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Murali R, Selenica P, Brown DN, Cheetham RK, Chandramohan R, Claros NL, Bouvier N, Cheng DT, Soslow RA, Weigelt B, McCluggage WG. Somatic genetic alterations in synchronous and metachronous low-grade serous tumours and high-grade carcinomas of the adnexa. Histopathology 2019; 74:638-650. [PMID: 30565721 DOI: 10.1111/his.13796] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 11/17/2018] [Indexed: 12/22/2022]
Abstract
AIMS Low-grade serous carcinomas (LGSCs) and their precursors serous borderline tumours (SBTs) characteristically harbour mutations in BRAF, KRAS or NRAS but rarely in TP53, whereas high-grade serous carcinomas (HGSCs) are characterised by frequent TP53 mutations but rare BRAF, KRAS or NRAS mutations. In a small subset of cases, LGSCs and/or SBTs develop into high-grade tumours, including HGSCs and poorly differentiated carcinomas (PDCs). Here, we sought to define the repertoire of somatic genetic alterations in low-grade serous tumours and synchronous or metachronous high-grade adnexal carcinomas. METHODS AND RESULTS DNA extracted from five SBTs/LGSCs and synchronous or metachronous HGSCs/PDCs and matched normal tissue was subjected to massively parallel sequencing targeting all exons and selected non-coding regions of 341 cancer-related genes. The low-grade and high-grade tumours from a given case were related, and shared mutations and copy number alterations. Progression from low-grade to high-grade lesions was observed, and involved the acquisition of additional mutations and/or copy number alterations, or shifts from subclonal to clonal mutations. Only two (an HGSC and a PDC) of the five high-grade tumours investigated harboured TP53 mutations, whereas NRAS and KRAS hotspot mutations were seen in two HGSCs and one HGSC, respectively. CONCLUSIONS Our results suggest that progression from SBT to HGSC may take place in a subset of cases, and that at least some of the rare HGSCs lacking TP53 mutations may be derived from a low-grade serous precursor.
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Affiliation(s)
- Rajmohan Murali
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Pier Selenica
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David N Brown
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Raghu Chandramohan
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nidia L Claros
- Marie-Josee and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nancy Bouvier
- Marie-Josee and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Robert A Soslow
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Britta Weigelt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - W Glenn McCluggage
- Department of Pathology, Belfast Health and Social Care Trust, Belfast, UK
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2
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Quigley DA, Dang HX, Zhao SG, Lloyd P, Aggarwal R, Alumkal JJ, Foye A, Kothari V, Perry MD, Bailey AM, Playdle D, Barnard TJ, Zhang L, Zhang J, Youngren JF, Cieslik MP, Parolia A, Beer TM, Thomas G, Chi KN, Gleave M, Lack NA, Zoubeidi A, Reiter RE, Rettig MB, Witte O, Ryan CJ, Fong L, Kim W, Friedlander T, Chou J, Li H, Das R, Li H, Moussavi-Baygi R, Goodarzi H, Gilbert LA, Lara PN, Evans CP, Goldstein TC, Stuart JM, Tomlins SA, Spratt DE, Cheetham RK, Cheng DT, Farh K, Gehring JS, Hakenberg J, Liao A, Febbo PG, Shon J, Sickler B, Batzoglou S, Knudsen KE, He HH, Huang J, Wyatt AW, Dehm SM, Ashworth A, Chinnaiyan AM, Maher CA, Small EJ, Feng FY. Genomic Hallmarks and Structural Variation in Metastatic Prostate Cancer. Cell 2018; 174:758-769.e9. [PMID: 30033370 PMCID: PMC6425931 DOI: 10.1016/j.cell.2018.06.039] [Citation(s) in RCA: 370] [Impact Index Per Article: 61.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 06/11/2018] [Accepted: 06/21/2018] [Indexed: 01/01/2023]
Abstract
While mutations affecting protein-coding regions have been examined across many cancers, structural variants at the genome-wide level are still poorly defined. Through integrative deep whole-genome and -transcriptome analysis of 101 castration-resistant prostate cancer metastases (109X tumor/38X normal coverage), we identified structural variants altering critical regulators of tumorigenesis and progression not detectable by exome approaches. Notably, we observed amplification of an intergenic enhancer region 624 kb upstream of the androgen receptor (AR) in 81% of patients, correlating with increased AR expression. Tandem duplication hotspots also occur near MYC, in lncRNAs associated with post-translational MYC regulation. Classes of structural variations were linked to distinct DNA repair deficiencies, suggesting their etiology, including associations of CDK12 mutation with tandem duplications, TP53 inactivation with inverted rearrangements and chromothripsis, and BRCA2 inactivation with deletions. Together, these observations provide a comprehensive view of how structural variations affect critical regulators in metastatic prostate cancer.
