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Maioru OV, Radoi VE, Coman MC, Hotinceanu IA, Dan A, Eftenoiu AE, Burtavel LM, Bohiltea LC, Severin EM. Developments in Genetics: Better Management of Ovarian Cancer Patients. Int J Mol Sci 2023; 24:15987. [PMID: 37958970 PMCID: PMC10647767 DOI: 10.3390/ijms242115987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 10/22/2023] [Accepted: 11/03/2023] [Indexed: 11/15/2023] Open
Abstract
The purpose of this article is to highlight the new advancements in molecular and diagnostic genetic testing and to properly classify all ovarian cancers. In this article, we address statistics, histopathological classification, molecular pathways implicated in ovarian cancer, genetic screening panels, details about the genes, and also candidate genes. We hope to bring new information to the medical field so as to better prevent and diagnose ovarian cancer.
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Affiliation(s)
- Ovidiu-Virgil Maioru
- Department of Medical Genetics, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania; (O.-V.M.); (M.-C.C.); (A.D.); (A.-E.E.); (L.-M.B.); (L.-C.B.); (E.-M.S.)
| | - Viorica-Elena Radoi
- Department of Medical Genetics, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania; (O.-V.M.); (M.-C.C.); (A.D.); (A.-E.E.); (L.-M.B.); (L.-C.B.); (E.-M.S.)
- “Alessandrescu-Rusescu” National Institute for Maternal and Child Health, 20382 Bucharest, Romania
| | - Madalin-Codrut Coman
- Department of Medical Genetics, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania; (O.-V.M.); (M.-C.C.); (A.D.); (A.-E.E.); (L.-M.B.); (L.-C.B.); (E.-M.S.)
| | - Iulian-Andrei Hotinceanu
- Department of Medical Genetics, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania; (O.-V.M.); (M.-C.C.); (A.D.); (A.-E.E.); (L.-M.B.); (L.-C.B.); (E.-M.S.)
| | - Andra Dan
- Department of Medical Genetics, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania; (O.-V.M.); (M.-C.C.); (A.D.); (A.-E.E.); (L.-M.B.); (L.-C.B.); (E.-M.S.)
| | - Anca-Elena Eftenoiu
- Department of Medical Genetics, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania; (O.-V.M.); (M.-C.C.); (A.D.); (A.-E.E.); (L.-M.B.); (L.-C.B.); (E.-M.S.)
| | - Livia-Mălina Burtavel
- Department of Medical Genetics, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania; (O.-V.M.); (M.-C.C.); (A.D.); (A.-E.E.); (L.-M.B.); (L.-C.B.); (E.-M.S.)
| | - Laurentiu-Camil Bohiltea
- Department of Medical Genetics, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania; (O.-V.M.); (M.-C.C.); (A.D.); (A.-E.E.); (L.-M.B.); (L.-C.B.); (E.-M.S.)
- “Alessandrescu-Rusescu” National Institute for Maternal and Child Health, 20382 Bucharest, Romania
| | - Emilia-Maria Severin
- Department of Medical Genetics, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania; (O.-V.M.); (M.-C.C.); (A.D.); (A.-E.E.); (L.-M.B.); (L.-C.B.); (E.-M.S.)
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Li J, Greytak SR, Guan P, Engel KB, Goerlitz DS, Islam M, Varghese RS, Moore HM, Ressom HW. Formalin Fixation, Delay to Fixation, and Time in Fixative Adversely Impact Copy Number Variation Analysis by aCGH. Biopreserv Biobank 2023; 21:407-416. [PMID: 36169416 PMCID: PMC10460690 DOI: 10.1089/bio.2022.0036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Although molecular profiling of DNA isolated from formalin-fixed, paraffin-embedded (FFPE) tumor specimens has become more common in recent years, it remains unclear how discrete FFPE processing variables may affect detection of copy number variation (CNV). To better understand such effects, array comparative genomic hybridization (aCGH) profiles of FFPE renal cell carcinoma specimens that experienced different delays to fixation (DTFs; 1, 2, 3, and 12 hours) and times in fixative (TIFs; 6, 12, 23, and 72 hours) were compared to snap-frozen tumor and blood specimens from the same patients. A greater number of regions containing CNVs relative to commercial reference DNA were detected in DNA from FFPE tumor specimens than snap-frozen tumor specimens even though they originated from the same tumor blocks. Extended DTF and TIF affected the number of DNA segments with a copy number status that differed between FFPE and frozen tumor specimens; a DTF ≥3 hours led to more segments, while a TIF of 72 hours led to fewer segments. Importantly, effects were not random as a higher guanine-cytosine (GC) content and/or a higher percentage of repeats were observed among stable regions. While limiting aCGH analysis to FFPE specimens with a DTF <3 hours and a TIF <72 hours may circumvent some effects, results from FFPE specimens should be validated against fresh or frozen specimens whenever possible.
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Affiliation(s)
- James Li
- Department of Biostatistics, Bioinformatics, and Biomathematics, Georgetown University, Washington, District of Columbia, USA
| | | | - Ping Guan
- Biorepositories & Biospecimen Research Branch, National Cancer Institute, Bethesda, Maryland, USA
| | | | - David S. Goerlitz
- Department of Biostatistics, Bioinformatics, and Biomathematics, Georgetown University, Washington, District of Columbia, USA
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, District of Columbia, USA
| | - Md Islam
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, District of Columbia, USA
| | - Rency S. Varghese
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, District of Columbia, USA
| | - Helen M. Moore
- Biorepositories & Biospecimen Research Branch, National Cancer Institute, Bethesda, Maryland, USA
| | - Habtom W. Ressom
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, District of Columbia, USA
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Practical forensic use of kinship determination using high-density SNP profiling based on a microarray platform, focusing on low-quantity DNA. Forensic Sci Int Genet 2022; 61:102752. [DOI: 10.1016/j.fsigen.2022.102752] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 07/16/2022] [Accepted: 07/27/2022] [Indexed: 11/20/2022]
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4
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Fostira F, Papadimitriou M, Papadimitriou C. Current practices on genetic testing in ovarian cancer. ANNALS OF TRANSLATIONAL MEDICINE 2021; 8:1703. [PMID: 33490215 PMCID: PMC7812194 DOI: 10.21037/atm-20-1422] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Epithelial ovarian cancer (EOC) is probably the tumor type with the highest percentage of hereditary cases observed, irrespectively of selection criteria. A fourth to a fifth of unselected epithelial EOC patients carry pathogenic variants (PVs) in a number of genes, the majority of which encode for proteins involved in DNA repair pathways. BRCA1 and BRCA2 predisposing PVs were the first to be associated to ovarian cancer, with the advent in DNA sequencing technologies leading to the discovery and association of additional genes which compromise the homologous recombination (HR) pathway. In addition, PVs genes involved in mismatch repair (MMR) pathway, account for 10–15% of hereditary EOC. The identification of women with HR deficient ovarian cancers has significant clinical implications concerning chemotherapy regimen planning and development and use of targeted therapies as well. More specifically, in patients with BRCA1/2 PVs or HR deficiency maintenance treatment with poly(ADP-ribose) polymerase (PARP) inhibitors, either in the first line setting or in recurrent disease, improves the progression-free survival. But also patients with HR proficient tumors show a benefit. Therefore, genetic testing in ovarian cancer has a prognostic and predictive value. In this review, we discuss which ovarian cancer patients should be referred for genetic counseling and how to perform genetic testing. We also discuss the timing of genetic testing and its clinical relevance to BRCA status.
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Affiliation(s)
- Florentia Fostira
- InRaSTES, Molecular Diagnostics Laboratory, National Centre for Scientific Research NCSR Demokritos, Athens, Greece
| | - Marios Papadimitriou
- Oncology Unit, Aretaieion University Hospital, National and Kapodistrian University of Athens School of Medicine, Athens, Greece
| | - Christos Papadimitriou
- Oncology Unit, Aretaieion University Hospital, National and Kapodistrian University of Athens School of Medicine, Athens, Greece
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Through the looking glass and what you find there: making sense of comparative genomic hybridization and fluorescence in situ hybridization for melanoma diagnosis. Mod Pathol 2020; 33:1318-1330. [PMID: 32066861 DOI: 10.1038/s41379-020-0490-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 01/10/2020] [Accepted: 01/11/2020] [Indexed: 12/11/2022]
Abstract
Melanoma is the leading cause of death among cutaneous neoplasms. Best outcome relies on early detection and accurate pathologic diagnosis. For the great majority of melanocytic tumors, histopathologic examination can reliably distinguish nevi from melanomas. However, there is a subset of melanocytic tumors that cannot be definitively classified as benign or malignant using histopathological criteria alone. These tumors are usually diagnosed using terms that imply various degrees of uncertainty in regards to their malignant potential and create the possibility for over or undertreatment. For such tumors, additional ancillary tests would be beneficial in adjudicating a more definitive diagnosis. In recent years, DNA-based molecular ancillary tests, specifically comparative genomic hybridization and fluorescence in situ hybridization, have been developed to help guide the diagnosis of ambiguous melanocytic proliferations. This study will present an updated overview of these two major ancillary tests, which are currently being used in clinical practice to assist in the diagnosis of challenging melanocytic neoplasms.
