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MERLION LUNG CANCER STUDY_2_DNA

ABSTRACT: East-Asian (EA) patients with Non Small Cell Lung Cancer (NSCLC) are associated with a high proportion of non-smoking women, EGFR activating somatic mutations, and clinical responses to tyrosine kinase inhibitors. We identify copy number alterations specific to EA and Western European (WE) NSCLCs and conducted an integrative analysis using transcritomic data for identifying copy-number-driven candidate genes. Samples were hybridized to Affymetrix Genome-Wide Human SNP 6.0 arrays according to the manufacturer’s specifications in the same center.

ORGANISM(S): Homo sapiens

PROVIDER: GSE33848 | GEO | 2011/11/22

SECONDARY ACCESSION(S): PRJNA148175

REPOSITORIES: GEO

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MERLION LUNG CANCER STUDY_2_DNA

Project description:East-Asian (EA) patients with Non Small Cell Lung Cancer (NSCLC) are associated with a high proportion of non-smoking women, EGFR activating somatic mutations, and clinical responses to tyrosine kinase inhibitors. We identify copy number alterations specific to EA and Western European (WE) NSCLCs and conducted an integrative analysis using transcritomic data for identifying copy-number-driven candidate genes. Samples were hybridized to Affymetrix Genome-Wide Human SNP 6.0 arrays according to the manufacturer’s specifications in the same center. 226 lung adenocarcinomas (90 East-Asian and 136 Western-European) were analyzed for copy-number aberrations (CNAs) using a common high resolution SNP microarray platform.

2011-11-22 | E-GEOD-33848 | biostudies-arrayexpress

Copy number profiling of prostate cancers from 40 African American patients

Project description:African American (AA) men have a significantly higher mortality rate from prostate cancer (PCa) compared to European American (EA) men. AA men are twice as likely to die from PCa compared to EA men and 8 times as likely as Asian American men to die from PCa. The biological basis for these differences in PCa mortality are unclear. We carried out Copy Number Alteration (CNA) studies on a new set of 40 highly tumor-enriched primary PCas and matched benign prostate tissues from AA men using high resolution Affymetrix 6.0 SNP arrays and expression array analysis using RNAs (GSE71016) from the same tissues using high purity tumors from AA men and matched benign tissue. We have confirmed the specific loss of 4p16.3 described previously and identified a novel tumor suppressor gene, RGS12 at this locus that shows significantly decreased expression in AA PCa but not EA EA PCa.

2018-06-06 | GSE95726 | GEO

Genomic profiles vary with race and subtype in young African American and European American breast cancer (SNP)

Project description:In the United States, African-American (AA) women are more likely to develop early-onset breast cancer and have historically poorer outcomes due to this disease compared to European-American (EA) women. Here, we analyzed genomic profiles of breast tumors from young women (<50 years old), matched by tumor subtype, histological grade, and ethnicity (African-American, AA, compared to European-American, EA). DNA copy number alterations (CNAs) were analyzed on the Affymetrix Human SNP Array v 6.0 platform. The study provides insight into the genetic component of ethnicity-related breast cancer health disparities. DNA copy number alterations (CNAs) and genotypes were analyzed using the Affymetrix SNP 6.0 platform. Breast tumor samples from young women (< 50 years old) were matched as follows: a matched pair consists of one AA and one EA sample, matched for tumor grade and tumor subtype (based on immunohistochemical analysis of ER, PR, and HER2 status). DNA from forty-four samples (22 AA, 22 EA) was analyzed on the Affymetrix SNP 6.0 array according to manufacturer’s directions.

2013-01-29 | E-GEOD-26232 | biostudies-arrayexpress

Genomic profiles vary with race and subtype in young African American and European American breast cancer (SNP)