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Affiliation(s)
- David A Quigley
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco (UCSF), San Francisco, CA, USA; Department of Epidemiology and Biostatistics, UCSF, San Francisco, CA, USA
| | - Ha X Dang
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO, USA; Department of Internal Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Shuang G Zhao
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
| | - Paul Lloyd
- Division of Hematology and Oncology, Department of Medicine, UCSF, San Francisco, CA, USA
| | - Rahul Aggarwal
- Division of Hematology and Oncology, Department of Medicine, UCSF, San Francisco, CA, USA
| | - Joshi J Alumkal
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA; Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR, USA
| | - Adam Foye
- Division of Hematology and Oncology, Department of Medicine, UCSF, San Francisco, CA, USA
| | - Vishal Kothari
- Department of Radiation Oncology, UCSF, San Francisco, CA, USA
| | - Marc D Perry
- Department of Radiation Oncology, UCSF, San Francisco, CA, USA
| | - Adina M Bailey
- Division of Hematology and Oncology, Department of Medicine, UCSF, San Francisco, CA, USA
| | - Denise Playdle
- Division of Hematology and Oncology, Department of Medicine, UCSF, San Francisco, CA, USA
| | | | - Li Zhang
- Division of Hematology and Oncology, Department of Medicine, UCSF, San Francisco, CA, USA
| | - Jin Zhang
- Cancer Biology Division, Department of Radiation Oncology, Washington University in St. Louis, MO USA; Institute for Informatics (I(2)), Washington University in St. Louis, MO
| | - Jack F Youngren
- Division of Hematology and Oncology, Department of Medicine, UCSF, San Francisco, CA, USA
| | - Marcin P Cieslik
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA; Michigan Center for Translational Pathology, Ann Arbor, MI, USA
| | - Abhijit Parolia
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA; Michigan Center for Translational Pathology, Ann Arbor, MI, USA
| | - Tomasz M Beer
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - George Thomas
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA; Department of Pathology, Oregon Health and Science University, Portland, OR, USA
| | - Kim N Chi
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada; British Columbia Cancer Agency, Vancouver Centre, Vancouver, BC, Canada
| | - Martin Gleave
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Nathan A Lack
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Amina Zoubeidi
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Robert E Reiter
- Jonsson Comprehensive Cancer Center, Department of Urology, UCLA, Los Angeles, CA, USA; VA Greater Los Angeles Healthcare System, Department of Medicine, Los Angeles, CA, USA
| | - Matthew B Rettig
- Jonsson Comprehensive Cancer Center, Department of Urology, UCLA, Los Angeles, CA, USA
| | - Owen Witte
- Department of Microbiology, Immunology, and Molecular Genetics at the David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Charles J Ryan
- Division of Hematology, Oncology, and Transplant, Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Lawrence Fong
- Division of Hematology and Oncology, Department of Medicine, UCSF, San Francisco, CA, USA
| | - Won Kim
- Division of Hematology and Oncology, Department of Medicine, UCSF, San Francisco, CA, USA
| | - Terence Friedlander
- Division of Hematology and Oncology, Department of Medicine, UCSF, San Francisco, CA, USA
| | - Jonathan Chou
- Division of Hematology and Oncology, Department of Medicine, UCSF, San Francisco, CA, USA
| | - Haolong Li
- Department of Radiation Oncology, UCSF, San Francisco, CA, USA
| | - Rajdeep Das
- Department of Radiation Oncology, UCSF, San Francisco, CA, USA
| | - Hui Li
- Department of Radiation Oncology, UCSF, San Francisco, CA, USA
| | | | - Hani Goodarzi
- Department of Biophysics and Biochemistry, UCSF, San Francisco, CA, USA; Department of Urology, UCSF, San Francisco, CA, USA
| | - Luke A Gilbert
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco (UCSF), San Francisco, CA, USA; Department of Urology, UCSF, San Francisco, CA, USA
| | - Primo N Lara
- Division of Hematology Oncology, Department of Internal Medicine, University of California Davis, Sacramento, CA, USA; Comprehensive Cancer Center, University of California Davis, Sacramento, CA, USA
