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Sangaralingam A, Dayem Ullah AZ, Marzec J, Gadaleta E, Nagano A, Ross-Adams H, Wang J, Lemoine NR, Chelala C. 'Multi-omic' data analysis using O-miner. Brief Bioinform 2019; 20:130-143. [PMID: 28981577 PMCID: PMC6357557 DOI: 10.1093/bib/bbx080] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Indexed: 12/19/2022] Open
Abstract
Innovations in -omics technologies have driven advances in biomedical research. However, integrating and analysing the large volumes of data generated from different high-throughput -omics technologies remain a significant challenge to basic and clinical scientists without bioinformatics skills or access to bioinformatics support. To address this demand, we have significantly updated our previous O-miner analytical suite, to incorporate several new features and data types to provide an efficient and easy-to-use Web tool for the automated analysis of data from '-omics' technologies. Created from a biologist's perspective, this tool allows for the automated analysis of large and complex transcriptomic, genomic and methylomic data sets, together with biological/clinical information, to identify significantly altered pathways and prioritize novel biomarkers/targets for biological validation. Our resource can be used to analyse both in-house data and the huge amount of publicly available information from array and sequencing platforms. Multiple data sets can be easily combined, allowing for meta-analyses. Here, we describe the analytical pipelines currently available in O-miner and present examples of use to demonstrate its utility and relevance in maximizing research output. O-miner Web server is free to use and is available at http://www.o-miner.org.
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Affiliation(s)
| | | | - Jacek Marzec
- Barts Cancer Institute, Queen Mary University of London
| | | | - Ai Nagano
- Barts Cancer Institute, Queen Mary University of London
| | | | - Jun Wang
- Barts Cancer Institute, Queen Mary University of London
| | | | - Claude Chelala
- Barts Cancer Institute, co-Lead of the Computational Biology Centre at the Life Science Initiative, Queen Mary University of London
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2
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Tokutomi N, Moyret‐Lalle C, Puisieux A, Sugano S, Martinez P. Quantifying local malignant adaptation in tissue-specific evolutionary trajectories by harnessing cancer's repeatability at the genetic level. Evol Appl 2019; 12:1062-1075. [PMID: 31080515 PMCID: PMC6503823 DOI: 10.1111/eva.12781] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 12/03/2018] [Accepted: 02/07/2019] [Indexed: 02/06/2023] Open
Abstract
Cancer is a potentially lethal disease, in which patients with nearly identical genetic backgrounds can develop a similar pathology through distinct combinations of genetic alterations. We aimed to reconstruct the evolutionary process underlying tumour initiation, using the combination of convergence and discrepancies observed across 2,742 cancer genomes from nine tumour types. We developed a framework using the repeatability of cancer development to score the local malignant adaptation (LMA) of genetic clones, as their potential to malignantly progress and invade their environment of origin. Using this framework, we found that premalignant skin and colorectal lesions appeared specifically adapted to their local environment, yet insufficiently for full cancerous transformation. We found that metastatic clones were more adapted to the site of origin than to the invaded tissue, suggesting that genetics may be more important for local progression than for the invasion of distant organs. In addition, we used network analyses to investigate evolutionary properties at the system-level, highlighting that different dynamics of malignant progression can be modelled by such a framework in tumour-type-specific fashion. We find that occurrence-based methods can be used to specifically recapitulate the process of cancer initiation and progression, as well as to evaluate the adaptation of genetic clones to given environments. The repeatability observed in the evolution of most tumour types could therefore be harnessed to better predict the trajectories likely to be taken by tumours and preneoplastic lesions in the future.
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Affiliation(s)
- Natsuki Tokutomi
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier SciencesThe University of TokyoTokyoJapan
| | - Caroline Moyret‐Lalle
- Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon BérardCancer Research Center of LyonLyonFrance
| | - Alain Puisieux
- Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon BérardCancer Research Center of LyonLyonFrance
| | - Sumio Sugano
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier SciencesThe University of TokyoTokyoJapan
| | - Pierre Martinez
- Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon BérardCancer Research Center of LyonLyonFrance
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3
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Martinez P, Kimberley C, BirkBak NJ, Marquard A, Szallasi Z, Graham TA. Quantification of within-sample genetic heterogeneity from SNP-array data. Sci Rep 2017; 7:3248. [PMID: 28607403 PMCID: PMC5468233 DOI: 10.1038/s41598-017-03496-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 05/03/2017] [Indexed: 01/17/2023] Open
Abstract
Intra-tumour genetic heterogeneity (ITH) fosters drug resistance and is a critical hurdle to clinical treatment. ITH can be well-measured using multi-region sampling but this is costly and challenging to implement. There is therefore a need for tools to estimate ITH in individual samples, using standard genomic data such as SNP-arrays, that could be implemented routinely. We designed two novel scores S and R, respectively based on the Shannon diversity index and Ripley's L statistic of spatial homogeneity, to quantify ITH in single SNP-array samples. We created in-silico and in-vitro mixtures of tumour clones, in which diversity was known for benchmarking purposes. We found significant but highly-variable associations of our scores with diversity in-silico (p < 0.001) and moderate associations in-vitro (p = 0.015 and p = 0.085). Our scores were also correlated to previous ITH estimates from sequencing data but heterogeneity in the fraction of tumour cells present across samples hampered accurate quantification. The prognostic potential of both scores was moderate but significantly predictive of survival in several tumour types (corrected p = 0.03). Our work thus shows how individual SNP-arrays reveal intra-sample clonal diversity with moderate accuracy.
