1
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Ogbonnaya CN, Alsaedi BSO, Alhussaini AJ, Hislop R, Pratt N, Steele JD, Kernohan N, Nabi G. Radiogenomics Map-Based Molecular and Imaging Phenotypical Characterization in Localised Prostate Cancer Using Pre-Biopsy Biparametric MR Imaging. Int J Mol Sci 2024; 25:5379. [PMID: 38791417 PMCID: PMC11121591 DOI: 10.3390/ijms25105379] [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: 04/13/2024] [Revised: 05/06/2024] [Accepted: 05/13/2024] [Indexed: 05/26/2024] Open
Abstract
To create a radiogenomics map and evaluate the correlation between molecular and imaging phenotypes in localized prostate cancer (PCa), using radical prostatectomy histopathology as a reference standard. Radiomic features were extracted from T2-weighted (T2WI) and Apparent Diffusion Coefficient (ADC) images of clinically localized PCa patients (n = 15) across different Gleason score-based risk categories. DNA extraction was performed on formalin-fixed, paraffin-embedded (FFPE) samples. Gene expression analysis of androgen receptor expression, apoptosis, and hypoxia was conducted using the Chromosome Analysis Suite (ChAS) application and OSCHIP files. The relationship between gene expression alterations and textural features was assessed using Pearson's correlation analysis. Receiver operating characteristic (ROC) analysis was utilized to evaluate the predictive accuracy of the model. A significant correlation was observed between radiomic texture features and copy number variation (CNV) of genes associated with apoptosis, hypoxia, and androgen receptor (p-value ≤ 0.05). The identified radiomic features, including Sum Entropy ADC, Inverse Difference ADC, Sum Variance T2WI, Entropy T2WI, Difference Variance T2WI, and Angular Secondary Moment T2WI, exhibited potential for predicting cancer grade and biological processes such as apoptosis and hypoxia. Incorporating radiomics and genomics into a prediction model significantly improved the prediction of prostate cancer grade (clinically significant prostate cancer), yielding an AUC of 0.95. Radiomic texture features significantly correlate with genotypes for apoptosis, hypoxia, and androgen receptor expression in localised prostate cancer. Integration of these into the prediction model improved prediction accuracy of clinically significant prostate cancer.
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Affiliation(s)
- Chidozie N. Ogbonnaya
- Division of Imaging Science and Technology, School of Medicine, University of Dundee, Dundee DD1 4HN, UK; (C.N.O.); (A.J.A.); (J.D.S.)
| | | | - Abeer J. Alhussaini
- Division of Imaging Science and Technology, School of Medicine, University of Dundee, Dundee DD1 4HN, UK; (C.N.O.); (A.J.A.); (J.D.S.)
| | - Robert Hislop
- Cytogenetic, Human Genetics Unit, NHS Tayside, Ninewells Hospital and Medical School, Dundee DD1 9SY, UK; (R.H.); (N.P.)
| | - Norman Pratt
- Cytogenetic, Human Genetics Unit, NHS Tayside, Ninewells Hospital and Medical School, Dundee DD1 9SY, UK; (R.H.); (N.P.)
| | - J. Douglas Steele
- Division of Imaging Science and Technology, School of Medicine, University of Dundee, Dundee DD1 4HN, UK; (C.N.O.); (A.J.A.); (J.D.S.)
| | - Neil Kernohan
- Department of Pathology, NHS Tayside, Ninewells Hospital and Medical School, Dundee DD1 9SY, UK;
| | - Ghulam Nabi
- Division of Imaging Science and Technology, School of Medicine, University of Dundee, Dundee DD1 4HN, UK; (C.N.O.); (A.J.A.); (J.D.S.)
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2
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Susman S, Berindan-Neagoe I, Petrushev B, Pirlog R, Florian IS, Mihu CM, Berce C, Craciun L, Grewal R, Tomuleasa C. The role of the pathology department in the preanalytical phase of molecular analyses. Cancer Manag Res 2018; 10:745-753. [PMID: 29695931 PMCID: PMC5903845 DOI: 10.2147/cmar.s150851] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
After introducing the new molecules for the treatment of patients with tumoral pathology, the therapeutical decision will be taken depending on the molecular profile performed upon the harvested tissues. This major modification makes the molecular and morphological analysis an essential part in the clinical management of patients and the pathologist plays an important role in this process. The quality and reproducibility of the results are imperative today and they depend on both the reliability of the molecular techniques and the quality of the tissue we use in the process. Also, the genomics and proteomics techniques, used increasingly often, require high-quality tissues, and pathology laboratories play a very significant role in the management of all phases of this process. In this paper the parameters which must be followed in order to obtain optimal results within the techniques which analyze nucleic acids and proteins were reviewed.
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Affiliation(s)
- Sergiu Susman
- Department of Pathology, Imogen Research Center.,Department of Morphological Sciences
| | | | - Bobe Petrushev
- Research Center for Functional Genomics and Translational Medicine
| | | | - Ioan-Stefan Florian
- Department of Neurosurgery, Iuliu Hatieganu University of Medicine and Pharmacy
| | | | - Cristian Berce
- Research Center for Functional Genomics and Translational Medicine
| | | | - Ravnit Grewal
- Department of Hematology, Ion Chiricuta Oncology Institute
| | - Ciprian Tomuleasa
- Research Center for Functional Genomics and Translational Medicine.,Department of Hematology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania.,Department of Haematopathology, Tygerberg Academic Hospital, Tygerberg, South Africa
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3
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Jung HS, Lefferts JA, Tsongalis GJ. Utilization of the oncoscan microarray assay in cancer diagnostics. ACTA ACUST UNITED AC 2017. [DOI: 10.1186/s41241-016-0007-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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4
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Kader T, Goode DL, Wong SQ, Connaughton J, Rowley SM, Devereux L, Byrne D, Fox SB, Mir Arnau G, Tothill RW, Campbell IG, Gorringe KL. Copy number analysis by low coverage whole genome sequencing using ultra low-input DNA from formalin-fixed paraffin embedded tumor tissue. Genome Med 2016; 8:121. [PMID: 27846907 PMCID: PMC5111221 DOI: 10.1186/s13073-016-0375-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 10/26/2016] [Indexed: 11/10/2022] Open
Abstract
Unlocking clinically translatable genomic information, including copy number alterations (CNA), from formalin-fixed paraffin-embedded (FFPE) tissue is challenging due to low yields and degraded DNA. We describe a robust, cost-effective low-coverage whole genome sequencing (LC WGS) method for CNA detection using 5 ng of FFPE-derived DNA. CN profiles using 100 ng or 5 ng input DNA were highly concordant and comparable with molecular inversion probe (MIP) array profiles. LC WGS improved CN profiles of samples that performed poorly using MIP arrays. Our technique enables identification of driver and prognostic CNAs in archival patient samples previously deemed unsuitable for genomic analysis due to DNA limitations.
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Affiliation(s)
- Tanjina Kader
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC, Australia.,The Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - David L Goode
- The Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia.,Bioinformatics and Cancer Genomics Laboratory, Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC, Australia
| | - Stephen Q Wong
- Molecular Biomarkers and Translational Genomics Laboratory, Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC, Australia
| | - Jacquie Connaughton
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC, Australia
| | - Simone M Rowley
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC, Australia
| | - Lisa Devereux
- LifePool, Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC, Australia
| | - David Byrne
- Pathology, Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC, Australia
| | - Stephen B Fox
- Pathology, Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC, Australia
| | - Gisela Mir Arnau
- Molecular Genomics Core Facility, Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC, Australia
| | - Richard W Tothill
- The Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia.,Molecular Imaging and Targeted Therapeutics Laboratory, Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC, Australia.,Department of Pathology, University of Melbourne, Parkville, VIC, Australia
| | - Ian G Campbell
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC, Australia.,The Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia.,Department of Pathology, University of Melbourne, Parkville, VIC, Australia
| | - Kylie L Gorringe
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC, Australia. .,The Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia. .,Department of Pathology, University of Melbourne, Parkville, VIC, Australia.
