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 G Einspahr, Anil P Rama Rao, Brian J. Nickoloff, John Carpten, Jeffrey Trent, David S Alberts, Michael Bittner

Research output: Contribution to journalArticle

25 Citations (Scopus)

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
JournalNucleic Acids Research
Volume38
Issue number2
DOIs
StatePublished - Oct 29 2009

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Paraffin Embedding
DNA Fragmentation
Oligonucleotide Array Sequence Analysis
Formaldehyde
Exons
Comparative Genomic Hybridization
DNA
Neoplasms
Gene Dosage
Deoxyribonucleases
Squamous Cell Carcinoma
Colorectal Neoplasms
Regression Analysis
Technology
Biopsy
Cell Line
Skin
Genes

ASJC Scopus subject areas

  • Genetics

Cite this

Random DNA fragmentation allows detection of single-copy, single-exon alterations of copy number by oligonucleotide array CGH in clinical FFPE samples. / Hostetter, Galen; Kim, Su Young; Savage, Stephanie; Gooden, Gerald C.; Barrett, Michael; Zhang, Jian; Alla, Lalitamba; Watanabe, April; Einspahr, Janine G; Rama Rao, Anil P; Nickoloff, Brian J.; Carpten, John; Trent, Jeffrey; Alberts, David S; Bittner, Michael.

In: Nucleic Acids Research, Vol. 38, No. 2, gkp881, 29.10.2009.

Research output: Contribution to journalArticle

Hostetter, G, Kim, SY, Savage, S, Gooden, GC, Barrett, M, Zhang, J, Alla, L, Watanabe, A, Einspahr, JG, Rama Rao, AP, Nickoloff, BJ, Carpten, J, Trent, J, Alberts, DS & 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, vol. 38, no. 2, gkp881. https://doi.org/10.1093/nar/gkp881
Hostetter, Galen ; Kim, Su Young ; Savage, Stephanie ; Gooden, Gerald C. ; Barrett, Michael ; Zhang, Jian ; Alla, Lalitamba ; Watanabe, April ; Einspahr, Janine G ; Rama Rao, Anil P ; Nickoloff, Brian J. ; Carpten, John ; Trent, Jeffrey ; Alberts, David S ; Bittner, Michael. / Random DNA fragmentation allows detection of single-copy, single-exon alterations of copy number by oligonucleotide array CGH in clinical FFPE samples. In: Nucleic Acids Research. 2009 ; Vol. 38, No. 2.
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