Detecting Copy Number Variations in PDX Cells

DNA was extracted from PDX cells at low (p3), middle (p15) and high (p30) in vitro passages using DNeasy Blood and Tissue Kit (Qiagen). For analysis, genomic DNA was hybridized to an Affymetrix CytoScan HD chip (Affymetrix) containing approximately 2.6 million markers of which almost 750,000 are SNPs. Constitutional copy number variants were removed by filtering against the Database of Genomic Variants (Oct. 2016). Copy number variation analyses were performed using ChAS software. The analyses of xenografts and the corresponding patient tumors were reported previously^{10 (link)}.

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Persson C.U., von Stedingk K., Bexell D., Merselius M., Braekeveldt N., Gisselsson D., Arsenian-Henriksson M., Påhlman S, & Wigerup C. (2017). Neuroblastoma patient-derived xenograft cells cultured in stem-cell promoting medium retain tumorigenic and metastatic capacities but differentiate in serum. Scientific Reports, 7, 10274.

Publication 2017

DNeasy Blood and Tissue Kit CytoScan HD chip

Blood Chip Copy number variation Genomic Patient Snps Tissue Tumors Xenografts

Corresponding Organization :

Other organizations : Lund University, Karolinska Institutet

Top 5 similar protocols

Variable analysis

independent variables

In vitro passage number (low (p3), middle (p15), high (p30))

dependent variables

Copy number variation in genomic DNA

control variables

DNA extraction using DNeasy Blood and Tissue Kit (Qiagen)
Genomic DNA hybridization to Affymetrix CytoScan HD chip (Affymetrix)
Filtering against Database of Genomic Variants (Oct. 2016) to remove constitutional copy number variants
Copy number variation analyses using ChAS software

controls

The analyses of xenografts and the corresponding patient tumors were reported previously (link provided)

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