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5
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Obulkasim A, Ylstra B, van Essen HF, Benner C, Stenning S, Langley R, Allum W, Cunningham D, Inam I, Hewitt LC, West NP, Meijer GA, van de Wiel MA, Grabsch HI. Reduced genomic tumor heterogeneity after neoadjuvant chemotherapy is related to favorable outcome in patients with esophageal adenocarcinoma. Oncotarget 2016; 7:44084-44095. [PMID: 27286451 PMCID: PMC5190081 DOI: 10.18632/oncotarget.9857] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2016] [Accepted: 04/29/2016] [Indexed: 11/25/2022] Open
Abstract
Neoadjuvant chemo(radio)therapy followed by surgery is the standard of care for patients with locally advanced resectable esophageal adenocarcinoma (EAC). There is increasing evidence that drug resistance might be related to genomic heterogeneity. We investigated whether genomic tumor heterogeneity is different after cytotoxic chemotherapy and is associated with EAC patient survival. We used arrayCGH and a quantitative assessment of the whole genome DNA copy number aberration patterns ('DNA copy number entropy') to establish the level of genomic tumor heterogeneity in 80 EAC treated with neoadjuvant chemotherapy followed by surgery (CS group) or surgery alone (S group). The association between DNA copy number entropy, clinicopathological variables and survival was investigated.DNA copy number entropy was reduced after chemotherapy, even if there was no morphological evidence of response to therapy (p<0.001). Low DNA copy number entropy was associated with improved survival in the CS group (p=0.011) but not in the S group (p=0.396).Our results suggest that cytotoxic chemotherapy reduces DNA copy number entropy, which might be a more sensitive tumor response marker than changes in the morphological tumor phenotype. The use of DNA copy number entropy in clinical practice will require validation of our results in a prospective study.
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Affiliation(s)
- Askar Obulkasim
- Department of Epidemiology and Biostatistics, VU University Medical Center, Amsterdam, NL
| | - Bauke Ylstra
- Department of Pathology, VU University Medical Center, Amsterdam, NL
| | | | - Christian Benner
- Department of Pathology, VU University Medical Center, Amsterdam, NL
| | - Sally Stenning
- MRC Clinical Trials Unit at University College London, London, UK
| | - Ruth Langley
- MRC Clinical Trials Unit at University College London, London, UK
| | - William Allum
- Department of Surgery, Royal Marsden NHS Foundation Trust, London, UK
| | - David Cunningham
- Department of Gastrointestinal Oncology, Royal Marsden NHS Foundation Trust, London and Surrey, UK
| | - Imran Inam
- Section of Pathology and Tumour Biology, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - Lindsay C. Hewitt
- Section of Pathology and Tumour Biology, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
- Department of Pathology and GROW School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, NL
| | - Nicolas P. West
- Section of Pathology and Tumour Biology, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - Gerrit A. Meijer
- Department of Pathology, VU University Medical Center, Amsterdam, NL
| | - Mark A. van de Wiel
- Department of Epidemiology and Biostatistics, VU University Medical Center, Amsterdam, NL
- Department of Mathematics, VU University, Amsterdam, NL
| | - Heike I. Grabsch
- Section of Pathology and Tumour Biology, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
- Department of Pathology and GROW School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, NL
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6
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Forero-Castro M, Robledo C, Benito R, Abáigar M, África Martín A, Arefi M, Fuster JL, de las Heras N, Rodríguez JN, Quintero J, Riesco S, Hermosín L, de la Fuente I, Recio I, Ribera J, Labrador J, Alonso JM, Olivier C, Sierra M, Megido M, Corchete-Sánchez LA, Ciudad Pizarro J, García JL, Ribera JM, Hernández-Rivas JM. Genome-Wide DNA Copy Number Analysis of Acute Lymphoblastic Leukemia Identifies New Genetic Markers Associated with Clinical Outcome. PLoS One 2016; 11:e0148972. [PMID: 26872047 PMCID: PMC4752220 DOI: 10.1371/journal.pone.0148972] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 01/26/2016] [Indexed: 01/13/2023] Open
Abstract
Identifying additional genetic alterations associated with poor prognosis in acute lymphoblastic leukemia (ALL) is still a challenge. Aims: To characterize the presence of additional DNA copy number alterations (CNAs) in children and adults with ALL by whole-genome oligonucleotide array (aCGH) analysis, and to identify their associations with clinical features and outcome. Array-CGH was carried out in 265 newly diagnosed ALLs (142 children and 123 adults). The NimbleGen CGH 12x135K array (Roche) was used to analyze genetic gains and losses. CNAs were analyzed with GISTIC and aCGHweb software. Clinical and biological variables were analyzed. Three of the patients showed chromothripsis (cth6, cth14q and cth15q). CNAs were associated with age, phenotype, genetic subtype and overall survival (OS). In the whole cohort of children, the losses on 14q32.33 (p = 0.019) and 15q13.2 (p = 0.04) were related to shorter OS. In the group of children without good- or poor-risk cytogenetics, the gain on 1p36.11 was a prognostic marker independently associated with shorter OS. In adults, the gains on 19q13.2 (p = 0.001) and Xp21.1 (p = 0.029), and the loss of 17p (p = 0.014) were independent markers of poor prognosis with respect to OS. In summary, CNAs are frequent in ALL and are associated with clinical parameters and survival. Genome-wide DNA copy number analysis allows the identification of genetic markers that predict clinical outcome, suggesting that detection of these genetic lesions will be useful in the management of patients newly diagnosed with ALL.
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Affiliation(s)
- Maribel Forero-Castro
- IBSAL, IBMCC, University of Salamanca, CSIC, Cancer Research Center, Salamanca, Spain
- School of Biological Sciences (GEBIMOL), Pedagogical and Technological University of Colombia (UPTC), Tunja, Colombia
| | - Cristina Robledo
- IBSAL, IBMCC, University of Salamanca, CSIC, Cancer Research Center, Salamanca, Spain
| | - Rocío Benito
- IBSAL, IBMCC, University of Salamanca, CSIC, Cancer Research Center, Salamanca, Spain
| | - María Abáigar
- IBSAL, IBMCC, University of Salamanca, CSIC, Cancer Research Center, Salamanca, Spain
| | - Ana África Martín
- IBSAL, IBMCC, University of Salamanca, CSIC, Cancer Research Center, Salamanca, Spain
- Department of Hematology, University Hospital of Salamanca, Salamanca, Spain
| | - Maryam Arefi
- Department of Hematology, Clinical University Hospital of Valladolid, Valladolid, Spain
| | - José Luis Fuster
- Department of Pediatric Oncohematology, Clinical University Hospital Virgen de la Arrixaca, Murcia, Spain
| | | | - Juan N. Rodríguez
- Department of Hematology, Juan Ramón Jiménez Hospital, Huelva, Spain
| | | | - Susana Riesco
- Department of Pediatric Oncohematology, University Hospital of Salamanca, Salamanca, Spain
| | - Lourdes Hermosín
- Department of Hematology, Jerez Hospital, Jerez de la Frontera, Cádiz, Spain
| | | | - Isabel Recio
- Department of Hematology, Nuestra Señora de Sonsoles Hospital, Avila, Spain
| | - Jordi Ribera
- Department of Hematology, ICO-Hospital Germans Trias i Pujol, Josep Carreras Research Institute, Badalona, Spain
| | - Jorge Labrador
- Department of Hematology, University Hospital of Burgos, Burgos, Spain
| | - José M. Alonso
- Department of Hematology, Rio Carrión Hospital, Palencia, Spain
| | - Carmen Olivier
- Department of Hematology, General Hospital of Segovia, Segovia, Spain
| | - Magdalena Sierra
- Department of Hematology, Virgen de la Concha Hospital, Zamora, Spain
| | - Marta Megido
- Department of Hematology, Bierzo Hospital, León/Ponferrada, Spain
| | | | - Juana Ciudad Pizarro
- Cytometry Service (NUCLEUS Research Support Platform), University of Salamanca (USAL), Salamanca, Spain
| | - Juan Luis García
- Institute of Health Science Studies of Castile and León (IESCYL), Salamanca, Spain
| | - José M. Ribera
- Department of Hematology, ICO-Hospital Germans Trias i Pujol, Josep Carreras Research Institute, Badalona, Spain
| | - Jesús M. Hernández-Rivas
- IBSAL, IBMCC, University of Salamanca, CSIC, Cancer Research Center, Salamanca, Spain
- Department of Hematology, University Hospital of Salamanca, Salamanca, Spain
- * E-mail:
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7
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Biesma HD, Schouten PC, Lacle MM, Sanders J, Brugman W, Kerkhoven R, Mandjes I, van der Groep P, van Diest PJ, Linn SC. Copy number profiling by array comparative genomic hybridization identifies frequently occurring BRCA2-like male breast cancer. Genes Chromosomes Cancer 2015; 54:734-44. [DOI: 10.1002/gcc.22284] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 06/25/2015] [Indexed: 11/08/2022] Open
Affiliation(s)
- Hedde D. Biesma
- Department of Molecular Pathology; Netherlands Cancer Institute; Amsterdam The Netherlands
| | - Philip C. Schouten
- Department of Molecular Pathology; Netherlands Cancer Institute; Amsterdam The Netherlands
| | - Miangela M. Lacle
- Department of Pathology; University Medical Center Utrecht; The Netherlands
| | - Joyce Sanders
