Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Novel Rare Copy Number Variants Associated with Tetralogy of Fallot in the Han Chinese Population

ABSTRACT: Tetralogy of Fallot (TOF), the most frequent cyanotic congenital heart disease, occurs as a simplex trait of unknown etiology in the majority of cases. Studies of non-Asian populations suggest that approximately 10% of TOF cases carry a de novo rare copy number variant (CNV) thought to underlie the malformation. A genome-wide CNV analysis was performed in 303 TOF and 302 controls of Han Chinese as well as compared to 1,000 common Chinese database and revealed 166 rare CNVs identified in TOF patients with 119 CNVs further evaluated as potential “TOF-specific CNVs”; 98 were validated by qPCR, and 44 CNVs showed positive results on validation (positive rate 46.9%, 44/98). The genes related to the clinical phenotypes (subpulmonary VSD, bicuspid pulmonary valve, aortic valve overriding more than 75%, and right aortic arch) and the specific CNVs were included in integrating gene-gene interaction network analysis that identified the genes covering the specific CNVs directly or indirectly correlated to TOF and the signaling pathways. Thus, this study identified novel TOF-specific/associate CNVs in the Han Chinese that occurring at higher frequency in the Han Chinese (28.4% in Chr 1-20 and 42.9% in all chromosomes) is reflective of the increased prevalence of TOF in China. These novel CNVs identify new candidate genes for TOF. Our findings provide new insight into the contribution of CNVs to the genetic basis of TOF and identify new genetic loci potentially important to the pathogenesis of TOF

ORGANISM(S): Homo sapiens

PROVIDER: GSE151767 | GEO | 2021/01/01

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

A Map of Copy Number Variations in Chinese Populations

Project description:It has been shown that the human genome contains extensive copy number variations (CNVs). Investigating the medical and evolutionary impacts of CNVs requires the knowledge of locations, sizes and frequency distribution of CNVs within and between populations. However, CNV study of Chinese populations has been underrepresented considering the same efforts in other populations. Here we constructed a Chinese CNV map by using Affymetrix SNP 6 array. We did population analysis with other HapMap populations and identified population specific CNVs as well as candidate CNV regions under selection. Our results serve as a useful resource in further evolutionary and medical studies.

2011-12-31 | GSE30481 | GEO

A Map of Copy Number Variations in Chinese Populations

2011-12-31 | E-GEOD-30481 | biostudies-arrayexpress

Identification of copy number variation using aCGH in Chinese chicken breeds

Project description: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.

2014-10-10 | GSE49889 | GEO

Identification of copy number variation using aCGH in Chinese chicken breeds

2014-10-10 | E-GEOD-49889 | biostudies-arrayexpress

Population Structure, and Selection Signatures underlying High-Altitude Adaptation Inferred from Genome-Wide Copy Number Variations in Chinese Indigenous Cattle

Project description: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. We successfully detected the genome-wide CNVs of 318 individuals from 24 Chinese indigenous cattle breeds and 37 yaks as outgroups. A total of 5,818 autosomal CNV regions (683 bp - 4,477,860 bp in size), covering ~14.34% of the bovine genome (UMD3.1), were identified, showing abundant CNV resources. Neighbor-joining clustering, principal component analysis (PCA), and population admixture analysis based on these CNVs support that most Chinese cattle breeds are hybrids of Bos taurus taurus (hereinafter to be referred as Bos taurus) and Bos taurus indicus (Bos indicus). The distribution patterns of the CNVs could to some extent be related to the geographical backgrounds of the habitat of the breeds, and admixture among cattle breeds from different districts. We analyzed the selective signatures of CNVs positively involved in high-altitude adaptation using pairwise Fst analysis within breeds with a strong Bos taurus background (taurine-type breeds) and within Bos taurus×Bos indicus hybrids, respectively. CNV-overlapping genes with strong selection signatures (at top 0.5% of Fst value), including LETM1 (Fst = 0.490), TXNRD2 (Fst=0.440) and STUB1 (Fst=0.420) within taurine-type breeds, and NOXA1 (Fst = 0.233), RUVBL1 (Fst=0.222) and SLC4A3 (Fst=0.154) within hybrids, were potentially involved in the adaptation to hypoxia. Thus, we provide a new profile of population structure from the CNV aspects of Chinese indigenous cattle and new insights into high-altitude adaptation in cattle.

