect for the mutation c.579G>A (p.Trp193Ter) in NCF1. We analyzed various genetic markers in the NCF1 region, including two single nucleotide polymorphisms (SNPs) in NCF1 and two short tandem repeats (STRs) located near NCF1. Most patients were homozygous for the c.579G>A mutation, but three patients were hemizygotes, with a deletion of NCF1 on the other allele, and three patients were compound heterozygotes with another mutation in NCF1. All Kavkazi Jewish patients had a c.295G_c.345T SNP combination in NCF1 and shared a common number of repeats in STR3. In addition, 90% of the Kavkazi Jewish patients shared a common number of repeats in STR1. This uniformity indicates that the c.579G>A mutation in NCF1 was introduced some 1200-2300 years ago in the Kavkazi Jewish population. Variation amongst the other investigated populations from the Middle East indicates that this mutation exists in these non-Kavkazi populations already for more than 5000 years.

Previous research, using habituation techniques with multiple rodent species as subjects, has demonstrated (from kin to across species) the greater perceptual similarity in the qualities of individual odours of more closely genetically related individuals ('odour–genes covariance', abbreviated 'OGC'). This predictable relationship between individual genotypes and individual odours has only been assessed in rodents in which the genetic similarities and dissimilarities are known either through laboratory breeding or by selecting odour donors from different populations or species. To study OGC within a natural population of rodents, we genotyped Spalax galili blind mole rats using ten microsatellite markers, and conducted pairwise genetic distance comparisons to estimate genetic similarity and to calculate the relatedness coefficient between pairs of individuals. We then used habituation-generalization techniques to assess whether perceived odour similarities covaried with the genetic similarities we had identified. Indeed, animals treated odours from genetically closer donors as more similar than odours from less genetically similar donors. The results suggest an accurate and subtle ability to resolve genetically determined odour distinctions among familially unrelated animals within a population. Graded differential responses to conspecific odours based on degrees of similarity between other individuals' odours and one's own have been demonstrated in kinship and species discriminations and preferences. The evidence presented here provides the basis for hypothesizing a similar process that could promote optimal outbreeding and inclusive fitness within populations of conspecifics. The evolutionary implications of these findings are discussed.

Background Dandy-Walker malformation features agenesis/hypoplasia of the cerebellar vermis, cystic dilatation of the fourth ventricle and enlargement of posterior fossa. Although Dandy-Walker malformation is relatively common and several genes were linked to the syndrome, the genetic cause in the majority of cases is unknown. Objective To identify the mutated gene responsible for Dandy-Walker malformation, kidney disease and bone marrow failure in four patients from two unrelated families. Methods Medical assessment, sonographic, MRI and pathological studies were used to define phenotype. Chromosomal microarray analysis and whole-exome sequence were performed to unravel the genotype. Results We report four subjects from two unrelated families with homozygous mutations in the Exocyst Complex Component 3-Like-2 gene ( EXOC3L2 ). EXOC3L2 functions in trafficking of post-Golgi vesicles to the plasma membrane. In the first family a missense mutation in a highly conserved amino acid, p.Leu41Gln, was found in three fetuses; all had severe forms of Dandy-Walker malformation that was detectable by prenatal ultrasonography and confirmed by autopsy. In the second family, the affected child carried a nonsense mutation, p.Arg72*, and no detected protein. He had peritrigonal and cerebellar white matter abnormalities with enlargement of the ventricular trigones, developmental delay, pituitary hypoplasia, severe renal dysplasia and bone marrow failure. Conclusion We propose that biallelic EXOC3L2 mutations lead to a novel syndrome that affects hindbrain development, kidney and possibly the bone marrow.

