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DOI: 10.1038/nbt.3432
¤ OpenAccess: Green
This work has “Green” OA status. This means it may cost money to access on the publisher landing page, but there is a free copy in an OA repository.
Haplotyping germline and cancer genomes with high-throughput linked-read sequencing
Grace Zheng,Billy T. Lau,Michael Schnall-Levin,Mirna Jarosz,John Bell,Christopher M. Hindson,Sofia Kyriazopoulou-Panagiotopoulou,Donald A Masquelier,Landon Merrill,Jessica M. Terry,Patrice A Mudivarti,Paul W. Wyatt,Rajiv Bharadwaj,Anthony J. Makarewicz,Yuan Li,Phillip Belgrader,Andrew D.F. Price,Adam Lowe,Patrick Marks,Gerard M Vurens,Paul Hardenbol,Luz Montesclaros,Melissa Luo,Lawrence Greenfield,Alexander Wong,David Birch,S. W. Short,Keith P. Bjornson,Pranav Patel,Erik Hopmans,Christina M. Wood,Sukhvinder Kaur,Glenn K. Lockwood,David Stafford,Joshua P Delaney,Indira Wu,Heather Ordonez,Susan M. Grimes,Stephanie Greer,Josephine Y Lee,Kamila Belhocine,Kristina Giorda,Haynes Heaton,Geoffrey P. McDermott,Zachary Bent,Francesca Meschi,Nikola O. Kondov,Ryan J. Wilson,Jorge Bernate,Shawn Gauby,Alex Kindwall,Clara Bermejo,Adrian Fehr,Adrian Chan,Serge Saxonov,Kevin Ness,Benjamin J. Hindson,Hanlee P. Ji
Haplotype
Genome
Biology
2016
Haplotyping of human chromosomes is a prerequisite for cataloguing the full repertoire of genetic variation. We present a microfluidics-based, linked-read sequencing technology that can phase and haplotype germline and cancer genomes using nanograms of input DNA. This high-throughput platform prepares barcoded libraries for short-read sequencing and computationally reconstructs long-range haplotype and structural variant information. We generate haplotype blocks in a nuclear trio that are concordant with expected inheritance patterns and phase a set of structural variants. We also resolve the structure of the EML4-ALK gene fusion in the NCI-H2228 cancer cell line using phased exome sequencing. Finally, we assign genetic aberrations to specific megabase-scale haplotypes generated from whole-genome sequencing of a primary colorectal adenocarcinoma. This approach resolves haplotype information using up to 100 times less genomic DNA than some methods and enables the accurate detection of structural variants.
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“Haplotyping germline and cancer genomes with high-throughput linked-read sequencing” is a paper by Grace Zheng Billy T. Lau Michael Schnall-Levin Mirna Jarosz John Bell Christopher M. Hindson Sofia Kyriazopoulou-Panagiotopoulou Donald A Masquelier Landon Merrill Jessica M. Terry Patrice A Mudivarti Paul W. Wyatt Rajiv Bharadwaj Anthony J. Makarewicz Yuan Li Phillip Belgrader Andrew D.F. Price Adam Lowe Patrick Marks Gerard M Vurens Paul Hardenbol Luz Montesclaros Melissa Luo Lawrence Greenfield Alexander Wong David Birch S. W. Short Keith P. Bjornson Pranav Patel Erik Hopmans Christina M. Wood Sukhvinder Kaur Glenn K. Lockwood David Stafford Joshua P Delaney Indira Wu Heather Ordonez Susan M. Grimes Stephanie Greer Josephine Y Lee Kamila Belhocine Kristina Giorda Haynes Heaton Geoffrey P. McDermott Zachary Bent Francesca Meschi Nikola O. Kondov Ryan J. Wilson Jorge Bernate Shawn Gauby Alex Kindwall Clara Bermejo Adrian Fehr Adrian Chan Serge Saxonov Kevin Ness Benjamin J. Hindson Hanlee P. Ji published in 2016. It has an Open Access status of “green”. You can read and download a PDF Full Text of this paper here.