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 T.; Zhang, Jian; Alla, Lalitamba; Watanabe, April; Einspahr, Janine G.; Nickoloff, Brian J.; Carpten, John D.; Trent, Jeffrey M.; Alberts, David S.; Bittner, Michael

doi:10.1093/nar/gkp881

Cited by 33 publications

(37 citation statements)

References 23 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Several research groups have shown copy number analysis DNA from FFPE tissue on high-resolution, dual channel oligonucleotide array comparative genomic hybridization (aCGH) arrays (Hostetter et al, 2010;Brosens et al, 2010) and SNP-based platforms (Thompson et al, 2005;Tuefferd et al, 2008;Alvarez et al, 2010) is feasible. Despite these results, large series of highresolution SNP data with DNA from FFPE archival tissue have thus far not been reported.…”

Section: Introductionmentioning

confidence: 99%

CGH arrays compared for DNA isolated from formalin‐fixed, paraffin‐embedded material

Krijgsman

Israeli

Haan

et al. 2011

Genes Chromosomes & Cancer

View full text Add to dashboard Cite

Formalin-fixed, paraffin-embedded (FFPE) archival tissue is an important source of DNA material. The most commonly used technique to identify copy number aberrations from chromosomal DNA in tumorigenesis is array comparative genomic hybridization (aCGH). Although copy number analysis using DNA from FFPE archival tissue is challenging, several research groups have reported high quality and reproducible DNA copy number results using aCGH. Aim of this study is to compare the commercially available aCGH platforms suitable for high-resolution copy number analysis using FFPE-derived DNA. Two dual channel aCGH platforms (Agilent and NimbleGen) and a single channel SNP-based platform (Affymetrix) were evaluated using seven FFPE colon cancer samples, and median absolute deviation (MAD), deflection, signal-to-noise ratio, and DNA input requirements were used as quality criteria. Large differences were observed between platforms; Agilent and NimbleGen showed better MAD values (0.13 for both) compared with Affymetrix (0.22). On the contrary, Affymetrix showed a better deflection of 0.94, followed by 0.71 for Agilent and 0.51 for NimbleGen. This resulted in signal-to-nose ratios that were comparable between the three commercially available platforms. Interestingly, DNA input amounts from FFPE material lower than recommended still yielded high quality profiles on all platforms. Copy number analysis using DNA derived from FFPE archival material is feasible using all three high-resolution copy number platforms and shows reproducible results, also with DNA input amounts lower than recommended.

show abstract

Section: Introductionmentioning

confidence: 99%

CGH arrays compared for DNA isolated from formalin‐fixed, paraffin‐embedded material

Krijgsman

Israeli

Haan

et al. 2011

Genes Chromosomes & Cancer

View full text Add to dashboard Cite

show abstract

“…Archival FFPE tissue is often the only source of material for study (Blow 2007). The use of such samples has been challenging due to poor DNA quality; hence, array CGH results, for example, have been variable (Mc Sherry et al 2007;Hostetter et al 2010;Krijgsman et al 2012;Warren et al 2012). To make large archival sample series accessible for genome research, a robust technique is required that performs well on diverse sample types, with high resolution, quality and reproducibility, and at low cost without the necessity for a (matched) normal sample.…”

mentioning

confidence: 99%

DNA copy number analysis of fresh and formalin-fixed specimens by shallow whole-genome sequencing with identification and exclusion of problematic regions in the genome assembly