The biological role of the mitochondrial DNA (mtDNA) control region in mtDNA replication remains unclear. In a worldwide survey of mtDNA variation in the general population, we have identified a novel large control region deletion spanning positions 16154 to 16307 (m.16154_16307del154). The population prevalence of this deletion is low, since it was only observed in 1 out of over 120,000 mtDNA genomes studied. The deletion is present in a nonheteroplasmic state, and was transmitted by a mother to her two sons with no apparent past or present disease conditions. The identification of this large deletion in healthy individuals challenges the current view of the control region as playing a crucial role in the regulation of mtDNA replication, and supports the existence of a more complex system of multiple or epigenetically-determined replication origins. Hum Mutat 0,1–5, 2008. © 2008 Wiley-Liss, Inc.

Inherited optic neuropathies are a heterogeneous group of disorders characterized by mild to severe visual loss, colour vision deficit, central or paracentral visual field defects and optic disc pallor. Optic atrophies can be classified into isolated or non-syndromic and syndromic forms. While multiple modes of inheritance have been reported, autosomal dominant optic atrophy and mitochondrial inherited Leber's hereditary optic neuropathy are the most common forms. Optic atrophy type 1, caused by mutations in the OPA1 gene is believed to be the most common hereditary optic neuropathy, and most patients inherit a mutation from an affected parent. In this study we used whole-exome sequencing to investigate the genetic aetiology in a patient affected with isolated optic atrophy. Since the proband was the only affected individual in his extended family, and was a product of consanguineous marriage, homozygosity mapping followed by whole-exome sequencing were pursued. Exome results identified a novel de novo OPA1 mutation in the proband. We conclude, that though de novo OPA1 mutations are uncommon, testing of common optic atrophy-associated genes such as mitochondrial mutations and OPA1 gene sequencing should be performed first in single individuals presenting with optic neuropathy, even when dominant inheritance is not apparent.

A recent meta-analysis described a variant (p.Ile2984Val) in the cubilin gene (CUBN) that is associated with levels of albuminuria in the general population and in diabetics.We implemented a Linkage Disequilibrium (LD) search with data from the 1000 Genomes Project, on African and European population genomic sequences.We found that the p.Ile2984Val variation is part of a larger haplotype in European populations and it is almost absent in west Africans. This haplotype contains 19 single nucleotide polymorphisms (SNPs) in very high LD, three of which are missense mutations (p.Leu2153Phe, p.Ile2984Val, p.Glu3002Gly), and two have not been previously reported. Notably, this European haplotype is absent in west African populations, and the frequency of each individual polymorphism differs significantly in Africans.Genotyping of these variants in existing African origin sample sets coupled to measurements of urine albumin excretion levels should reveal which is the most likely functional candidate for albuminuria risk. The unique haplotypic structure of CUBN in different populations may leverage the effort to identify the functional variant and to shed light on evolution of the CUBN gene locus.

The origin and history of the Ashkenazi Jewish population have long been of great interest, and advances in high-throughput genetic analysis have recently provided a new approach for investigating these topics. We and others have argued on the basis of genome-wide data that the Ashkenazi Jewish population derives its ancestry from a combination of sources tracing to both Europe and the Middle East. It has been claimed, however, through a reanalysis of some of our data, that a large part of the ancestry of the Ashkenazi population originates with the Khazars, a Turkic-speaking group that lived to the north of the Caucasus region ~1,000 years ago. Because the Khazar population has left no obvious modern descendants that could enable a clear test for a contribution to Ashkenazi Jewish ancestry, the Khazar hypothesis has been difficult to examine using genetics. Furthermore, because only limited genetic data have been available from the Caucasus region, and because these data have been concentrated in populations that are genetically close to populations from the Middle East, the attribution of any signal of Ashkenazi-Caucasus genetic similarity to Khazar ancestry rather than shared ancestral Middle Eastern ancestry has been problematic. Here, through integration of genotypes from newly collected samples with data from several of our past studies, we have assembled the largest data set available to date for assessment of Ashkenazi Jewish genetic origins. This data set contains genome-wide single-nucleotide polymorphisms in 1,774 samples from 106 Jewish and non-Jewish populations that span the possible regions of potential Ashkenazi ancestry: Europe, the Middle East, and the region historically associated with the Khazar Khaganate. The data set includes 261 samples from 15 populations from the Caucasus region and the region directly to its north, samples that have not previously been included alongside Ashkenazi Jewish samples in genomic studies. Employing a variety of standard techniques for the analysis of population-genetic structure, we found that Ashkenazi Jews share the greatest genetic ancestry with other Jewish populations and, among non-Jewish populations, with groups from Europe and the Middle East. No particular similarity of Ashkenazi Jews to populations from the Caucasus is evident, particularly populations that most closely represent the Khazar region. Thus, analysis of Ashkenazi Jews together with a large sample from the region of the Khazar Khaganate corroborates the earlier results that Ashkenazi Jews derive their ancestry primarily from populations of the Middle East and Europe, that they possess considerable shared ancestry with other Jewish populations, and that there is no indication of a significant genetic contribution either from within or from north of the Caucasus region.