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Affiliation(s)
- Pierre Martinez
- Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Center of Lyon, Lyon, France.
- Evolution and Cancer laboratory, Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, EC1M 6BQ, London, UK.
| | - Christopher Kimberley
- Evolution and Cancer laboratory, Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, EC1M 6BQ, London, UK
| | - Nicolai J BirkBak
- Centre for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark
| | - Andrea Marquard
- Centre for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark
| | - Zoltan Szallasi
- Centre for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark
- Children's Hospital Informatics Program at the Harvard-MIT Division of Health Sciences and Technology (CHIP@HST), Harvard Medical School, Boston, MA, USA
| | - Trevor A Graham
- Evolution and Cancer laboratory, Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, EC1M 6BQ, London, UK
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4
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Kanu N, Grönroos E, Martinez P, Burrell RA, Yi Goh X, Bartkova J, Maya-Mendoza A, Mistrík M, Rowan AJ, Patel H, Rabinowitz A, East P, Wilson G, Santos CR, McGranahan N, Gulati S, Gerlinger M, Birkbak NJ, Joshi T, Alexandrov LB, Stratton MR, Powles T, Matthews N, Bates PA, Stewart A, Szallasi Z, Larkin J, Bartek J, Swanton C. SETD2 loss-of-function promotes renal cancer branched evolution through replication stress and impaired DNA repair. Oncogene 2015; 34:5699-708. [PMID: 25728682 PMCID: PMC4660036 DOI: 10.1038/onc.2015.24] [Citation(s) in RCA: 128] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Revised: 12/29/2014] [Accepted: 01/06/2015] [Indexed: 12/13/2022]
Abstract
Defining mechanisms that generate intratumour heterogeneity and branched evolution may inspire novel therapeutic approaches to limit tumour diversity and adaptation. SETD2 (Su(var), Enhancer of zeste, Trithorax-domain containing 2) trimethylates histone-3 lysine-36 (H3K36me3) at sites of active transcription and is mutated in diverse tumour types, including clear cell renal carcinomas (ccRCCs). Distinct SETD2 mutations have been identified in spatially separated regions in ccRCC, indicative of intratumour heterogeneity. In this study, we have addressed the consequences of SETD2 loss-of-function through an integrated bioinformatics and functional genomics approach. We find that bi-allelic SETD2 aberrations are not associated with microsatellite instability in ccRCC. SETD2 depletion in ccRCC cells revealed aberrant and reduced nucleosome compaction and chromatin association of the key replication proteins minichromosome maintenance complex component (MCM7) and DNA polymerase δ hindering replication fork progression, and failure to load lens epithelium-derived growth factor and the Rad51 homologous recombination repair factor at DNA breaks. Consistent with these data, we observe chromosomal breakpoint locations are biased away from H3K36me3 sites in SETD2 wild-type ccRCCs relative to tumours with bi-allelic SETD2 aberrations and that H3K36me3-negative ccRCCs display elevated DNA damage in vivo. These data suggest a role for SETD2 in maintaining genome integrity through nucleosome stabilization, suppression of replication stress and the coordination of DNA repair.
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Affiliation(s)
- N Kanu
- UCL Cancer Institute, Paul O'Gorman Building, London, UK
| | - E Grönroos
- Cancer Research UK London Research Institute, London, UK
| | - P Martinez
- Cancer Research UK London Research Institute, London, UK
| | - R A Burrell
- Cancer Research UK London Research Institute, London, UK
| | - X Yi Goh
- Cancer Research UK London Research Institute, London, UK
| | - J Bartkova
- Danish Cancer Society Research Center, Copenhagen, Denmark
| | - A Maya-Mendoza
- Danish Cancer Society Research Center, Copenhagen, Denmark
| | - M Mistrík
- Faculty of Medicine and Dentistry, Institute of Molecular and Translational Medicine, Palacky University, Olomouc, Czech Republic
| | - A J Rowan
- Cancer Research UK London Research Institute, London, UK
| | - H Patel
- Cancer Research UK London Research Institute, London, UK
| | - A Rabinowitz
- Cancer Research UK London Research Institute, London, UK
| | - P East
- Cancer Research UK London Research Institute, London, UK
| | - G Wilson
- Cancer Research UK London Research Institute, London, UK
| | - C R Santos
- Cancer Research UK London Research Institute, London, UK
| | - N McGranahan
- Cancer Research UK London Research Institute, London, UK
| | - S Gulati
- Cancer Research UK London Research Institute, London, UK
| | - M Gerlinger
- Cancer Research UK London Research Institute, London, UK
| | - N J Birkbak
- UCL Cancer Institute, Paul O'Gorman Building, London, UK
- Cancer Research UK London Research Institute, London, UK
- Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, Kongens Lyngby, Denmark
| | - T Joshi
- Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, Kongens Lyngby, Denmark
| | - L B Alexandrov
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridgeshire, UK
| | - M R Stratton
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridgeshire, UK
| | - T Powles
- Barts Cancer Institute, Experimental Cancer Medicine Centre, Queen Mary University of London, London, UK
| | - N Matthews
- Cancer Research UK London Research Institute, London, UK
| | - P A Bates
- Cancer Research UK London Research Institute, London, UK
| | - A Stewart
- Cancer Research UK London Research Institute, London, UK
| | - Z Szallasi
- Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, Kongens Lyngby, Denmark
- Children's Hospital Boston, Informatics—Enders 1506, Boston, MA, USA
| | - J Larkin
- Department of Medicine, The Royal Marsden Hospital, London, UK
| | - J Bartek
- Danish Cancer Society Research Center, Copenhagen, Denmark
- Faculty of Medicine and Dentistry, Institute of Molecular and Translational Medicine, Palacky University, Olomouc, Czech Republic
| | - C Swanton
- UCL Cancer Institute, Paul O'Gorman Building, London, UK
- Cancer Research UK London Research Institute, London, UK
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Alentorn A, Dehais C, Ducray F, Carpentier C, Mokhtari K, Figarella-Branger D, Chinot O, Cohen-Moyal E, Ramirez C, Loiseau H, Elouahdani-Hamdi S, Beauchesne P, Langlois O, Desenclos C, Guillamo JS, Dam-Hieu P, Ghiringhelli F, Colin P, Godard J, Parker F, Dhermain F, Carpentier AF, Frenel JS, Menei P, Bauchet L, Faillot T, Fesneau M, Fontaine D, Motuo-Fotso MJ, Vauleon E, Gaultier C, Le Guerinel C, Gueye EM, Noel G, Desse N, Durando X, Barrascout E, Wager M, Ricard D, Carpiuc I, Delattre JY, Idbaih A. Allelic loss of 9p21.3 is a prognostic factor in 1p/19q codeleted anaplastic gliomas. Neurology 2015; 85:1325-31. [PMID: 26385879 DOI: 10.1212/wnl.0000000000002014] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2014] [Accepted: 06/17/2015] [Indexed: 12/18/2022] Open
Abstract
OBJECTIVES We aimed to study the potential clinical relevance of 9p allelic loss, with or without copy number variation, in 1p/19q codeleted anaplastic oligodendroglial tumors (AOTs). METHODS This study enrolled 216 patients with 1p/19q codeleted AOT. The prognostic value of 9p allelic loss was investigated using a French nation-wide prospective registry, POLA (prise en charge des tumeurs oligodendrogliales anaplasiques) and high-density single nucleotide polymorphism arrays. We validated our results using the Repository of Molecular Brain Neoplasia Data (REMBRANDT) dataset. RESULTS The minimal common region of allelic loss in chromosome arm 9p was 9p21.3. Allelic loss of 9p21.3, detected in 41.7% of tumors, was associated with shorter progression-free and overall survival rates in univariate (p = 0.008 and p < 0.001, respectively) and multivariate analyses (p = 0.009 and p = 0.009, respectively). This finding was validated in the REMBRANDT dataset in univariate and multivariate analysis (p = 0.01 and p = 0.01, respectively). CONCLUSION Our study highlights a novel potential prognostic biomarker in 1p/19q codeleted AOT. Further prospective studies are warranted to investigate our finding.
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Affiliation(s)
| | | | | | | | | | | | - Olivier Chinot
- Authors' affiliations are listed at the end of the article
| | | | - Carole Ramirez
- Authors' affiliations are listed at the end of the article
| | - Hugues Loiseau
- Authors' affiliations are listed at the end of the article
| | | | | | | | | | | | - Phong Dam-Hieu
- Authors' affiliations are listed at the end of the article
| | | | - Philippe Colin
- Authors' affiliations are listed at the end of the article
| | - Joel Godard
- Authors' affiliations are listed at the end of the article
| | - Fabrice Parker
- Authors' affiliations are listed at the end of the article
| | | | | | | | - Philippe Menei
- Authors' affiliations are listed at the end of the article
| | - Luc Bauchet
- Authors' affiliations are listed at the end of the article
| | | | | | - Denys Fontaine
- Authors' affiliations are listed at the end of the article
| | | | - Elodie Vauleon
- Authors' affiliations are listed at the end of the article
| | | | | | | | - Georges Noel
- Authors' affiliations are listed at the end of the article
| | - Nicolas Desse
- Authors' affiliations are listed at the end of the article
| | - Xavier Durando
- Authors' affiliations are listed at the end of the article
| | | | - Michel Wager
- Authors' affiliations are listed at the end of the article
| | - Damien Ricard
- Authors' affiliations are listed at the end of the article
| | - Ioana Carpiuc
- Authors' affiliations are listed at the end of the article
| | | | - Ahmed Idbaih
- Authors' affiliations are listed at the end of the article.