| | - Christopher P Evans
- Comprehensive Cancer Center, University of California Davis, Sacramento, CA, USA; Department of Urologic Surgery, University of California Davis, Sacramento, CA, USA
| | - Theodore C Goldstein
- Division of Hematology and Oncology, Department of Medicine, UCSF, San Francisco, CA, USA; UC Sant Cruz Genome Institute and Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Joshua M Stuart
- UC Sant Cruz Genome Institute and Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Scott A Tomlins
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA; Department of Urology, University of Michigan, Ann Arbor, MI, USA
| | - Daniel E Spratt
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
| | | | | | | | | | | | | | | | | | | | | | - Karen E Knudsen
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Housheng H He
- Princess Margaret Cancer Centre/University Health Network, Toronto, ON, Canada
| | - Jiaoti Huang
- Department of Pathology, Duke University, Durham, NC, USA
| | - Alexander W Wyatt
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Scott M Dehm
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA; Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Alan Ashworth
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco (UCSF), San Francisco, CA, USA; Division of Hematology and Oncology, Department of Medicine, UCSF, San Francisco, CA, USA
| | - Arul M Chinnaiyan
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA; Michigan Center for Translational Pathology, Ann Arbor, MI, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA; Howard Hughes Medical Institute, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Urology, University of Michigan, Ann Arbor, MI, USA; Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI, USA.
| | - Christopher A Maher
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO, USA; Department of Internal Medicine, Washington University in St. Louis, St. Louis, MO, USA.
| | - Eric J Small
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco (UCSF), San Francisco, CA, USA; Division of Hematology and Oncology, Department of Medicine, UCSF, San Francisco, CA, USA.
| | - Felix Y Feng
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco (UCSF), San Francisco, CA, USA; Division of Hematology and Oncology, Department of Medicine, UCSF, San Francisco, CA, USA; Department of Radiation Oncology, UCSF, San Francisco, CA, USA; Department of Urology, UCSF, San Francisco, CA, USA.
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3
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Ross-Innes CS, Becq J, Warren A, Cheetham RK, Northen H, O'Donovan M, Malhotra S, di Pietro M, Ivakhno S, He M, Weaver JMJ, Lynch AG, Kingsbury Z, Ross M, Humphray S, Bentley D, Fitzgerald RC. Whole-genome sequencing provides new insights into the clonal architecture of Barrett's esophagus and esophageal adenocarcinoma. Nat Genet 2015; 47:1038-1046. [PMID: 26192915 PMCID: PMC4556068 DOI: 10.1038/ng.3357] [Citation(s) in RCA: 202] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 06/23/2015] [Indexed: 12/14/2022]
Abstract
The molecular genetic relationship between esophageal adenocarcinoma (EAC) and its precursor lesion, Barrett's esophagus, is poorly understood. Using whole-genome sequencing on 23 paired Barrett's esophagus and EAC samples, together with one in-depth Barrett's esophagus case study sampled over time and space, we have provided the following new insights: (i) Barrett's esophagus is polyclonal and highly mutated even in the absence of dysplasia; (ii) when cancer develops, copy number increases and heterogeneity persists such that the spectrum of mutations often shows surprisingly little overlap between EAC and adjacent Barrett's esophagus; and (iii) despite differences in specific coding mutations, the mutational context suggests a common causative insult underlying these two conditions. From a clinical perspective, the histopathological assessment of dysplasia appears to be a poor reflection of the molecular disarray within the Barrett's epithelium, and a molecular Cytosponge technique overcomes sampling bias and has the capacity to reflect the entire clonal architecture.