We study Phylotree, a comprehensive representation of the phylogeny of global human mitochondrial DNA (mtDNA) variations, to better understand the mtDNA substitution mechanism and its most influential factors. We consider a substitution model, where a set of genetic features may predict the rate at which mtDNA substitutions occur. To find an appropriate model, an exhaustive analysis on the effect of multiple factors on the substitution rate is performed through Negative Binomial and Poisson regressions. We examine three different inclusion options for each categorical factor: omission, inclusion as an explanatory variable, and by-value partitioning. The examined factors include genes, codon position, a CpG indicator, directionality, nucleotide, amino acid, codon, and context (neighboring nucleotides), in addition to other site based factors. Partitioning a model by a factor's value results in several sub-models (one for each value), where the likelihoods of the sub-models can be combined to form a score for the entire model. Eventually, the leading models are considered as viable candidates for explaining mtDNA substitution rates.Initially, we introduce a novel clustering technique on genes, based on three similarity tests between pairs of genes, supporting previous results regarding gene functionalities in the mtDNA. These clusters are then used as a factor in our models. We present leading models for the protein coding genes, rRNA and tRNA genes and the control region, showing it is disadvantageous to separate the models of transitions/transversions, or synonymous/non-synonymous substitutions. We identify a context effect that cannot be attributed solely to protein level constraints or CpG pairs. For protein-coding genes, we show that the substitution model should be partitioned into sub-models according to the codon position and input codon; additionally we confirm that gene identity and cluster have no significant effect once the above factors are accounted for.We leverage the large, high-confidence Phylotree mtDNA phylogeny to develop a new statistical approach. We model the substitution rates using regressions, allowing consideration of many factors simultaneously. This admits the use of model selection tools helping to identify the set of factors best explaining the mutational dynamics when considered in tandem.

