Evaluation of whole genome amplification protocols for array and oligonucleotide CGH.
Genome-based technologies such as genomic arrays and next generation sequencing are poised to make significant contributions to clinical oncology. However, translation of these technologies to the clinic will require that they produce high-quality reproducible data from small archived tumor specimens and biopsies. Herein, we report on a systematic and comprehensive microarray analysis comparing multiple whole genome amplification methods using a variety of difficult clinical specimens, including formalin-fixed and paraffin-embedded tissues. Quantitative analysis and clustering suggest that Sigma's whole genome amplification protocol performed best on all specimens and, moreover, worked well with a formalin-fixed, paraffin-embedded biopsy.
Hittelman
Adam
A
Department of Urology University of California at San Francisco Comprehensive Cancer Center, San Francisco, CA, USA.
Sridharan
Shivaranjani
S
Roy
Ritu
R
Fridlyand
Jane
J
Loda
Massimo
M
Collins
Colin
C
Paris
Pamela L
PL
D005260:Female; D015894:Genome, Human; D006801:Humans; D008297:Male; D021141:Nucleic Acid Amplification Techniques / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis; D009841:Oligonucleotides / Q000737:chemistry*; D012680:Sensitivity and Specificity
D009841:Oligonucleotides