- Department of Pathology; Netherlands Cancer Institute; Amsterdam The Netherlands
| | - Wim Brugman
- Genomics Core Facility, Netherlands Cancer Institute; Amsterdam The Netherlands
| | - Ron Kerkhoven
- Genomics Core Facility, Netherlands Cancer Institute; Amsterdam The Netherlands
| | - Ingrid Mandjes
- Data Center, Netherlands Cancer Institute; Amsterdam The Netherlands
| | | | - Paul J. van Diest
- Department of Pathology; University Medical Center Utrecht; The Netherlands
| | - Sabine C. Linn
- Department of Molecular Pathology; Netherlands Cancer Institute; Amsterdam The Netherlands
- Department of Pathology; University Medical Center Utrecht; The Netherlands
- Department of Medical Oncology; Netherlands Cancer Institute; Amsterdam The Netherlands
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8
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Kalmár A, Péterfia B, Hollósi P, Wichmann B, Bodor A, Patai ÁV, Schöller A, Krenács T, Tulassay Z, Molnár B. Bisulfite-Based DNA Methylation Analysis from Recent and Archived Formalin-Fixed, Paraffin Embedded Colorectal Tissue Samples. Pathol Oncol Res 2015; 21:1149-1156. [PMID: 25991403 DOI: 10.1007/s12253-015-9945-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Accepted: 05/05/2015] [Indexed: 01/11/2023]
Abstract
We aimed to test the applicability of formalin-fixed and paraffin-embedded (FFPE) tissue samples for gene specific DNA methylation analysis after using two commercially available DNA isolation kits. Genomic DNA was isolated from 5 colorectal adenocarcinomas and 5 normal adjacent tissues from "recent", collected within 6 months, and "archived", collected more than 5 years ago, FFPE tissues using either High Pure FFPET DNA Isolation kit or QIAamp DNA FFPE Tissue kit. DNA methylation analysis of MAL, SFRP1 and SFRP2 genes, known to be hypermethylated in CRC, was performed using methylation-sensitive high resolution melting (MS-HRM) analysis and sequencing. QIAamp (Q) method resulted in slightly higher recovery in archived (HP: 1.22 ± 3.18 μg DNA; Q: 3.00 ± 4.04 μg DNA) and significantly (p < 0.05) higher recovery in recent samples compared to High Pure method (HP) (HP: 4.10 ± 2.91 μg DNA; Q: 11.51 ± 7.50 μg DNA). Both OD260/280 and OD260/230 ratios were lower, but still high in the High Pure isolated archived and recent samples compared to those isolated with QIAamp. Identical DNA methylation patterns were detected for all 3 genes tested by MS-HRM with both isolation kits in the recent group. However, despite of higher DNA recovery in QIAamp slightly more reproducible methylation results were obtained from High Pure isolated archived samples. Sequencing confirmed DNA hypermethylation in CRCs. In conclusion, reproducible DNA methylation patterns were obtained from recent samples using both isolation kits. However, long term storage may affect the reliability of the results leading to moderate differences between the efficiency of isolation kits.
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Affiliation(s)
- Alexandra Kalmár
- 2nd Department of Internal Medicine, Semmelweis University, Szentkirályi utca 46, 1088, Budapest, Hungary,
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9
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Schouten PC, Grigoriadis A, Kuilman T, Mirza H, Watkins JA, Cooke SA, van Dyk E, Severson TM, Rueda OM, Hoogstraat M, Verhagen CVM, Natrajan R, Chin SF, Lips EH, Kruizinga J, Velds A, Nieuwland M, Kerkhoven RM, Krijgsman O, Vens C, Peeper D, Nederlof PM, Caldas C, Tutt AN, Wessels LF, Linn SC. Robust BRCA1-like classification of copy number profiles of samples repeated across different datasets and platforms. Mol Oncol 2015; 9:1274-86. [PMID: 25825120 PMCID: PMC5528812 DOI: 10.1016/j.molonc.2015.03.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 03/01/2015] [Accepted: 03/11/2015] [Indexed: 11/30/2022] Open
Abstract
Breast cancers with BRCA1 germline mutation have a characteristic DNA copy number (CN) pattern. We developed a test that assigns CN profiles to be 'BRCA1-like' or 'non-BRCA1-like', which refers to resembling a BRCA1-mutated tumor or resembling a tumor without a BRCA1 mutation, respectively. Approximately one third of the BRCA1-like breast cancers have a BRCA1 mutation, one third has hypermethylation of the BRCA1 promoter and one third has an unknown reason for being BRCA1-like. This classification is indicative of patients' response to high dose alkylating and platinum containing chemotherapy regimens, which targets the inability of BRCA1 deficient cells to repair DNA double strand breaks. We investigated whether this classification can be reliably obtained with next generation sequencing and copy number platforms other than the bacterial artificial chromosome (BAC) array Comparative Genomic Hybridization (aCGH) on which it was originally developed. We investigated samples from 230 breast cancer patients for which a CN profile had been generated on two to five platforms, comprising low coverage CN sequencing, CN extraction from targeted sequencing panels (CopywriteR), Affymetrix SNP6.0, 135K/720K oligonucleotide aCGH, Affymetrix Oncoscan FFPE (MIP) technology, 3K BAC and 32K BAC aCGH. Pairwise comparison of genomic position-mapped profiles from the original aCGH platform and other platforms revealed concordance. For most cases, biological differences between samples exceeded the differences between platforms within one sample. We observed the same classification across different platforms in over 80% of the patients and kappa values of at least 0.36. Differential classification could be attributed to CN profiles that were not strongly associated to one class. In conclusion, we have shown that the genomic regions that define our BRCA1-like classifier are robustly measured by different CN profiling technologies, providing the possibility to retro- and prospectively investigate BRCA1-like classification across a wide range of CN platforms.
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Affiliation(s)
- Philip C Schouten
- Department of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Anita Grigoriadis
- Breakthrough Breast Cancer Research Unit, Department of Research Oncology, Guy's Hospital, King's College London School of Medicine, London, United Kingdom
| | - Thomas Kuilman
- Division of Molecular Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Hasan Mirza
- Breakthrough Breast Cancer Research Unit, Department of Research Oncology, Guy's Hospital, King's College London School of Medicine, London, United Kingdom
| | - Johnathan A Watkins
- Breakthrough Breast Cancer Research Unit, Department of Research Oncology, Guy's Hospital, King's College London School of Medicine, London, United Kingdom
| | - Saskia A Cooke
- Breakthrough Breast Cancer Research Unit, Department of Research Oncology, Guy's Hospital, King's College London School of Medicine, London, United Kingdom
| | - Ewald van Dyk
- Department of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Tesa M Severson
- Department of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Oscar M Rueda
- Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Cambridge, UK
| | - Marlous Hoogstraat
- Department of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands; Department of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, The Netherlands; Department of Medical Oncology, University Medical Center Utrecht, Utrecht, The Netherlands; Netherlands Center for Personalized Cancer Treatment, Utrecht, The Netherlands
| | - Caroline V M Verhagen
- Division of Biological Stress Response, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Rachael Natrajan
- The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, UK
| | - Suet-Feung Chin
- Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Cambridge, UK
| | - Esther H Lips
- Department of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Janneke Kruizinga
- Genomics Core Facility, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Arno Velds
- Genomics Core Facility, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Marja Nieuwland
- Genomics Core Facility, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Ron M Kerkhoven
- Genomics Core Facility, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Oscar Krijgsman
- Division of Molecular Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Conchita Vens
- Division of Biological Stress Response, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Daniel Peeper
- Division of Molecular Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Petra M Nederlof
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Carlos Caldas
- Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Cambridge, UK; Department of Oncology, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK; Cambridge Experimental Cancer Medicine Centre and NIHR Cambridge Biomedical, Research Centre, Cambridge University Hospitals NHS, Cambridge, UK
| | - Andrew N Tutt
- Breakthrough Breast Cancer Research Unit, Department of Research Oncology, Guy's Hospital, King's College London School of Medicine, London, United Kingdom
| | - Lodewyk F Wessels
- Department of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, The Netherlands; Faculty of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, Delft, The Netherlands
| | - Sabine C Linn
- Department of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands; Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands; Division of Medical Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands.