No AccessJournal of UrologyAdult Urology1 May 2021Mutations in HOGA1 do Not Confer a Dominant Phenotype Manifesting as Kidney Stone Disease Roi Bar, Efrat Ben-Shalom, Mordechai Duvdevani, Ruth Belostotsky, Martin R Pollak, David B. Mount, Ruth Bar-Gal, Ehud Gnessin, Shay Tzur, Gary C Curhan, and Yaacov Frishberg Roi BarRoi Bar Division of Pediatric Nephrology, Shaare Zedek Medical Center, Jerusalem, Israel Equal study contribution. More articles by this author , Efrat Ben-ShalomEfrat Ben-Shalom Division of Pediatric Nephrology, Shaare Zedek Medical Center, Jerusalem, Israel Equal study contribution. More articles by this author , Mordechai DuvdevaniMordechai Duvdevani Department of Urology, Hadassah Hebrew University Hospital, Jerusalem, Israel More articles by this author , Ruth BelostotskyRuth Belostotsky Division of Pediatric Nephrology, Shaare Zedek Medical Center, Jerusalem, Israel More articles by this author , Martin R PollakMartin R Pollak Division of Nephrology, Beth Israel Deaconess Medical Center, Boston, Massachusetts More articles by this author , David B. MountDavid B. Mount Division of Nephrology, Brigham and Women’s Hospital, Boston, Massachusetts More articles by this author , Ruth Bar-GalRuth Bar-Gal Division of Pediatric Nephrology, Shaare Zedek Medical Center, Jerusalem, Israel More articles by this author , Ehud GnessinEhud Gnessin Department of Urology, Shaare Zedek Medical Center, Jerusalem, Israel More articles by this author , Shay TzurShay Tzur Genomic Research Department, Emedgene Technologies, Tel Aviv, Israel More articles by this author , Gary C CurhanGary C Curhan Division of Nephrology, Brigham and Women’s Hospital, Boston, Massachusetts More articles by this author , and Yaacov FrishbergYaacov Frishberg †Correspondence: Division of Pediatric Nephrology, Shaare Zedek Medical Center, Shmu’el Bait St 12, Jerusalem, 9103102, Israel telephone: 972 2 6666144; FAX: 972 2 6555484; E-mail Address: [email protected] Division of Pediatric Nephrology, Shaare Zedek Medical Center, Jerusalem, Israel More articles by this author View All Author Informationhttps://doi.org/10.1097/JU.0000000000001528AboutFull TextPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail Abstract Purpose: The etiology of calcium-oxalate kidney stone formation remains elusive. Biallelic mutations in HOGA1 are responsible for primary hyperoxaluria type 3 and result in oxalate overproduction and kidney stone disease. Our previous study showed that carriers of HOGA1 mutations have elevated urinary levels of oxalate precursors. In this study we explored the possibility that mutations in HOGA1 confer a dominant phenotype in the form of kidney stone disease or hyperoxaluria. Materials and Methods: An observational analytic case control study was designed to determine the prevalence of pathogenic HOGA1 mutations among adults with calcium-oxalate kidney stone disease. Given the high prevalence of HOGA1 mutations among Ashkenazi Jews, this group was evaluated separately. Carrier frequency of any of the 52 reported pathogenic mutations was compared to data derived from gnomAD for the corresponding ethnic group. Sanger sequencing of HOGA1 gene was performed on DNA samples from the following groups: 60 Ashkenazi Jews and 86 nonAshkenazi calcium-oxalate stone formers, 150 subjects with low and 150 with high urinary oxalate levels. Results: The carrier prevalence of pathogenic mutations among the Ashkenazi Jews was 1.7% compared to 2.8% in the corresponding control group (p=0.9 OR=0.6 95% CI 0.01–3.51). We did not detect any mutation among the nonAshkenazi study group. No correlation was detected between hyperoxaluria and HOGA1 variants. Conclusions: This study shows that mutations in HOGA1 do not confer a dominant phenotype in the form of calcium-oxalate kidney stone disease or hyperoxaluria. References 1. : Urologic diseases in America project: prevalence of kidney stones in the United States. Eur Urol 2012; 62: 160. Google Scholar 2. : Quality of life of patients with nephrolithiasis and recurrent painful renal colic. Nephron