Journal
NATURE BIOTECHNOLOGY
Volume 34, Issue 3, Pages 303-+Publisher
NATURE PORTFOLIO
DOI: 10.1038/nbt.3432
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Funding
- US National Institutes of Health [NHGRI P01HG000205, NCI R33CA174575, NHGRI R01HG006137]
- American Cancer Society [RSG-13-297-01-TBG]
- Doris Duke Clinical Foundation
- Clayville Foundation
- Seiler Foundation
- Howard Hughes Medical Institute
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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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