GEO DataSets

(Submitter supplied) Structural and functional impacts of copy number variations (CNVs) on livestock genomes are not yet well understood. In this study, we have identified 1853 CNV regions (CNVRs) using population-scale sequencing data generated from 75 cattle of 8 breeds (Holstein, Angus, Jersey, Limousin, Romagnola, Brahman, Gir and Nelore). Individual genome sequence coverage ranged from 4 to 30 fold, with a mean of 11.8 fold. more...

Organism:

Bos taurus

Type:

Genome variation profiling by genome tiling array

Platform:

GPL11314

25 Samples

Download data: BED, PAIR

(Submitter supplied) Copy number variations (CNVs) affect a wide range of phenotypic traits; however, CNVs in or near segmental duplication regions are often intractable. Using a read depth approach based on next-generation sequencing, we examined genome-wide copy number differences among five taurine (three Angus, one Holstein and one Hereford) and one indicine (Nelore) cattle. Within mapped chromosomal sequence, we identified 1,265 CNV regions comprising ~55.6 Mbp sequence-476 of which (~38%) have not previously been reported. more...

Organism:

Bos taurus

Type:

Genome variation profiling by genome tiling array

Platform:

GPL11314

5 Samples

Download data: PAIR, TXT

(Submitter supplied) Genomic structural variation is an important and abundant source of genetic and phenotypic variation. Here we describe the first systematic and genome-wide analysis of copy number variations (CNVs) in modern domesticated cattle using array comparative genomic hybridization (array CGH), quantitative PCR (qPCR) and fluorescent in situ hybridization (FISH). The array CGH panel included 90 animals from 11 Bos taurus, 3 Bos indicus and 3 composite breeds for beef, dairy or dual purpose. more...

Organism:

Bos taurus

Type:

Genome variation profiling by genome tiling array

Platforms:

GPL9865 GPL9866

90 Samples

Download data: PAIR, TXT

(Submitter supplied) CNV plays an important role in the chicken genomic studies,it is imperative need to investigate the extent and pattern of CNVs using array comparative genomic hybridization (aCGH) in chinese chicken breeds for future studies associating phenotype to genome architecture. we describe systematic and genome-wide analysis of CNVs loci in five Chinese indigenous chicken breeds were evaluated by aCGH.

Organism:

Gallus gallus

Type:

Genome variation profiling by genome tiling array

Platform:

GPL9799

10 Samples

Download data: PAIR

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Gallus gallus

Type:

Genome variation profiling by genome tiling array

Platforms:

GPL18174 GPL18175

11 Samples

Download data: PAIR, TXT

(Submitter supplied) Copy number variation (CNV) is important and widespread in the genome, and is a major cause of disease and phenotypic diversity. Herein, we perform a genome-wide analysis of CNVs in the 12 diversified chicken genomes based on next-generation sequencing. We apply aCGH experiments to confirm our predicted CNVs. Results from aCGH agree well with our findings and the Pearson’s correlation values between the test and reference samples range from 0.644 to 0.722.

Organism:

Gallus gallus

Type:

Genome variation profiling by genome tiling array

Platform:

GPL18175

3 Samples

Download data: TXT

(Submitter supplied) Copy number variation (CNV) is important and widespread in the genome, and is a major cause of disease and phenotypic diversity. Herein, we perform a genome-wide analysis of CNVs in the 12 diversified chicken genomes based on next-generation sequencing. We apply aCGH experiments to confirm our predicted CNVs. Results from aCGH agree well with our findings and the Pearson’s correlation values between the test and reference samples range from 0.395 to 0.740.

Organism:

Gallus gallus

Type:

Genome variation profiling by genome tiling array

Platform:

GPL18174

8 Samples

Download data: PAIR

(Submitter supplied) Since CNVs play a vital role in genomic studies, it is an imperative need to develop a comprehensive, more accurate and higher resolution porcine CNV map with practical significance in follow-up CNV functional analyses To detect CNV of pigs, we performed high density aCGH data of diverse pig breeds in the framework of the pig draft genome sequence (Sscrofa10.2)

Organism:

Sus scrofa

Type:

Genome variation profiling by genome tiling array

Platform:

GPL17469

12 Samples

Download data: TXT

(Submitter supplied) Chromosomal structural variation can cause alterations in gene dosage and gene regulation between genomes. Structural variants producing a change in the number of copies of a genomic region are termed copy number variants (CNVs). CNVs have been demonstrated to have causative effects on both Mendelian and complex traits, including susceptibility to infectious diseases. We are interested in mapping CNVs to domesticated chicken breeds to help determine structural variation between genomes that influences economically important traits. more...

Organism:

Gallus gallus

Type:

Genome variation profiling by genome tiling array

Platform:

GPL11041

24 Samples

Download data: TXT

(Submitter supplied) Duplicated sequences are the important source of gene innovation and structural variation within mammalian genomes. Using a read depth approach based on next-generation sequencing, we performed a genome-wide analysis of segmental duplications (SDs) and associated copy number variants (CNVs) in water buffalo (Bubalus bubalis). Aligning to the UMD3.1 cattle genome, we estimated 44.6 Mb (~1.73% of cattle genome) segmental duplications in the autosomes and X chromosome using the sequencing reads of Olimpia (the sequenced water buffalo). more...