Clin Pract 2007; 106: 91. Google Scholar 3. : Nephrolithiasis and loss of kidney function. Curr Opin Nephrol Hypertens 2013; 22: 390. Google Scholar 4. : Alberta Kidney Disease Network: kidney stones and cardiovascular events: a cohort study. Clin J Am Soc Nephrol 2014; 9: 506. Google Scholar 5. : History of kidney stones and risk of coronary heart disease. JAMA 2013; 310: 408. Google Scholar 6. : Urinary stone composition in Israel: current status and variation with age and sex-a Bicester study. J Endourology 2013; 27: 1539. Google Scholar 7. : Clinical practice. Calcium kidney stones. N Engl J Med 2010; 363: 954. Google Scholar 8. : Kidney stone disease. J Clin Invest 2005; 115: 2598. Google Scholar 9. : 24-h uric acid excretion and the risk of kidney stones. Kidney Int 2008; 73: 489. Google Scholar 10. : Primary hyperoxaluria type III gene HOGA1 (formerly DHDPSL) as a possible risk factor for calcium oxalate urolithiasis. CJASN 2011; 6: 2289. Google Scholar 11. : Primary hyperoxaluria type III—a model for studying perturbations in glyoxylate metabolism. J Mol Med 2012; 90: 1497. Google Scholar 12. : 4-Hydroxy-2-oxoglutarate aldolase inactivity in primary hyperoxaluria type 3 and glyoxylate reductase inhibition. Biochim Biophys Acta 2012; 1822: 1544. Google Scholar 13. : Mutations in DHDPSL are responsible for primary hyperoxaluria type III. Am J Hum Genet 2010; 87: 392. Google Scholar 14. : Novel findings in patients with primary hyperoxaluria type III and implications for advanced molecular testing strategies. Eur J Hum Genet 2013; 21: 162. Google Scholar 15. : 4-hydroxyglutamate is a biomarker for primary hyperoxaluria type 3. J Inherit Met Dis Rep 2015; 15: 1. Google Scholar 16. : WINPEPI updated: computer programs for epidemiologists, and their teaching potential. Epidemiol Perspect Innov 2011; 8: 1. Google Scholar 17. : A population-genetic perspective on the similarities and differences among worldwide human populations. Hum Biol 2011; 83: 659. Google Scholar Supported by the Israel Science Foundation. © 2021 by American Urological Association Education and Research, Inc.FiguresReferencesRelatedDetails Volume 205Issue 5May 2021Page: 1394-1399Supplementary Materials Advertisement Copyright & Permissions© 2021 by American Urological Association Education and Research, Inc.Keywordscalcium oxalatekidney calculiprimaryhyperoxaluriaMetricsAuthor Information Roi Bar Division of Pediatric Nephrology, Shaare Zedek Medical Center, Jerusalem, Israel Equal study contribution. More articles by this author Efrat Ben-Shalom Division of Pediatric Nephrology, Shaare Zedek Medical Center, Jerusalem, Israel Equal study contribution. More articles by this author Mordechai Duvdevani Department of Urology, Hadassah Hebrew University Hospital, Jerusalem, Israel More articles by this author Ruth Belostotsky Division of Pediatric Nephrology, Shaare Zedek Medical Center, Jerusalem, Israel More articles by this author Martin R Pollak Division of Nephrology, Beth Israel Deaconess Medical Center, Boston, Massachusetts More articles by this author David B. Mount Division of Nephrology, Brigham and Women’s Hospital, Boston, Massachusetts More articles by this author Ruth Bar-Gal Division of Pediatric Nephrology, Shaare Zedek Medical Center, Jerusalem, Israel More articles by this author Ehud Gnessin Department of Urology, Shaare Zedek Medical Center, Jerusalem, Israel More articles by this author Shay Tzur Genomic Research Department, Emedgene Technologies, Tel Aviv, Israel More articles by this author Gary C Curhan Division of Nephrology, Brigham and Women’s Hospital, Boston, Massachusetts More articles by this author Yaacov Frishberg Division of Pediatric Nephrology, Shaare Zedek Medical Center, Jerusalem, Israel †Correspondence: Division of Pediatric Nephrology, Shaare Zedek Medical Center, Shmu’el Bait St 12, Jerusalem, 9103102, Israel telephone: 972 2 6666144; FAX: 972 2 6555484; E-mail Address: [email protected] More articles by this author Expand All Supported by the Israel Science Foundation. Advertisement Loading ...

