Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Rare and novel variants identified in Black Parkinson’s disease patients

ABSTRACT: Targeted resequencing identifies rare and novel sequence variants in Black South African and Nigerian Parkinson’s disease patients

PROVIDER: PRJEB30330 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ERR3013350.fastq.gz	Fastqsanger.gz
	ERR3013360.fastq.gz	Fastqsanger.gz
	ERR3013370.fastq.gz	Fastqsanger.gz
	ERR3013380.fastq.gz	Fastqsanger.gz
	ERR3013390.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 47

Similar Datasets

Higher self renewal and oncogenic potential of keratinocytes from Black versus White populations linked to the hydroxysteroid dehydrogenase HSD17B7 gene.

Project description:Genotyping of 62 foreskin-derived human primary fibroblasts from individuals of Black African versus Caucasian ancestries.

2021-05-12 | GSE156977 | GEO

Higher self renewal and oncogenic potential of keratinocytes from Black versus White populations linked to the hydroxysteroid dehydrogenase HSD17B7 gene

Project description:Transcriptomic profiling of 54 foreskin-derived human primary keratinocytes from individuals of Black African versus Caucasian ancestries.

2021-05-12 | GSE156011 | GEO

Engaging Black Men in Colorectal Cancer Screening

Project description:To determine the unmet needs, attitudes, barriers and facilitators of African American (AA)/ Black men use of colorectal cancer screening and describe how community leaders such as barbers may act as Community Champions to educate and facilitate screening participation.

| 70579 | ecrin-mdr-crc

Rare-intronic-variants-of-TCF7L2

Project description:Rare intronic variants of TCF7L2 arising by selective sweeps in an indigenous population from Mexico

| PRJEB13132 | ENA

NINDS Parkinson’s Disease

Project description:NINDS Parkinson’s Disease

| PRJNA330889 | ENA

Rare de novo copy number variants in patients with congenital pulmonary atresia

Project description:Ongoing studies using genomic microarrays and next-generation sequencing have demonstrated that the genetic contributions to cardiovascular diseases have been significantly ignored in the past. The aim of this study was to identify rare copy number variants in individuals with congenital pulmonary atresia (PA). Based on the hypothesis that rare structural variants encompassing key genes play an important role in heart development in PA patients, we performed high-resolution genome-wide microarrays for copy number variations (CNVs) in 82 PA patient-parent trios and 189 controls with an Illumina SNP array platform. CNVs were identified in 17/82 patients (20.7%), and eight of these CNVs (9.8%) are considered potentially pathogenic. Five de novo CNVs occurred at two known congenital heart disease (CHD) loci (16p13.1 and 22q11.2). Two de novo CNVs that may affect folate and vitamin B12 metabolism were identified for the first time. A de novo 1-Mb deletion at 17p13.2 may represent a rare genomic disorder that involves mild intellectual disability and associated facial features. high-resolution genome-wide microarrays for copy number variations (CNVs) in 82 PA patient-parent trios and 189 controls with an Illumina SNP array platform. Only 21 samples with potentially pathogenic CNVs are included in this records

2014-04-02 | E-GEOD-56422 | biostudies-arrayexpress

Transcriptome sequencing of a large human family identifies the impact of rare non-coding variants

Project description:We have combined high-quality genome sequencing and RNA-sequencing data within a 17-individual, three generation family. Using these data, we have contrasted cis-acting expression, allele-specific expression and splicing quantitative trait loci (collectively termed eQTLs) within the family to eQTLs discovered within a cell-type and ethnicity-matched population sample. We identified that eQTL that exhibit larger effects in the family compared to the population are enriched for rare regulatory and splicing variants and were more likely to influence essential genes. In addition, we identify several large effect-size eQTLs within the family for genes involved in complex disease. Through analysis of eQTLs in a large family we also report the utility of non-coding genome annotation to predicting the effect of rare non-coding variants. We find that a combination of distance to the transcription start site, evolutionary constraint and epigenetic annotation is considerably more informative for predicting the consequence of rare non-coding variants than for common variants. In summary, through transcriptome analyses within a large family we are able to identify the contribution of rare non-coding variants to expression phenotypes and further demonstrate the predictive potential of diverse non-coding genome annotation for interpretation of the impact of rare non-coding variants. RNA-Sequencing of CEPH/UTAH family 1463

2014-09-01 | E-GEOD-56961 | biostudies-arrayexpress

Cooperation Between PRMT1 and PRMT6 Drives Lung Cancer Health Disparities Among Black/African American Men

Project description:SUMMARY Non-Hispanic Black/African American (Black/AA) men in the United States have disproportionally higher incidence and mortality rates of lung cancer compared to non-Hispanic White (NHW) men. Biological factors are believed to play critical roles in driving the disparities. Nevertheless, large-scale genomic studies fail to identify significant somatic differences in lung cancer driver genes contributing to the disparities. Elevated expression of protein arginine methyltransferases (PRMTs) correlating with poorer prognosis is observed in many cancer types. Here, we observed a higher PRMT6 expression in lung cancer of Black/AA men compared to NHW men. PRMT6 formed a heteromer complex with PRMT1 to catalyze arginine methylation of interleukin enhancer-binding factor 2 essential for cell proliferation. Disrupting PRMT1/PRMT6 heteromer complex by a competitive peptide reduced cell proliferation in non-small cell lung cancer cell lines and lung cancer patient-derived organoids. This work implicates that PRMT1/PRMT6 heteromer complex contributes to poorer lung cancer outcomes in Black/AA men vs. NHW men that could serve as a target to eliminate cancer health disparities.

2023-12-15 | MSV000093674 | MassIVE

Rare LRP6 variants identified in spina bifida patients.

Project description:Several single-nucleotide variants (SNVs) in low-density lipoprotein receptor-related protein 6 (Lrp6) cause neural tube defects (NTDs) in mice. We therefore examined LRP6 in 192 unrelated infants from California with the NTD, spina bifida, and found four heterozygous missense SNVs, three of which were predicted to be deleterious, among NTD cases and not in 190 ethnically matched nonmalformed controls. Parents and siblings could not be tested because of the study design. Like Crooked tail and Ringleschwanz mouse variants, the p.Tyr544Cys Lrp6 protein failed to bind the chaperone protein mesoderm development and impaired Lrp6 subcellular localization to the plasma membrane of MDCK II cells. Only the p.Tyr544Cys Lrp6 variant downregulated canonical Wnt signaling in a TopFlash luciferase reporter in vitro assay. In contrast, three Lrp6 mutants (p.Ala3Val, p.Tyr544Cys, and p.Arg1574Leu) increased noncanonical Wnt/planar cell polarity (PCP) signaling in an Ap1-luciferase assay. Thus, LRP6 variants outside of YWTD repeats could potentially predispose embryos to NTDs, whereas Lrp6 modulation of Wnt/PCP signaling would be more essential than its canonical pathway role in neural tube closure.

| S-EPMC4361299 | biostudies-literature

Bovine nose tissues: Yellow nose vs. Black nose

Project description:The coat color of mammals is determined by the melanogenesis pathway, which is responsible for maintaining the balance between black-brown eumelanin and yellow-reddish phaeomelanin. It is also believed that the color of the bovine nose is regulated in a similar manner; however, the molecular mechanism underlying pigment deposition in the black nose has yet to be elucidated. The aim of the present study was to identify melanogenesis-associated genes that are differentially expressed in the black vs. yellow nose of native Korean cows.

2013-12-26 | GSE53657 | GEO

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