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6
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Marquard AM, Eklund AC, Joshi T, Krzystanek M, Favero F, Wang ZC, Richardson AL, Silver DP, Szallasi Z, Birkbak NJ. Pan-cancer analysis of genomic scar signatures associated with homologous recombination deficiency suggests novel indications for existing cancer drugs. Biomark Res 2015; 3:9. [PMID: 26015868 PMCID: PMC4443545 DOI: 10.1186/s40364-015-0033-4] [Citation(s) in RCA: 210] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 03/25/2015] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Ovarian and triple-negative breast cancers with BRCA1 or BRCA2 loss are highly sensitive to treatment with PARP inhibitors and platinum-based cytotoxic agents and show an accumulation of genomic scars in the form of gross DNA copy number aberrations. Cancers without BRCA1 or BRCA2 loss but with accumulation of similar genomic scars also show increased sensitivity to platinum-based chemotherapy. Therefore, reliable biomarkers to identify DNA repair-deficient cancers prior to treatment may be useful for directing patients to platinum chemotherapy and possibly PARP inhibitors. Recently, three SNP array-based signatures of chromosomal instability were published that each quantitate a distinct type of genomic scar considered likely to be caused by improper DNA repair. They measure telomeric allelic imbalance (named NtAI), large scale transition (named LST), and loss of heterozygosity (named HRD-LOH), and it is suggested that these signatures may act as biomarkers for the state of DNA repair deficiency in a given cancer. RESULTS We explored the pan-cancer distribution of scores of the three signatures utilizing a panel of 5371 tumors representing 15 cancer types from The Cancer Genome Atlas, and found a good correlation between scores of the three signatures (Spearman's ρ 0.73-0.87). In addition we found that cancer types ordinarily receiving platinum as standard of care have higher median scores of all three signatures. Interestingly, we also found that smaller subpopulations of high-scoring tumors exist in most cancer types, including those for which platinum chemotherapy is not standard therapy. CONCLUSIONS Within several cancer types that are not ordinarily treated with platinum chemotherapy, we identified tumors with high levels of the three genomic biomarkers. These tumors represent identifiable subtypes of patients which may be strong candidates for clinical trials with PARP inhibitors or platinum-based chemotherapeutic regimens.
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Affiliation(s)
- Andrea M Marquard
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet 8, 2800 Lyngby, Denmark
| | - Aron C Eklund
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet 8, 2800 Lyngby, Denmark
| | - Tejal Joshi
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet 8, 2800 Lyngby, Denmark
| | - Marcin Krzystanek
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet 8, 2800 Lyngby, Denmark
| | - Francesco Favero
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet 8, 2800 Lyngby, Denmark
| | - Zhigang C Wang
- Department of Cancer Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, 02215 Boston, Massachusetts USA.,Department of Surgery, Brigham and Women's Hospital, 75 Francis Street, 02115 Boston, Massachusetts USA
| | - Andrea L Richardson
- Department of Pathology, Brigham and Women's Hospital, 75 Francis Street, 02115 Boston, Massachusetts USA
| | - Daniel P Silver
- Department of Cancer Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, 02215 Boston, Massachusetts USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, 02215 Boston, Massachusetts USA
| | - Zoltan Szallasi
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet 8, 2800 Lyngby, Denmark.,Harvard Medical School, Children's Hospital Informatics Program at the Harvard-Massachusetts Institute of Technology Division of Health Sciences and Technology (CHIP@HST), 320 Longwood Avenue, Boston, Massachusetts USA
| | - Nicolai J Birkbak
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet 8, 2800 Lyngby, Denmark
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7
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McGranahan N, Favero F, de Bruin EC, Birkbak NJ, Szallasi Z, Swanton C. Clonal status of actionable driver events and the timing of mutational processes in cancer evolution. Sci Transl Med 2015; 7:283ra54. [PMID: 25877892 PMCID: PMC4636056 DOI: 10.1126/scitranslmed.aaa1408] [Citation(s) in RCA: 534] [Impact Index Per Article: 53.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Deciphering whether actionable driver mutations are found in all or a subset of tumor cells will likely be required to improve drug development and precision medicine strategies. We analyzed nine cancer types to determine the subclonal frequencies of driver events, to time mutational processes during cancer evolution, and to identify drivers of subclonal expansions. Although mutations in known driver genes typically occurred early in cancer evolution, we also identified later subclonal "actionable" mutations, including BRAF (V600E), IDH1 (R132H), PIK3CA (E545K), EGFR (L858R), and KRAS (G12D), which may compromise the efficacy of targeted therapy approaches. More than 20% of IDH1 mutations in glioblastomas, and 15% of mutations in genes in the PI3K (phosphatidylinositol 3-kinase)-AKT-mTOR (mammalian target of rapamycin) signaling axis across all tumor types were subclonal. Mutations in the RAS-MEK (mitogen-activated protein kinase kinase) signaling axis were less likely to be subclonal than mutations in genes associated with PI3K-AKT-mTOR signaling. Analysis of late mutations revealed a link between APOBEC-mediated mutagenesis and the acquisition of subclonal driver mutations and uncovered putative cancer genes involved in subclonal expansions, including CTNNA2 and ATXN1. Our results provide a pan-cancer census of driver events within the context of intratumor heterogeneity and reveal patterns of tumor evolution across cancers. The frequent presence of subclonal driver mutations suggests the need to stratify targeted therapy response according to the proportion of tumor cells in which the driver is identified.
