Project description:The conservation and development of chicken has considerably affected human activities, but the admixture history of chicken breeds has so far been poorly demonstrated especially for Chinese indigenous breeds. Using genotypes from 580961 single nucleotide polymorphism markers scored in 1201 animals, we evaluate the genetic diversity (heterozygosity and proportion of polymorphic markers), Linkage disequilibrium (LD) decay, population structure (principal component analysis and neighbor-joining tree), genetic differentiation (FST and genetic distance) and migration events (Treemix and f-statistics) of eight domesticated chicken breeds. All population analytical methods reveal patterns of hybridization which occurred after divergence in Tibetan chicken. We argue that chicken migration and admixture followed by trade have been important forces in shaping modern Chinese chicken genomic variation. Moreover, isolation by distance may play critical role in the shaping genomic variation within Eurasia continent chicken breeds.

2019-10-07 | GSE127968 | GEO

Affymetrix SNP array data for HNSCC samples

Project description:Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from cryopreserved HNSCC samples.

2016-03-29 | GSE74555 | GEO

Affymetrix SNP array data for chicken responses to glycoconjugate vaccination against Campylobacter jejuni

Project description:Affymetrix SNP array data for chicken responses to glycoconjugate vaccination against Campylobacter jejuni

| PRJNA752761 | ENA

Affymetrix SNP array data for 30 NSCLC samples

Project description:In cancer, proto-oncogenes are often altered by genomic amplification. Recent studies have highlighted a role for PDGFRA as an oncogene in non-small cell lung cancer. To characterize 4q12 copy number status in NSCLC, both previously published (Weir et al. PMID 17982442) and unpublished Affymetrix 250K SNP array data for 733 NSCLC samples (628 primary samples, 105 cell lines) were evaluated for copy number aberrations. 4q12 amplifications overlapping the PDGFRA/KIT locus were observed in 31 (4.2%) NSCLC samples. SNP array and FISH analysis indicate that 4q12 is amplified in 3-7% of lung adenocarcinomas and 8-10% of lung squamous cell carcinomas. In addition, the NSCLC cell line NCI-H1703 exhibits focal amplification of PDGFRA and is dependent on PDGFRα activity for cell growth. Treatment of NCI-H1703 cells with PDGFRA-specific shRNAs or with the PDGFRα/KIT small molecule inhibitors imatinib or sunitinib leads to cell growth inhibition. However, these observations do not extend to NSCLC cell lines with lower-amplitude and broader gains of chromosome 4q. Together these observations implicate PDGFRA and KIT as potential oncogenes in NSCLC, but further study is needed to define the specific characteristics of those tumors that could respond to PDGFRα/KIT inhibitors.

2009-09-15 | GSE17429 | GEO

Affymetrix SNP array data for a pediatric acute lymphoblastic leukemia samples

Project description:Affymetrix SNP array data for a pediatric acute lymphoblastic leukemia samples

| PRJNA506710 | ENA

Affymetrix SNP Data array data of pancreatic cancer PDX models

Project description:Affymetrix SNP Data array data of pancreatic cancer PDX models

| PRJNA803543 | ENA