2020-02-21 | GSE142218 | GEO

Genome-wide copy number variation in Chinese schizophrenia trios

Project description:To reveal the risk CNVs of SZ in Chinese population, we recrited and enrolled 100 Chinese family trios with a schizophrenia affected children and both of their father and mother. SZ was diagnosed according to DSM-IV criteria by two independent psychiatrists. There gDNA we screen the genome-wide CNV using Agilent SurePrint G3 Human CGH Microarray Kit (1x1M) and Agilent sex-matched human DNA was used as reference. The CNV were called by ADM-2 statistical algorithms with a threshold of 6.0. We compared the burden of large rare CNVs and found that SZ probands carried more duplications and less deletions. Furtherly, we performed familial inheritance analysis of transmission disequilibrium and de novo CNV detection, validated several associated CNV loci with SZ susceptibility and also identify eight novel loci conferring risk of SZ

2021-10-01 | E-MTAB-8075 | biostudies-arrayexpress

The effects of chromosomal copy number variations (CNV) on transcriptional programs at single cell resolution in multiple myeloma

Project description:Chromosome copy number variations (CNV) are a near-universal feature of cancer however their specific effects on cellular function are poorly understood. Single-cell RNA sequencing (scRNA-seq) can reveal cellular gene expression however cannot directly link this to CNVs. Here we report scRNA-seq normalization methods that improve inter-cellular expression alignment, increasing the sensitivity of scRNA-seq for CNV detection. We additionally report sciCNV, a tool for inferring CNVs from scRNA-seq data. Together, these tools enable simultaneous profiling of DNA CNV and RNA within single cells. We apply these tools to multiple myeloma and examine the roles of pan cancer CNVs +8q and +1q. Cells with +8q23-24 upregulate MYC, MYC-target genes, mRNA translation, protein synthesis capacity and DEPTOR; and show reduced transcriptome size. Cells with +1q21-44 reconfigure translation to suppress unfolded protein stress and show increased proliferation, oxidative phosphorylation and MCL1. Overall, we report scRNA-seq methods that can reveal the function of CNVs in cancer.

2020-01-13 | GSE141299 | GEO

De novo assembled individual genome does not show advantage against standard reference genome: a demonstration of Chinese Han Population

Project description:We compared standard human reference genome GRCh38 and de novo assembled reference genome HX1 in precision medicine applications for specific ethnics. In order to quantify the HX1 misassembled genes and HX1-specific contigs, we performed RNA-seq and RNC-seq on hepatocellular carcinoma cell lines (MHCC97H, MHCCLM3 and MHCCLM6) which were derived from Chinese Han individuals. In which, RNC-seq datasets of MHCC97H and MHCCLM3 had been published. We found that a considerable fraction of HX1 misassembled genes was expressed in the Chinese Han samples. Furthermore, we found no HX1-specific contigs yielded more than 2.27 FPKM (minimun FPKM of 1 copy/cell transcript) in the Chinese Han sampels.

2019-06-01 | GSE121013 | GEO

Inhibitory Role of Notch1 in Calcific Aortic Valve Disease

Project description:Aortic valve calcification is the most common form of valvular heart disease, but the mechanisms of calcific aortic valve disease (CAVD) are unknown. NOTCH1 mutations are associated with aortic valve malformations and adult-onset calcification in families with inherited disease. The Notch signaling pathway is critical for multiple cell differentiation processes, but its role in the development of CAVD is not well understood. The aim of this study was to investigate the molecular changes that occur with inhibition of Notch signaling in the aortic valve. Notch signaling pathway members are expressed in adult aortic valve cusps, and examination of diseased human aortic valves revealed decreased expression of NOTCH1 in areas of calcium deposition. To identify downstream mediators of Notch1, we examined gene expression changes that occur with chemical inhibition of Notch signaling in rat aortic valve interstitial cells (AVICs). We found significant downregulation of Sox9 along with several cartilage-specific genes that were direct targets of the transcription factor, Sox9. Loss of expression Sox9 has been published to be associated with aortic valve calcification. Utilizing an in vitro porcine aortic valve calcification model system, inhibition of Notch activity resulted in accelerated calcification while stimulation of Notch signaling attenuated the calcific process. Finally, the addition of Sox9 was able to prevent the calcification of porcine AVICs that occurs with Notch inhibition. In conclusion, loss of Notch signaling contributes to aortic valve calcification via a Sox9-dependent mechanism. 3 samples of aortic valve interstitial cells treated with DAPT were compared with 3 samples of aortic valve interstitial cells treated with DMSO

2011-08-25 | E-GEOD-31668 | biostudies-arrayexpress

CGH analyses for the Chinese indigenous pig breeds and commercial pig breeds [Agilent]

Project description: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) 9 Chinese indigenous pig, one Chinese wild boar and 2 commercial pigs were detected using one pig of Duroc as reference. These 12 animals include 1 wild pig, 2 pigs each from Yorkshire and Landrace as the representatives of modern commercial breeds and 9 unrelated individuals selected from 6 Chinese indigenous breeds (2- Tibetan pig, 2- Diannan small-ear pig, 2-Meishan pig, 1- Min pig, 1-Daweizi pig, and 1-Rongchang pig).

2015-06-29 | E-GEOD-49299 | biostudies-arrayexpress

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