Dataset features

Specifications


Application: SNP array data analysis, aCGH data analysis
Number of samples: 45
Release date: May 16 2009
Last update date: Dec 22 2017
Access: Public
Diseases: Multiple Myeloma, Myopathies, Structural, Congenital
Dataset link Integrated genomics approach to detect allelic imbalances in multiple myeloma, SNP data

Experimental Protocol


Pathological bone marrow specimens from 41 MM and four plasma cell leukemia (PCL) patients at diagnosis. 250 nanograms of genomic DNA was processed and, in accordance with the manufacturer's protocols, 40 micrograms of fragmented biotin-labelled DNA were hybridized on GeneChip Human Mapping 50K XbaI Arrays (Affymetrix Inc.). The arrays were scanned using the GeneChip Scanner 3000 7G. The images were acquired using Affymetrix GeneChip® Operating Software (GCOS version 1.4). Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using GTYPE 4.1 and Affymetrix Copy Number Analysis Tool (CNAT 4.0.1) softwares. Genomic Smoothing analysis was performed by using the smoothing window of 0 Mb, and inferred copy number states were derived from a Hidden Markov Model (HMM) based algorithm implemented in CNAT 4.0.1. Circular Binary Segmentation (Ohlsen et al., 2004) was applied using DNAcopy package for R Bioconductor on raw data. FBN procedure was finally applied to infer exact local copy number as described in the mentioned Reference.

Repositories


GEO

GSE16121

ArrayExpress

E-GEOD-16121

BioProject

PRJNA122809

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Contact


Luca Agnelli
Antonino Neri