Genome-wide, high-resolution detection of copy number, loss of heterozygosity, and genotypes from formalin-fixed, paraffin-embedded tumor tissue using microarrays.
Formalin-fixed, paraffin-embedded (FFPE) material tends to yield degraded DNA and is thus suboptimal for use in many downstream applications. We describe an integrated analysis of genotype, loss of heterozygosity (LOH), and copy number for DNA derived from FFPE tissues using oligonucleotide microarrays containing over 500K single nucleotide polymorphisms. A prequalifying PCR test predicted the performance of FFPE DNA on the microarrays better than age of FFPE sample. Although genotyping efficiency and reliability were reduced for FFPE DNA when compared with fresh samples, closer examination revealed methods to improve performance at the expense of variable reduction in resolution. Important steps were also identified that enable equivalent copy number and LOH profiles from paired FFPE and fresh frozen tumor samples. In conclusion, we have shown that the Mapping 500K arrays can be used with FFPE-derived samples to produce genotype, copy number, and LOH predictions, and we provide guidelines and suggestions for application of these samples to this integrated system.
Jacobs
Sharoni
S
Affymetrix, Inc., Santa Clara, California 95051, USA. sharoni_jacobs@affymetrix.com
Thompson
Ella R
ER
Nannya
Yasuhito
Y
Yamamoto
Go
G
Pillai
Raji
R
Ogawa
Seishi
S
Bailey
Dione K
DK
Campbell
Ian G
IG
D001943:Breast Neoplasms / Q000235:genetics / Q000473:pathology; D018269:Carcinoma, Endometrioid / Q000235:genetics; D002874:Chromosome Mapping; D015179:Colorectal Neoplasms / Q000235:genetics / Q000473:pathology; D004273:DNA, Neoplasm / Q000235:genetics / Q000302:isolation & purification; D005260:Female; D005557:Formaldehyde; D018628:Gene Dosage; D015894:Genome, Human; D005838:Genotype; D006801:Humans; D019656:Loss of Heterozygosity; D018895:Microsatellite Repeats; D009369:Neoplasms / Q000235:genetics* / Q000473:pathology; D020411:Oligonucleotide Array Sequence Analysis; D010051:Ovarian Neoplasms / Q000235:genetics; D016612:Paraffin Embedding; D016133:Polymerase Chain Reaction; D016707:Tissue Fixation
D004273:DNA, Neoplasm; D005557:Formaldehyde