Comparative analyses across cattle genders and breeds reveal the pitfalls caused by false positive and lineage-differential copy number variations

被引：21

作者：

Zhou, Yang ^{[1
,2
]}

Utsunomiya, Yuri T. ^{[3
]}

Xu, Lingyang ^{[1
,4
]}

Hay, El Hamidi Abdel ^{[1
]}

Bickhart, Derek M. ^{[1
]}

Sonstegard, Tad S. ^{[1
,6
]}

Van Tassell, Curtis P. ^{[1
]}

Garcia, Jose Fernando ^{[3
,5
]}

Liu, George E. ^{[1
]}

机构：

[1] ARS, Anim Genom & Improvement Lab, BARC, USDA, Beltsville, MD 20705 USA

[2] Northwest A&F Univ, Coll Anim Sci & Technol, Shaanxi Key Lab Agr Mol Biol, Yangling 712100, Shaanxi, Peoples R China

[3] UNESP Univ Estadual Paulista, Fac Ciencias Agr & Vet, Dept Med Vet Prevent & Reprod Anim, BR-14884900 Sao Paulo, Brazil

[4] Chinese Acad Agr Sci, Inst Anim Sci, Beijing 100193, Peoples R China

[5] UNESP Univ Estadual Paulista, Fac Med Vet Aracatuba, Dept Apoio Prod & Saude Anim, BR-16050680 Sao Paulo, Brazil

[6] Recombinetics Inc, St Paul, MN 55104 USA

来源：

SCIENTIFIC REPORTS | 2016年 / 6卷

基金：

美国食品与农业研究所;

关键词：

GENOME-WIDE DETECTION; SEGMENTAL DUPLICATIONS; STRUCTURAL VARIATION; ASSEMBLY ERRORS; HOLSTEIN CATTLE; INTEGRATED MAP; BLACK ANGUS; SNP; VARIANTS; SEQUENCE;

D O I：

10.1038/srep29219

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

We compared CNV region (CNVR) results derived from 1,682 Nellore cattle with equivalent results derived from our previous analysis of Bovine HapMap samples. By comparing CNV segment frequencies between different genders and groups, we identified 9 frequent, false positive CNVRs with a total length of 0.8 Mbp that were likely caused by assembly errors. Although there was a paucity of lineage specific events, we did find one 54 kb deletion on chr5 significantly enriched in Nellore cattle. A few highly frequent CNVRs present in both datasets were detected within genomic regions containing olfactory receptor, ATP-binding cassette, and major histocompatibility complex genes. We further evaluated their impacts on downstream bioinformatics and CNV association analyses. Our results revealed pitfalls caused by false positive and lineage-differential copy number variations and will increase the accuracy of future CNV studies in both taurine and indicine cattle.

引用

页数：9

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