Genome‐wide copy number alterations detection in fresh frozen and matched FFPE samples using SNP 6.0 arrays

Tuefferd, Marianne; Bondt, An De; Wyngaert, Ilse Van den; Talloen, Willem; Verbeke, Tobias; Carvalho, Benilton; Clevert, Djork-Arné; Alifano, Marco; Raghavan, Nandini; Amaratunga, Dhammika; Göhlmann, Hinrich W. H.; Broët, Philippe; Camilleri-Broët, Sophie

doi:10.1002/gcc.20599

Cited by 47 publications

(50 citation statements)

References 30 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…For instance, tumor 007 performed quite well in the Infinium assay without undergoing DNA restoration (Supplementary Figure 3) with several amplifications, including at 7p11.2, 12p12.1, 16p12.1, 16p13.3 and 16p13.2, being mapped using both restored and nonrestored DNA. Others have reported reasonable success of FFPE samples in SNP array experiments, [14][15][16][17][18][19] so this is not unexpected. However, the clarity and magnitude of the amplification may be enhanced in LRR plots of restored DNA (for instance for the high-level CNAs on 16p).…”

Section: Discussionmentioning

confidence: 57%

“…Comparative analyses of matched pairs of FF and FFPE tumors demonstrate that SNP array technology can yield reasonable DNA copy number data. [14][15][16][17][18][19] However, reduced data quality obtained from FFPE samples on SNP arrays can lead to the false detection of copy number aberrations (CNAs) that are not identified using oligonucleotide aCGH platforms or using matched FF tumors on SNP-based microarrays. 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.…”

mentioning

confidence: 99%

See 1 more Smart Citation

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

Section: Discussionmentioning

confidence: 57%

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

show abstract

“…To define the chromosome 3 copy number and loss of heterozygosity status and to detect other abnormalities, genetic analyses of the patients' tumors and the corresponding xenografts were done using Affymetrix Genome-Wide SNP Arrays 6.0. DNA was purified as described (9), and loss of heterozygosity of chromosome 3 was detected with single-nucleotide polymorphisms (SNP) as described (10). Data were analyzed using Partek Genomic Suite software, version 6.4, build 6.09.0129 (Partek, Inc.) using Partek's default parameters.…”

Section: Translational Relevancementioning

confidence: 99%

Establishment and Characterization of a Panel of Human Uveal Melanoma Xenografts Derived from Primary and/or Metastatic Tumors

Némati

Sastre-Garau

Laurent

et al. 2010

Clinical Cancer Research

136

View full text Add to dashboard Cite

Purpose: Uveal melanoma is the most common primary intraocular malignant tumor in adults and is defined by a poor natural outcome, as 50% of patients die from metastases. The aim of this study was to develop and characterize a panel of human uveal melanoma xenografts transplanted into immunodeficient mice.Experimental Design: Ninety tumor specimens were grafted into severe combined immunodeficient mice, and 25 transplantable xenografts were then established (28%). Relationship between tumor graft and clinical, biological, and therapeutic features of the patients included were investigated. Characterization of 16 xenografts included histology, molecular analyses by immunohistochemistry, genetic alteration analysis (single-nucleotide polymorphism), and specific tumor antigen expression by quantitative reverse transcription-PCR. Pharmacologic characterization (chemosensitivity) was also done in four models using two drugs, temozolomide and fotemustine, currently used in the clinical management of uveal melanoma.Results: Take rate of human uveal melanoma was 28% (25 of 90). Tumor take was independent of size, histologic parameters, or chromosome 3 monosomy but was significantly higher in metastatic tumors. Interestingly, in vivo tumor growth was prognostic for a lower metastasis-free survival in patients with primary tumors. A high concordance between the patients' tumors and their corresponding xenografts was found for all parameters tested (histology, genetic profile, and tumor antigen expression). Finally, the four xenografts studied displayed different response profiles to chemotherapeutic agents.Conclusions: Based on these results, this panel of 16 uveal melanoma xenografts represents a useful preclinical tool for both pharmacologic and biological assessments. Clin Cancer Res; 16(8); 2352-62. ©2010 AACR.Uveal melanoma is the most common primary intraocular malignant tumor in adults. Despite the increased diagnostic accuracy and the development of conservative and effective treatments on primary tumor sites, such as plaque radiotherapy and photon beam therapy, the mortality remains stable and 50% of patients die from metastases that frequently involve the liver. Chemotherapy, such as oral temozolomide and intra-arterial fotemustine used at the metastatic stage, induces very low response rates, 14.3% and 36%, respectively, and a median survival time of 6.7 and 15 months (1-3). No postoperative adjuvant therapies are currently available to decrease the risk of metastases. Several prognostic factors of disseminated relapse after initial ophthalmologic treatment have been determined, including location with respect to the equator, monosomy 3, and retinal detachment (4). However, no effect of these prognostic markers on patient care can be envisaged in the absence of effective systemic therapies.The growing body of knowledge about molecular and genetics events involved in oncogenesis and tumor progression has led to the identification of new therapeutic targets and therapeutic agents. Preclinical investigatio...

show abstract

“…When degraded DNA is used with the Affymetrix GeneChip system the intensities of probe signals hybridized to long fragments tend to be weakened, which would cause artificial copy number change. To resolve this problem, previous studies modified the extraction protocol and/or filtered out signals expected to result from hybridization of long DNA fragments (20)(21)(22)(23)33). Referring to these studies, we have adopted the modifications described above.…”

Section: Discussionmentioning

confidence: 99%

Intracystic Papillary Carcinoma of Breast Harbors Significant Genomic Alteration Compared with Intracystic Papilloma: Genome-wide Copy Number and LOH Analysis Using High-Density Single-Nucleotide Polymorphism Microarrays

et al. 2011

View full text Add to dashboard Cite

Running title Molecular-cytogenetic Profile of ICPTs KEY WORDS Intracystic papillary tumor, breast cancer, array CGH, GeneChip®, FFPE 2 ABSTRACTPurpose: Intracystic papillary breast tumors consist of benign papilloma, carcinoma in situ and carcinoma with invasion. Using high-density single-nucleotide polymorphism arrays, this study aimed to determine the profile of genomic alterations in these lesions and to identify novel diagnostic criteria. Methods: Ten samples of intracystic papillary tumor, which included five papillomas (Pap), three papillary carcinomas in situ (PurePC) and two papillary carcinomas with invasion (PCinv), were studied. DNA was extracted from tumor and normal tissues that were microdissected from the same formalin-fixed paraffin embedded blocks. Using probe intensity and genotype data from high-density oligonucleotide SNP microarrays (Affymetrix® GeneChip Genome-wide Human 5.0), paired copy number and LOH analysis was performed using Partek Genomic Suite Software. Results: Quality control (QC) call rate, which is an index measuring the quality of a SNP microarray experiment, ranged from 70.75% to 91.93%, mean 80.72%. The mean total genomic alteration rate (sum of amplifications, deletions and copy-neutral loss of heterogeneity) with respect to the whole genome was 2.87%,

show abstract

Genome‐wide copy number alterations detection in fresh frozen and matched FFPE samples using SNP 6.0 arrays

Cited by 47 publications

References 30 publications

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

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

Establishment and Characterization of a Panel of Human Uveal Melanoma Xenografts Derived from Primary and/or Metastatic Tumors

Intracystic Papillary Carcinoma of Breast Harbors Significant Genomic Alteration Compared with Intracystic Papilloma: Genome-wide Copy Number and LOH Analysis Using High-Density Single-Nucleotide Polymorphism Microarrays

Contact Info

Product

Resources

About