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Affiliation(s)
- Caryn S Ross-Innes
- Medical Research Council Cancer Unit, Hutchison/Medical Research Council Research Centre, University of Cambridge, Cambridge, UK
| | - Jennifer Becq
- Illumina, Chesterford Research Park, Little Chesterford, UK
| | - Andrew Warren
- Illumina, Chesterford Research Park, Little Chesterford, UK
| | | | - Helen Northen
- Illumina, Chesterford Research Park, Little Chesterford, UK
| | - Maria O'Donovan
- Department of Histopathology, Addenbrooke's Hospital, Cambridge, UK
| | - Shalini Malhotra
- Department of Histopathology, Addenbrooke's Hospital, Cambridge, UK
| | - Massimiliano di Pietro
- Medical Research Council Cancer Unit, Hutchison/Medical Research Council Research Centre, University of Cambridge, Cambridge, UK
| | - Sergii Ivakhno
- Illumina, Chesterford Research Park, Little Chesterford, UK
| | - Miao He
- Illumina, Chesterford Research Park, Little Chesterford, UK
| | - Jamie M J Weaver
- Medical Research Council Cancer Unit, Hutchison/Medical Research Council Research Centre, University of Cambridge, Cambridge, UK
| | - Andy G Lynch
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Zoya Kingsbury
- Illumina, Chesterford Research Park, Little Chesterford, UK
| | - Mark Ross
- Illumina, Chesterford Research Park, Little Chesterford, UK
| | - Sean Humphray
- Illumina, Chesterford Research Park, Little Chesterford, UK
| | - David Bentley
- Illumina, Chesterford Research Park, Little Chesterford, UK
| | - Rebecca C Fitzgerald
- Medical Research Council Cancer Unit, Hutchison/Medical Research Council Research Centre, University of Cambridge, Cambridge, UK
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4
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Chien J, Sicotte H, Fan JB, Humphray S, Cunningham JM, Kalli KR, Oberg AL, Hart SN, Li Y, Davila JI, Baheti S, Wang C, Dietmann S, Atkinson EJ, Asmann YW, Bell DA, Ota T, Tarabishy Y, Kuang R, Bibikova M, Cheetham RK, Grocock RJ, Swisher EM, Peden J, Bentley D, Kocher JPA, Kaufmann SH, Hartmann LC, Shridhar V, Goode EL. TP53 mutations, tetraploidy and homologous recombination repair defects in early stage high-grade serous ovarian cancer. Nucleic Acids Res 2015; 43:6945-58. [PMID: 25916844 PMCID: PMC4538798 DOI: 10.1093/nar/gkv111] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Revised: 01/23/2015] [Accepted: 02/02/2015] [Indexed: 12/30/2022] Open
Abstract
To determine early somatic changes in high-grade serous ovarian cancer (HGSOC), we performed whole genome sequencing on a rare collection of 16 low stage HGSOCs. The majority showed extensive structural alterations (one had an ultramutated profile), exhibited high levels of p53 immunoreactivity, and harboured a TP53 mutation, deletion or inactivation. BRCA1 and BRCA2 mutations were observed in two tumors, with nine showing evidence of a homologous recombination (HR) defect. Combined Analysis with The Cancer Genome Atlas (TCGA) indicated that low and late stage HGSOCs have similar mutation and copy number profiles. We also found evidence that deleterious TP53 mutations are the earliest events, followed by deletions or loss of heterozygosity (LOH) of chromosomes carrying TP53, BRCA1 or BRCA2. Inactivation of HR appears to be an early event, as 62.5% of tumours showed a LOH pattern suggestive of HR defects. Three tumours with the highest ploidy had little genome-wide LOH, yet one of these had a homozygous somatic frame-shift BRCA2 mutation, suggesting that some carcinomas begin as tetraploid then descend into diploidy accompanied by genome-wide LOH. Lastly, we found evidence that structural variants (SV) cluster in HGSOC, but are absent in one ultramutated tumor, providing insights into the pathogenesis of low stage HGSOC.