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Affiliation(s)
- Nicholas McGranahan
- Cancer Research UK London Research Institute, London WC2A 3LY, UK. Centre for Mathematics and Physics in the Life Sciences and Experimental Biology (CoMPLEX), University College London, London WC1E 6BT, UK
| | - Francesco Favero
- Cancer System Biology, Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby 2800, Denmark
| | - Elza C de Bruin
- UCL Cancer Institute, CRUK Lung Cancer Centre of Excellence, Paul O'Gorman Building, Huntley Street, London WC1E 6DD, UK
| | - Nicolai Juul Birkbak
- Cancer Research UK London Research Institute, London WC2A 3LY, UK. Cancer System Biology, Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby 2800, Denmark. UCL Cancer Institute, CRUK Lung Cancer Centre of Excellence, Paul O'Gorman Building, Huntley Street, London WC1E 6DD, UK
| | - Zoltan Szallasi
- Cancer System Biology, Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby 2800, Denmark. Children's Hospital Informatics Program, Harvard Medical School, Boston, MA 02115, USA
| | - Charles Swanton
- Cancer Research UK London Research Institute, London WC2A 3LY, UK. UCL Cancer Institute, CRUK Lung Cancer Centre of Excellence, Paul O'Gorman Building, Huntley Street, London WC1E 6DD, UK.
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8
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de Bruin EC, McGranahan N, Mitter R, Salm M, Wedge DC, Yates L, Jamal-Hanjani M, Shafi S, Murugaesu N, Rowan AJ, Grönroos E, Muhammad MA, Horswell S, Gerlinger M, Varela I, Jones D, Marshall J, Voet T, Van Loo P, Rassl DM, Rintoul RC, Janes SM, Lee SM, Forster M, Ahmad T, Lawrence D, Falzon M, Capitanio A, Harkins TT, Lee CC, Tom W, Teefe E, Chen SC, Begum S, Rabinowitz A, Phillimore B, Spencer-Dene B, Stamp G, Szallasi Z, Matthews N, Stewart A, Campbell P, Swanton C. Spatial and temporal diversity in genomic instability processes defines lung cancer evolution. Science 2014; 346:251-6. [PMID: 25301630 PMCID: PMC4636050 DOI: 10.1126/science.1253462] [Citation(s) in RCA: 871] [Impact Index Per Article: 79.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Spatial and temporal dissection of the genomic changes occurring during the evolution of human non-small cell lung cancer (NSCLC) may help elucidate the basis for its dismal prognosis. We sequenced 25 spatially distinct regions from seven operable NSCLCs and found evidence of branched evolution, with driver mutations arising before and after subclonal diversification. There was pronounced intratumor heterogeneity in copy number alterations, translocations, and mutations associated with APOBEC cytidine deaminase activity. Despite maintained carcinogen exposure, tumors from smokers showed a relative decrease in smoking-related mutations over time, accompanied by an increase in APOBEC-associated mutations. In tumors from former smokers, genome-doubling occurred within a smoking-signature context before subclonal diversification, which suggested that a long period of tumor latency had preceded clinical detection. The regionally separated driver mutations, coupled with the relentless and heterogeneous nature of the genome instability processes, are likely to confound treatment success in NSCLC.
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Affiliation(s)
- Elza C de Bruin
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London WC1E 6BT, UK
| | - Nicholas McGranahan
- Cancer Research UK London Research Institute, London WC2A 3LY, UK. Centre for Mathematics and Physics in the Life Science and Experimental Biology (CoMPLEX), University College London, London WC1E 6BT, UK
| | - Richard Mitter
- Cancer Research UK London Research Institute, London WC2A 3LY, UK
| | - Max Salm
- Cancer Research UK London Research Institute, London WC2A 3LY, UK
| | - David C Wedge
- Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
| | - Lucy Yates
- Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK. University of Cambridge, Cambridge CB2 1TN, UK
| | - Mariam Jamal-Hanjani
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London WC1E 6BT, UK
| | - Seema Shafi
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London WC1E 6BT, UK
| | - Nirupa Murugaesu
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London WC1E 6BT, UK
| | - Andrew J Rowan
- Cancer Research UK London Research Institute, London WC2A 3LY, UK
| | - Eva Grönroos
- Cancer Research UK London Research Institute, London WC2A 3LY, UK
| | - Madiha A Muhammad
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London WC1E 6BT, UK
| | - Stuart Horswell
- Cancer Research UK London Research Institute, London WC2A 3LY, UK
| | - Marco Gerlinger
- Cancer Research UK London Research Institute, London WC2A 3LY, UK
| | - Ignacio Varela
- Instituto de Biomedicina y Biotecnología de Cantabria (CSIC-UC-Sodercan), Departamento de Biología Molecular, Universidad de Cantabria, Santander, Spain
| | - David Jones
- Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
| | - John Marshall
- Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
| | - Thierry Voet
- Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK. Department of Human Genetics, University of Leuven, 3000 Leuven, Belgium
| | - Peter Van Loo
- Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK. Department of Human Genetics, University of Leuven, 3000 Leuven, Belgium
| | - Doris M Rassl
- Papworth Hospital NHS Foundation Trust, Cambridge CB23 3RE, UK
| | | | - Sam M Janes
- Lungs for Living Research Centre, University College London, London WC1E 6BT, UK
| | - Siow-Ming Lee
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London WC1E 6BT, UK. University College London Hospitals, London NW1 2BU, UK
| | - Martin Forster
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London WC1E 6BT, UK. University College London Hospitals, London NW1 2BU, UK
| | - Tanya Ahmad
- University College London Hospitals, London NW1 2BU, UK
| | | | - Mary Falzon
- University College London Hospitals, London NW1 2BU, UK
| | | | | | | | - Warren Tom
- Thermo Fisher Scientific, Carlsbad, CA 92008, USA
| | - Enock Teefe
- Thermo Fisher Scientific, Carlsbad, CA 92008, USA
| | | | - Sharmin Begum
- Cancer Research UK London Research Institute, London WC2A 3LY, UK
| | - Adam Rabinowitz
- Cancer Research UK London Research Institute, London WC2A 3LY, UK
| | | | | | - Gordon Stamp
- Cancer Research UK London Research Institute, London WC2A 3LY, UK
| | - Zoltan Szallasi
- Technical University of Denmark, 2800 Kongens Lyngby, Denmark. Children's Hospital Informatics Program, Harvard Medical School, Boston, MA 02115, USA
| | - Nik Matthews
- Cancer Research UK London Research Institute, London WC2A 3LY, UK
| | - Aengus Stewart
- Cancer Research UK London Research Institute, London WC2A 3LY, UK
| | | | - Charles Swanton
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London WC1E 6BT, UK. Cancer Research UK London Research Institute, London WC2A 3LY, UK.
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9
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Lönnstedt IM, Caramia F, Li J, Fumagalli D, Salgado R, Rowan A, Salm M, Kanu N, Savas P, Horswell S, Gade S, Loibl S, Neven P, Sotiriou C, Swanton C, Loi S, Speed TP. Deciphering clonality in aneuploid breast tumors using SNP array and sequencing data. Genome Biol 2014; 15:470. [PMID: 25270265 PMCID: PMC4220069 DOI: 10.1186/s13059-014-0470-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Accepted: 09/15/2014] [Indexed: 12/30/2022] Open
Abstract
Intra-tumor heterogeneity concerns the existence of genetically different subclones within the same tumor. Single sample quantification of heterogeneity relies on precise determination of chromosomal copy numbers throughout the genome, and an assessment of whether identified mutation variant allele fractions match clonal or subclonal copy numbers. We discuss these issues using data from SNP arrays, whole exome sequencing and pathologist purity estimates on several breast cancers characterized by ERBB2 amplification. We show that chromosomal copy numbers can only be estimated from SNP array signals or sequencing depths for subclonal tumor samples with simple subclonal architectures under certain assumptions.
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Affiliation(s)
- Ingrid M Lönnstedt
- />Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052 Australia
- />University of Melbourne, Melbourne, VIC 3010 Australia
- />Division of Research and Cancer Medicine, Peter MacCallum Cancer Centre, East Melbourne, VIC 3002 Australia
| | - Franco Caramia
- />Division of Research and Cancer Medicine, Peter MacCallum Cancer Centre, East Melbourne, VIC 3002 Australia
| | - Jason Li
- />Division of Research and Cancer Medicine, Peter MacCallum Cancer Centre, East Melbourne, VIC 3002 Australia
| | - Debora Fumagalli
- />Breast Cancer Translational Research Laboratory, Institut Jules Bordet, Brussels, Belgium
| | - Roberto Salgado
- />Breast Cancer Translational Research Laboratory, Institut Jules Bordet, Brussels, Belgium
| | - Andrew Rowan
- />Cancer Research UK, London Research Institute, Translational Cancer Therapeutics Laboratory, 44 Lincoln’s Inn Fields, London, WC2A 3LY UK
| | - Max Salm
- />Bioinformatics and BioStatistics, Cancer Research UK, Lincoln’s Inn Fields, Holborn, London WC2A 3LY UK
| | - Nnennaya Kanu
- />Translational Cancer Therapeutics Laboratory, UCL Cancer Institute, Paul O’Gorman Building, University College London, 72 Huntley Street, London, WC1E 6DD UK
| | - Peter Savas
- />Division of Research and Cancer Medicine, Peter MacCallum Cancer Centre, East Melbourne, VIC 3002 Australia
| | - Stuart Horswell
- />Bioinformatics and BioStatistics, Cancer Research UK, Lincoln’s Inn Fields, Holborn, London WC2A 3LY UK
| | - Stephan Gade
- />German Breast Group (GBG), Neu Isenburg, Germany
| | | | - Patrick Neven
- />Multidisciplinary Breast Centre and Gynaecological Oncology, KU Leuven, University of Leuven, Department of Oncology, B-3000 Leuven, Belgium
| | - Christos Sotiriou
- />Breast Cancer Translational Research Laboratory, Institut Jules Bordet, Brussels, Belgium
| | - Charles Swanton
- />Cancer Research UK, London Research Institute, Translational Cancer Therapeutics Laboratory, 44 Lincoln’s Inn Fields, London, WC2A 3LY UK
