Haplotyping germline and cancer genomes using high-throughput linked-read sequencing

By Grace X. Y. Zheng, Billy T. Lau, Michael Schnall-Levin, M. Jarosz, John M. Bell, Christopher M. Hindson, S. Kyriazopoulou-Panagiotopoulou, D. Masquelier, Landon Merrill, Jessica M. Terry and 48 more. Nature Biotechnology, 2016

625 citations recorded by the source corpus.

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.

Subfields: Cancer Research, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/3d6d17843c3bbb5a30134ec9d1b71c4a632486d1

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Citations in the corpus

Integrating Hi-C links with assembly graphs for chromosome-scale assembly (2018, background): “…clones (Venter et al. , 1996; Gnerre et al. , 2011), optical maps (Schwartz et al. , 1993; Dong et al. , 2013; Shelton et al. , 2015), linked reads (Zheng et al. , 2016; Weisenfeld et al. , 2017; Yeo et al. , 2017), or chromosomal conformation capture (Simonis et al. , 2006) to order and orient…”
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TGS-GapCloser: A fast and accurate gap closer for large genomes with low coverage of error-prone long reads (2020, neutral): “…in genome sequencing, recent state-of-the-art techniques, such as third-generationsingle-moleculelongreads(TGS)[2,3],syntheticlong read (SLR) libraries [4–6], Hi-C [7], and BioNano physical maps [8], have provided long-range genome information to help increase the contiguity of genome assemblies.”
SvABA: genome-wide detection of structural variants and indels by local assembly (2018, background): “Linked reads are also particularly useful for long-range haplotyping of detected variants (Zheng et al. 2016).”
A reference data set of 5.4 million phased human variants validated by genetic inheritance from sequencing a three-generation 17-member pedigree (2016, positive): “Additionally, because every one of the variants in this catalog is phased, this data set provides a resource to accurately assess emerging technologies designed to provide phasing information (Kitzman et al. 2011; Suk et al. 2011; Zheng et al. 2016).”
Opportunities and challenges in long-read sequencing data analysis (2020, background): “…the potential for accurately assembling and re-assembling genomes [17, 29–32], methylomes [33, 34], variants [18], isoforms [35, 36], haplotypes [37–39], or species [40, 41], tools to analyse the sequencing data provided by long-read sequencing platforms are being actively developed, especially…”
Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation (2016, methodology): “Alternatively, secondary information from technologies like 10x Genomics (Zheng et al. 2016) or Hi-C (Selvaraj et al. 2013) could be used to guide walks through the Canu graph.”
HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies (2017, methodology): “We also used HapCUT2 to assemble haplotypes from 10X Genomics linked-read data (Zheng et al. 2016), which is based on a similar idea as the fosmid-based dilution pool approach.”
Insights into human genetic variation and population history from 929 diverse genomes (2019, methodology): “We constructed 10x Genomics linked-read libraries (14) and sequenced these on IlluminaHiSeq Xmachines for 26 individuals from 13 globally representative populations to physically resolve their haplotype phase and to aid analyses of structural variation.”
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