Browse
Submit Data
Databases
API
Help

Dataset Information

8 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A definitive haplotype map of structural variations determined by microarray analysis of duplicated haploid genomes.

ABSTRACT: Complete hydatidiform moles (CHMs) are tissues carrying duplicated haploid genomes derived from single sperms, and detecting copy number variations (CNVs) in CHMs is assumed to be sensitive and straightforward methods. We genotyped 108 CHM genomes using Affymetrix SNP 6.0 (GEO#: GSE18642) and Illumina 1 M-duo (GEO#: GSE54948). After quality control, we obtained 84 definitive haplotype consisting of 1.7 million SNPs and 2339 CNV regions. The results are presented in the database of our web site (http://orca.gen.kyushu-u.ac.jp/cgi-bin/gbrowse/humanBuild37D4_1/).

SUBMITTER: Tahira T

PROVIDER: S-EPMC4535890 | biostudies-literature | 2014 Dec

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

A definitive haplotype map of structural variations determined by microarray analysis of duplicated haploid genomes.

Tahira Tomoko T Yahara Koji K Kukita Yoji Y Higasa Koichiro K Kato Kiyoko K Wake Norio N Hayashi Kenshi K

Genomics data 20140424

Complete hydatidiform moles (CHMs) are tissues carrying duplicated haploid genomes derived from single sperms, and detecting copy number variations (CNVs) in CHMs is assumed to be sensitive and straightforward methods. We genotyped 108 CHM genomes using Affymetrix SNP 6.0 (GEO#: GSE18642) and Illumina 1 M-duo (GEO#: GSE54948). After quality control, we obtained 84 definitive haplotype consisting of 1.7 million SNPs and 2339 CNV regions. The results are presented in the database of our web site ( ...[more]

PMID: 26484070

Similar Datasets

A definitive haplotype map as determined by genotyping duplicated haploid genomes finds a predominant haplotype preference at copy-number variation events.

Project description:The majority of complete hydatidiform moles (CHMs) harbor duplicated haploid genomes that originate from sperm. This makes CHMs more advantageous than conventional diploid cells for determining haplotypes of SNPs and copy-number variations (CNVs), because all of the genetic variants in a CHM genome are homozygous. Here we report SNP and CNV haplotype structures determined by analysis of 100 CHMs from Japanese subjects via high-density DNA arrays. The obtained haplotype map should be useful as a reference for the haplotype structure of Asian populations. We resolved common CNV regions (merged CNV segments across the examined samples) into CNV events (clusters of CNV segments) on the basis of mutual overlap and found that the haplotype backgrounds of different CNV events within the same CNV region were predominantly similar, perhaps because of inherent structural instability.

| S-EPMC3032077 | biostudies-literature

Whole-genome definitive haplotypes of SNPs and CNVs determined by genotyping duplicated haploid genomes

Project description:Copy number variations (CNVs) constitute the largest portion of the human genome variation. We determined a genome-wide high resolution SNP/CNV haplotype structure of Asians, by analyzing a collection of complete hydatidiform moles (CHMs) of Japanese, using high-density DNA arrays. CHMs are tissues carrying duplicated haploid genomes derived from single sperms, and are suitable material for the detection of CNVs, because they are expected to reveal greater signal to noise ratio in hybridization experiments. Also, the absence of heterozygosity ensures straightforward CNV interpretation without being bothered by overlapping CNV segments. We genotyped 100 CHM genomes using Affymetrix SNP 6.0 and Illumina 1M-duo, created a definitive haplotype map including 1.7 million SNPs and 2339 CNV region (CNVR) that is presented as D-HaploDB Phase 4.1.

2014-02-13 | GSE54948 | GEO

Whole-genome definitive haplotypes of SNPs and CNVs determined by genotyping duplicated haploid genomes

2014-02-13 | E-GEOD-54948 | biostudies-arrayexpress

Definitive SNP/CNV haplotype map of Asians determined using a collection of complete hydatidiform moles

Project description:This SuperSeries is composed of the following subset Series: GSE18642: Definitive SNP/CNV haplotype map of Asians determined using a collection of complete hydatidiform moles (Affymetrix) GSE18663: Definitive SNP/CNV haplotype map of Asians determined using a collection of complete hydatidiform moles (Illumina) Refer to individual Series

2010-05-17 | E-GEOD-18701 | biostudies-arrayexpress

Definitive SNP/CNV haplotype map of Asians determined using a collection of complete hydatidiform moles

Project description:This SuperSeries is composed of the SubSeries listed below.