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Brown J, Stepien AJ, Willem P. Landscape of copy number aberrations in esophageal squamous cell carcinoma from a high endemic region of South Africa. BMC Cancer 2020; 20:281. [PMID: 32252688 PMCID: PMC7137242 DOI: 10.1186/s12885-020-06788-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 03/26/2020] [Indexed: 02/08/2023] Open
Abstract
Background Esophageal squamous cell carcinoma (ESCC) is an aggressive cancer with one of the highest world incidences in the Eastern Cape region of South Africa. Several genome wide studies have been performed on ESCC cohorts from Asian countries, North America, Malawi and other parts of the world but none have been conducted on ESCC tumors from South Africa to date, where the molecular pathology and etiology of this disease remains unclear. We report here tumor associated copy number changes observed in 51 ESCC patients’ samples from the Eastern Cape province of South Africa. Methods We extracted tumor DNA from 51 archived ESCC specimens and interrogated tumor associated DNA copy number changes using Affymetrix® 500 K SNP array technology. The Genomic Identification of Significant Targets in Cancer (GISTIC 2.0) algorithm was applied to identify significant focal regions of gains and losses. Gains of the top recurrent cancer genes were validated by fluorescence in situ hybridization and their protein expression assessed by immunohistochemistry. Results Twenty-three significant focal gains were identified across samples. Gains involving the CCND1, MYC, EGFR and JAG1 loci recapitulated those described in studies on Asian and Malawian cohorts. The two most significant gains involved the chromosomal sub-bands 3q28, encompassing the TPRG1 gene and 11q13.3 including the CTTN, PPFIA1and SHANK2 genes. There was no significant homozygous loss and the most recurrent hemizygous deletion involved the B3GAT1 gene on chromosome 11q25. Focal gains on 11q13.3 in 37% of cases (19/51), consistently involved CTTN and SHANK2 genes. Twelve of these cases (23,5%), had a broader region of gain that also included the CCND1, FGF19, FGF4 and FGF3 genes. SHANK2 and CTTN are co-amplified in several cancers, these proteins interact functionally together and are involved in cell motility. Immunohistochemistry confirmed both Shank2 (79%) and cortactin (69%) protein overexpression in samples with gains of these genes. In contrast, cyclin D1 (65%) was moderately expressed in samples with CCND1 DNA gain. Conclusions This study reports copy number changes in a South African ESCC cohort and highlights similarities and differences with cohorts from Asia and Malawi. Our results strongly suggest a role for CTTN and SHANK2 in the pathogenesis of ESCC in South Africa.
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Affiliation(s)
- Jacqueline Brown
- School of Pathology, Department of Molecular Medicine and Haematology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg and the National Health Laboratory Services, Johannesburg, South Africa.
| | - Andrzej J Stepien
- Department of Anatomical Pathology, School of Medicine, Faculty of Health Science, Walter Sisulu University, National Health Laboratory Services/NMAH, Mthatha, South Africa
| | - Pascale Willem
- School of Pathology, Department of Molecular Medicine and Haematology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg and the National Health Laboratory Services, Johannesburg, South Africa
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Mathieson W, Thomas G. Using FFPE Tissue in Genomic Analyses: Advantages, Disadvantages and the Role of Biospecimen Science. CURRENT PATHOBIOLOGY REPORTS 2019. [DOI: 10.1007/s40139-019-00194-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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8
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Kanagal-Shamanna R, Hodge JC, Tucker T, Shetty S, Yenamandra A, Dixon-McIver A, Bryke C, Huxley E, Lennon PA, Raca G, Xu X, Jeffries S, Quintero-Rivera F, Greipp PT, Slovak ML, Iqbal MA, Fang M. Assessing copy number aberrations and copy neutral loss of heterozygosity across the genome as best practice: An evidence based review of clinical utility from the cancer genomics consortium (CGC) working group for myelodysplastic syndrome, myelodysplastic/myeloproliferative and myeloproliferative neoplasms. Cancer Genet 2018; 228-229:197-217. [PMID: 30377088 DOI: 10.1016/j.cancergen.2018.07.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Revised: 07/27/2018] [Accepted: 07/30/2018] [Indexed: 12/16/2022]
Abstract
Multiple studies have demonstrated the utility of chromosomal microarray (CMA) testing to identify clinically significant copy number alterations (CNAs) and copy-neutral loss-of-heterozygosity (CN-LOH) in myeloid malignancies. However, guidelines for integrating CMA as a standard practice for diagnostic evaluation, assessment of prognosis and predicting treatment response are still lacking. CMA has not been recommended for clinical work-up of myeloid malignancies by the WHO 2016 or the NCCN 2017 guidelines but is a suggested test by the European LeukaemiaNet 2013 for the diagnosis of primary myelodysplastic syndrome (MDS). The Cancer Genomics Consortium (CGC) Working Group for Myeloid Neoplasms systematically reviewed peer-reviewed literature to determine the power of CMA in (1) improving diagnostic yield, (2) refining risk stratification, and (3) providing additional genomic information to guide therapy. In this manuscript, we summarize the evidence base for the clinical utility of array testing in the workup of MDS, myelodysplastic/myeloproliferative neoplasms (MDS/MPN) and myeloproliferative neoplasms (MPN). This review provides a list of recurrent CNAs and CN-LOH noted in this disease spectrum and describes the clinical significance of the aberrations and how they complement gene mutation findings by sequencing. Furthermore, for new or suspected diagnosis of MDS or MPN, we present suggestions for integrating genomic testing methods (CMA and mutation testing by next generation sequencing) into the current standard-of-care clinical laboratory testing (karyotype, FISH, morphology, and flow).
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Affiliation(s)
- Rashmi Kanagal-Shamanna
- Department of Hematopathology, The University of Texas M.D. Anderson Cancer Center, Houston TX, USA.
| | - Jennelle C Hodge
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA; Department of Pediatrics, University of California Los Angeles, Los Angeles, CA, USA; Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Tracy Tucker
- Department of Pathology and Laboratory Medicine, Cancer Genetics Laboratory, British Columbia Cancer Agency, Vancouver, BC Canada
| | - Shashi Shetty
- Department of Pathology, UHCMC, University Hospitals and Case Western Reserve University, Cleveland, OH, USA
| | - Ashwini Yenamandra
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Christine Bryke
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Emma Huxley
- West Midlands Regional Genetics Laboratory, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | | | - Gordana Raca
- Department of Pathology and Laboratory Medicine, Children's Hospital of Los Angeles, Los Angeles, CA, USA
| | - Xinjie Xu
- ARUP Laboratories, University of Utah, Salt Lake City, UT, USA
| | - Sally Jeffries
- West Midlands Regional Genetics Laboratory, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - Fabiola Quintero-Rivera
- Department of Pathology and Laboratory Medicine, UCLA Clinical Genomics Center, University of California Los Angeles, Los Angeles, CA, USA
| | - Patricia T Greipp
- Department of Laboratory Medicine and Pathology, Genomics Laboratory, Mayo Clinic, Rochester, MN, USA
| | - Marilyn L Slovak
- TriCore Reference Laboratories, University of New Mexico, Albuquerque, NM, USA
| | - M Anwar Iqbal
- University of Rochester Medical Center, Rochester, NY, USA
| | - Min Fang
- Fred Hutchinson Cancer Research Center and University of Washington, Seattle, WA, USA.
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Zhang C, Cerveira E, Rens W, Yang F, Lee C. Multicolor Fluorescence In Situ Hybridization (FISH) Approaches for Simultaneous Analysis of the Entire Human Genome. CURRENT PROTOCOLS IN HUMAN GENETICS 2018; 99:e70. [PMID: 30215889 DOI: 10.1002/cphg.70] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Analysis of the organization of the human genome is vital for understanding genetic diversity, human evolution, and disease pathogenesis. A number of approaches, such as multicolor fluorescence in situ hybridization (FISH) assays, cytogenomic microarray (CMA), and next-generation sequencing (NGS) technologies, are available for simultaneous analysis of the entire human genome. Multicolor FISH-based spectral karyotyping (SKY), multiplex FISH (M-FISH), and Rx-FISH may provide rapid identification of interchromosomal and intrachromosomal rearrangements as well as the origin of unidentified extrachromosomal elements. Recent advances in molecular cytogenetics have made it possible to efficiently examine the entire human genome in a single experiment at much higher resolution and specificity using CMA and NGS technologies. Here, we present an overview of the approaches available for genome-wide analyses. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Chengsheng Zhang
- Jackson Laboratory for Genomic Medicine, Farmington, Connecticut
| | - Eliza Cerveira
- Jackson Laboratory for Genomic Medicine, Farmington, Connecticut
| | - Willem Rens
- University of Cambridge, Cambridge, United Kingdom
| | | | - Charles Lee
- Jackson Laboratory for Genomic Medicine, Farmington, Connecticut
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Quality and concordance of genotyping array data of 12,064 samples from 5840 cancer patients. Genomics 2018; 111:950-957. [PMID: 29902512 DOI: 10.1016/j.ygeno.2018.06.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 05/21/2018] [Accepted: 06/05/2018] [Indexed: 12/21/2022]
Abstract
Genotyping arrays characterize genome-wide SNPs for a study cohort and were the primary technology behind genome wide association studies over the last decade. The Cancer Genome Atlas (TCGA) is one of the largest cancer consortium studies, and it collected genotyping data for all of its participants. Using TCGA SNP data genotyped using the Affymetrix 6.0 SNP array from 12,064 samples, we conducted a comprehensive comparisons across DNA sources (tumor tissue, normal tissue, and blood) and sample storage protocols (formalin-fixed paraffin-embedded (FFPE) vs. freshly frozen (FF)), examining genotypes, transition/transversion ratios, and mutation catalogues. During the analysis, we made important observations in relevance to the data quality issues. SNP concordance was excellent between blood and normal tissues, and slightly lower between blood and tumor tissue due to potential somatic mutations in the tumors. The observed poor SNP concordance between FFPE and FF samples suggested a batch effect. The transition/transversion ratio, a metric commonly used for quality control purpose in exome sequencing projects, appeared less applicable for genotyping array data due to the whole-genome coverage built into the array design. Moreover, there were substantially more loss of heterozygosity events than gain of heterozygosity when comparing tumors relative to normal tissues and blood. This might be a consequence of extensive copy number deletions in tumors. In summary, our thorough evaluation calls for more adequate quality control practices and provides guidelines for improved application of TCGA genotyping data.