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10
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Abstract
Background With one million new cases of colorectal cancer (CRC) diagnosed annually in the world, CRC is the third most commonly diagnosed cancer in the Western world. Patients with stage I-III CRC can be cured with surgery but are at risk for recurrence. Colorectal cancer is characterized by the presence of chromosomal deletions and gains. Large genomic profiling studies have however not been conducted in this disease. The number of a specific genetic aberration in a tumour sample could correlate with recurrence-free survival or overall survival, possibly leading to its use as biomarker for therapeutic decisions. At this point there are not sufficient markers for prediction of disease recurrence in colorectal cancer, which can be used in the clinic to discriminate between stage II patients who will benefit from adjuvant chemotherapy. For instance, the benefit of adjuvant chemotherapy has been most clearly demonstrated in stage III disease with an approximately 30 percent relative reduction in the risk of disease recurrence. The benefits of adjuvant chemotherapy in stage II disease are less certain, the risk for relapse is much smaller in the overall group and the specific patients at risk are hard to identify. Materials and Methods In this study, array-comparative genomic hybridization analysis (array-CGH) was applied to study high-resolution DNA copy number alterations in 93 colon carcinoma samples. These genomic data were combined with parameters like KRAS mutation status, microsatellite status and clinicopathological characteristics. Results Both large and small chromosomal losses and gains were identified in our sample cohort. Recurrent gains were found for chromosome 1q, 7, 8q, 13 and 20 and losses were mostly found for 1p, 4, 8p, 14, 15, 17p, 18, 21 and 22. Data analysis demonstrated that loss of chromosome 4 is linked to a worse prognosis in our patients series. Besides these alterations, two interesting small regions of overlap were identified, which could be associated with disease recurrence. Gain of the 16p13.3 locus (including the RNA binding protein, fox-1 homolog gene, RBFOX1) was linked with a worse recurrence-free survival in our patient cohort. On the other hand, loss of RBFOX1 was only found in patients without disease recurrence. Most interestingly, above mentioned characteristics were also found in stage II patients, for whom there is a high medical need for the identification of new prognostic biomarkers. Conclusions In conclusion, copy number variation of the 16p13.3 locus seems to be an important parameter for prediction of disease recurrence in colon cancer.
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11
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Hastings RJ, Bown N, Tibiletti MG, Debiec-Rychter M, Vanni R, Espinet B, van Roy N, Roberts P, van den Berg-de-Ruiter E, Bernheim A, Schoumans J, Chatters S, Zemanova Z, Stevens-Kroef M, Simons A, Heim S, Salido M, Ylstra B, Betts DR. Guidelines for cytogenetic investigations in tumours. Eur J Hum Genet 2015; 24:6-13. [PMID: 25804401 DOI: 10.1038/ejhg.2015.35] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 01/19/2015] [Accepted: 02/03/2015] [Indexed: 12/31/2022] Open
Affiliation(s)
- Rosalind J Hastings
- Women's Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Trust, Oxford, UK
| | - Nick Bown
- Northern Genetics Service, Institute of Genomic Medicine, Central Parkway, Newcastle, UK
| | - Maria G Tibiletti
- UO Anatomia Patologica, Ospedale di Circolo-Polo Universitario, Varese, Italy
| | - Maria Debiec-Rychter
- Laboratory for Genetics of Malignant Disorders, Department of Human Genetics, University Hospital Gasthuisberg, UZ Leuven, Leuven, Belgium
| | - Roberta Vanni
- Department of Biomedical Sciences, University of Cagliari, Cittadella Universitaria, Monserrato, Italy
| | - Blanca Espinet
- Laboratori de Citogenètica Molecular, Servei de Patologia, Hospital del Mar, Barcelona, Spain
| | - Nadine van Roy
- Centre for Medical Genetics, University Hospital Ghent, Ghent, Belgium
| | - Paul Roberts
- Cytogenetics Department, St James's Hospital, Leeds, UK
| | - Eva van den Berg-de-Ruiter
- Department of Genetics, University of Groningen, University Medical Centre Groningen, RB Groningen, The Netherlands
| | - Alain Bernheim
- Génétique des tumeurs (INSERM U985), Laboratoire de Cytogénétique, Pathologie Moléculaire Gustave Roussy, Paris-Villejuif, France
| | - Jacqueline Schoumans
- Cancer Cytogenetic Unit, Lausanne University Hospital, CHUV, Lausanne, Switzerland
| | - Steve Chatters
- Haematology, Cellular and Molecular Diagnostic Service, Great Ormond St Hospital, London, UK
| | - Zuzana Zemanova
- Center of Oncocytogenetics, Institute of Clinical Biochemistry and Laboratory Diagnostics, General University Hospital and First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Marian Stevens-Kroef
- Radboud University Nijmegen Medical Centre Department of Human Genetics, HB Nijmegen, The Netherlands
| | - Annet Simons
- Radboud University Nijmegen Medical Centre Department of Human Genetics, HB Nijmegen, The Netherlands
| | - Sverre Heim
- Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Marta Salido
- Laboratori de Citogenètica Molecular, Servei de Patologia, Hospital del Mar, Barcelona, Spain
| | - Bauke Ylstra
- Department of Pathology, Cancer Center Amsterdam, VU University Medical Center, MB Amsterdam, The Netherlands
| | - David R Betts
- Department of Clinical Genetics, Our Lady's Children's Hospital, Crumlin, Dublin, Ireland
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12
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Kuilman T, Velds A, Kemper K, Ranzani M, Bombardelli L, Hoogstraat M, Nevedomskaya E, Xu G, de Ruiter J, Lolkema MP, Ylstra B, Jonkers J, Rottenberg S, Wessels LF, Adams DJ, Peeper DS, Krijgsman O. CopywriteR: DNA copy number detection from off-target sequence data. Genome Biol 2015; 16:49. [PMID: 25887352 PMCID: PMC4396974 DOI: 10.1186/s13059-015-0617-1] [Citation(s) in RCA: 160] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2015] [Accepted: 02/20/2015] [Indexed: 12/13/2022] Open
Abstract
Current methods for detection of copy number variants (CNV) and aberrations (CNA) from targeted sequencing data are based on the depth of coverage of captured exons. Accurate CNA determination is complicated by uneven genomic distribution and non-uniform capture efficiency of targeted exons. Here we present CopywriteR, which eludes these problems by exploiting 'off-target' sequence reads. CopywriteR allows for extracting uniformly distributed copy number information, can be used without reference, and can be applied to sequencing data obtained from various techniques including chromatin immunoprecipitation and target enrichment on small gene panels. CopywriteR outperforms existing methods and constitutes a widely applicable alternative to available tools.
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Affiliation(s)
- Thomas Kuilman
- Division of Molecular Oncology, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands.
| | - Arno Velds
- Central Genomic Facility, Netherlands Cancer Institute, Amsterdam, The Netherlands.
| | - Kristel Kemper
- Division of Molecular Oncology, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands.
| | - Marco Ranzani
- Experimental Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, UK.
| | - Lorenzo Bombardelli
- Division of Molecular Genetics, Netherlands Cancer Institute, Amsterdam, The Netherlands.
| | - Marlous Hoogstraat
- Division of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, The Netherlands.
| | - Ekaterina Nevedomskaya
- Division of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, The Netherlands.
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands.
| | - Guotai Xu
- Division of Molecular Oncology, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands.
| | - Julian de Ruiter
- Division of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, The Netherlands.
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands.
| | - Martijn P Lolkema
- Center for Personalized Cancer Treatment, Amsterdam, The Netherlands.
| | - Bauke Ylstra
- Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands.
| | - Jos Jonkers
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands.
| | - Sven Rottenberg
- Division of Molecular Oncology, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands.
- Vetsuisse Faculty, Institute of Animal Pathology, University of Bern, Bern, Switzerland.
| | - Lodewyk F Wessels
- Division of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, The Netherlands.
| | - David J Adams
- Experimental Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, UK.
| | - Daniel S Peeper
- Division of Molecular Oncology, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands.
| | - Oscar Krijgsman
- Division of Molecular Oncology, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands.
