Microarray Analysis of Copy Number Variants on the Human Y Chromosome Reveals Novel and Frequent Duplications Overrepresented in Specific Haplogroups

PloS One
Martin M JohanssonElena Jazin

Abstract

The human Y chromosome is almost always excluded from genome-wide investigations of copy number variants (CNVs) due to its highly repetitive structure. This chromosome should not be forgotten, not only for its well-known relevance in male fertility, but also for its involvement in clinical phenotypes such as cancers, heart failure and sex specific effects on brain and behaviour. We analysed Y chromosome data from Affymetrix 6.0 SNP arrays and found that the signal intensities for most of 8179 SNP/CN probes in the male specific region (MSY) discriminated between a male, background signals in a female and an isodicentric male containing a large deletion of the q-arm and a duplication of the p-arm of the Y chromosome. Therefore, this SNP/CN platform is suitable for identification of gain and loss of Y chromosome sequences. In a set of 1718 males, we found 25 different CNV patterns, many of which are novel. We confirmed some of these variants by PCR or qPCR. The total frequency of individuals with CNVs was 14.7%, including 9.5% with duplications, 4.5% with deletions and 0.7% exhibiting both. Hence, a novel observation is that the frequency of duplications was more than twice the frequency of deletions. Another striking result was t...Continue Reading

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Citations

Jun 1, 2016·Molecular Psychiatry·I KushimaN Ozaki
Nov 7, 2016·Human Genetics·Francesc Calafell, Maarten H D Larmuseau
Aug 17, 2019·Journal of Assisted Reproduction and Genetics·Vertika SinghKiran Singh
Feb 1, 2018·Annals of Human Biology·Maarten H D Larmuseau, Claudio Ottoni
Jan 18, 2021·Journal of Assisted Reproduction and Genetics·Xiangyin LiuYang Yu
Nov 12, 2020·Revista Da Sociedade Brasileira De Medicina Tropical·Oscar LassenAdela Sembaj

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Datasets Mentioned

BETA
GSE21661

Methods Mentioned

BETA
Genotyping
PCR
electrophoresis
traditional
chip
PCA

Software Mentioned

UCSC genome browser
GIGAS
Statistical Package for Social Sciences Statistical Software
JMP
Affymetrix
SPSS
AMY
Affymetrix Genotyping Console

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