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Reference Size Matching, Whole-Genome Amplification, and Fluorescent Labeling as a Method for Chromosomal Microarray Analysis of Clinically Actionable Copy Number Alterations in Formalin-Fixed, Paraffin-Embedded Tumor Tissue. J Mol Diagn 2018; 20:279-288. [DOI: 10.1016/j.jmoldx.2018.01.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 01/01/2018] [Accepted: 01/09/2018] [Indexed: 12/14/2022] Open
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Ellison G, Ahdesmäki M, Luke S, Waring PM, Wallace A, Wright R, Röthlisberger B, Ludin K, Merkelbach-Bruse S, Heydt C, Ligtenberg MJL, Mensenkamp AR, de Castro DG, Jones T, Vivancos A, Kondrashova O, Pauwels P, Weyn C, Hahnen E, Hauke J, Soong R, Lai Z, Dougherty B, Carr TH, Johnson J, Mills J, Barrett JC. An evaluation of the challenges to developing tumor BRCA1 and BRCA2 testing methodologies for clinical practice. Hum Mutat 2017; 39:394-405. [PMID: 29215764 PMCID: PMC5838520 DOI: 10.1002/humu.23375] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 11/06/2017] [Accepted: 11/26/2017] [Indexed: 01/19/2023]
Abstract
Ovarian cancer patients with germline or somatic pathogenic variants benefit from treatment with poly ADP ribose polymerase (PARP) inhibitors. Tumor BRCA1/2 testing is more challenging than germline testing as the majority of samples are formalin-fixed paraffin embedded (FFPE), the tumor genome is complex, and the allelic fraction of somatic variants can be low. We collaborated with 10 laboratories testing BRCA1/2 in tumors to compare different approaches to identify clinically important variants within FFPE tumor DNA samples. This was not a proficiency study but an inter-laboratory comparison to identify common issues. Each laboratory received the same tumor DNA samples ranging in genotype, quantity, quality, and variant allele frequency (VAF). Each laboratory performed their preferred next-generation sequencing method to report on the variants. No false positive results were reported in this small study and the majority of methods detected the low VAF variants. A number of variants were not detected due to the bioinformatics analysis, variant classification, or insufficient DNA. The use of hybridization capture or short amplicon methods are recommended based on a bioinformatic assessment of the data. The study highlights the importance of establishing standards and standardization for tBRCA testing particularly when the test results dictate clinical decisions regarding life extending therapies.
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Affiliation(s)
- Gillian Ellison
- Precision Medicine and Genomics, IMED Biotech Unit, AstraZeneca, Macclesfield, UK
| | - Miika Ahdesmäki
- Translational Science, Oncology, IMED Biotech Unit, AstraZeneca, Cambridge, UK
| | - Sally Luke
- R&D Information, AstraZeneca, Cambridge, UK
| | - Paul M Waring
- Department of Pathology, University of Melbourne, Parkville, Melbourne, Victoria, Australia
| | - Andrew Wallace
- Genomic Diagnostics Laboratory, Manchester Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, Saint Mary's Hospital, Manchester, UK
| | - Ronnie Wright
- Genomic Diagnostics Laboratory, Manchester Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, Saint Mary's Hospital, Manchester, UK
| | - Benno Röthlisberger
- Kantonsspital Aarau, Institut für Labormedizin, Abteilung für Medizinische Genetik, Aarau, Switzerland
| | - Katja Ludin
- Kantonsspital Aarau, Institut für Labormedizin, Abteilung für Medizinische Genetik, Aarau, Switzerland
| | | | - Carina Heydt
- Institute of Pathology, University Hospital Cologne, Cologne, Germany
| | - Marjolijn J L Ligtenberg
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Arjen R Mensenkamp
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - David Gonzalez de Castro
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK.,The Centre for Molecular Pathology, The Royal Marsden NHS FT, Sutton, UK
| | - Thomas Jones
- The Centre for Molecular Pathology, The Royal Marsden NHS FT, Sutton, UK
| | - Ana Vivancos
- Laboratory 2.01, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Olga Kondrashova
- Department of Pathology, University of Melbourne, Parkville, Melbourne, Victoria, Australia
| | - Patrick Pauwels
- Center for Oncological Research (CORE), Pathology Department, University Hospital Antwerp (UZA), Edegem, Belgium
| | - Christine Weyn
- Center for Oncological Research (CORE), Pathology Department, University Hospital Antwerp (UZA), Edegem, Belgium
| | - Eric Hahnen
- Center for Hereditary Breast and Ovarian Cancer and Center for Integrated Oncology (CIO), Medical Faculty, University Hospital Cologne, Cologne, Germany
| | - Jan Hauke
- Center for Hereditary Breast and Ovarian Cancer and Center for Integrated Oncology (CIO), Medical Faculty, University Hospital Cologne, Cologne, Germany
| | - Richie Soong
- Cancer Science Institute of Singapore, and Department of Pathology, National University of Singapore, Singapore, Singapore
| | - Zhongwu Lai
- Bioscience, Oncology, IMED Biotech Unit, AstraZeneca, IMED Oncology, Waltham, Massachusetts
| | - Brian Dougherty
- Translational Science, Oncology, IMED Biotech Unit, AstraZeneca, Waltham, Massachusetts
| | - T Hedley Carr
- Translational Science, Oncology, IMED Biotech Unit, AstraZeneca, Cambridge, UK
| | - Justin Johnson
- Translational Science, Oncology, IMED Biotech Unit, AstraZeneca, Waltham, Massachusetts
| | - John Mills
- Precision Medicine and Genomics, IMED Biotech Unit, AstraZeneca, Macclesfield, UK
| | - J Carl Barrett
- Translational Science, Oncology, IMED Biotech Unit, AstraZeneca, Waltham, Massachusetts
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Iddawela M, Rueda O, Eremin J, Eremin O, Cowley J, Earl HM, Caldas C. Integrative analysis of copy number and gene expression in breast cancer using formalin-fixed paraffin-embedded core biopsy tissue: a feasibility study. BMC Genomics 2017; 18:526. [PMID: 28697743 PMCID: PMC5506605 DOI: 10.1186/s12864-017-3867-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 06/16/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND An absence of reliable molecular markers has hampered individualised breast cancer treatments, and a major limitation for translational research is the lack of fresh tissue. There are, however, abundant banks of formalin-fixed paraffin-embedded (FFPE) tissue. This study evaluated two platforms available for the analysis of DNA copy number and gene expression using FFPE samples. METHODS The cDNA-mediated annealing, selection, extension, and ligation assay (DASL™) has been developed for gene expression analysis and the Molecular Inversion Probes assay (Oncoscan™), were used for copy number analysis using FFPE tissues. Gene expression and copy number were evaluated in core-biopsy samples from patients with breast cancer undergoing neoadjuvant chemotherapy (NAC). RESULTS Forty-three core-biopsies were evaluated and characteristic copy number changes in breast cancers, gains in 1q, 8q, 11q, 17q and 20q and losses in 6q, 8p, 13q and 16q, were confirmed. Regions that frequently exhibited gains in tumours showing a pathological complete response (pCR) to NAC were 1q (55%), 8q (40%) and 17q (40%), whereas 11q11 (37%) gain was the most frequent change in non-pCR tumours. Gains associated with poor survival were 11q13 (62%), 8q24 (54%) and 20q (47%). Gene expression assessed by DASL correlated with immunohistochemistry (IHC) analysis for oestrogen receptor (ER) [area under the curve (AUC) = 0.95], progesterone receptor (PR)(AUC = 0.90) and human epidermal growth factor type-2 receptor (HER-2) (AUC = 0.96). Differential expression analysis between ER+ and ER- cancers identified over-expression of TTF1, LAF-4 and C-MYB (p ≤ 0.05), and between pCR vs non-pCRs, over-expression of CXCL9, AREG, B-MYB and under-expression of ABCG2. CONCLUSION This study was an integrative analysis of copy number and gene expression using FFPE core biopsies and showed that molecular marker data from FFPE tissues were consistent with those in previous studies using fresh-frozen samples. FFPE tissue can provide reliable information and will be a useful tool in molecular marker studies. TRIAL REGISTRATION Trial registration number ISRCTN09184069 and registered retrospectively on 02/06/2010.
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Affiliation(s)
- Mahesh Iddawela
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE UK
- Department of Oncology, University of Cambridge, Addenbrooke’s Hospital, Hills Road, Cambridge, UK
- Cambridge Breast Unit, Addenbrooke’s Hospital, Cambridge University Hospitals NHS Foundation Trust, NIHR Cambridge Biomedical Research Centre and Cambridge Experimental Cancer Medicine Centre, Cambridge, UK
- Department of Anatomy & Developmental Biology, Monash University, Clayton, VIC 3800 Australia
- School of Clinical Sciences, Monash University, Clayton, Australia
| | - Oscar Rueda
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE UK
| | - Jenny Eremin
- Research and Development, Lincoln Breast Unit, Lincoln County Hospital, Lincoln, UK
- Nottingham Digestive Disease Centre, Faculty of Medicine and Health Sciences, University of Nottingham, Queen’s Medical Centre, Nottingham, UK
| | - Oleg Eremin
- Research and Development, Lincoln Breast Unit, Lincoln County Hospital, Lincoln, UK
- Nottingham Digestive Disease Centre, Faculty of Medicine and Health Sciences, University of Nottingham, Queen’s Medical Centre, Nottingham, UK
| | - Jed Cowley
- PathLinks, Lincoln County Hospital, Lincoln, UK
| | - Helena M. Earl
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE UK
- Department of Oncology, University of Cambridge, Addenbrooke’s Hospital, Hills Road, Cambridge, UK
- Cambridge Breast Unit, Addenbrooke’s Hospital, Cambridge University Hospitals NHS Foundation Trust, NIHR Cambridge Biomedical Research Centre and Cambridge Experimental Cancer Medicine Centre, Cambridge, UK
| | - Carlos Caldas
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE UK
- Department of Oncology, University of Cambridge, Addenbrooke’s Hospital, Hills Road, Cambridge, UK
- Cambridge Breast Unit, Addenbrooke’s Hospital, Cambridge University Hospitals NHS Foundation Trust, NIHR Cambridge Biomedical Research Centre and Cambridge Experimental Cancer Medicine Centre, Cambridge, UK
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The Utilization of Formalin Fixed-Paraffin-Embedded Specimens in High Throughput Genomic Studies. Int J Genomics 2017; 2017:1926304. [PMID: 28246590 PMCID: PMC5299160 DOI: 10.1155/2017/1926304] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 01/09/2017] [Indexed: 01/09/2023] Open
Abstract
High throughput genomic assays empower us to study the entire human genome in short time with reasonable cost. Formalin fixed-paraffin-embedded (FFPE) tissue processing remains the most economical approach for longitudinal tissue specimen storage. Therefore, the ability to apply high throughput genomic applications to FFPE specimens can expand clinical assays and discovery. Many studies have measured the accuracy and repeatability of data generated from FFPE specimens using high throughput genomic assays. Together, these studies demonstrate feasibility and provide crucial guidance for future studies using FFPE specimens. Here, we summarize the findings of these studies and discuss the limitations of high throughput data generated from FFPE specimens across several platforms that include microarray, high throughput sequencing, and NanoString.