2013-01-29 | GSE26232 | GEO

Korean Lung Adenocarcinoma proteogenomics

Project description:Never-smoker lung adenocarcinoma (NSLA) is prevalent in Asian populations and even more in women. Since epidermal growth factor receptor (EGFR) mutations or anaplastic lymphoma kinase (ALK) fusions are major alterations found in NSLA, studies have focused on NSLA with EGFR and ALK alteration (EA), but not for NSLA without EGFR and ALK alteration (NENA). To reveal the proteogenomic landscape of NENA, we selected 101 NSLA tissues without EGFR and ALK by targeted sequencing of 1597 FFPE samples, and performed multiomics analyses including whole genome, transcriptome, methylation EPIC array, total proteome, and phosphoproteome. Genome analysis revealed that TP53 (25%), KRAS (22%), ROS1 fusion (13%), SETD2 (11%), and ERRB2 (9%) were the most frequently mutated genes in NENA. Proteogenomic impact analysis found that STK11 and ERBB2 somatic mutations had more profound effects on cancer-associated genes in NENA. From DNA copy number alteration analysis, we identified 22 prognostic proteins whose expression was controlled through transcriptome from copy number alterations Intriguingly, from gene set enrichment analysis, estrogen signaling emerged as the key pathway activated in NENA compared with EA. Evidence from multiomics analysis including copy number gains in chromosomes 14 and 21, STK11 mutation, and DNA hypomethylation of LLGL2 and ST14, also supported the increased estrogen signaling. Finally, the saracatinib, an Src inhibitor, was suggested as a potential drug for targeting activated estrogen signaling in NENA. Taken together, the proteogenomic landscape for NENA from this study will enhance our understanding of the etiology of NSLA.

2024-03-12 | PXD033360 | Pride

Single-cell transcriptomics of East-Asian pancreatic islets cells

Project description:Single-cell RNA-seq (scRNA-seq) of pancreatic islets have reported on α- and β-cell gene expression in mice and subjects of predominantly European ancestry. We aimed to assess these findings in East-Asian islet-cells. 448 islet-cells were captured from three East-Asian non-diabetic subjects for scRNA-seq. Hierarchical clustering using pancreatic cell lineage genes was used to assign cells into cell-types. Differentially expressed transcripts between α- and β-cells were detected using ANOVA and in silico replications of mouse and human islet cell genes were performed. We identified 118 α, 105 β, 6 δ endocrine cells and 47 exocrine cells. Besides INS and GCG, 26 genes showed differential expression between α- and β-cells. 10 genes showed concordant expression as reported in rodents, while FAM46A was significantly discordant. Comparing our East-Asian data with data from primarily European subjects, we replicated several genes implicated in nuclear receptor activations, acute phase response pathway, glutaryl-CoA/tryptophan degradations and EIF2/AMPK/mTOR signaling. Additionally, we identified protein ubiquitination to be associated among East-Asian β-cells. We report on East-Asian α- and β-cell gene signatures and substantiate several genes/pathways. We identify expression signatures in East-Asian β-cells that perhaps reflects increased susceptibility to cell-death and warrants future validations to fully appreciate their role in East-Asian diabetes pathogenesis.

2017-08-11 | GSE97655 | GEO

Genomewide copy number profiles for breast cancer from Taiwanese women

Project description:The incidence of breast cancer has been rapidly increasing in East Asia. This is the first study of genome wide copy number of breast cancer in East Asia. We conducted this study to compare the genetic alterations between East and West.

2021-05-05 | GSE80526 | GEO

Discovery of common Asian copy number variants using high-resolution array CGH

Project description:Discovery of common Asian copy number variants using a novel integrated high-resolution array CGH and massively parallel DNA sequencing. We attempted to discover common Asian copy number variants (CNVs) from the DNA of 30 Asian women (10 Korean, 10 CHB (HapMap), 10 JPT (HapMap)) using a custom-designed 24M-oligonucleotide Agilent platform (1.1M X 24 slides). The reference sample for aCGH was NA10851 (HapMap CEPH). In addition to the 30 women, 3 more individuals were analyzed as controls (AK1 (Kim, J.I. et al., 2009 Nature), NA12878 and NA19240).

2010-01-13 | GSE19651 | GEO

A framework for identification of actionable cancer genome dependencies in small cell lung cancer

Project description:We analyzed copy numbers of 60 SCLC cell lines using 6.0 SNP-arrays. For a subgroup of 36 cell lines, previously published copy number data was utilized. CEL and SEG files are included for all cell lines, for which copy number data were not publicly available.

2012-09-21 | GSE40142 | GEO

Affymetrix SNP6.0 on Ollier disease-related tumors

Project description:Mutations in the PTH1R gene were reported but these mutations are limited to a small subgroup of patients. The etiology of Ollier disease is unknown. We therefore undertook genome-wide copy number and loss of heterozygosity (LOH) analysis using Affymetrix SNP 6.0 arrays on 37 tumors of 28 Ollier patients in combination with expression array using Illumina Beadarray v3.0 for 7 tumors of 6 patients. We used Affymetrix SNP 6.0 to find out LOH and copy number alterations in Ollier tumors.

2011-08-26 | GSE22984 | GEO

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