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SNP array analysis of lung cancer NCI-H1395, diluted to different tumor cell concentrations

ABSTRACT: In vitro mix of DNA from patient-matched lung cancer and blood cell lines, representing 30,50,70,100% tumor cell tissue, analyzed on Affymetrix 6.0 arrays.

ORGANISM(S): Homo sapiens

PROVIDER: GSE29172 | GEO | 2011/09/09

SECONDARY ACCESSION(S): PRJNA139979

REPOSITORIES: GEO

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SNP array analysis of lung cancer NCI-H1395, diluted to different tumor cell concentrations

Project description:In vitro mix of DNA from patient-matched lung cancer and blood cell lines, representing 30,50,70,100% tumor cell tissue, analyzed on Affymetrix 6.0 arrays. Lung cancer cell line H-1395 and patient-matched blood cell line BL1395 were obtained from ATCC and cultured according to their recommendations. DNA extraction was performed using the DNeasy Tissue Kit (Qiagen, Hilden, Germany). DNA from patient-matched Lung cancer and Blood cell lines NCI-H1395 and NCI-BL1395 were mixed to simulate tumor tissue with 30,50,70,100% cancer cells. The DNA ratio was adjusted to compensate for NCI-H1395 being nearly triploid. DNA was analyzed on Affymetrix SNP6.0 microarrays according to the manufacturer's protocol.

2011-09-08 | E-GEOD-29172 | biostudies-arrayexpress

Affymetrix SNP array data for 29 MCL cases

2013-11-04 | GSE46969 | GEO

Affymetrix SNP 6.0 array data from neuroendocrine primary tumor and its metastasis

2012-07-17 | GSE39371 | GEO

Affymetrix SNP array data for 29 MCL cases

Project description:DNA from four 29 cases, 38 tumor samples (23 PB, 12 LN, 1 Tonsil, 1 colonic biopsy, 1 spleen) and 29 normal DNA from the same patients were analyzed with Affymetrix SNP 6.0 platform for copy number alterations study. Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from blood samples, lymph nodes and other tissues like spleen, tonsil and colonic biopsy Copy number analysis of Affymetrix SNP 6.0 arrays was performed for 29 MCL cases samples and their respective matched non-tumor DNA, which were used as references for copy number inference.

2013-11-04 | E-GEOD-46969 | biostudies-arrayexpress

Affymetrix SNP-array data for splenic diffuse red pulp lymphoma samples

Project description:Deep characterization of a large series of splenic diffuse red pulp lymphomas DNA from 5 tumor samples, corresponding to 4 cases, were analyzed with Affymetrix SNP 6.0 platform for copy number alteration study.

2017-12-23 | GSE65052 | GEO

Affymetrix SNP array data for hepatocellular carcinoma tissue

Project description:Genetic variations play an important role in tumor development and metastasis. Hepatocellular carcinoma (HCC) is one of leading cause of cancer-related death. Despite improvements in surveillance and clinical treatment strategies, the prognosis of HCC remains dismal. Affymetrix SNP 6.0 array were used to evaluate the genetic characteristics of tumor DNA in 30 HBV-related HCC patients who were underwent liver transplantation. Recurrence related SNPs were selected and validated.

2012-10-26 | GSE29667 | GEO

Affymetrix SNP 6.0

Project description:Affymetrix SNP 6.0

| EGAD00010001253 | EGA

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

Affymetrix SNP 6.0 array data from neuroendocrine primary tumor and its metastasis

Project description:Reports on common mutations in neuroendocrine tumors (NET) are rare and clonality of NET metastases has not been investigated in this tumor entity yet. We selected a NET and a the corresponding lymph node and liver metastases as well as the derivative cell lines to screen for somatic mutations in the primary NET and to track the fate of genetic changes (by Affymetrix SNP 6.0 micorarray and targeted resequencing by 454 GS FLX) and during metastasis and in vitro progression. using Affymetrix SNP 6.0 Arrays. Affymetrix SNP 6.0 arrays were performed according to the manufacturer's directions on DNA extracted from cryo material or cell lines. Copy number analysis of Affymetrix SNP 6.0 arrays was performed for 4 samples. 60 samples from HapMap database were used as references for copy number inference.

2012-07-16 | E-GEOD-39371 | biostudies-arrayexpress

Affymetrix SNP array data for hepatocellular carcinoma tissue

2012-10-26 | E-GEOD-29667 | biostudies-arrayexpress

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