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Abstract
Copy number variations (CNVs) in the genomes have been suggested to play important roles in human evolution, genetic diversity, and disease susceptibility. A number of assays have been developed for the detection of CNVs, including fluorescent in situ hybridization (FISH), array-based comparative genomic hybridization (aCGH), PCR-based assays, and next-generation sequencing (NGS). In this chapter, we describe a microarray method that has been used for the detection of genome-wide CNVs, loss of heterozygosity (LOH), and uniparental disomy (UPD) associated with constitutional and neoplastic disorders.
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Affiliation(s)
- Chengsheng Zhang
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, 06032, USA.
| | - Eliza Cerveira
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, 06032, USA
| | - Mallory Romanovitch
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, 06032, USA
| | - Qihui Zhu
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, 06032, USA
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Greytak SR, Engel KB, Bass BP, Moore HM. Accuracy of Molecular Data Generated with FFPE Biospecimens: Lessons from the Literature. Cancer Res 2015; 75:1541-7. [PMID: 25836717 DOI: 10.1158/0008-5472.can-14-2378] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 12/22/2014] [Indexed: 12/15/2022]
Abstract
Formalin-fixed and paraffin-embedded (FFPE) tissue biospecimens are a valuable resource for molecular cancer research. Although much can be gained from their use, it remains unclear whether the genomic and expression profiles obtained from FFPE biospecimens accurately reflect the physiologic condition of the patient from which they were procured, or if such profiles are confounded by biologic effects from formalin fixation and processing. To assess the physiologic accuracy of genomic and expression data generated with FFPE specimens, we surveyed the literature for articles investigating genomic and expression endpoints in case-matched FFPE and fresh or frozen human biospecimens using the National Cancer Institute's Biospecimen Research Database (http://biospecimens.cancer.gov/brd). Results of the survey revealed that the level of concordance between differentially preserved biospecimens varied among analytical parameters and platforms but also among reports, genes/transcripts of interest, and tumor status. The identified analytical techniques and parameters that resulted in strong correlations between FFPE and frozen biospecimens may provide guidance when optimizing molecular protocols for FFPE use; however, discrepancies reported for similar assays also illustrate the importance of validating protocols optimized for use with FFPE specimens with a case-matched fresh or frozen cohort for each platform, gene or transcript, and FFPE processing regime. On the basis of evidence published to date, validation of analytical parameters with a properly handled frozen cohort is necessary to ensure a high degree of concordance and confidence in the results obtained with FFPE biospecimens.
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Affiliation(s)
| | | | | | - Helen M Moore
- Biorepositories and Biospecimen Research Branch, Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, Maryland.
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Zheng J, Li F, Liu J, Xu Z, Zhang H, Fu Q, Wang J, Sun K. Investigation of Somatic NKX2-5 Mutations in Chinese Children with Congenital Heart Disease. Int J Med Sci 2015; 12:538-43. [PMID: 26180509 PMCID: PMC4502057 DOI: 10.7150/ijms.11700] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 05/18/2015] [Indexed: 11/15/2022] Open
Abstract
The purposes of this study are to investigate somatic NKX2-5 mutations in Chinese children with congenital heart disease (CHD) and assess the reliability of somatic mutation detection in formalin-fixed, paraffin-embedded (FFPE) tissues. The study cohort included frozen and FFPE cardiac tissues as well as blood samples from 85 Chinese children with CHD who had the cardiac operations. The right atrial appendage far from the diseased heart was used as normal control. Genomic DNA was isolated from cardiac tissues and blood samples using TIANamp Blood DNA kit. Two exons and exon-intron boundaries of NKX2-5 were amplified by polymerase chain reaction (PCR) and sequenced by dideoxynucleotide chain termination approach. The acquired sequences were aligned with GenBank sequences to identify the sequence variations. No somatic mutation in the NKX2-5 gene was observed in both frozen and FFPE cardiac tissues in 85 Chinese children with CHD. Nonetheless, a common single nucleotide polymorphism (SNP), c.63 A > G (E21E), was identified in all the three kinds of DNA samples with the same allele frequency 82.3%. Moreover, another common SNP c.606 G > C (L202L) was found in 2.3% of our patients. There were no significant differences in the allele frequencies of two SNPs between the cardiac diseased tissues and right atrial appendage (P > 0.05). PCR artefact as mutations was not found in the FFPE tissues stored for one year. Our findings demonstrate that somatic NKX2-5 mutations do not represent an important aetiologic pathway in Chinese children with congenital heart disease.
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Affiliation(s)
- Jiayi Zheng
- 1. Institute of Pediatric Translational Medicine, Shanghai Children's Medical Center Affiliated to School of Medicine, Shanghai Jiao Tong University, Shanghai, China. ; 2. Department of Pediatric Cardiology, Shanghai Children's Medical Center Affiliated to School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Fen Li
- 2. Department of Pediatric Cardiology, Shanghai Children's Medical Center Affiliated to School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jinfen Liu
- 3. Department of Cardiothoracic Surgery, Shanghai Children's Medical Center Affiliated to School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Zhiwei Xu
- 3. Department of Cardiothoracic Surgery, Shanghai Children's Medical Center Affiliated to School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Haibo Zhang
- 3. Department of Cardiothoracic Surgery, Shanghai Children's Medical Center Affiliated to School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Qihua Fu
- 1. Institute of Pediatric Translational Medicine, Shanghai Children's Medical Center Affiliated to School of Medicine, Shanghai Jiao Tong University, Shanghai, China. ; 4. Clinical Laboratory, Shanghai Children's Medical Center Affiliated to School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jian Wang
- 5. Molecular Diagnostics Laboratory, Shanghai Children's Medical Center Affiliated to School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Kun Sun
- 6. Pediatric Cardiology Department, Xinhua Hospital Affiliated to School of Medicine, Shanghai Jiao Tong University, Shanghai, China
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Dumenil TD, Wockner LF, Bettington M, McKeone DM, Klein K, Bowdler LM, Montgomery GW, Leggett BA, Whitehall VLJ. Genome-wide DNA methylation analysis of formalin-fixed paraffin embedded colorectal cancer tissue. Genes Chromosomes Cancer 2014; 53:537-48. [PMID: 24677610 DOI: 10.1002/gcc.22164] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Revised: 02/26/2014] [Accepted: 02/27/2014] [Indexed: 01/24/2023] Open
Abstract
Formalin fixation and embedding of clinical tissue samples in paraffin is a common method for archiving biological material. These samples are often well annotated and provide an invaluable resource for research. However, this process of fixation and storage of tissue leads to DNA damage and fragmentation. The use of DNA from formalin fixed, paraffin-embedded (FFPE) tissue to interrogate methylation levels on a genome-wide scale can pose challenges. We compared fresh and matched FFPE tissue DNA samples using the Illumina Infinium HD Human Methylation 450K BeadChip platform with a companion application for repair and "restoration" of DNA from FFPE tissue. Our results showed good correlation between fresh and FFPE sample data. FFPE DNA captured 99% of the CpG sites on the array on average. Significant cancer subgroups based on the CpG island methylator phenotype (CIMP) were clearly distinguished for both fresh and FFPE sample sets with cluster and scaling analysis. The DNA methylation status for the five standard CIMP panel genes which was evaluated for all samples by the MethyLight assay was correctly assigned in both fresh and FFPE samples by the array data. We conclude that the "restoration" method followed by assay on the Infinium HD Human Methylation 450K microarray can produce good quality data for DNA from FFPE samples.
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Affiliation(s)
- Troy D Dumenil
- Conjoint Gastroenterology Laboratory, Royal Brisbane and Women's Hospital, Clinical Research Centre and QIMR Berghofer Medical Research Institute, Brisbane, Australia
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Holliday C, Rummel S, Hooke JA, Shriver CD, Ellsworth DL, Ellsworth RE. Genomic instability in the breast microenvironment? A critical evaluation of the evidence. Expert Rev Mol Diagn 2014; 9:667-78. [DOI: 10.1586/erm.09.55] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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20
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Rodrigues MJ, Gentien D, Stern MH, Desjardins L, Couturier J. Genomic amplification is not a frequent event in uveal melanomas. THE AMERICAN JOURNAL OF PATHOLOGY 2013; 183:638. [PMID: 23885717 DOI: 10.1016/j.ajpath.2013.04.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Accepted: 04/01/2013] [Indexed: 06/02/2023]
Abstract
This Correspondence relates to the article by Lake et al that reported copy number and genotyping analysis on formalin-fixed, paraffin-embedded samples using genome-wide SNP arrays version 6.0.
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21
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Evaluating the repair of DNA derived from formalin-fixed paraffin-embedded tissues prior to genomic profiling by SNP-CGH analysis. J Transl Med 2013; 93:701-10. [PMID: 23568031 DOI: 10.1038/labinvest.2013.54] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
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 high-level 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.
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22
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Jacobs S. Data analysis considerations for detecting copy number changes in formalin-fixed, paraffin-embedded tissues. Cold Spring Harb Protoc 2012; 2012:1203-1209. [PMID: 23118356 DOI: 10.1101/pdb.ip071761] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The Whole Genome Sampling Analysis (WGSA) assay in combination with Affymetrix GeneChip Mapping Arrays is used for copy number analysis of high-quality DNA samples (i.e., samples that have been collected from blood, fresh or frozen tissue, or cell lines). Formalin-fixed, paraffin-embedded (FFPE) samples, however, represent the most prevalent form of archived clinical samples, but they provide additional challenges for molecular assays. FFPE processing usually results in the degradation of FFPE DNA and in the contamination and chemical modification of these DNA samples. In this article, we describe the steps needed to obtain reliable copy number predictions from degraded and contaminated FFPE samples.
