Random DNA fragmentation allows detection of single-copy, single-exon alterations of copy number by oligonucleotide array CGH in clinical FFPE samples

Galen Hostetter, Su Young Kim, Stephanie Savage, Gerald C. Gooden, Michael Barrett, Jian Zhang, Lalitamba Alla, April Watanabe, Janine Einspahr, Anil Prasad, Brian J. Nickoloff, John Carpten, Jeffrey Trent, David Alberts, Michael Bittner

Research output: Contribution to journalArticle

Abstract

Genomic technologies, such as array comparative genomic hybridization (aCGH), increasingly offer definitive gene dosage profiles in clinical samples. Historically, copy number profiling was limited to large fresh-frozen tumors where intact DNA could be readily extracted. Genomic analyses of pre-neoplastic tumors and diagnostic biopsies are often limited to DNA processed by formalin-fixation and paraffin-embedding (FFPE). We present specialized protocols for DNA extraction and processing from FFPE tissues utilizing DNase processing to generate randomly fragmented DNA. The protocols are applied to FFPE clinical samples of varied tumor types, from multiple institutions and of varied block age. Direct comparative analyses with regression coefficient were calculated on splitsample (portion fresh/portion FFPE) of colorectal tumor samples. We show equal detection of a homozygous loss of SMAD4 at the exon-level in the SW480 cell line and gene-specific alterations in the split tumor samples. aCGH application to a set of archival FFPE samples of skin squamous cell carcinomas detected a novel hemizygous deletion in INPP5A on 10q26.3. Finally we present data on derivative of log ratio, a particular sensitive detector of measurement variance, for 216 sequential hybridizations to assess protocol reliability over a wide range of FFPE samples.

Original languageEnglish (US)
Article numbergkp881
Pages (from-to)e9.1-e9.12
JournalNucleic acids research
Volume38
Issue number2
DOIs
StatePublished - Oct 29 2009

ASJC Scopus subject areas

  • Genetics

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    Hostetter, G., Kim, S. Y., Savage, S., Gooden, G. C., Barrett, M., Zhang, J., Alla, L., Watanabe, A., Einspahr, J., Prasad, A., Nickoloff, B. J., Carpten, J., Trent, J., Alberts, D., & Bittner, M. (2009). Random DNA fragmentation allows detection of single-copy, single-exon alterations of copy number by oligonucleotide array CGH in clinical FFPE samples. Nucleic acids research, 38(2), e9.1-e9.12. [gkp881]. https://doi.org/10.1093/nar/gkp881