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Affiliation(s)
- Jeremy Chien
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Hugues Sicotte
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | | | - Sean Humphray
- Illumina Cambridge Ltd, Little Chesterford, Essex CB10 1, UK
| | - Julie M Cunningham
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | | | - Ann L Oberg
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Steven N Hart
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Ying Li
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Jaime I Davila
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Saurabh Baheti
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Chen Wang
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Sabine Dietmann
- Wellcome Trust, Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge CB2 1TN, UK
| | | | - Yan W Asmann
- Department of Health Sciences Research, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Debra A Bell
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Takayo Ota
- Department of Internal Medicine, Rinku General Medical Center, Izumi-sano, 598-8577, Japan
| | - Yaman Tarabishy
- Department of Pathology and Immunology, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Rui Kuang
- Department of Biomedical Informatics and Computational Biology, University of Minnesota, Minneapolis, MN 55414, USA
| | | | | | | | - Elizabeth M Swisher
- Department of Obstetrics and Gynecology, University of Washington, Seattle, WA 98109, USA
| | - John Peden
- Illumina Cambridge Ltd, Little Chesterford, Essex CB10 1, UK
| | - David Bentley
- Illumina Cambridge Ltd, Little Chesterford, Essex CB10 1, UK
| | | | | | - Lynn C Hartmann
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Viji Shridhar
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Ellen L Goode
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
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Leonard B, Hart SN, Burns MB, Carpenter MA, Temiz NA, Rathore A, Vogel RI, Nikas JB, Law EK, Brown WL, Li Y, Zhang Y, Maurer MJ, Oberg AL, Cunningham JM, Shridhar V, Bell DA, April C, Bentley D, Bibikova M, Cheetham RK, Fan JB, Grocock R, Humphray S, Kingsbury Z, Peden J, Chien J, Swisher EM, Hartmann LC, Kalli KR, Goode EL, Sicotte H, Kaufmann SH, Harris RS. APOBEC3B upregulation and genomic mutation patterns in serous ovarian carcinoma. Cancer Res 2013; 73:7222-31. [PMID: 24154874 DOI: 10.1158/0008-5472.can-13-1753] [Citation(s) in RCA: 129] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Ovarian cancer is a clinically and molecularly heterogeneous disease. The driving forces behind this variability are unknown. Here, we report wide variation in the expression of the DNA cytosine deaminase APOBEC3B, with elevated expression in the majority of ovarian cancer cell lines (three SDs above the mean of normal ovarian surface epithelial cells) and high-grade primary ovarian cancers. APOBEC3B is active in the nucleus of several ovarian cancer cell lines and elicits a biochemical preference for deamination of cytosines in 5'-TC dinucleotides. Importantly, examination of whole-genome sequence from 16 ovarian cancers reveals that APOBEC3B expression correlates with total mutation load as well as elevated levels of transversion mutations. In particular, high APOBEC3B expression correlates with C-to-A and C-to-G transversion mutations within 5'-TC dinucleotide motifs in early-stage high-grade serous ovarian cancer genomes, suggesting that APOBEC3B-catalyzed genomic uracil lesions are further processed by downstream DNA "repair" enzymes including error-prone translesion polymerases. These data identify a potential role for APOBEC3B in serous ovarian cancer genomic instability.
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Affiliation(s)
- Brandon Leonard
- Authors' Affiliations: Biochemistry, Molecular Biology and Biophysics Department; Masonic Cancer Center, University of Minnesota, Minneapolis; Division of Biomedical Statistics and Informatics, Department of Health Sciences Research; Medical Genome Facility and Department of Laboratory Medicine and Pathology; Department of Laboratory Medicine and Pathology; Division of Medical Oncology, Department of Oncology; Division of Epidemiology, Department of Health Sciences Research; Division of Oncology Research, Department of Oncology; Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic; Women's Cancer Program, Mayo Clinic Cancer Center, Rochester, Minnesota; Department of Cancer Biology, University of Kansas, Kansas City, Kansas; Department of Obstetrics & Gynecology, University of Washington School of Medicine, Seattle, Washington; and Illumina Cambridge Ltd, Chesterford Research Park, Little Chesterford, Cambridge, United Kingdom