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Use of formalin-fixed paraffin-embedded tumor tissue as a DNA source in molecular epidemiological studies of pediatric CNS tumors. ACTA ACUST UNITED AC 2012; 21:105-13. [PMID: 22555093 DOI: 10.1097/pdm.0b013e3182340a78] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Formalin-fixed paraffin-embedded tissue (FFPET) samples are a potential source of DNA for molecular epidemiological studies. However, the use of FFPET samples can be restricted by the yield and quality of DNA isolated. The aim of this study was to examine whether FFPET biopsies from pediatric central nervous system tumors were a feasible alternative to archival frozen tissue when characterizing common gene polymorphisms. DNA was isolated from 50 frozen pediatric central nervous system tumor biopsies and matched FFPET samples. Real-time polymerase chain reaction (PCR) was used to quantify DNA and characterize GSTT1, GSTM1, GSTP1, and MTHFR gene polymorphisms. The use of whole-genome amplification (WGA) to increase DNA yields was also investigated. The results showed that DNA isolated from FFPET samples was more fragmented and provided smaller yields than DNA isolated from frozen samples. Attempts to increase the DNA yield from FFPET using WGA were unsuccessful. DNA from FFPET samples was successfully genotyped for the GSTP1 Ile105Val and MTHFR 677 C>T polymorphisms in 98% of samples and was 100% concordant with the results from frozen tissue. However, DNA from FFPET performed poorly in real-time PCR assays for GSTM1 and GSTT1 deletion polymorphisms. Our investigations show that DNA extracted from FFPET is substantially fragmented and not readily amplified using WGA. In addition, careful validation of PCR assays should be carried out due to the variable amplification of fragmented FFPET DNA.
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Pedeutour F, Maire G, Pierron A, Thomas DM, Garsed DW, Bianchini L, Duranton-Tanneur V, Cortes-Maurel A, Italiano A, Squire JA, Coindre JM. A newly characterized human well-differentiated liposarcoma cell line contains amplifications of the 12q12-21 and 10p11-14 regions. Virchows Arch 2012; 461:67-78. [DOI: 10.1007/s00428-012-1256-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Revised: 05/16/2012] [Accepted: 05/21/2012] [Indexed: 12/14/2022]
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Analysis of KLLN as a high-penetrance breast cancer predisposition gene. Breast Cancer Res Treat 2012; 134:543-7. [PMID: 22580995 DOI: 10.1007/s10549-012-2088-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2012] [Accepted: 04/30/2012] [Indexed: 01/24/2023]
Abstract
KLLN is a p53 target gene with DNA binding function and represents a highly plausible candidate breast cancer predisposition gene. We screened for predisposing variants in 860 high-risk breast cancer families using high resolution melt analysis. A germline c.339_340delAG variant predicted to cause premature termination of the protein after 57 alternative amino acid residues was identified in 3/860 families who tested negative for BRCA1 and BRCA2 mutations and in 1/84 sporadic breast cancer cases. However, the variant was also detected in 2/182 families with known BRCA1 or BRCA2 mutations and in 2/464 non-cancer controls. Furthermore, loss of the mutant allele was detected in 2/2 breast tumors. Our data suggest that pathogenic mutations in KLLN are rare in breast cancer families and the c.339_340delAG variant does not represent a high-penetrance breast cancer risk allele.
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Abstract
Formalin is the most commonly used tissue fixative worldwide. While it offers excellent morphological preservation for routine histology, it has detrimental effects on nucleic acids. Most studies of nucleic acids have therefore used fresh frozen tissue, the collection and storage of which is resource intensive. The ability to use modern genomic, transcriptomic and epigenomic methods with nucleic acids derived from formalin-fixed, paraffin-embedded (FFPE) tissues would allow enormous archives of routinely stored tissues (usually with well-annotated clinical data) to be used for translational research. This paper outlines the effects of formalin on nucleic acids, describes ways of minimizing nucleic acid degradation and optimizing extraction, and reviews recent studies that have used contemporary techniques to analyse FFPE-derived nucleic acids (with a focus on malignant tissue sources). Simple tips are also offered to ensure the utility of your institution's samples for future studies, and broadly applicable guidelines are listed for those contemplating their own study using FFPE-derived material.
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Affiliation(s)
- Adam Frankel
- University of Queensland, Ipswich Road, Woolloongabba,Brisbane, Qld 4102, Australia.
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Sato-Otsubo A, Sanada M, Ogawa S. Single-nucleotide polymorphism array karyotyping in clinical practice: where, when, and how? Semin Oncol 2012; 39:13-25. [PMID: 22289488 DOI: 10.1053/j.seminoncol.2011.11.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Single-nucleotide polymorphism array (SNP-A) karyotyping is a new technology that has enabled genome-wide detection of genetic lesions in human cancers, including hematopoietic neoplasms. Taking advantage of very large numbers of allele-specific probes synthesized on microarrays at high density, copy number alterations as well as allelic imbalances can be sensitively detected in a genome-wide manner at unprecedented resolutions. Most importantly, SNP-A karyotyping represents the only platform currently available for genome-scale detection of copy neutral loss of heterozygosity (CN-LOH) or uniparental disomy (UPD), which is widely observed in cancer genomes. Although not applicable to detection of balanced translocations, which are commonly found in hematopoietic malignancies, SNP-A karyotyping technology complements and even outperforms conventional metaphase karyotyping, potentially allowing for more accurate genetic diagnosis of hematopoietic neoplasms in clinical practice. Here, we review the current status of SNP-A karyotyping and its application to hematopoietic neoplasms.
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Affiliation(s)
- Aiko Sato-Otsubo
- Cancer Genomics Project, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
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The utility and limitation of single nucleotide polymorphism analysis on whole genome amplified mesenchymal tumour DNA in formalin fixed tumour samples. Pathology 2012; 44:33-41. [DOI: 10.1097/pat.0b013e32834e411e] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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Oikawa M, Yoshiura KI, Kondo H, Miura S, Nagayasu T, Nakashima M. Significance of genomic instability in breast cancer in atomic bomb survivors: analysis of microarray-comparative genomic hybridization. Radiat Oncol 2011; 6:168. [PMID: 22152285 PMCID: PMC3280193 DOI: 10.1186/1748-717x-6-168] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2011] [Accepted: 12/07/2011] [Indexed: 01/04/2023] Open
Abstract
Background It has been postulated that ionizing radiation induces breast cancers among atomic bomb (A-bomb) survivors. We have reported a higher incidence of HER2 and C-MYC oncogene amplification in breast cancers from A-bomb survivors. The purpose of this study was to clarify the effect of A-bomb radiation exposure on genomic instability (GIN), which is an important hallmark of carcinogenesis, in archival formalin-fixed paraffin-embedded (FFPE) tissues of breast cancer by using microarray-comparative genomic hybridization (aCGH). Methods Tumor DNA was extracted from FFPE tissues of invasive ductal cancers from 15 survivors who were exposed at 1.5 km or less from the hypocenter and 13 calendar year-matched non-exposed patients followed by aCGH analysis using a high-density oligonucleotide microarray. The total length of copy number aberrations (CNA) was used as an indicator of GIN, and correlation with clinicopathological factors were statistically tested. Results The mean of the derivative log ratio spread (DLRSpread), which estimates the noise by calculating the spread of log ratio differences between consecutive probes for all chromosomes, was 0.54 (range, 0.26 to 1.05). The concordance of results between aCGH and fluorescence in situ hybridization (FISH) for HER2 gene amplification was 88%. The incidence of HER2 amplification and histological grade was significantly higher in the A-bomb survivors than control group (P = 0.04, respectively). The total length of CNA tended to be larger in the A-bomb survivors (P = 0.15). Correlation analysis of CNA and clinicopathological factors revealed that DLRSpread was negatively correlated with that significantly (P = 0.034, r = -0.40). Multivariate analysis with covariance revealed that the exposure to A-bomb was a significant (P = 0.005) independent factor which was associated with larger total length of CNA of breast cancers. Conclusions Thus, archival FFPE tissues from A-bomb survivors are useful for genome-wide aCGH analysis. Our results suggested that A-bomb radiation may affect the increased amount of CNA as a hallmark of GIN and, subsequently, be associated with a higher histologic grade in breast cancer found in A-bomb survivors.
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Affiliation(s)
- Masahiro Oikawa
- Department of Human Genetics, Atomic Bomb Disease Institute, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
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Thompson ER, Boyle SE, Johnson J, Ryland GL, Sawyer S, Choong DY, kConFab, Chenevix-Trench G, Trainer AH, Lindeman GJ, Mitchell G, James PA, Campbell IG. Analysis of RAD51C germline mutations in high-risk breast and ovarian cancer families and ovarian cancer patients. Hum Mutat 2011; 33:95-9. [DOI: 10.1002/humu.21625] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2011] [Accepted: 09/16/2011] [Indexed: 11/10/2022]
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Stokes A, Drozdov I, Guerra E, Ouzounis CA, Warnakulasuriya S, Gleeson MJ, McGurk M, Tavassoli M, Odell EW. Copy number and loss of heterozygosity detected by SNP array of formalin-fixed tissues using whole-genome amplification. PLoS One 2011; 6:e24503. [PMID: 21966361 PMCID: PMC3180289 DOI: 10.1371/journal.pone.0024503] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2011] [Accepted: 08/11/2011] [Indexed: 12/18/2022] Open
Abstract
The requirement for large amounts of good quality DNA for whole-genome applications prohibits their use for small, laser capture micro-dissected (LCM), and/or rare clinical samples, which are also often formalin-fixed and paraffin-embedded (FFPE). Whole-genome amplification of DNA from these samples could, potentially, overcome these limitations. However, little is known about the artefacts introduced by amplification of FFPE-derived DNA with regard to genotyping, and subsequent copy number and loss of heterozygosity (LOH) analyses. Using a ligation adaptor amplification method, we present data from a total of 22 Affymetrix SNP 6.0 experiments, using matched paired amplified and non-amplified DNA from 10 LCM FFPE normal and dysplastic oral epithelial tissues, and an internal method control. An average of 76.5% of SNPs were called in both matched amplified and non-amplified DNA samples, and concordance was a promising 82.4%. Paired analysis for copy number, LOH, and both combined, showed that copy number changes were reduced in amplified DNA, but were 99.5% concordant when detected, amplifications were the changes most likely to be 'missed', only 30% of non-amplified LOH changes were identified in amplified pairs, and when copy number and LOH are combined ∼50% of gene changes detected in the unamplified DNA were also detected in the amplified DNA and within these changes, 86.5% were concordant for both copy number and LOH status. However, there are also changes introduced as ∼20% of changes in the amplified DNA are not detected in the non-amplified DNA. An integrative network biology approach revealed that changes in amplified DNA of dysplastic oral epithelium localize to topologically critical regions of the human protein-protein interaction network, suggesting their functional implication in the pathobiology of this disease. Taken together, our results support the use of amplification of FFPE-derived DNA, provided sufficient samples are used to increase power and compensate for increased error rates.