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13
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Haan JC, Labots M, Rausch C, Koopman M, Tol J, Mekenkamp LJM, van de Wiel MA, Israeli D, van Essen HF, van Grieken NCT, Voorham QJM, Bosch LJW, Qu X, Kabbarah O, Verheul HMW, Nagtegaal ID, Punt CJA, Ylstra B, Meijer GA. Genomic landscape of metastatic colorectal cancer. Nat Commun 2014; 5:5457. [PMID: 25394515 PMCID: PMC4243240 DOI: 10.1038/ncomms6457] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2014] [Accepted: 10/02/2014] [Indexed: 12/21/2022] Open
Abstract
Response to drug therapy in individual colorectal cancer (CRC) patients is associated with tumour biology. Here we describe the genomic landscape of tumour samples of a homogeneous well-annotated series of patients with metastatic CRC (mCRC) of two phase III clinical trials, CAIRO and CAIRO2. DNA copy number aberrations of 349 patients are determined. Within three treatment arms, 194 chromosomal subregions are associated with progression-free survival (PFS; uncorrected single-test P-values <0.005). These subregions are filtered for effect on messenger RNA expression, using an independent data set from The Cancer Genome Atlas which returned 171 genes. Three chromosomal regions are associated with a significant difference in PFS between treatment arms with or without irinotecan. One of these regions, 6q16.1–q21, correlates in vitro with sensitivity to SN-38, the active metabolite of irinotecan. This genomic landscape of mCRC reveals a number of DNA copy number aberrations associated with response to drug therapy. Response to drug therapy in colorectal cancer (CRC) patients has been associated with tumour heterogeneity. Here the authors analyse DNA copy number aberrations in primary tumours from CRC patients and identify genetic variants that influence drug response.
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Affiliation(s)
- Josien C Haan
- Department of Pathology, VU University Medical Center, PO Box 7057, 1007 MB Amsterdam, The Netherlands
| | - Mariette Labots
- Department of Medical Oncology, VU University Medical Center, PO Box 7057, 1007 MB Amsterdam, The Netherlands
| | - Christian Rausch
- Department of Pathology, VU University Medical Center, PO Box 7057, 1007 MB Amsterdam, The Netherlands
| | - Miriam Koopman
- Department of Medical Oncology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Jolien Tol
- Department of Medical Oncology, Radboud University Medical Centre, Route 452, PO Box 9101, 6500 HB Nijmegen, The Netherlands
| | - Leonie J M Mekenkamp
- Department of Pathology, Radboud University Medical Centre, Huispost 824, PO Box 9101, 6500 HB Nijmegen, The Netherlands
| | - Mark A van de Wiel
- Department of Epidemiology and Biostatistics, VU University Medical Center, PO Box 7057, 1007 MB Amsterdam, The Netherlands
| | - Danielle Israeli
- Department of Pathology, VU University Medical Center, PO Box 7057, 1007 MB Amsterdam, The Netherlands
| | - Hendrik F van Essen
- Department of Pathology, VU University Medical Center, PO Box 7057, 1007 MB Amsterdam, The Netherlands
| | - Nicole C T van Grieken
- Department of Pathology, VU University Medical Center, PO Box 7057, 1007 MB Amsterdam, The Netherlands
| | - Quirinus J M Voorham
- Department of Pathology, VU University Medical Center, PO Box 7057, 1007 MB Amsterdam, The Netherlands
| | - Linda J W Bosch
- Department of Pathology, VU University Medical Center, PO Box 7057, 1007 MB Amsterdam, The Netherlands
| | - Xueping Qu
- Oncology Biomarker Development, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080 USA
| | - Omar Kabbarah
- Oncology Biomarker Development, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080 USA
| | - Henk M W Verheul
- Department of Medical Oncology, VU University Medical Center, PO Box 7057, 1007 MB Amsterdam, The Netherlands
| | - Iris D Nagtegaal
- Department of Pathology, Radboud University Medical Centre, Huispost 824, PO Box 9101, 6500 HB Nijmegen, The Netherlands
| | - Cornelis J A Punt
- Department of Medical Oncology, Academic Medical Center, PO Box 22660, 1100 DD Amsterdam, The Netherlands
| | - Bauke Ylstra
- Department of Pathology, VU University Medical Center, PO Box 7057, 1007 MB Amsterdam, The Netherlands
| | - Gerrit A Meijer
- Department of Pathology, VU University Medical Center, PO Box 7057, 1007 MB Amsterdam, The Netherlands
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14
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DNA copy number analysis of fresh and formalin-fixed specimens by shallow whole-genome sequencing with identification and exclusion of problematic regions in the genome assembly. Genome Res 2014; 24:2022-32. [PMID: 25236618 PMCID: PMC4248318 DOI: 10.1101/gr.175141.114] [Citation(s) in RCA: 350] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Detection of DNA copy number aberrations by shallow whole-genome sequencing (WGS) faces many challenges, including lack of completion and errors in the human reference genome, repetitive sequences, polymorphisms, variable sample quality, and biases in the sequencing procedures. Formalin-fixed paraffin-embedded (FFPE) archival material, the analysis of which is important for studies of cancer, presents particular analytical difficulties due to degradation of the DNA and frequent lack of matched reference samples. We present a robust, cost-effective WGS method for DNA copy number analysis that addresses these challenges more successfully than currently available procedures. In practice, very useful profiles can be obtained with ∼0.1× genome coverage. We improve on previous methods by first implementing a combined correction for sequence mappability and GC content, and second, by applying this procedure to sequence data from the 1000 Genomes Project in order to develop a blacklist of problematic genome regions. A small subset of these blacklisted regions was previously identified by ENCODE, but the vast majority are novel unappreciated problematic regions. Our procedures are implemented in a pipeline called QDNAseq. We have analyzed over 1000 samples, most of which were obtained from the fixed tissue archives of more than 25 institutions. We demonstrate that for most samples our sequencing and analysis procedures yield genome profiles with noise levels near the statistical limit imposed by read counting. The described procedures also provide better correction of artifacts introduced by low DNA quality than prior approaches and better copy number data than high-resolution microarrays at a substantially lower cost.
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15
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Minca EC, Tubbs RR, Portier BP, Wang Z, Lanigan C, Aronow ME, Triozzi PL, Singh A, Cook JR, Saunthararajah Y, Plesec TP, Schoenfield L, Cawich V, Sulpizio S, Schultz RA. Genomic microarray analysis on formalin-fixed paraffin-embedded material for uveal melanoma prognostication. Cancer Genet 2014; 207:306-15. [PMID: 25442074 DOI: 10.1016/j.cancergen.2014.08.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Revised: 07/07/2014] [Accepted: 08/21/2014] [Indexed: 11/30/2022]
Abstract
Cytogenetic alterations are strong outcome prognosticators in uveal melanoma (UVM). Monosomy 3 (-3) and MYC amplification at 8q24 are commonly tested by fluorescence in situ hybridization (FISH). Alternatively, microarray analysis provides whole genome data, detecting partial chromosome loss, loss of heterozygosity (LOH), or abnormalities unrepresented by FISH probes. Nonfixed frozen tissue is conventionally used for microarray analysis but may not always be available. We assessed the feasibility of genomic microarray analysis for high resolution interrogation of UVM using formalin-fixed paraffin-embedded tissue (FFPET) as an alternative to frozen tissue (FZT). Enucleations from 44 patients (clinical trial NCT00952939) yielded sufficient DNA from FFPET (n = 34) and/or frozen tissue (n = 41) for comparative genomic hybridization and select single nucleotide polymorphism analysis (CGH/SNP) on Roche-NimbleGen OncoChip arrays. CEP3 FISH analysis was performed on matched cytology ThinPrep material. CGH/SNP analysis was successful in 30 of 34 FFPET and 41 of 41 FZT samples. Of 27 paired FFPET/FZT samples, 26 (96.3%) were concordant for at least four of six major recurrent abnormalities (-3, +8q, -1p, +6p, -6q, -8p), and 25 of 27 (92.6%) were concordant for -3. Results of CGH/SNP were concordant with the CEP3 FISH results in 27 of 30 (90%) FFPET and 38 of 41 (92.6%) FZT cases; partial -3q was detected in two CEP3 FISH-negative cases and whole chromosome 3, 4, and 6 SNP-LOH in one case. CGH detection of -3, +8q, -8p on FFPET and FZT showed significant correlation with the clinical outcome measures (metastasis development, time to progression, survival). Results of the UVM genotyping by CGH/SNP on FFPET are highly concordant with those of the FZT analysis and with those of the CEP3 FISH analysis, and therefore CGH/SNP is a practical method for UVM prognostication. Genome-wide coverage provides additional data with potential relevance to UVM biology, diagnosis, and prognosis.