2010-05-17 | GSE18701 | GEO

Definitive SNP/CNV haplotype map of Asians determined using a collection of complete hydatidiform moles (Illumina)

Project description:Copy number variations (CNVs) are abundant, possibly variable among populations, and can confer various phenotypic variations such as risk to complex disease. We determined a genome-wide high resolution SNP/CNV haplotype structure of Asians, by analyzing a collection of complete hydatidiform moles (CHMs) of Japanese, using high-density DNA arrays. CHMs are tissues carrying duplicated haploid genomes that originated from single sperm, and have advantages as materials over conventional diploid cells in detecting CNVs by hybridization, because greater S/N ratios are expected, and overlapping CNV segments are independently detected without being bothered by possible heterozygous situations. Overall occupancy of CNV segments per haploid found here was at a level similar to previous reports. Approximately a half of our polymorphic CNV regions have not been described in the previous report for Asians, but the frequencies of most of these new CNV regions were low. The limited number of examined samples is likely to be the reason that they have escaped detection in the previous report. Many common CNV regions are resolvable to clusters of CNV segmets (that is, CNV events) on the basis of mutual overlap of the segments. The similarity of haplotype backgrounds surrounding different CNV events within the same CNV regions suggests that ancestral recurrences of CNV events were predominantly haplotype preferential. Illumina Human1M-Duov3 BeadChip analyses were performed according to the manufacturer's directions on DNA extracted from 5 complete hydatidiform moles (CHMs) tissues collected throughout Japan.

2010-05-17 | E-GEOD-18663 | biostudies-arrayexpress

Definitive SNP/CNV haplotype map of Asians determined using a collection of complete hydatidiform moles (Illumina)

2010-05-17 | GSE18663 | GEO

Definitive SNP/CNV haplotype map of Asians determined using a collection of complete hydatidiform moles (Affymetrix)

2010-05-17 | GSE18642 | GEO

Structural variations in plant genomes.

Project description:Differences between plant genomes range from single nucleotide polymorphisms to large-scale duplications, deletions and rearrangements. The large polymorphisms are termed structural variants (SVs). SVs have received significant attention in human genetics and were found to be responsible for various chronic diseases. However, little effort has been directed towards understanding the role of SVs in plants. Many recent advances in plant genetics have resulted from improvements in high-resolution technologies for measuring SVs, including microarray-based techniques, and more recently, high-throughput DNA sequencing. In this review we describe recent reports of SV in plants and describe the genomic technologies currently used to measure these SVs.

| S-EPMC4110416 | biostudies-literature

Structural variations in papaya genomes.

Project description:BackgroundStructural variations (SVs) are a type of mutations that have not been widely detected in plant genomes and studies in animals have shown their role in the process of domestication. An in-depth study of SVs will help us to further understand the impact of SVs on the phenotype and environmental adaptability during papaya domestication and provide genomic resources for the development of molecular markers.ResultsWe detected a total of 8083 SVs, including 5260 deletions, 552 tandem duplications and 2271 insertions with deletion being the predominant, indicating the universality of deletion in the evolution of papaya genome. The distribution of these SVs is non-random in each chromosome. A total of 1794 genes overlaps with SV, of which 1350 genes are expressed in at least one tissue. The weighted correlation network analysis (WGCNA) of these expressed genes reveals co-expression relationship between SVs-genes and different tissues, and functional enrichment analysis shows their role in biological growth and environmental responses. We also identified some domesticated SVs genes related to environmental adaptability, sexual reproduction, and important agronomic traits during the domestication of papaya. Analysis of artificially selected copy number variant genes (CNV-genes) also revealed genes associated with plant growth and environmental stress.ConclusionsSVs played an indispensable role in the process of papaya domestication, especially in the reproduction traits of hermaphrodite plants. The detection of genome-wide SVs and CNV-genes between cultivated gynodioecious populations and wild dioecious populations provides a reference for further understanding of the evolution process from male to hermaphrodite in papaya.

| S-EPMC8108470 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data