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Affiliation(s)
- Angela Stokes
- Department of Oral Pathology, King's College London Dental Institute, London, United Kingdom.
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Ngamphiw C, Assawamakin A, Xu S, Shaw PJ, Yang JO, Ghang H, Bhak J, Liu E, Tongsima S. PanSNPdb: the Pan-Asian SNP genotyping database. PLoS One 2011; 6:e21451. [PMID: 21731755 PMCID: PMC3121791 DOI: 10.1371/journal.pone.0021451] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2011] [Accepted: 05/27/2011] [Indexed: 01/07/2023] Open
Abstract
The HUGO Pan-Asian SNP consortium conducted the largest survey to date of human genetic diversity among Asians by sampling 1,719 unrelated individuals among 71 populations from China, India, Indonesia, Japan, Malaysia, the Philippines, Singapore, South Korea, Taiwan, and Thailand. We have constructed a database (PanSNPdb), which contains these data and various new analyses of them. PanSNPdb is a research resource in the analysis of the population structure of Asian peoples, including linkage disequilibrium patterns, haplotype distributions, and copy number variations. Furthermore, PanSNPdb provides an interactive comparison with other SNP and CNV databases, including HapMap3, JSNP, dbSNP and DGV and thus provides a comprehensive resource of human genetic diversity. The information is accessible via a widely accepted graphical interface used in many genetic variation databases. Unrestricted access to PanSNPdb and any associated files is available at: http://www4a.biotec.or.th/PASNP.
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Affiliation(s)
- Chumpol Ngamphiw
- National Center for Genetic Engineering and Biotechnology (BIOTEC), Klong Luang, Pathumthani, Thailand
- Inter-Department Program of BioMedical Sciences, Faculty of Graduate School, Chulalongkorn University, Bangkok, Thailand
| | - Anunchai Assawamakin
- National Center for Genetic Engineering and Biotechnology (BIOTEC), Klong Luang, Pathumthani, Thailand
| | - Shuhua Xu
- Chinese Academy of Sciences and Max Planck Society (CAS-MPG) Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Philip J. Shaw
- National Center for Genetic Engineering and Biotechnology (BIOTEC), Klong Luang, Pathumthani, Thailand
| | - Jin Ok Yang
- Korean BioInformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Yuseong-gu, Deajeon, South Korea
| | - Ho Ghang
- Personal Genomics Institute, Genome Research Foundation, Suwon, South Korea
| | - Jong Bhak
- Personal Genomics Institute, Genome Research Foundation, Suwon, South Korea
- Theragen BiO Institute, TheragenEtex, Suwon, South Korea
| | - Edison Liu
- Genome Institute of Singapore, Singapore, Singapore
| | - Sissades Tongsima
- National Center for Genetic Engineering and Biotechnology (BIOTEC), Klong Luang, Pathumthani, Thailand
- * E-mail:
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Oikawa M, Nagayasu T, Yano H, Hayashi T, Abe K, Kinoshita A, Yoshiura KI. 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. Breast J 2011; 17:427-30. [PMID: 21651641 DOI: 10.1111/j.1524-4741.2011.01110.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Clevert DA, Mitterecker A, Mayr A, Klambauer G, Tuefferd M, De Bondt A, Talloen W, Göhlmann H, Hochreiter S. cn.FARMS: a latent variable model to detect copy number variations in microarray data with a low false discovery rate. Nucleic Acids Res 2011; 39:e79. [PMID: 21486749 PMCID: PMC3130288 DOI: 10.1093/nar/gkr197] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Cost-effective oligonucleotide genotyping arrays like the Affymetrix SNP 6.0 are still the predominant technique to measure DNA copy number variations (CNVs). However, CNV detection methods for microarrays overestimate both the number and the size of CNV regions and, consequently, suffer from a high false discovery rate (FDR). A high FDR means that many CNVs are wrongly detected and therefore not associated with a disease in a clinical study, though correction for multiple testing takes them into account and thereby decreases the study's discovery power. For controlling the FDR, we propose a probabilistic latent variable model, 'cn.FARMS', which is optimized by a Bayesian maximum a posteriori approach. cn.FARMS controls the FDR through the information gain of the posterior over the prior. The prior represents the null hypothesis of copy number 2 for all samples from which the posterior can only deviate by strong and consistent signals in the data. On HapMap data, cn.FARMS clearly outperformed the two most prevalent methods with respect to sensitivity and FDR. The software cn.FARMS is publicly available as a R package at http://www.bioinf.jku.at/software/cnfarms/cnfarms.html.
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Affiliation(s)
- Djork-Arné Clevert
- Institute of Bioinformatics, Johannes Kepler University Linz, Linz, Austria
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Hagleitner MM, Coenen MJH, Jeuken JWM, Flucke U, Schreuder HWB, te Loo DMWM, Hoogerbrugge PM. Taqman genotyping assays can be used on decalcified and paraffin-embedded tissue from patients with osteosarcoma. Pediatr Blood Cancer 2011; 56:35-8. [PMID: 20848662 DOI: 10.1002/pbc.22654] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2010] [Accepted: 04/23/2010] [Indexed: 11/09/2022]
Abstract
BACKGROUND In cancers like osteosarcoma with a 5-year overall survival of 50-60%, archived histological specimens can be a useful source of biological material. However, this material generally has been decalcified and formalin-fixed for many years. In our study, we investigated whether DNA obtained from these tissues can be used for reliable single nucleotide polymorphism (SNP) genotyping. PROCEDURE We studied two SNPs in the drug transporter MDR1 using Taqman® SNP genotyping assays. Genotypes of the germ line DNA derived from freshly isolated DNA of 20 surviving patients with osteosarcoma were compared with genotypes obtained from archived material from decalcified formalin-fixed, paraffin-embedded (FFPE) blocks of the same patients. RESULTS Decalcified FFPE-derived DNA yielded smaller PCR fragments compared to DNA extracted from peripheral blood cells, with a reliable size of ∼200 bp. However, we were able to evaluate each SNP in 19 of 20 cases included in this study. All successfully genotyped samples showed 100% concordance between genotypes obtained from DNA of FFPE tissue and the genotypes obtained from DNA of blood from the same patients. CONCLUSIONS In conclusion, we have demonstrated that decalcified FFPE tissue can be used for genetic polymorphism analysis using Taqman® allelic discrimination assays. This forms a unique opportunity to combine new insights in genetic research with historical patient cohorts.
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Affiliation(s)
- Melanie M Hagleitner
- Department of Pediatric Hematology and Oncology, Radboud University Nijmegen Medical Centre, Nijmegen, Netherlands.
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Tuefferd M, de Bondt A, Van den Wyngaert I, Talloen W, Göhlmann H. Microarray profiling of DNA extracted from FFPE tissues using SNP 6.0 Affymetrix platform. Methods Mol Biol 2011; 724:147-160. [PMID: 21370012 DOI: 10.1007/978-1-61779-055-3_10] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
High-density oligonucleotide microarrays are commonly used for GWAS studies as well as for tumor genome alteration identifications. The recent Affymetrix Genome-Wide SNP 6.0 microarray generation has two major advantages: (1) showing high genome coverage and (2) starting with very small amount of DNA material. The hybridization protocol needs to be standardized and highly reproducible, as DNA is first digested by restriction enzymes and then PCR-amplified to reduce genome complexity. Especially the restriction digestion step is highly sensitive to degradation of the initial material. The stronger the sample is degraded, the lower the number of restriction sites still present in the genome, and hence the less-efficient amplification step.Paraffin-embedded material generally only allows to extract partially degraded DNA, and therefore is difficult to analyze using SNP array technology. We and others (Jacobs et al., Cancer Res 67:2544-2551, 2007; Tuefferd et al., Genes Chromosomes Cancer 47:957-964, 2008) have shown that target preparation protocol can be adjusted to improve hybridization performances. The final in silico data analysis procedure should be modified accordingly to extract most of the biological information from the signal measured. By optimizing these crucial steps, it is possible to use Affymetrix SNP array 6.0 -technology in the context of genome variation, even for FFPE partially degraded material. This opens a lot of potential for large retrospective series of samples.
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Affiliation(s)
- Marianne Tuefferd
- Johnson & Johnson Pharmaceutical Research & Development, Beerse, Belgium.
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Reproducibility and performance of virtual karyotyping with SNP microarrays for the detection of chromosomal imbalances in formalin-fixed paraffin-embedded tissues. ACTA ACUST UNITED AC 2010; 19:127-34. [PMID: 20736741 DOI: 10.1097/pdm.0b013e3181d527c5] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND Chromosomal imbalances are commonly seen in cancer and inherited genetic diseases. These imbalances may assist in the diagnosis, prognosis, and/or therapeutic management of certain neoplasms. Several methods for detecting chromosomal imbalances, such as, fluorescent in situ hybridization, array comparative genomic hybridization, and single nucleotide polymorphism (SNP) arrays have proven useful in formalin-fixed paraffin-embedded (FFPE) tissues. Here, we report the performance and reproducibility of virtual karyotyping of FFPE tissues with Affymetrix SNP arrays. METHODS Virtual karyotypes from 442 FFPE tumor samples were generated using the Affymetrix GeneChip Mapping 10K Xba 2.0 and/or 250K Nsp SNP mapping arrays. Samples ranged from a few weeks to 17 years in archival storage. Virtual karyotypes were assessed for copy number changes, loss of heterozygosity, and acquired uniparental disomy. RESULTS Overall, 75.3% of samples produced interpretable virtual karyotypes with the 10K arrays and 76.7% in the 250K arrays. Parameters for the selection of samples for hybridization were determined, which increased the success rate in both platforms to 81.3 and 92.6%, respectively. FFPE virtual karyotypes generated with both 10K Xba 2.0 and 250K Nsp arrays showed 100% concordance in intralaboratory and interlaboratory reproducibility studies. Samples older than 7 years showed decreased performance. CONCLUSIONS SNP arrays are a reliable, reproducible, and robust platform for the virtual karyotyping of FFPE tumor tissues with performance characteristics adequate for clinical application. Parameters that most significantly affected sample performance were sample age and storage conditions.