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Affiliation(s)
- Eugen C Minca
- Departments of Molecular and Anatomic Pathology, Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Raymond R Tubbs
- Departments of Molecular and Anatomic Pathology, Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Bryce P Portier
- Departments of Molecular and Anatomic Pathology, Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Zhen Wang
- Departments of Molecular and Anatomic Pathology, Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Christopher Lanigan
- Departments of Molecular and Anatomic Pathology, Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Mary E Aronow
- Cole Eye Institute, Cleveland Clinic, Cleveland, OH, USA
| | | | - Arun Singh
- Cole Eye Institute, Cleveland Clinic, Cleveland, OH, USA
| | - James R Cook
- Departments of Molecular and Anatomic Pathology, Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
| | | | - Thomas P Plesec
- Departments of Molecular and Anatomic Pathology, Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Lynn Schoenfield
- Departments of Molecular and Anatomic Pathology, Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Victoria Cawich
- Signature Genomics Laboratories, Perkin Elmer, Spokane, WA, USA
| | - Scott Sulpizio
- Signature Genomics Laboratories, Perkin Elmer, Spokane, WA, USA
| | - Roger A Schultz
- Signature Genomics Laboratories, Perkin Elmer, Spokane, WA, USA.
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16
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Gebauer N, Gebauer J, Hardel TT, Bernard V, Biersack H, Lehnert H, Rades D, Feller AC, Thorns C. Prevalence of targetable oncogenic mutations and genomic alterations in Epstein–Barr virus-associated diffuse large B-cell lymphoma of the elderly. Leuk Lymphoma 2014; 56:1100-6. [DOI: 10.3109/10428194.2014.944522] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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17
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Caretti V, Sewing ACP, Lagerweij T, Schellen P, Bugiani M, Jansen MHA, van Vuurden DG, Navis AC, Horsman I, Vandertop WP, Noske DP, Wesseling P, Kaspers GJL, Nazarian J, Vogel H, Hulleman E, Monje M, Wurdinger T. Human pontine glioma cells can induce murine tumors. Acta Neuropathol 2014; 127:897-909. [PMID: 24777482 DOI: 10.1007/s00401-014-1272-4] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Revised: 03/07/2014] [Accepted: 03/20/2014] [Indexed: 01/12/2023]
Abstract
Diffuse intrinsic pontine glioma (DIPG), with a median survival of only 9 months, is the leading cause of pediatric brain cancer mortality. Dearth of tumor tissue for research has limited progress in this disease until recently. New experimental models for DIPG research are now emerging. To develop preclinical models of DIPG, two different methods were adopted: cells obtained at autopsy (1) were directly xenografted orthotopically into the pons of immunodeficient mice without an intervening cell culture step or (2) were first cultured in vitro and, upon successful expansion, injected in vivo. Both strategies resulted in pontine tumors histopathologically similar to the original human DIPG tumors. However, following the direct transplantation method all tumors proved to be composed of murine and not of human cells. This is in contrast to the indirect method that included initial in vitro culture and resulted in xenografts comprising human cells. Of note, direct injection of cells obtained postmortem from the pons and frontal lobe of human brains not affected by cancer did not give rise to neoplasms. The murine pontine tumors exhibited an immunophenotype similar to human DIPG, but were also positive for microglia/macrophage markers, such as CD45, CD68 and CD11b. Serial orthotopic injection of these murine cells results in lethal tumors in recipient mice. Direct injection of human DIPG cells in vivo can give rise to malignant murine tumors. This represents an important caveat for xenotransplantation models of DIPG. In contrast, an initial in vitro culture step can allow establishment of human orthotopic xenografts. The mechanism underlying this phenomenon observed with direct xenotransplantation remains an open question.
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Affiliation(s)
- Viola Caretti
- Departments of Neurology, Neurosurgery and Pediatrics, Stanford University School of Medicine, Stanford, USA,
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18
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Jonker MJ, de Leeuw WC, Marinković M, Wittink FRA, Rauwerda H, Bruning O, Ensink WA, Fluit AC, Boel CH, Jong MD, Breit TM. Absence/presence calling in microarray-based CGH experiments with non-model organisms. Nucleic Acids Res 2014; 42:e94. [PMID: 24771343 PMCID: PMC4066771 DOI: 10.1093/nar/gku343] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Structural variations in genomes are commonly studied by (micro)array-based comparative genomic hybridization. The data analysis methods to infer copy number variation in model organisms (human, mouse) are established. In principle, the procedures are based on signal ratios between test and reference samples and the order of the probe targets in the genome. These procedures are less applicable to experiments with non-model organisms, which frequently comprise non-sequenced genomes with an unknown order of probe targets. We therefore present an additional analysis approach, which does not depend on the structural information of a reference genome, and quantifies the presence or absence of a probe target in an unknown genome. The principle is that intensity values of target probes are compared with the intensities of negative-control probes and positive-control probes from a control hybridization, to determine if a probe target is absent or present. In a test, analyzing the genome content of a known bacterial strain: Staphylococcus aureus MRSA252, this approach proved to be successful, demonstrated by receiver operating characteristic area under the curve values larger than 0.9995. We show its usability in various applications, such as comparing genome content and validating next-generation sequencing reads from eukaryotic non-model organisms.
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Affiliation(s)
- Martijs J Jonker
- MicroArray Department & Integrative Bioinformatics Unit (MAD-IBU), Swammerdam Institute for Life Sciences (SILS), Faculty of Science (FNWI), University of Amsterdam (UvA), 1098 XH, Amsterdam, the Netherlands Netherlands Bioinformatics Centre (NBIC), 6525 GA, Nijmegen, the Netherlands
| | - Wim C de Leeuw
- MicroArray Department & Integrative Bioinformatics Unit (MAD-IBU), Swammerdam Institute for Life Sciences (SILS), Faculty of Science (FNWI), University of Amsterdam (UvA), 1098 XH, Amsterdam, the Netherlands Netherlands Bioinformatics Centre (NBIC), 6525 GA, Nijmegen, the Netherlands
| | - Marino Marinković
- MicroArray Department & Integrative Bioinformatics Unit (MAD-IBU), Swammerdam Institute for Life Sciences (SILS), Faculty of Science (FNWI), University of Amsterdam (UvA), 1098 XH, Amsterdam, the Netherlands Department of Aquatic Ecology and Ecotoxicology, Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, the Netherlands
| | - Floyd R A Wittink
- MicroArray Department & Integrative Bioinformatics Unit (MAD-IBU), Swammerdam Institute for Life Sciences (SILS), Faculty of Science (FNWI), University of Amsterdam (UvA), 1098 XH, Amsterdam, the Netherlands
| | - Han Rauwerda
- MicroArray Department & Integrative Bioinformatics Unit (MAD-IBU), Swammerdam Institute for Life Sciences (SILS), Faculty of Science (FNWI), University of Amsterdam (UvA), 1098 XH, Amsterdam, the Netherlands Netherlands Bioinformatics Centre (NBIC), 6525 GA, Nijmegen, the Netherlands
| | - Oskar Bruning
- MicroArray Department & Integrative Bioinformatics Unit (MAD-IBU), Swammerdam Institute for Life Sciences (SILS), Faculty of Science (FNWI), University of Amsterdam (UvA), 1098 XH, Amsterdam, the Netherlands Netherlands Bioinformatics Centre (NBIC), 6525 GA, Nijmegen, the Netherlands
| | - Wim A Ensink
- MicroArray Department & Integrative Bioinformatics Unit (MAD-IBU), Swammerdam Institute for Life Sciences (SILS), Faculty of Science (FNWI), University of Amsterdam (UvA), 1098 XH, Amsterdam, the Netherlands
| | - Ad C Fluit
- Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - C H Boel
- Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Mark de Jong
- MicroArray Department & Integrative Bioinformatics Unit (MAD-IBU), Swammerdam Institute for Life Sciences (SILS), Faculty of Science (FNWI), University of Amsterdam (UvA), 1098 XH, Amsterdam, the Netherlands
| | - Timo M Breit
- MicroArray Department & Integrative Bioinformatics Unit (MAD-IBU), Swammerdam Institute for Life Sciences (SILS), Faculty of Science (FNWI), University of Amsterdam (UvA), 1098 XH, Amsterdam, the Netherlands Netherlands Bioinformatics Centre (NBIC), 6525 GA, Nijmegen, the Netherlands
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19
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High fidelity copy number analysis of formalin-fixed and paraffin-embedded tissues using Affymetrix Cytoscan HD chip. PLoS One 2014; 9:e92820. [PMID: 24699316 PMCID: PMC3974686 DOI: 10.1371/journal.pone.0092820] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Accepted: 02/26/2014] [Indexed: 11/19/2022] Open
Abstract
Detection of human genome copy number variation (CNV) is one of the most important analyses in diagnosing human malignancies. Genome CNV detection in formalin-fixed and paraffin-embedded (FFPE) tissues remains challenging due to suboptimal DNA quality and failure to use appropriate baseline controls for such tissues. Here, we report a modified method in analyzing CNV in FFPE tissues using microarray with Affymetrix Cytoscan HD chips. Gel purification was applied to select DNA with good quality and data of fresh frozen and FFPE tissues from healthy individuals were included as baseline controls in our data analysis. Our analysis showed a 91% overlap between CNV detection by microarray with FFPE tissues and chromosomal abnormality detection by karyotyping with fresh tissues on 8 cases of lymphoma samples. The CNV overlap between matched frozen and FFPE tissues reached 93.8%. When the analyses were restricted to regions containing genes, 87.1% concordance between FFPE and fresh frozen tissues was found. The analysis was further validated by Fluorescence In Situ Hybridization on these samples using probes specific for BRAF and CITED2. The results suggested that the modified method using Affymetrix Cytoscan HD chip gave rise to a significant improvement over most of the previous methods in terms of accuracy in detecting CNV in FFPE tissues. This FFPE microarray methodology may hold promise for broad application of CNV analysis on clinical samples.
