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Haplotyping germline and cancer genomes with high-throughput linked-read sequencing
Open accessAbstract
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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Metadata
- Authors
- Zheng, G. X. Y., Lau, B. T., Schnall-Levin, M., Jarosz, M., Bell, J. M., Hindson, C. M., Kyriazopoulou-Panagiotopoulou, S., Masquelier, D. A., Merrill, L., Terry, J. M., Mudivarti, P. A., Wyatt, P. W., Bharadwaj, R., Makarewicz, A. J., Li, Y., Belgrader, P., Price, A. D., Lowe, A. J., Marks, P., Vurens, G. M., Hardenbol, P., Montesclaros, L., Luo, M., Greenfield, L., Wong, A., Birch, D. E., Short, S. W., Bjornson, K. P., Patel, P., Hopmans, E. S., Wood, C., Kaur, S., Lockwood, G. K., Stafford, D., Delaney, J. P., Wu, I., Ordonez, H. S., Grimes, S. M., Greer, S., Lee, J. Y., Belhocine, K., Giorda, K. M., Heaton, W. H., McDermott, G. P., Bent, Z. W., Meschi, F., Kondov, N. O., Wilson, R., Bernate, J. A., Gauby, S., Kindwall, A., Bermejo, C., Fehr, A. N., Chan, A., Saxonov, S., Ness, K. D., Hindson, B. J., & Ji, H. P.
- Venue
- Nature Biotechnology
- Published
- 2016-02-01
- Volume
- 34
- Issue
- 3
- Pages
- 303-311
- ISSN
- 0733-222X (ISSN-L)
- 1087-0156
- 1546-1696
- OpenAlex
- W2264578395
- Cited by
- 677
- References
- 10
- FWCI
- 40.93
- Type
- journal article
- Language
- en
- Open access
- green
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