- />UCL Cancer Institute, Paul O’Gorman Building, University College London, 72 Huntley Street, London, WC1E 6DD UK
| | - Sherene Loi
- />University of Melbourne, Melbourne, VIC 3010 Australia
- />Division of Research and Cancer Medicine, Peter MacCallum Cancer Centre, East Melbourne, VIC 3002 Australia
| | - Terence P Speed
- />Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052 Australia
- />Department of Mathematics and Statistics, University of Melbourne, Melbourne, VIC 3010 Australia
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10
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Liu Y, Wang M, Feng H, Li A. Comprehensive study of tumour single nucleotide polymorphism array data reveals significant driver aberrations and disrupted signalling pathways in human hepatocellular cancer. IET Syst Biol 2014; 8:24-32. [PMID: 25014222 DOI: 10.1049/iet-syb.2013.0027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The authors describe an integrated method for analysing cancer driver aberrations and disrupted pathways by using tumour single nucleotide polymorphism (SNP) arrays. The authors new method adopts a novel statistical model to explicitly quantify the SNP signals, and therefore infers the genomic aberrations, including copy number alteration and loss of heterozygosity. Examination on the dilution series dataset shows that this method can correctly identify the genomic aberrations even with the existence of severe normal cell contamination in tumour sample. Furthermore, with the results of the aberration identification obtained from multiple tumour samples, a permutation-based approach is proposed for identifying the statistically significant driver aberrations, which are further incorporated with the known signalling pathways for pathway enrichment analysis. By applying the approach to 286 hepatocellular tumour samples, they successfully uncover numerous driver aberration regions across the cancer genome, for example, chromosomes 4p and 5q, which harbour many known hepatocellular cancer related genes such as alpha-fetoprotein (AFP) and ectodermal-neural cortex (ENC1). In addition, they identify nine disrupted pathways that are highly enriched by the driver aberrations, including the systemic lupus erythematosus pathway, the vascular endothelial growth factor (VEGF) signalling pathway and so on. These results support the feasibility and the utility of the proposed method on the characterisation of the cancer genome and the downstream analysis of the driver aberrations and the disrupted signalling pathways.
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Affiliation(s)
- Yuanning Liu
- School of Information Science and Technology, University of Science and Technology of China, Hefei AH230027, People's Republic of China
| | - Minghui Wang
- Centers for Biomedical Engineering, University of Science and Technology of China, Hefei AH230027, People's Republic of China
| | - Huanqing Feng
- School of Information Science and Technology, University of Science and Technology of China, Hefei AH230027, People's Republic of China
| | - Ao Li
- Centers for Biomedical Engineering, University of Science and Technology of China, Hefei AH230027, People's Republic of China.
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11
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Genome-wide identification of somatic aberrations from paired normal-tumor samples. PLoS One 2014; 9:e87212. [PMID: 24498045 PMCID: PMC3907544 DOI: 10.1371/journal.pone.0087212] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Accepted: 12/26/2013] [Indexed: 12/13/2022] Open
Abstract
Genomic copy number alteration and allelic imbalance are distinct features of cancer cells, and recent advances in the genotyping technology have greatly boosted the research in the cancer genome. However, the complicated nature of tumor usually hampers the dissection of the SNP arrays. In this study, we describe a bioinformatic tool, named GIANT, for genome-wide identification of somatic aberrations from paired normal-tumor samples measured with SNP arrays. By efficiently incorporating genotype information of matched normal sample, it accurately detects different types of aberrations in cancer genome, even for aneuploid tumor samples with severe normal cell contamination. Furthermore, it allows for discovery of recurrent aberrations with critical biological properties in tumorigenesis by using statistical significance test. We demonstrate the superior performance of the proposed method on various datasets including tumor replicate pairs, simulated SNP arrays and dilution series of normal-cancer cell lines. Results show that GIANT has the potential to detect the genomic aberration even when the cancer cell proportion is as low as 5∼10%. Application on a large number of paired tumor samples delivers a genome-wide profile of the statistical significance of the various aberrations, including amplification, deletion and LOH. We believe that GIANT represents a powerful bioinformatic tool for interpreting the complex genomic aberration, and thus assisting both academic study and the clinical treatment of cancer.
