Computational protocol: Clonal Evolution through Loss of Chromosomes and Subsequent Polyploidization in Chondrosarcoma

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Protocol publication

[…] SNP array analysis was used for combined DNA copy number and LOH investigation in cases 1–16. DNA previously extracted for array CGH was used for the present analysis. The DNA had been extracted from fresh frozen tumor biopsies using the DNeasy Tissue Kit including the optional RNaseH treatment, according to the manufacturer's instructions (Qiagen, Valencia, CA, USA). Quality and concentration of the extracted DNA were ascertained using a NanoDrop ND-1000 (Thermo Fisher Scientific Inc., Waltham, MA, USA). Tumor DNA was hybridized onto Illumina Human Omni-Quad v1.0 BeadChip or Human CNV370-Quad v3.0 BeadChip (Illumina, San Diego, CA, USA), containing 1.2 million and 370,000 markers, respectively, following standard protocols supplied by the manufacturer. Data were extracted from the GenomeStudio software (Illumina), and subsequently normalized and segmented using thresholded quantile normalization (tQN) and BAFsegmentation, respectively , . Base pair positions are indicated according to the NCBI build 36 (hg18). SNP array data have been deposited in the Gene Expression Omnibus (GEO) database, www.ncbi.nlm.nih.gov/geo (accession no. GSE25985). […]

Pipeline specifications

Software tools GenomeStudio, tQN
Databases GEO
Application aCGH data analysis
Diseases Chondrosarcoma, Leukemia, Lymphoid, Neoplasms