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20
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Genomic profiling reveals extensive heterogeneity in somatic DNA copy number aberrations of canine hemangiosarcoma. Chromosome Res 2014; 22:305-19. [PMID: 24599718 DOI: 10.1007/s10577-014-9406-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Revised: 01/22/2014] [Accepted: 01/23/2014] [Indexed: 01/08/2023]
Abstract
Canine hemangiosarcoma is a highly aggressive vascular neoplasm associated with extensive clinical and anatomical heterogeneity and a grave prognosis. Comprehensive molecular characterization of hemangiosarcoma may identify novel therapeutic targets and advanced clinical management strategies, but there are no published reports of tumor-associated genome instability and disrupted gene dosage in this cancer. We performed genome-wide microarray-based somatic DNA copy number profiling of 75 primary intra-abdominal hemangiosarcomas from five popular dog breeds that are highly predisposed to this disease. The cohort exhibited limited global genomic instability, compared to other canine sarcomas studied to date, and DNA copy number aberrations (CNAs) were predominantly of low amplitude. Recurrent imbalances of several key cancer-associated genes were evident; however, the global penetrance of any single CNA was low and no distinct hallmark aberrations were evident. Copy number gains of dog chromosomes 13, 24, and 31, and loss of chromosome 16, were the most recurrent CNAs involving large chromosome regions, but their relative distribution within and between cases suggests they most likely represent passenger aberrations. CNAs involving CDKN2A, VEGFA, and the SKI oncogene were identified as potential driver aberrations of hemangiosarcoma development, highlighting potential targets for therapeutic modulation. CNA profiles were broadly conserved between the five breeds, although subregional variation was evident, including a near twofold lower incidence of VEGFA gain in Golden Retrievers versus other breeds (22 versus 40 %). These observations support prior transcriptional studies suggesting that the clinical heterogeneity of this cancer may reflect the existence of multiple, molecularly distinct subtypes of canine hemangiosarcoma.
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Idris SF, Ahmad SS, Scott MA, Vassiliou GS, Hadfield J. The role of high-throughput technologies in clinical cancer genomics. Expert Rev Mol Diagn 2014; 13:167-81. [DOI: 10.1586/erm.13.1] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Genomic instability: a stronger prognostic marker than proliferation for early stage luminal breast carcinomas. PLoS One 2013; 8:e76496. [PMID: 24143191 PMCID: PMC3797106 DOI: 10.1371/journal.pone.0076496] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Accepted: 08/27/2013] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND The accurate prognosis definition to tailor treatment for early luminal invasive breast carcinoma patients remains challenging. MATERIALS AND METHODS Two hundred fourteen early luminal breast carcinomas were genotyped with single nucleotide polymorphisms (SNPs) array to determine the number of chromosomal breakpoints as a marker of genomic instability. Proliferation was assessed by KI67 (immunohistochemistry) and genomic grade index (transcriptomic analysis). IHC3 (IHC4 score for HER2 negative tumors) was also determined. RESULTS In the training set (109 cases), the optimal cut-off was 34 breakpoints with a specificity of 0.94 and a sensitivity of 0.57 (Area under the curve (AUC): 0.81[0.71; 0.91]). In the validation set (105 cases), the outcome of patients with > 34 breakpoints (11 events / 22 patients) was poorer (logrank test p < 0.001; Relative Risk (RR): 3.7 [1.73; 7.92]), than that of patients with < 34 breakpoints (19 events / 83 patients).Whereas genomic grade and KI67 had a significant prognostic value in univariate analysis in contrast to IHC3 that failed to have a statistical significant prognostic value in this series, the number of breakpoints remained the only significant parameter predictive of outcome (RR: 3.47, Confidence Interval (CI [1.29; 9.31], p = 0.014)) in multivariate analysis . CONCLUSION Genomic instability, defined herein as a high number of chromosomal breakpoints, in early stage luminal breast carcinoma is a stronger prognostic marker than proliferation.
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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: 1.8] [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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Schouten PC, van Dyk E, Braaf LM, Mulder L, Lips EH, de Ronde JJ, Holtman L, Wesseling J, Hauptmann M, Wessels LFA, Linn SC, Nederlof PM. Platform comparisons for identification of breast cancers with a BRCA-like copy number profile. Breast Cancer Res Treat 2013; 139:317-27. [PMID: 23670131 DOI: 10.1007/s10549-013-2558-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Accepted: 04/29/2013] [Indexed: 12/28/2022]
Abstract
Previously, we employed bacterial artificial chromosome (BAC) array comparative genomic hybridization (aCGH) profiles from BRCA1 and -2 mutation carriers and sporadic tumours to construct classifiers that identify tumour samples most likely to harbour BRCA1 and -2 mutations, designated 'BRCA1 and -2-like' tumours, respectively. The classifiers are used in clinical genetics to evaluate unclassified variants, and patients for which no good quality germline DNA is available. Furthermore, we have shown that breast cancer patients with BRCA-like tumour aCGH profiles benefit substantially from platinum-based chemotherapy, potentially due to their inability to repair DNA double strand breaks (DSB), providing a further important clinical application for the classifiers. The BAC array technology has been replaced with oligonucleotide arrays. To continue clinical use of existing classifiers, we mapped oligonucleotide aCGH data to the BAC domain, such that the oligonucleotide profiles can be employed as in the BAC classifier. We demonstrate that segmented profiles derived from oligonucleotide aCGH show high correlation with BAC aCGH profiles. Furthermore, we trained a support vector machine score to objectify aCGH profile quality. Using the mapped oligonucleotide aCGH data, we show equivalence in classification of biologically relevant cases between BAC and oligonucleotide data. Furthermore, the predicted benefit of DSB inducing chemotherapy due to a homologous recombination defect is retained. We conclude that oligonucleotide aCGH data can be mapped to and used in the previously developed and validated BAC aCGH classifiers. Our findings suggest that it is possible to map copy number data from any other technology in a similar way.
