Izvorni znanstveni članak
https://doi.org/10.3325/cmj.2015.56.194
Structural variation on the human Y chromosome from population-scale resequencing
Jose Rodrigo Flores Espinosa
; 1The Wellcome Trust Sanger Institute, Hinxton, UK
Qasim Ayub
; 1The Wellcome Trust Sanger Institute, Hinxton, UK
Yuan Chen
; 1The Wellcome Trust Sanger Institute, Hinxton, UK
Yali Xue
; 1The Wellcome Trust Sanger Institute, Hinxton, UK
Chris Tyler-Smith
; 1The Wellcome Trust Sanger Institute, Hinxton, UK
Sažetak
Aim To investigate the information about Y-structural variants
(SVs) in the general population that could be obtained
by low-coverage whole-genome sequencing.
Methods We investigated SVs on the male-specific portion
of the Y chromosome in the 70 individuals from Africa,
Europe, or East Asia sequenced as part of the 1000 Genomes
Pilot project, using data from this project and from additional
studies on the same samples. We applied a combination
of read-depth and read-pair methods to discover
candidate Y-SVs, followed by validation using information
from the literature, independent sequence and single nucleotide
polymorphism-chip data sets, and polymerase
chain reaction experiments.
Results We validated 19 Y-SVs, 2 of which were novel. Nonreference
allele counts ranged from 1 to 64. The regions
richest in variation were the heterochromatic segments
near the centromere or the DYZ19 locus, followed by the
ampliconic regions, but some Y-SVs were also present in
the X-transposed and X-degenerate regions. In all, 5 of the
27 protein-coding gene families on the Y chromosome
varied in copy number.
Conclusions We confirmed that Y-SVs were readily detected
from low-coverage sequence data and were abundant
on the chromosome. We also reported both common and
rare Y-SVs that are novel
Ključne riječi
Hrčak ID:
144065
URI
Datum izdavanja:
15.6.2015.
Posjeta: 936 *