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Nat Biotechnol. 2016 Mar;34(3):303-11. doi: 10.1038/nbt.3432. Epub 2016 Feb 1.

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

Author information

1
10X Genomics, Pleasanton, California, USA.
2
Stanford Genome Technology Center, Stanford University, Palo Alto, California, USA.
3
Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, California, USA.

Abstract

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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PMID:
26829319
PMCID:
PMC4786454
DOI:
10.1038/nbt.3432
[Indexed for MEDLINE]
Free PMC Article

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