Abstract Pheochromocytoma (PCC) is a rare, mostly benign tumour of the adrenal medulla. Hereditary PCC accounts for ~35% of cases and has been associated with germline mutations in several cancer susceptibility genes (e.g., KIF1B , SDHB , VHL , SDHD , RET ). We performed whole-exome sequencing in a family with four PCC-affected patients in two consecutive generations and identified a potential novel candidate pathogenic variant in the REXO2 gene that affects splicing (c.531-1G&gt;T (NM 015523.3)), which co-segregated with the phenotype in the family. REXO2 encodes for RNA exonuclease 2 protein and localizes to 11q23, a chromosomal region displaying allelic imbalance in PCC. REXO2 protein has been associated with DNA repair, replication and recombination processes and thus its inactivation may contribute to tumorigenesis. While the study suggests that this novel REXO2 gene variant underlies PCC in this family, additional functional studies are required in order to establish the putative role of the REXO2 gene in PCC predisposition.

The mitochondrial DNA (mtDNA) control region is a highly variable segment that contains functional elements that control mtDNA transcription and replication. By analysis of the polymorphic nucleotide spectrum of that segment, we aimed to identify the most conserved sites that should be associated with these elements. For that aim, we analyzed 50 033 human mtDNA control region sequences (mtDNA positions 16 066–16 374). We identified 10 conserved tri-nucleotides, one conserved tetra-nucleotide, and one conserved penta-nucleotide, containing six repetitions of the motif CAT, and two of its complement motif ATG (p value < 2 × 10 − 4). Three other appearances of the tri-nucleotide CAT were almost perfectly preserved. The positions of the preserved CAT elements are associated with the location of previously identified termination-associated sequences (TAS) which are the binding locations for proteins involved in mtDNA replication. We, therefore, hypothesize that the CAT tri-nucleotide elements within the control region may be the binding sites for TAS proteins and are directly involved in mtDNA transcription and replication.

Summary Whole-exome sequencing for clinical applications is now an integral part of medical genetics practice. Though most studies are performed in order to establish diagnoses in individuals with rare and clinically unrecognizable disorders, due to the constantly decreasing costs and commercial availability, whole-exome sequencing has gradually become the initial tool to study patients with clinically recognized disorders when more than one gene is responsible for the phenotype or in complex phenotypes, when variants in more than one gene can be the cause for the disease. Here we report a patient presenting with a complex phenotype consisting of severe, adult-onset, dilated cardiomyopathy, hearing loss and developmental delay, in which exome sequencing revealed two genetic variants that are inherited from a healthy mother: a novel missense variant in the CASK gene, mutations in which cause a spectrum of neurocognitive manifestations, and a second variant, in MYBPC3 , that is associated with hereditary cardiomyopathy. We conclude that although the potential for co-occurrence of rare diseases is higher when analyzing undefined phenotypes in consanguineous families, it should also be given consideration in the genetic evaluation of complex phenotypes in non-consanguineous families.

doi:10.1371/journal.pgen.0030104 Correction for: Citation: Behar DM, Rosset S, Blue-Smith J, Balanovsky O, Tzur S, et al. (2007) The Genographic Project public participation mitochondrial DNA database. PLoS Genet 3(6): e104. doi:10.1371/journal.pgen.0030104 The original version of Dataset S1 was truncated. The full dataset follows: Dataset S1The Genographic Project Open Resource Mitochondrial DNA Database (Consented Database) (10.5 MB XLS) Click here for additional data file.(10M, xls)

