Dataset features

Specifications


Dataset type: SNP genotyping by SNP array, Variation
Number of samples: 27
Release date: Aug 10 2009
Last update date: Aug 21 2013
Access: Public
Diseases: Neoplasms, Leukemia-Lymphoma, Adult T-Cell, Precursor T-Cell Lymphoblastic Leukemia-Lymphoma
Chemicals: Zinc
Dataset link WT1 mutations in T-ALL

Experimental Protocol


DNA samples from pediatric T-ALL patients (n=9) obtained at diagnosis, remission and relapse were analyzed with the GeneChip Human Mapping 250K Sty Array (Affymetrix, Santa Clara, California), which contains 238,000 SNPs. Copy number and LOH analysis was performed with dCHIP. Probe intensity data for each array was normalized to a baseline array with median signal intensity using the “invariant set” model, as previously described 11. We used matched remission samples as a reference for copy number estimation and loss of heterozygosity (LOH) analysis. LOH was analyzed using a Hidden Markov Model in dChip and an inferred LOH call threshold of 0.5.

Repositories


GEO

GSE15931

BioProject

PRJNA116945

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Contact


Adolfo Ferrando