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6
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Saunders CT, Wong WSW, Swamy S, Becq J, Murray LJ, Cheetham RK. Strelka: accurate somatic small-variant calling from sequenced tumor-normal sample pairs. ACTA ACUST UNITED AC 2012; 28:1811-7. [PMID: 22581179 DOI: 10.1093/bioinformatics/bts271] [Citation(s) in RCA: 1115] [Impact Index Per Article: 92.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
MOTIVATION Whole genome and exome sequencing of matched tumor-normal sample pairs is becoming routine in cancer research. The consequent increased demand for somatic variant analysis of paired samples requires methods specialized to model this problem so as to sensitively call variants at any practical level of tumor impurity. RESULTS We describe Strelka, a method for somatic SNV and small indel detection from sequencing data of matched tumor-normal samples. The method uses a novel Bayesian approach which represents continuous allele frequencies for both tumor and normal samples, while leveraging the expected genotype structure of the normal. This is achieved by representing the normal sample as a mixture of germline variation with noise, and representing the tumor sample as a mixture of the normal sample with somatic variation. A natural consequence of the model structure is that sensitivity can be maintained at high tumor impurity without requiring purity estimates. We demonstrate that the method has superior accuracy and sensitivity on impure samples compared with approaches based on either diploid genotype likelihoods or general allele-frequency tests. AVAILABILITY The Strelka workflow source code is available at ftp://strelka@ftp.illumina.com/. CONTACT csaunders@illumina.com
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7
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Murchison EP, Schulz-Trieglaff OB, Ning Z, Alexandrov LB, Bauer MJ, Fu B, Hims M, Ding Z, Ivakhno S, Stewart C, Ng BL, Wong W, Aken B, White S, Alsop A, Becq J, Bignell GR, Cheetham RK, Cheng W, Connor TR, Cox AJ, Feng ZP, Gu Y, Grocock RJ, Harris SR, Khrebtukova I, Kingsbury Z, Kowarsky M, Kreiss A, Luo S, Marshall J, McBride DJ, Murray L, Pearse AM, Raine K, Rasolonjatovo I, Shaw R, Tedder P, Tregidgo C, Vilella AJ, Wedge DC, Woods GM, Gormley N, Humphray S, Schroth G, Smith G, Hall K, Searle SMJ, Carter NP, Papenfuss AT, Futreal PA, Campbell PJ, Yang F, Bentley DR, Evers DJ, Stratton MR. Genome sequencing and analysis of the Tasmanian devil and its transmissible cancer. Cell 2012; 148:780-91. [PMID: 22341448 PMCID: PMC3281993 DOI: 10.1016/j.cell.2011.11.065] [Citation(s) in RCA: 238] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2011] [Revised: 11/03/2011] [Accepted: 11/29/2011] [Indexed: 01/23/2023]
Abstract
The Tasmanian devil (Sarcophilus harrisii), the largest marsupial carnivore, is endangered due to a transmissible facial cancer spread by direct transfer of living cancer cells through biting. Here we describe the sequencing, assembly, and annotation of the Tasmanian devil genome and whole-genome sequences for two geographically distant subclones of the cancer. Genomic analysis suggests that the cancer first arose from a female Tasmanian devil and that the clone has subsequently genetically diverged during its spread across Tasmania. The devil cancer genome contains more than 17,000 somatic base substitution mutations and bears the imprint of a distinct mutational process. Genotyping of somatic mutations in 104 geographically and temporally distributed Tasmanian devil tumors reveals the pattern of evolution and spread of this parasitic clonal lineage, with evidence of a selective sweep in one geographical area and persistence of parallel lineages in other populations. PaperClip
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8
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Ivakhno S, Royce T, Cox AJ, Evers DJ, Cheetham RK, Tavaré S. CNAseg—a novel framework for identification of copy number changes in cancer from second-generation sequencing data. Bioinformatics 2010; 26:3051-8. [DOI: 10.1093/bioinformatics/btq587] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