et al. 2014

View full text Add to dashboard Cite

Detection of DNA copy number aberrations by shallow whole-genome sequencing (WGS) faces many challenges, including lack of completion and errors in the human reference genome, repetitive sequences, polymorphisms, variable sample quality, and biases in the sequencing procedures. Formalin-fixed paraffin-embedded (FFPE) archival material, the analysis of which is important for studies of cancer, presents particular analytical difficulties due to degradation of the DNA and frequent lack of matched reference samples. We present a robust, cost-effective WGS method for DNA copy number analysis that addresses these challenges more successfully than currently available procedures. In practice, very useful profiles can be obtained with~0.13 genome coverage. We improve on previous methods by first implementing a combined correction for sequence mappability and GC content, and second, by applying this procedure to sequence data from the 1000 Genomes Project in order to develop a blacklist of problematic genome regions. A small subset of these blacklisted regions was previously identified by ENCODE, but the vast majority are novel unappreciated problematic regions. Our procedures are implemented in a pipeline called QDNAseq. We have analyzed over 1000 samples, most of which were obtained from the fixed tissue archives of more than 25 institutions. We demonstrate that for most samples our sequencing and analysis procedures yield genome profiles with noise levels near the statistical limit imposed by read counting. The described procedures also provide better correction of artifacts introduced by low DNA quality than prior approaches and better copy number data than high-resolution microarrays at a substantially lower cost.

show abstract

“…20 Oligonucleotide aCGH platforms developed by Agilent or Nimblegen are thus considered as the more robust at tolerating degraded DNA from FFPE tissue samples than SNP arrays. They provide both high resolution and precision for detecting high-level amplifications, single-copy alterations, and resolving chromosomal break points, 20,21 but lack the capacity for detecting copy neutral LOH.…”

mentioning

confidence: 99%

Evaluating the repair of DNA derived from formalin-fixed paraffin-embedded tissues prior to genomic profiling by SNP–CGH analysis

Hosein

Song

Reed

et al. 2013

Laboratory Investigation

View full text Add to dashboard Cite

Pathology archives contain vast resources of clinical material in the form of formalin-fixed paraffin-embedded (FFPE) tissue samples. Owing to the methods of tissue fixation and storage, the integrity of DNA and RNA available from FFPE tissue is compromized, which means obtaining informative data regarding epigenetic, genomic, and expression alterations can be challenging. Here, we have investigated the utility of repairing damaged DNA derived from FFPE tumors prior to single-nucleotide polymorphism (SNP) arrays for whole-genome DNA copy number analysis. DNA was extracted from FFPE samples spanning five decades, involving tumor material obtained from surgical specimens and postmortems. Various aspects of the protocol were assessed, including the method of DNA extraction, the role of Quality Control quantitative PCR (qPCR) in predicting sample success, and the effect of DNA restoration on assay performance, data quality, and the prediction of copy number aberrations (CNAs). DNA that had undergone the repair process yielded higher SNP call rates, reduced log R ratio variance, and improved calling of CNAs compared with matched FFPE DNA not subjected to repair. Reproducible mapping of genomic break points and detection of focal CNAs representing highlevel gains and homozygous deletions (HD) were possible, even on autopsy material obtained in 1974. For example, DNA amplifications at the ERBB2 and EGFR gene loci and a HD mapping to 13q14.2 were validated using immunohistochemistry, in situ hybridization, and qPCR. The power of SNP arrays lies in the detection of allele-specific aberrations; however, this aspect of the analysis remains challenging, particularly in the distinction between loss of heterozygosity (LOH) and copy neutral LOH. In summary, attempting to repair DNA that is damaged during fixation and storage may be a useful pretreatment step for genomic studies of large archival FFPE cohorts with long-term follow-up or for understanding rare cancer types, where fresh frozen material is scarce.

show abstract

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

Cited by 33 publications

References 23 publications

CGH arrays compared for DNA isolated from formalin‐fixed, paraffin‐embedded material

CGH arrays compared for DNA isolated from formalin‐fixed, paraffin‐embedded material

DNA copy number analysis of fresh and formalin-fixed specimens by shallow whole-genome sequencing with identification and exclusion of problematic regions in the genome assembly

Evaluating the repair of DNA derived from formalin-fixed paraffin-embedded tissues prior to genomic profiling by SNP–CGH analysis

Contact Info

Product

Resources

About