Organism:

Bubalus bubalis

Type:

Genome variation profiling by genome tiling array

Platform:

GPL25422

14 Samples

Download data: TXT

(Submitter supplied) Copy number variation (CNV) is an important type of genetic variation contributing to phenotypic differences among mammals. Up to now, GWAS analysis using CNV called by array CGH is lacking in livestock like Holstein cattle. The objectives of this work are to identify CNVs using high-density aCGH data and explore functional CNVs which are associated with complex traits by GWAS method in Holstein cattle. more...

Organism:

Bos taurus

Type:

Genome variation profiling by genome tiling array; Third-party reanalysis

Platform:

GPL11314

41 Samples

Download data: PAIR

(Submitter supplied) Investigating genome-wide characteristics of CNVs in 6 horses representing 6 distinct breeds by using the aCGH method and performed GO and KEGG analysis for the CNVs genes.This result is an important complement to the mapping of horse whole-genome CNVs and helpful to study plateau horses’ adaption to the plateau’s environment.

Organism:

Equus caballus

Type:

Genome variation profiling by genome tiling array

Platform:

GPL17952

6 Samples

Download data: PAIR

(Submitter supplied) Copy number variations (CNVs) are an important source of genomic structural variation, and can be used as markers to investigate phenotypic and economic traits. CNVs also have functional effects on gene expression and can contribute to disease susceptibility in mammals. Currently, single nucleotide polymorphism genotyping arrays (SNP chips) are the technology of choice for identifying CNV variations. more...

Organism:

Bos taurus

Type:

Genome variation profiling by SNP array; SNP genotyping by SNP array

Platform:

GPL18258

12 Samples

Download data: CEL, TXT

(Submitter supplied) Copy number variations (CNVs) have been demonstrated as crucial substrates for evolution, adaptation and breed formation. Chinese indigenous cattle breeds exhibit a broad geographical distribution and diverse environmental adaptability. Here, we analyzed the population structure and adaptation to high altitude of Chinese indigenous cattle based on genome-wide CNVs derived from the high-density BovineHD SNP array. more...

Organism:

Bos indicus; Bos grunniens; Bos taurus

Type:

Genome variation profiling by SNP array

Platform:

GPL21267

355 Samples

Download data: IDAT, TXT

(Submitter supplied) Copy number variations (CNVs), which represent a significant source of genetic diversity in mammals, are currently being associated with phenotypes of clinical relevance, mostly in humans and mice. Notwithstanding, little is known about the extent of CNV that contributes to genetic variation in cattle. This study reports the highest resolution map of copy number variation in the cattle genome, with 304 CNV regions (CNVRs) being identified among the genomes of 20 bovine samples from 4 dairy and beef breeds. more...

Organism:

Bos taurus

Type:

Genome variation profiling by genome tiling array

Platforms:

GPL9220 GPL9219 GPL9221

114 Samples

Download data: PAIR

(Submitter supplied) Here we describe a genome-wide analysis of copy number variations (CNVs) in Chinese domestic cattle by using array comparative genomic hybridization (array CGH) and quantitative PCR (qPCR). We conducted array CGH analysis on 30 male cattle individuals, animals from consisting of 12 breeds of Bos taurus/Bos indicus, 1 Bos grunniens and and two ones of Bubalus bubalis breeds for with beef, and/or dairy or dual purpose. more...

Organism:

Bubalus bubalis; Bos taurus; Bos grunniens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL17177

30 Samples

Download data: PAIR, TXT

(Submitter supplied) Background: Detecting genetic variation is a critical step in elucidating the molecular mechanisms underlying phenotypic diversity. Until recently, such detection has mostly focused on single nucleotide polymorphisms (SNPs) because of the ease in screening complete genomes. Another type of variant, copy number variation (CNV), is emerging as a significant contributor to phenotypic variation in many species. more...

Organism:

Gallus gallus

Type:

Genome variation profiling by genome tiling array

Platform:

GPL15501

62 Samples

Download data: TXT

(Submitter supplied) Since CNVs play a vital role in genomic studies, it is an imperative need to develop a comprehensive, more accurate and higher resolution porcine CNV map with practical significance in follow-up CNV functional analyses To detect CNV of pigs, we performed high density aCGH data of diverse pig breeds in the framework of the pig draft genome sequence (Sscrofa10.2)

Organism:

Sus scrofa

Type:

Genome variation profiling by genome tiling array

Platform:

GPL17150

12 Samples

Download data: PAIR

(Submitter supplied) This study used the CanineHD genotyping array to investigate copy number variants in the dog genome in a total of 351 samples from 30 different breeds.

Organism:

Canis lupus familiaris

Type:

Genome variation profiling by SNP array; SNP genotyping by SNP array

Platform:

GPL17481

351 Samples

Download data: TXT

(Submitter supplied) We carried out a cross species cattle-sheep array comparative genome hybridization (aCGH) experiment in order to identify copy number variations (CNVs) in the sheep genome analysing animals of Italian dairy breeds (Sarda, Bagnolese, Laticauda, Massese and Valle del Belice) using a tiling oligonucleotide array with ~385,000 probes designed on the bovine genome. We identified 135 CNV regions (CNVRs) covering about 10.5 Mb of the virtual sheep genome referred to the bovine genome (0.398%) with a mean and median equal to 77.6 kb and 55.9 kb, respectively. more...

Organism:

Bos taurus; Ovis aries

Type:

Genome variation profiling by genome tiling array

Platform:

GPL10990

11 Samples

Download data: PAIR