2-AIN-506 a 2-AIN-252: Seminár z bioinformatiky (2) a (4)
Leto 2017

Grace X. Y. Zheng, Billy T. Lau, Michael Schnall-Levin, Mirna Jarosz, John M. Bell, Christopher M. Hindson, Sofia Kyriazopoulou-Panagiotopoulou, Donald A. Masquelier, Landon Merrill, Jessica M. Terry, Patrice A. Mudivarti, Paul W. Wyatt, Rajiv Bharadwaj, Anthony J. Makarewicz, Yuan Li, Phillip Belgrader, Andrew D. Price, Adam J. Lowe, Patrick Marks, Gerard M. Vurens, Paul Hardenbol, Luz Montesclaros, Melissa Luo, Lawrence Greenfield, Alexander Wong, David E. Birch, Steven W. Short, Keith P. Bjornson, Pranav Patel, Erik S. Hopmans, Christina Wood, Sukhvinder Kaur, Glenn K. Lockwood, David Stafford, Joshua P. Delaney, Indira Wu, Heather S. Ordonez, Susan M. Grimes, Stephanie Greer, Josephine Y. Lee, Kamila Belhocine, Kristina M. Giorda, William H. Heaton, Geoffrey P. McDermott, Zachary W. Bent, Francesca Meschi, Nikola O. Kondov, Ryan Wilson, Jorge A. Bernate, Shawn Gauby, Alex Kindwall, Clara Bermejo, Adrian N. Fehr, Adrian Chan, Serge Saxonov, Kevin D. Ness, Benjamin J. Hindson, Hanlee P. Ji. Haplotyping germline and cancer genomes with high-throughput linked-read sequencing. Nature biotechnology, 34(3):303-311. 2016.

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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.