2-AIN-505, 2-AIN-251: Seminár z bioinformatiky (1) a (3)
Zima 2019

Michal Levy-Sakin, Steven Pastor, Yulia Mostovoy, Le Li, Alden K. Y. Leung, Jennifer McCaffrey, Eleanor Young, Ernest T. Lam, Alex R. Hastie, Karen H. Y. Wong, Claire Y. L. Chung, Walfred Ma, Justin Sibert, Ramakrishnan Rajagopalan, Nana Jin, Eugene Y. C. Chow, Catherine Chu, Annie Poon, Chin Lin, Ahmed Naguib, Wei-Ping Wang, Han Cao, Ting-Fung Chan, Kevin Y. Yip, Ming Xiao, Pui-Yan Kwok. Genome maps across 26 human populations reveal population-specific patterns ofstructural variation. Nat Commun, 10(1):1025. 2019.

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Large structural variants (SVs) in the human genome are difficult to detect and
study by conventional sequencing technologies. With long-range genome analysis
platforms, such as optical mapping, one can identify large SVs (>2 kb) across the
genome in one experiment. Analyzing optical genome maps of 154 individuals from
the 26 populations sequenced in the 1000 Genomes Project, we find that
phylogenetic population patterns of large SVs are similar to those of single
nucleotide variations in 86% of the human genome, while ~2% of the genome has
high structural complexity. We are able to characterize SVs in many intractable
regions of the genome, including segmental duplications and subtelomeric,
pericentromeric, and acrocentric areas. In addition, we discover ~60 Mb of
non-redundant genome content missing in the reference genome sequence assembly.
Our results highlight the need for a comprehensive set of alternate haplotypes
from different populations to represent SV patterns in the genome.