Haplotyping germline and cancer genomes with high-throughput linked-read sequencing.

Autor: Zheng GX; 10X Genomics, Pleasanton, California, USA., Lau BT; Stanford Genome Technology Center, Stanford University, Palo Alto, California, USA., Schnall-Levin M; 10X Genomics, Pleasanton, California, USA., Jarosz M; 10X Genomics, Pleasanton, California, USA., Bell JM; Stanford Genome Technology Center, Stanford University, Palo Alto, California, USA., Hindson CM; 10X Genomics, Pleasanton, California, USA., Kyriazopoulou-Panagiotopoulou S; 10X Genomics, Pleasanton, California, USA., Masquelier DA; 10X Genomics, Pleasanton, California, USA., Merrill L; 10X Genomics, Pleasanton, California, USA., Terry JM; 10X Genomics, Pleasanton, California, USA., Mudivarti PA; 10X Genomics, Pleasanton, California, USA., Wyatt PW; 10X Genomics, Pleasanton, California, USA., Bharadwaj R; 10X Genomics, Pleasanton, California, USA., Makarewicz AJ; 10X Genomics, Pleasanton, California, USA., Li Y; 10X Genomics, Pleasanton, California, USA., Belgrader P; 10X Genomics, Pleasanton, California, USA., Price AD; 10X Genomics, Pleasanton, California, USA., Lowe AJ; 10X Genomics, Pleasanton, California, USA., Marks P; 10X Genomics, Pleasanton, California, USA., Vurens GM; 10X Genomics, Pleasanton, California, USA., Hardenbol P; 10X Genomics, Pleasanton, California, USA., Montesclaros L; 10X Genomics, Pleasanton, California, USA., Luo M; 10X Genomics, Pleasanton, California, USA., Greenfield L; 10X Genomics, Pleasanton, California, USA., Wong A; 10X Genomics, Pleasanton, California, USA., Birch DE; 10X Genomics, Pleasanton, California, USA., Short SW; 10X Genomics, Pleasanton, California, USA., Bjornson KP; 10X Genomics, Pleasanton, California, USA., Patel P; 10X Genomics, Pleasanton, California, USA., Hopmans ES; Stanford Genome Technology Center, Stanford University, Palo Alto, California, USA., Wood C; Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, California, USA., Kaur S; 10X Genomics, Pleasanton, California, USA., Lockwood GK; 10X Genomics, Pleasanton, California, USA., Stafford D; 10X Genomics, Pleasanton, California, USA., Delaney JP; 10X Genomics, Pleasanton, California, USA., Wu I; 10X Genomics, Pleasanton, California, USA., Ordonez HS; 10X Genomics, Pleasanton, California, USA., Grimes SM; Stanford Genome Technology Center, Stanford University, Palo Alto, California, USA., Greer S; Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, California, USA., Lee JY; 10X Genomics, Pleasanton, California, USA., Belhocine K; 10X Genomics, Pleasanton, California, USA., Giorda KM; 10X Genomics, Pleasanton, California, USA., Heaton WH; 10X Genomics, Pleasanton, California, USA., McDermott GP; 10X Genomics, Pleasanton, California, USA., Bent ZW; 10X Genomics, Pleasanton, California, USA., Meschi F; 10X Genomics, Pleasanton, California, USA., Kondov NO; 10X Genomics, Pleasanton, California, USA., Wilson R; 10X Genomics, Pleasanton, California, USA., Bernate JA; 10X Genomics, Pleasanton, California, USA., Gauby S; 10X Genomics, Pleasanton, California, USA., Kindwall A; 10X Genomics, Pleasanton, California, USA., Bermejo C; 10X Genomics, Pleasanton, California, USA., Fehr AN; 10X Genomics, Pleasanton, California, USA., Chan A; 10X Genomics, Pleasanton, California, USA., Saxonov S; 10X Genomics, Pleasanton, California, USA., Ness KD; 10X Genomics, Pleasanton, California, USA., Hindson BJ; 10X Genomics, Pleasanton, California, USA., Ji HP; Stanford Genome Technology Center, Stanford University, Palo Alto, California, USA.; Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, California, USA.
Jazyk: angličtina
Zdroj: Nature biotechnology [Nat Biotechnol] 2016 Mar; Vol. 34 (3), pp. 303-11. Date of Electronic Publication: 2016 Feb 01.
DOI: 10.1038/nbt.3432
Abstrakt: 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.
Databáze: MEDLINE
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