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12
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Tumor mutation burden forecasts outcome in ovarian cancer with BRCA1 or BRCA2 mutations. PLoS One 2013; 8:e80023. [PMID: 24265793 PMCID: PMC3827141 DOI: 10.1371/journal.pone.0080023] [Citation(s) in RCA: 115] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Accepted: 09/27/2013] [Indexed: 12/16/2022] Open
Abstract
Background Increased number of single nucleotide substitutions is seen in breast and ovarian cancer genomes carrying disease-associated mutations in BRCA1 or BRCA2. The significance of these genome-wide mutations is unknown. We hypothesize genome-wide mutation burden mirrors deficiencies in DNA repair and is associated with treatment outcome in ovarian cancer. Methods and Results The total number of synonymous and non-synonymous exome mutations (Nmut), and the presence of germline or somatic mutation in BRCA1 or BRCA2 (mBRCA) were extracted from whole-exome sequences of high-grade serous ovarian cancers from The Cancer Genome Atlas (TCGA). Cox regression and Kaplan-Meier methods were used to correlate Nmut with chemotherapy response and outcome. Higher Nmut correlated with a better response to chemotherapy after surgery. In patients with mBRCA-associated cancer, low Nmut was associated with shorter progression-free survival (PFS) and overall survival (OS), independent of other prognostic factors in multivariate analysis. Patients with mBRCA-associated cancers and a high Nmut had remarkably favorable PFS and OS. The association with survival was similar in cancers with either BRCA1 or BRCA2 mutations. In cancers with wild-type BRCA, tumor Nmut was associated with treatment response in patients with no residual disease after surgery. Conclusions Tumor Nmut was associated with treatment response and with both PFS and OS in patients with high-grade serous ovarian cancer carrying BRCA1 or BRCA2 mutations. In the TCGA cohort, low Nmut predicted resistance to chemotherapy, and for shorter PFS and OS, while high Nmut forecasts a remarkably favorable outcome in mBRCA-associated ovarian cancer. Our observations suggest that the total mutation burden coupled with BRCA1 or BRCA2 mutations in ovarian cancer is a genomic marker of prognosis and predictor of treatment response. This marker may reflect the degree of deficiency in BRCA-mediated pathways, or the extent of compensation for the deficiency by alternative mechanisms.
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13
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Martinez P, Birkbak NJ, Gerlinger M, McGranahan N, Burrell RA, Rowan AJ, Joshi T, Fisher R, Larkin J, Szallasi Z, Swanton C. Parallel evolution of tumour subclones mimics diversity between tumours. J Pathol 2013; 230:356-64. [PMID: 23716380 DOI: 10.1002/path.4214] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Revised: 05/17/2013] [Accepted: 05/22/2013] [Indexed: 01/17/2023]
Abstract
Intratumour heterogeneity (ITH) may foster tumour adaptation and compromise the efficacy of personalized medicine approaches. The scale of heterogeneity within a tumour (intratumour heterogeneity) relative to genetic differences between tumours (intertumour heterogeneity) is unknown. To address this, we obtained 48 biopsies from eight stage III and IV clear cell renal cell carcinomas (ccRCCs) and used DNA copy-number analyses to compare biopsies from the same tumour with 440 single tumour biopsies from the Cancer Genome Atlas (TCGA). Unsupervised hierarchical clustering of TCGA and multi-region ccRCC samples revealed segregation of samples from the same tumour into unrelated clusters; 25% of multi-region samples appeared more similar to unrelated samples than to any other sample originating from the same tumour. We found that the majority of recurrent DNA copy number driver aberrations in single biopsies were not present ubiquitously in late-stage ccRCCs and were likely to represent subclonal events acquired during tumour progression. Such heterogeneous subclonal genetic alterations within individual tumours may impair the identification of robust ccRCC molecular subtypes classified by distinct copy number alterations and clinical outcomes. The co-existence of distinct subclonal copy number events in different regions of individual tumours reflects the diversification of individual ccRCCs through multiple evolutionary routes and may contribute to tumour sampling bias and impact upon tumour progression and clinical outcome.
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14
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Ortiz-Estevez M, Aramburu A, Rubio A. Getting DNA copy numbers without control samples. Algorithms Mol Biol 2012; 7:19. [PMID: 22898240 PMCID: PMC3512512 DOI: 10.1186/1748-7188-7-19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2011] [Accepted: 06/15/2012] [Indexed: 01/30/2023] Open
Abstract
Background The selection of the reference to scale the data in a copy number analysis has paramount importance to achieve accurate estimates. Usually this reference is generated using control samples included in the study. However, these control samples are not always available and in these cases, an artificial reference must be created. A proper generation of this signal is crucial in terms of both noise and bias. We propose NSA (Normality Search Algorithm), a scaling method that works with and without control samples. It is based on the assumption that genomic regions enriched in SNPs with identical copy numbers in both alleles are likely to be normal. These normal regions are predicted for each sample individually and used to calculate the final reference signal. NSA can be applied to any CN data regardless the microarray technology and preprocessing method. It also finds an optimal weighting of the samples minimizing possible batch effects. Results Five human datasets (a subset of HapMap samples, Glioblastoma Multiforme (GBM), Ovarian, Prostate and Lung Cancer experiments) have been analyzed. It is shown that using only tumoral samples, NSA is able to remove the bias in the copy number estimation, to reduce the noise and therefore, to increase the ability to detect copy number aberrations (CNAs). These improvements allow NSA to also detect recurrent aberrations more accurately than other state of the art methods. Conclusions NSA provides a robust and accurate reference for scaling probe signals data to CN values without the need of control samples. It minimizes the problems of bias, noise and batch effects in the estimation of CNs. Therefore, NSA scaling approach helps to better detect recurrent CNAs than current methods. The automatic selection of references makes it useful to perform bulk analysis of many GEO or ArrayExpress experiments without the need of developing a parser to find the normal samples or possible batches within the data. The method is available in the open-source R package NSA, which is an add-on to the aroma.cn framework.
http://www.aroma-project.org/addons.
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