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Affiliation(s)
- Philip C Schouten
- Division of Molecular Pathology, Netherlands Cancer Institute, Plesmanlaan 121, 1066CX, Amsterdam, The Netherlands
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Swerdlow SH. Lymphoma classification and the tools of our trade: an introduction to the 2012 USCAP Long Course. Mod Pathol 2013; 26 Suppl 1:S1-S14. [PMID: 23281432 DOI: 10.1038/modpathol.2012.177] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The 2012 USCAP Long Course 'Malignant Lymphomas-Building on the Past, Moving to the Future' began with an introduction to lymphoma classification over the last half century and a discussion of our current diagnostic armamentarium, together with a look toward the future. The Rappaport classification, originally published in 1956, was a morphologic classification with few categories. The early 1970s saw a great and tumultuous revolution in the field with the publication of two functional lymphoma classifications that related the malignant lymphomas to the cells of the normal immune system-the Lukes/Collins classification from the United States and the Kiel classification from Professor Lennert and the European Lymphoma Club. With discord abounding, the NCI working formulation, published in 1982, satisfied some but was a step back to a morphologic-based classification. In 1994, the International Lymphoma Study Group published the REAL classification, which reflected state-of-the-art practice for that time, and was shortly followed by preparations for the modern World Health Organization (WHO) classification published in 2001 and revised in 2008. The WHO classification, created by hematopathologists working with the advice and consent of clinical hematologist/oncologists, recognizes numerous distinct entities, defined based on their histopathological, immunophenotypical, molecular/cytogenetic and clinical features. The classification requires use of a multiparameter approach to lymphoma diagnosis although we still rely heavily on histopathology. Immunophenotypical studies, whether using paraffin section immunohistochemistry and/or flow cytometry, are also critical in almost all circumstances. Molecular/cytogenetic techniques that are constantly changing have an increasingly important role, even if not always required. The full impact of next-generation sequencing is yet to be felt but we are beginning to catch a glimpse of what is in our future. Finally, one must not forget the great importance of clinical data in arriving at a diagnosis that best serves the patient, our ultimate goal.
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Affiliation(s)
- Steven H Swerdlow
- Division of Hematopathology, Department of Pathology, UPMC Health System-UPMC Presbyterian, University of Pittsburgh School of Medicine, 200 Lothrop Street, Pittsburgh, PA 15213, USA.
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Banerjee D. Array comparative genomic hybridization: an overview of protocols, applications, and technology trends. Methods Mol Biol 2013; 973:1-13. [PMID: 23412780 DOI: 10.1007/978-1-62703-281-0_1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
From the earliest observations of human chromosomes in the late 1800s to modern day next generation sequencing technologies, much has been learned about human cancers by the vigorous application of the techniques of the day. In general, resolution has improved tremendously, and correspondingly the size of the datasets generated has grown exponentially such that computational methods required to handle massive datasets have had to be devised. This chapter provides a brief synopsis of the evolution of such techniques as an introduction to the subsequent chapters that provide methods and applications, relevant to research, and clinical diagnostics.
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Affiliation(s)
- Diponkar Banerjee
- Department of Pathology and Laboratory Medicine, The Ottawa Hospital, Ottawa, BC, Canada.
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Campo E. Whole genome profiling and other high throughput technologies in lymphoid neoplasms--current contributions and future hopes. Mod Pathol 2013; 26 Suppl 1:S97-S110. [PMID: 23281439 DOI: 10.1038/modpathol.2012.179] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The development of high throughput technologies based on the knowledge of the human genome has opened the possibility to search for global genomic alterations in tumors responsible for their development and progression that may have important clinical implications. One of the major applications of this genomic knowledge has been the design of different types of microarray platforms for the analysis of DNA alterations and gene expression profiling (GEP). The main contributions of the DNA studies in lymphoid neoplasms include the definition of relatively characteristic genomic profiles for specific disease entities, the demonstration of common chromosomal alterations across entities, the identification of genes and pathways targeted by the altered chromosomal regions, and the identification of chromosomal alterations with prognostic implications. RNA GEP studies in these tumors have enhanced the molecular characterization of known entities and facilitated the recognition of new subtypes and categories of lymphoid neoplasms, the identification of new biomarkers and prognostic models, and the detection of oncogenic pathways with potential implications for targeted therapies. The recent development of the next generation sequencing (NGS) technologies and its application in lymphoid neoplasms already have provided an initial view of the complex landscape of somatic mutations in these tumors and some findings with important functional and clinical implications. This review addresses the major contributions and limitations of the microarray technologies in the understanding of lymphoid neoplasms and discusses how this knowledge may be transferred into the clinics. The initial results of the NGS studies are also presented.
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Affiliation(s)
- Elías Campo
- Haematopathology Section, Department of Anatomic Pathology, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, Barcelona, Spain.
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Krijgsman O, Israeli D, van Essen HF, Eijk PP, Berens MLM, Mellink CHM, Nieuwint AW, Weiss MM, Steenbergen RDM, Meijer GA, Ylstra B. Detection limits of DNA copy number alterations in heterogeneous cell populations. Cell Oncol (Dordr) 2012; 36:27-36. [PMID: 23117839 DOI: 10.1007/s13402-012-0108-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/15/2012] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Array Comparative Genomic Hybridization (aCGH) is a widely used technique to assess chromosomal copy number alterations. Chromosomal content, however, is often not uniform throughout cell populations. Here we evaluated to what extent aCGH can detect DNA copy number alterations in heterogeneous cell populations. A systematic evaluation is currently lacking, despite its importance in diagnostics and research. The detection limits reported are a compound of analytical software and laboratory techniques and do not account for the number of probes in relation to sample homogeneity. METHODS Detection limits were explored with DNA isolated from a patient with intellectual disability (ID) and from tumor cell line BT474. Both were diluted with increasing amounts of normal DNA to simulate different levels of cellularity. Samples were hybridized on microarrays containing 180,880 oligonucleotides evenly distributed over the genome (spacing ~17 kb). RESULTS Single copy number alterations, represented by down to 249 probes (4 Mb) and present in 10 % of a cell population, could be detected. Alterations encompassing as few as 14 probes (~238 Kb) could also be detected, but for this a 35 % mosaic level was required. CONCLUSIONS DNA copy number alterations can be detected in cell populations containing 10 % abnormal cells. Detection of sub-megabase alterations requires a higher percentage of abnormal cells or microarrays with a higher probe density.
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Affiliation(s)
- Oscar Krijgsman
- Department of Pathology, VU University Medical Center, MB, Amsterdam, The Netherlands
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Bierkens M, Krijgsman O, Wilting SM, Bosch L, Jaspers A, Meijer GA, Meijer CJLM, Snijders PJF, Ylstra B, Steenbergen RDM. Focal aberrations indicate EYA2 and hsa-miR-375 as oncogene and tumor suppressor in cervical carcinogenesis. Genes Chromosomes Cancer 2012; 52:56-68. [PMID: 22987659 DOI: 10.1002/gcc.22006] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2012] [Accepted: 08/08/2012] [Indexed: 01/06/2023] Open
Abstract
Cervical cancer results from persistent infection with high-risk human papillomavirus (hrHPV). Common genetic aberrations in cervical (pre)cancers encompass large genomic regions with numerous genes, hampering identification of driver genes. This study aimed to identify genes functionally involved in HPV-mediated transformation by analysis of focal aberrations (<3 Mb) in high-grade cervical intraepithelial neoplasia (hgCIN). Focal chromosomal aberrations were determined in high-resolution array comparative genomic hybridization data of 60 hgCIN. Genes located within focal aberrations were validated using 2 external gene expression datasets or qRT-PCR. Functional roles of candidate genes EYA2 (20q13) and hsa-miR-375 (2q35) were studied by siRNA-mediated knock-down and overexpression, respectively, in hrHPV-containing cell lines. We identified 74 focal aberrations encoding 305 genes. Concurrent altered expression in hgCIN and/or cervical carcinomas compared with normal cervical samples was shown for ATP13A3, HES1, OPA1, HRASLS, EYA2, ZMYND8, APOBEC2, and NCR2. Gene silencing of EYA2 significantly reduced viability, migratory capacity, and anchorage-independent growth of HPV16-transformed keratinocytes. For hsa-miR-375, a direct correlation between a (focal) loss and significantly reduced expression was found. Downregulation of hsa-miR-375 expression was confirmed in an independent series of cervical tissues. Ectopic expression of hsa-miR-375 in 2 cervical carcinoma cell lines reduced cellular viability. Our data provide a proof of concept that chromosomal aberrations are actively contributing to HPV-induced carcinogenesis and identify EYA2 and hsa-miR-375 as oncogene and tumor suppressor gene, respectively.
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Affiliation(s)
- Mariska Bierkens
- Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
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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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