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Kotliarov Y, Bozdag S, Cheng H, Wuchty S, Zenklusen JC, Fine HA. CNAReporter: a GenePattern pipeline for the generation of clinical reports of genomic alterations. BMC Med Genomics 2010; 3:11. [PMID: 20380730 PMCID: PMC2872651 DOI: 10.1186/1755-8794-3-11] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2009] [Accepted: 04/09/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Genomic copy number alterations are widely associated with a broad range of human tumors and offer the potential to be used as a diagnostic tool. Especially in the emerging era of personalized medicine medical informatics tools that allow the fast visualization and analysis of genomic alterations of a patient's genomic profile for diagnostic and potential treatment purposes increasingly gain importance. RESULTS We developed CNAReporter, a software tool that allows users to visualize SNP-specific data obtained from Affymetrix arrays and generate PDF-reports as output. We combined standard algorithms for the analysis of chromosomal alterations, utilizing the widely applied GenePattern framework. As an example, we show genome analyses of two patients with distinctly different CNA profiles using the tool. CONCLUSIONS Glioma subtypes, characterized by different genomic alterations, are often treated differently but can be difficult to differentiate pathologically. CNAReporter offers a user-friendly way to visualize and analyse genomic changes of any given tumor genomic profile, thereby leading to an accurate diagnosis and patient-specific treatment.
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Affiliation(s)
- Yuri Kotliarov
- Neuro-Oncology Branch, National Cancer Institute, National Institutes of Neurological Disorder and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
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Huang WY, Sheehy TM, Moore LE, Hsing AW, Purdue MP. Simultaneous recovery of DNA and RNA from formalin-fixed paraffin-embedded tissue and application in epidemiologic studies. Cancer Epidemiol Biomarkers Prev 2010; 19:973-7. [PMID: 20332269 PMCID: PMC2864144 DOI: 10.1158/1055-9965.epi-10-0091] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Analysis of DNA, RNA, and protein extracted from tissue specimens in epidemiologic studies is useful for assessing etiologic heterogeneity, mechanisms of carcinogenesis, and biomarkers for prognosis and prediction of treatment responses. Fresh-frozen tissue samples may provide optimal quality nucleic acids, but pose multiple logistical considerations, including rapid access to tissues before histopathologic examination and specialized equipment for freezing, transport, and storage; in addition, morphology is often compromised. In contrast, formalin-fixed paraffin-embedded (FFPE) tissue samples, including enormous archives of existing specimens, represent a valuable source of retrospective biological material for epidemiologic research, although presenting different limitations compared with frozen samples. Recent efforts have made progress toward enhancing the utility of FFPE specimens for molecular analyses, including DNA studies, and increasingly for RNA and other macromolecules. Here, we report the method that we used to simultaneously recover DNA and RNA from FFPE tissue specimens with appreciable quantity and quality and discuss briefly the application of tumor markers in epidemiologic studies.
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Affiliation(s)
- Wen-Yi Huang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, 6120 Executive Boulevard, EPS 8110, MSC 7240, Bethesda, MD 20892-7240, USA.
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Nasri S, Anjomshoaa A, Song S, Guilford P, McNoe L, Black M, Phillips V, Reeve A, Humar B. Oligonucleotide array outperforms SNP array on formalin-fixed paraffin-embedded clinical samples. ACTA ACUST UNITED AC 2010; 198:1-6. [DOI: 10.1016/j.cancergencyto.2009.12.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2009] [Accepted: 12/07/2009] [Indexed: 10/19/2022]
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Monzon FA, Alvarez K, Gatalica Z, Bridge JA, Nelson M, Kim HJ, Hagenkord JM. Detection of chromosomal aberrations in renal tumors: a comparative study of conventional cytogenetics and virtual karyotyping with single-nucleotide polymorphism microarrays. Arch Pathol Lab Med 2010; 133:1917-22. [PMID: 19961245 DOI: 10.5858/133.12.1917] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/18/2009] [Indexed: 11/06/2022]
Abstract
CONTEXT -Renal epithelial neoplasms have characteristic chromosomal imbalances, and we have shown previously that virtual karyotypes derived from single-nucleotide polymorphism microarrays can be performed on formalin-fixed, paraffin-embedded tissue. OBJECTIVE -To perform a direct comparison of virtual and conventional karyotypes to evaluate concordance of results. DESIGN -Twenty archival formalin-fixed, paraffin-embedded tumor samples with preexisting, conventional cytogenetic results were analyzed with Affymetrix 10K 2.0 or 250K Nsp single-nucleotide polymorphism microarrays. RESULTS -Nineteen samples yielded adequate virtual karyotypes for interpretation. Eight samples showed complete agreement between the 2 techniques, and 8 samples showed partial agreement. The disease-defining lesions (eg, loss of 3p for clear cell carcinoma) were identified in all 19 cases by virtual karyotypes and in 15 cases by conventional karyotypes. Virtual and conventional karyotypic findings were concordant in the identification of these disease-defining lesions in 86% (13 of 15) of cases. In 3 cases, virtual karyotypes identified lesions consistent with the morphologic diagnosis, whereas the conventional karyotypes were unsuccessful because of insufficient tumor representation or stromal overgrowth. Two cases with acquired uniparental disomy were identified by single-nucleotide polymorphism arrays, and 5 cases with translocations were identified by conventional karyotype. CONCLUSIONS -Our results show that both techniques are able to identify the characteristic chromosomal abnormality for renal tumor subtypes in most cases. Discrepancies can be explained by inherent limitations of each technique, inadequate tumor sampling, and tumor heterogeneity. We conclude that virtual karyotyping is a robust alternative to conventional cytogenetics for the evaluation of chromosomal anomalies in formalin-fixed, paraffin-embedded tissues from renal epithelial neoplasms.
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Affiliation(s)
- Federico A Monzon
- Department of Pathology, The Methodist Hospital Research Institute, The Methodist Hospital, Houston, Texas 77030, USA.
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Abstract
Exploiting the potential of omics for clinical diagnosis, prognosis, and therapeutic purposes has currently been receiving a lot of attention. In recent years, most of the effort has been put into demonstrating the possible clinical applications of the various omics fields. The cost-effectiveness analysis has been, so far, rather neglected. The cost of omics-derived applications is still very high, but future technological improvements are likely to overcome this problem. In this chapter, we will give a general background of the main omics fields and try to provide some examples of the most successful applications of omics that might be used in clinical diagnosis and in a therapeutic context.
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Affiliation(s)
- Ewa Gubb
- Bioinformatics, Parque Technológico de Bizkaia, Derio, Spain
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Li J, Yang T, Wang L, Yan H, Zhang Y, Guo Y, Pan F, Zhang Z, Peng Y, Zhou Q, He L, Zhu X, Deng H, Levy S, Papasian CJ, Drees BM, Hamilton JJ, Recker RR, Cheng J, Deng HW. Whole genome distribution and ethnic differentiation of copy number variation in Caucasian and Asian populations. PLoS One 2009; 4:e7958. [PMID: 19956714 PMCID: PMC2776354 DOI: 10.1371/journal.pone.0007958] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2008] [Accepted: 07/03/2009] [Indexed: 12/16/2022] Open
Abstract
Although copy number variation (CNV) has recently received much attention as a form of structure variation within the human genome, knowledge is still inadequate on fundamental CNV characteristics such as occurrence rate, genomic distribution and ethnic differentiation. In the present study, we used the Affymetrix GeneChip® Mapping 500K Array to discover and characterize CNVs in the human genome and to study ethnic differences of CNVs between Caucasians and Asians. Three thousand and nineteen CNVs, including 2381 CNVs in autosomes and 638 CNVs in X chromosome, from 985 Caucasian and 692 Asian individuals were identified, with a mean length of 296 kb. Among these CNVs, 190 had frequencies greater than 1% in at least one ethnic group, and 109 showed significant ethnic differences in frequencies (p<0.01). After merging overlapping CNVs, 1135 copy number variation regions (CNVRs), covering approximately 439 Mb (14.3%) of the human genome, were obtained. Our findings of ethnic differentiation of CNVs, along with the newly constructed CNV genomic map, extend our knowledge on the structural variation in the human genome and may furnish a basis for understanding the genomic differentiation of complex traits across ethnic groups.