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Pleasance ED, Cheetham RK, Stephens PJ, McBride DJ, Humphray SJ, Greenman CD, Varela I, Lin ML, Ordóñez GR, Bignell GR, Ye K, Alipaz J, Bauer MJ, Beare D, Butler A, Carter RJ, Chen L, Cox AJ, Edkins S, Kokko-Gonzales PI, Gormley NA, Grocock RJ, Haudenschild CD, Hims MM, James T, Jia M, Kingsbury Z, Leroy C, Marshall J, Menzies A, Mudie LJ, Ning Z, Royce T, Schulz-Trieglaff OB, Spiridou A, Stebbings LA, Szajkowski L, Teague J, Williamson D, Chin L, Ross MT, Campbell PJ, Bentley DR, Futreal PA, Stratton MR. A comprehensive catalogue of somatic mutations from a human cancer genome. Nature 2009; 463:191-6. [PMID: 20016485 DOI: 10.1038/nature08658] [Citation(s) in RCA: 1213] [Impact Index Per Article: 80.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2009] [Accepted: 11/04/2009] [Indexed: 02/07/2023]
Abstract
All cancers carry somatic mutations. A subset of these somatic alterations, termed driver mutations, confer selective growth advantage and are implicated in cancer development, whereas the remainder are passengers. Here we have sequenced the genomes of a malignant melanoma and a lymphoblastoid cell line from the same person, providing the first comprehensive catalogue of somatic mutations from an individual cancer. The catalogue provides remarkable insights into the forces that have shaped this cancer genome. The dominant mutational signature reflects DNA damage due to ultraviolet light exposure, a known risk factor for malignant melanoma, whereas the uneven distribution of mutations across the genome, with a lower prevalence in gene footprints, indicates that DNA repair has been preferentially deployed towards transcribed regions. The results illustrate the power of a cancer genome sequence to reveal traces of the DNA damage, repair, mutation and selection processes that were operative years before the cancer became symptomatic.
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Niemann S, Köser CU, Gagneux S, Plinke C, Homolka S, Bignell H, Carter RJ, Cheetham RK, Cox A, Gormley NA, Kokko-Gonzales P, Murray LJ, Rigatti R, Smith VP, Arends FPM, Cox HS, Smith G, Archer JAC. Genomic diversity among drug sensitive and multidrug resistant isolates of Mycobacterium tuberculosis with identical DNA fingerprints. PLoS One 2009; 4:e7407. [PMID: 19823582 PMCID: PMC2756628 DOI: 10.1371/journal.pone.0007407] [Citation(s) in RCA: 126] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2009] [Accepted: 09/04/2009] [Indexed: 12/19/2022] Open
Abstract
Background Mycobacterium tuberculosis complex (MTBC), the causative agent of tuberculosis (TB), is characterized by low sequence diversity making this bacterium one of the classical examples of a genetically monomorphic pathogen. Because of this limited DNA sequence variation, routine genotyping of clinical MTBC isolates for epidemiological purposes relies on highly discriminatory DNA fingerprinting methods based on mobile and repetitive genetic elements. According to the standard view, isolates exhibiting the same fingerprinting pattern are considered direct progeny of the same bacterial clone, and most likely reflect ongoing transmission or disease relapse within individual patients. Methodology/Principal Findings Here we further investigated this assumption and used massively parallel whole-genome sequencing to compare one drug-susceptible (K-1) and one multidrug resistant (MDR) isolate (K-2) of a rapidly spreading M. tuberculosis Beijing genotype clone from a high incidence region (Karakalpakstan, Uzbekistan). Both isolates shared the same IS6110 RFLP pattern and the same allele at 23 out of 24 MIRU-VNTR loci. We generated 23.9 million (K-1) and 33.0 million (K-2) paired 50 bp purity filtered reads corresponding to a mean coverage of 483.5 fold and 656.1 fold respectively. Compared with the laboratory strain H37Rv both Beijing isolates shared 1,209 SNPs. The two Beijing isolates differed by 130 SNPs and one large deletion. The susceptible isolate had 55 specific SNPs, while the MDR variant had 75 specific SNPs, including the five known resistance-conferring mutations. Conclusions Our results suggest that M. tuberculosis isolates exhibiting identical DNA fingerprinting patterns can harbour substantial genomic diversity. Because this heterogeneity is not captured by traditional genotyping of MTBC, some aspects of the transmission dynamics of tuberculosis could be missed or misinterpreted. Furthermore, a valid differentiation between disease relapse and exogenous reinfection might be impossible using standard genotyping tools if the overall diversity of circulating clones is limited. These findings have important implications for clinical trials of new anti-tuberculosis drugs.
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Affiliation(s)
- Stefan Niemann
- Molecular Mycobacteriology, Research Center Borstel, Borstel, Germany.
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