Background: Concealing coloration in rodents is well established.However, only a few studies examined how soil color, pelage color, hair-melanin content, and genetics (i.e., the causal chain) synergize to configure it.This study investigates the causal chain of dorsal coloration in Israeli subterranean blind mole rats, Spalax ehrenbergi. Methods:We examined pelage coloration of 128 adult animals from 11 populations belonging to four species of Spalax ehrenbergi superspecies (Spalax galili, Spalax golani, Spalax carmeli, and Spalax judaei) and the corresponding coloration of soil samples from the collection sites using a digital colorimeter.Additionally, we quantified hair-melanin contents of 67 animals using HPLC and sequenced the MC1R gene in 68 individuals from all four mole rat species.Results: Due to high variability of soil colors, the correlation between soil and pelage color coordinates was weak and significant only between soil hue and pelage lightness.Multiple stepwise forward regression revealed that soil lightness was significantly associated with all pelage color variables.Pelage color lightness among the four species increased with the higher southward aridity in accordance to Gloger's rule (darker in humid habitats and lighter in arid habitats).Darker and lighter pelage colors are associated with darker basalt and terra rossa, and lighter rendzina soils, respectively.Despite soil lightness varying significantly, pelage lightness and eumelanin converged among populations living in similar soil types.Partial sequencing of the MC1R gene identified three allelic variants, two of which were predominant in northern species (S. galili and S. golani), and the third was exclusive to southern species (S. carmeli and S. judaei), which might have caused the differences found in pheomelanin/eumelanin ratio.Conclusion/Significance: Darker dorsal pelage in darker basalt and terra rossa soils in the north and lighter pelage in rendzina and loess soils in the south reflect the combined results of crypsis and thermoregulatory function following Gloger's rule.

Whole exome sequencing is a diagnostic approach for the identification of molecular etiology in patients with suspected monogenic diseases. In this article we report on our experience with whole-exome sequencing (WES) of DNA samples taken from patients referred for genetic evaluation due to suspected undiagnosed genetic conditions.Exome enrichment was achieved by Nextera Rapid Capture Expanded Exome Kit. Whole-exome sequencing was performed on Illumina HiSeq 2500. Potentially damaging rare variants were selected for familial cosegregation analysis.A total of 39 patients presenting a wide range of phenotypes suspected to have a genetic cause were sent to WES. Approximately 80% were children with neurological phenotypes. Variations having a high probability of being causative were identified in 20 families, achieving a 51.3% molecular diagnostic rate. Among these, 7 exhibited autosomal dominant disease, 12 autosomal recessive diseases and one X-linked disease; 28% of the patients (11/39) were found to carry a novel mutation located in previously reported genes. Novel mutations located in genes not known to be associated with genetic disease were identified in 23% of the patients (9/39).Whole exome sequencing identified the underlying genetic cause in more than half of the patients referred for evaluation in the genetics clinic at the tertiary hospital. These data demonstrate the utility of WES as a powerful tool for effective diagnostics of monogenic genetic diseases.

Abstract We build on the up-to-date version of Phylotree, a comprehensive and continuously updating phylogeny of global human mtDNA variations (van Oven and Kayser 2009), to better understand the substitution mechanism of the mitochondrial DNA (mtDNA) and its most influential factors. We do so by composing Poisson and negative-binomial regression models relating the rate of occurrence of mtDNA substitutions to various factors. Important factors we identify include the identity of the codon at each position, confirming previous findings about the biological significance of different codons for the same amino acid. Importantly, we also identify a significant effect of neighboring sites. This effect cannot be attributed solely to CpG pairs. A similar effect of neighboring sites was recently described for autosomal DNA substitutions, and we speculate it is related to the basic mutational mechanism itself. Once codon composition and context are taken into account, there is no significant difference in substitution rate between different genes in mtDNA.

In brief: This study describes the first skeletal dysplasia caused by a mutation in a microRNA that is not simply inactivating, but modifies the repertoire of target genes.

Table S5. All control region models ordered by their minimal AIC score. (XLSX 64 kb)

Table S3. All rRNA models ordered by their minimal AIC score. (XLSX 65 kb)

Table S2. All protein coding genes models ordered by their minimal AIC score. (XLSB 1472 kb)

Table S4. All tRNA models ordered by their minimal AIC score. (XLSX 178 kb)

Table S1. Uncalibrated time estimations for each node in the Phylotree dataset. (XLSX 177 kb)