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Affiliation(s)
- Jian Li
- School of Medicine, University of Missouri Kansas City, Kansas City, Missouri, United States of America
| | - Tielin Yang
- School of Medicine, University of Missouri Kansas City, Kansas City, Missouri, United States of America
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education and Institute of Molecular Genetics, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shanxi, People's Republic of China
| | - Liang Wang
- School of Medicine, University of Missouri Kansas City, Kansas City, Missouri, United States of America
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education and Institute of Molecular Genetics, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shanxi, People's Republic of China
| | - Han Yan
- School of Medicine, University of Missouri Kansas City, Kansas City, Missouri, United States of America
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education and Institute of Molecular Genetics, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shanxi, People's Republic of China
| | - Yinping Zhang
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education and Institute of Molecular Genetics, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shanxi, People's Republic of China
| | - Yan Guo
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education and Institute of Molecular Genetics, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shanxi, People's Republic of China
| | - Feng Pan
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education and Institute of Molecular Genetics, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shanxi, People's Republic of China
| | - Zhixin Zhang
- School of Medicine, University of Missouri Kansas City, Kansas City, Missouri, United States of America
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education and Institute of Molecular Genetics, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shanxi, People's Republic of China
| | - Yumei Peng
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education and Institute of Molecular Genetics, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shanxi, People's Republic of China
| | - Qi Zhou
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education and Institute of Molecular Genetics, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shanxi, People's Republic of China
| | - Lina He
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education and Institute of Molecular Genetics, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shanxi, People's Republic of China
| | - Xuezhen Zhu
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education and Institute of Molecular Genetics, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shanxi, People's Republic of China
| | - Hongyi Deng
- School of Medicine, University of Missouri Kansas City, Kansas City, Missouri, United States of America
| | - Shawn Levy
- Vanderbilt Microarray Shared Resource, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Christopher J. Papasian
- School of Medicine, University of Missouri Kansas City, Kansas City, Missouri, United States of America
| | - Betty M. Drees
- School of Medicine, University of Missouri Kansas City, Kansas City, Missouri, United States of America
| | - James J. Hamilton
- School of Medicine, University of Missouri Kansas City, Kansas City, Missouri, United States of America
| | - Robert R. Recker
- Osteoporosis Research Center, Creighton University, Omaha, Nebraska, United States of America
| | - Jing Cheng
- National Engineering Research Center for Beijing Biochip Technology, Changping District, Beijing, People's Republic of China
| | - Hong-Wen Deng
- School of Medicine, University of Missouri Kansas City, Kansas City, Missouri, United States of America
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education and Institute of Molecular Genetics, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shanxi, People's Republic of China
- Laboratory of Molecular and Statistical Genetics, College of Life Sciences, Hunan Normal University, Changsha, Hunan, People's Republic of China
- * E-mail:
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Gorringe KL, Ramakrishna M, Williams LH, Sridhar A, Boyle SE, Bearfoot JL, Li J, Anglesio MS, Campbell IG. Are there any more ovarian tumor suppressor genes? A new perspective using ultra high-resolution copy number and loss of heterozygosity analysis. Genes Chromosomes Cancer 2009; 48:931-42. [DOI: 10.1002/gcc.20694] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
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Sircar K, Yoshimoto M, Monzon FA, Koumakpayi IH, Katz RL, Khanna A, Alvarez K, Chen G, Darnel AD, Aprikian AG, Saad F, Bismar TA, Squire JA. PTEN genomic deletion is associated with p-Akt and AR signalling in poorer outcome, hormone refractory prostate cancer. J Pathol 2009; 218:505-13. [PMID: 19402094 DOI: 10.1002/path.2559] [Citation(s) in RCA: 169] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
PTEN haploinsufficiency is common in hormone-sensitive prostate cancer, though the incidence of genomic deletion and its downstream effects have not been elucidated in clinical samples of hormone refractory prostate cancer (HRPC). Progression to androgen independence is pivotal in prostate cancer and mediated largely by the androgen receptor (AR). Since this process is distinct from metastatic progression, we examined alterations of the PTEN gene in locally advanced recurrent, non-metastatic human HRPC tissues. Retrospective analyses of PTEN deletion status were correlated with activated downstream phospho-Akt (p-Akt) pathway proteins and with the androgen receptor. The prevalence of PTEN genomic deletions in transurethral resection samples of 59 HRPC patients with known clinical outcome was assessed by four-colour FISH analyses. FISH was performed using six BAC clones spanning both flanking PTEN genomic regions and the PTEN gene locus, and a chromosome 10 centromeric probe. PTEN copy number was also evaluated in a subset of cases using single nucleotide polymorphism (SNP) arrays. In addition, the samples were immunostained with antibodies against p-Akt, p-mTOR, p-70S6, and AR. The PTEN gene was deleted in 77% of cases, with 25% showing homozygous deletions, 18% homozygous and hemizygous deletions, and 34% hemizygous deletions only. In a subset of the study group, SNP array analysis confirmed the FISH findings. PTEN genomic deletion was significantly correlated to the expression of downstream p-Akt (p < 0.0001), AR (p = 0.025), and to cancer-specific mortality (p = 0.039). PTEN deletion is common in HRPC, with bi-allelic loss correlating to disease-specific mortality and associated with Akt and AR deregulation.
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Affiliation(s)
- Kanishka Sircar
- The University of Texas MD Anderson Cancer Center, Department of Pathology, Houston, TX, USA
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Virtual-Karyotyping With SNP Microarrays in Morphologically Challenging Renal Cell Neoplasms. Am J Surg Pathol 2009; 33:1276-86. [DOI: 10.1097/pas.0b013e3181a2aa36] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Wang Y, Carlton VEH, Karlin-Neumann G, Sapolsky R, Zhang L, Moorhead M, Wang ZC, Richardson AL, Warren R, Walther A, Bondy M, Sahin A, Krahe R, Tuna M, Thompson PA, Spellman PT, Gray JW, Mills GB, Faham M. High quality copy number and genotype data from FFPE samples using Molecular Inversion Probe (MIP) microarrays. BMC Med Genomics 2009; 2:8. [PMID: 19228381 PMCID: PMC2649948 DOI: 10.1186/1755-8794-2-8] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2008] [Accepted: 02/19/2009] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND A major challenge facing DNA copy number (CN) studies of tumors is that most banked samples with extensive clinical follow-up information are Formalin-Fixed Paraffin Embedded (FFPE). DNA from FFPE samples generally underperforms or suffers high failure rates compared to fresh frozen samples because of DNA degradation and cross-linking during FFPE fixation and processing. As FFPE protocols may vary widely between labs and samples may be stored for decades at room temperature, an ideal FFPE CN technology should work on diverse sample sets. Molecular Inversion Probe (MIP) technology has been applied successfully to obtain high quality CN and genotype data from cell line and frozen tumor DNA. Since the MIP probes require only a small (approximately 40 bp) target binding site, we reasoned they may be well suited to assess degraded FFPE DNA. We assessed CN with a MIP panel of 50,000 markers in 93 FFPE tumor samples from 7 diverse collections. For 38 FFPE samples from three collections we were also able to asses CN in matched fresh frozen tumor tissue. RESULTS Using an input of 37 ng genomic DNA, we generated high quality CN data with MIP technology in 88% of FFPE samples from seven diverse collections. When matched fresh frozen tissue was available, the performance of FFPE DNA was comparable to that of DNA obtained from matched frozen tumor (genotype concordance averaged 99.9%), with only a modest loss in performance in FFPE. CONCLUSION MIP technology can be used to generate high quality CN and genotype data in FFPE as well as fresh frozen samples.
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Affiliation(s)
| | | | | | | | - Li Zhang
- MD Anderson Cancer Center, Houston, TX, USA
| | | | | | | | - Robert Warren
- University of California San Francisco, San Francisco, CA, USA
| | - Axel Walther
- Cancer Research UK, London Research Institute, London, UK
| | | | | | - Ralf Krahe
- MD Anderson Cancer Center, Houston, TX, USA
| | | | | | | | - Joe W Gray
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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Yu J, Miller R, Zhang W, Sharma M, Holtschlag V, Watson MA, McLeod HL. Copy-number analysis of topoisomerase and thymidylate synthase genes in frozen and FFPE DNAs of colorectal cancers. Pharmacogenomics 2009; 9:1459-66. [PMID: 18855534 DOI: 10.2217/14622416.9.10.1459] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Archived formalin-fixed, paraffin-embedded specimens represent an important resource for pharmacogenomic analysis in retrospective clinical studies but the quality of results from formalin-fixed, paraffin-embedded samples is of concern due to the fact of the degradation of DNAs and RNAs from formalin-fixed, paraffin-embedded tissues. METHODS In the present study, we used DNA from fresh frozen as well as formalin-fixed, paraffin-embedded tumor to detect copy-number changes in colorectal cancer, and our data shows that formalin-fixed, paraffin-embedded DNAs were able to deliver reliable copy-number data, and that quantitative PCR had the ability to detect copy-number changes from deletion to amplification, with high concordance of copy-number calls among formalin-fixed, paraffin-embedded and frozen DNAs. RESULTS The amplification of topoisomerase I and deletion of thymidylate synthase were found in 23% (12/52) and 27% (14/52) of colorectal cancers, but EGF receptor amplification was not common (5/52, <10%). Among 52 colorectal cancers, 31 tumors were both topoisomerase I and thymidylate synthase diploid, which may have a worse outcome for tumor chemotherapy; and there were five tumors with favorable genomics (topoisomerase I amplification and thymidylate synthase deletion). Furthermore, topoisomerase I-amplified tumors had a two-times higher RNA level and a nearly twofold higher protein expression level than did the diploid tumors (p < 0.001 and 0.01, respectively), but there were no correlations between copy-number status and RNA or protein level for thymidylate synthase. CONCLUSIONS Our study suggests a potential pharmacogenomic influence of topoisomerase I copy-number alteration on its RNA/protein expressions, which could be reflected on tumor response to chemotherapy in human colorectal cancer.
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Affiliation(s)
- Jinsheng Yu
- Washington University School of Medicine, Department of Pathology & Immunology, Saint Louis, MO, USA
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Corver WE, Middeldorp A, ter Haar NT, Jordanova ES, van Puijenbroek M, van Eijk R, Cornelisse CJ, Fleuren GJ, Morreau H, Oosting J, van Wezel T. Genome-wide allelic state analysis on flow-sorted tumor fractions provides an accurate measure of chromosomal aberrations. Cancer Res 2009; 68:10333-40. [PMID: 19074902 DOI: 10.1158/0008-5472.can-08-2665] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Chromosomal aberrations are a common characteristic of cancer and are associated with copy number abnormalities and loss of heterozygosity (LOH). Tumor heterogeneity, low tumor cell percentage, and lack of knowledge of the DNA content impair the identification of these alterations especially in aneuploid tumors. To accurately detect allelic changes in carcinomas, we combined flow-sorting and single nucleotide polymorphism arrays. Cells derived from archival cervical and colon cancers were flow-sorted based on differential vimentin and keratin expression and DNA content and analyzed on single nucleotide polymorphism arrays. A new algorithm, the lesser allele intensity ratio, was used to generate a molecular measure of chromosomal aberrations for each case. Flow-sorting significantly improved the detection of copy number abnormalities; 31.8% showed an increase in amplitude and 23.2% were missed in the unsorted fraction, whereas 15.9% were detected but interpreted differently. Integration of the DNA index in the analysis enabled the identification of the allelic state of chromosomal aberrations, such as LOH ([A]), copy-neutral LOH ([AA]), balanced amplifications ([AABB]), and allelic imbalances ([AAB] or [AAAB], etc.). Chromosomal segments were sharply defined. Fluorescence in situ hybridization copy numbers, as well as the high similarity between the DNA index and the allelic state index, which is the average of the allelic states across the genome, validated the method. This new approach provides an individual molecular measure of chromosomal aberrations and will likely have repercussions for preoperative molecular staging, classification, and prognostic profiling of tumors, particularly for heterogeneous aneuploid tumors, and allows the study of the underlying molecular genetic mechanisms and clonal evolution of tumor subpopulations.
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Affiliation(s)
- Willem E Corver
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands.
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