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Butler M, Konigshofer Y, Clement O, Liu L, Zhao C, Arcila ME, Zehir A, Kohle R, Magliocco AM, Gligorich K, Gloeckner C, Lovejoy AF, Hantash F, Sougnez C, Lennon N, Anekella B, Garlick R. Tumor mutational burden reference materials for assay standardization. J Clin Oncol 2019. [DOI: 10.1200/jco.2019.37.15_suppl.e14746] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
e14746 Background: Next Generation Sequencing based assays are designed to detect genomic aberrations in a limited number of target regions. However, there is a need for accurate measurement of tumor mutational burden (TMB) as low as 4 to as high as 50. As TMB assessment is added to various targeted panels, consistent results between panels are required to advance the broad use of this biomarker. Properly designed reference materials aid measurement standardization and are required to demonstrate assay concordance. We developed reference materials that vary in TMB score, tumor content 5-50% and are prepared in FFPE format. Methods: Seven lung and two breast tumor cell lines as well as matched “normal” lymphoblastoid cell lines were expanded in cell culture. Genomic DNA (gDNA) from each cell line was extracted. Tumor/normal mixes were made by mixing DNA and by embedding cells in FFPE blocks. Whole exome sequencing (WES) results were obtained using Agilent SureSelectXT for library construction and an Illumina Novaseq for sequencing. The Friends of Cancer Research TMB consensus method for analyzing WES data was used to filter variants and calculate TMB scores. Results: The cell lines were grown at large scale to produce extractable gDNA. 100% gDNA tumor, 30% gDNA tumor mixes and 30% FFPE cell line mixes were prepared. Preliminary results show that a clinically-relevant range of TMB values ranging from 4 to 35 mutations per million bases. The several thousand mutations that were observed across the lines were found in a variety of genes, which may explain why TMB in targeted panels is influenced by the specific target regions. Also, the initial results show that 30% cell line mixes showed similar TMB results to 100% gDNA. Conclusions: Our approach with wide ranging TMB values as tumor normal mixes is flexible and can be used to test different tumors and assays. For this study we established WES as the ground truth measurement for comparison to other assay formats and obtained comparison data from other panels. This approach also allows laboratories to test additional variables including formalin fixation, sample extraction, gene panel size, target regions, sequencing depth, filtering and limits of detection.
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Affiliation(s)
| | | | | | | | | | | | - Ahmet Zehir
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
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2
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Barretina J, Caponigro G, Stransky N, Venkatesan K, Margolin AA, Kim S, Wilson CJ, Lehár J, Kryukov GV, Sonkin D, Reddy A, Liu M, Murray L, Berger MF, Monahan JE, Morais P, Meltzer J, Korejwa A, Jané-Valbuena J, Mapa FA, Thibault J, Bric-Furlong E, Raman P, Shipway A, Engels IH, Cheng J, Yu GK, Yu J, Aspesi P, de Silva M, Jagtap K, Jones MD, Wang L, Hatton C, Palescandolo E, Gupta S, Mahan S, Sougnez C, Onofrio RC, Liefeld T, MacConaill L, Winckler W, Reich M, Li N, Mesirov JP, Gabriel SB, Getz G, Ardlie K, Chan V, Myer VE, Weber BL, Porter J, Warmuth M, Finan P, Harris JL, Meyerson M, Golub TR, Morrissey MP, Sellers WR, Schlegel R, Garraway LA. Addendum: The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature 2018; 565:E5-E6. [PMID: 30559381 DOI: 10.1038/s41586-018-0722-x] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jordi Barretina
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, 02115, USA.,Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, 02115, USA.,Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - Giordano Caponigro
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - Nicolas Stransky
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA
| | - Kavitha Venkatesan
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - Adam A Margolin
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA.,Sage Bionetworks, 1100 Fairview Ave. N., Seattle, Washington, 98109, USA
| | - Sungjoon Kim
- Genomics Institute of the Novartis Research Foundation, San Diego, California, 92121, USA
| | - Christopher J Wilson
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - Joseph Lehár
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - Gregory V Kryukov
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA
| | - Dmitriy Sonkin
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - Anupama Reddy
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - Manway Liu
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - Lauren Murray
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA
| | - Michael F Berger
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA.,Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, New York, 10065, USA
| | - John E Monahan
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - Paula Morais
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA
| | - Jodi Meltzer
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - Adam Korejwa
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA
| | - Judit Jané-Valbuena
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Felipa A Mapa
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - Joseph Thibault
- Genomics Institute of the Novartis Research Foundation, San Diego, California, 92121, USA
| | - Eva Bric-Furlong
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - Pichai Raman
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - Aaron Shipway
- Genomics Institute of the Novartis Research Foundation, San Diego, California, 92121, USA
| | - Ingo H Engels
- Genomics Institute of the Novartis Research Foundation, San Diego, California, 92121, USA
| | - Jill Cheng
- Novartis Institutes for Biomedical Research, Emeryville, California, 94608, USA
| | - Guoying K Yu
- Novartis Institutes for Biomedical Research, Emeryville, California, 94608, USA
| | - Jianjun Yu
- Novartis Institutes for Biomedical Research, Emeryville, California, 94608, USA
| | - Peter Aspesi
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - Melanie de Silva
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - Kalpana Jagtap
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - Michael D Jones
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - Li Wang
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - Charles Hatton
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Emanuele Palescandolo
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Supriya Gupta
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA
| | - Scott Mahan
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA
| | - Carrie Sougnez
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA
| | - Robert C Onofrio
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA
| | - Ted Liefeld
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA
| | - Laura MacConaill
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Wendy Winckler
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA
| | - Michael Reich
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA
| | - Nanxin Li
- Genomics Institute of the Novartis Research Foundation, San Diego, California, 92121, USA
| | - Jill P Mesirov
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA
| | - Stacey B Gabriel
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA
| | - Gad Getz
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA
| | - Kristin Ardlie
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA
| | - Vivien Chan
- Novartis Institutes for Biomedical Research, Emeryville, California, 94608, USA
| | - Vic E Myer
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - Barbara L Weber
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - Jeff Porter
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - Markus Warmuth
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - Peter Finan
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - Jennifer L Harris
- Genomics Institute of the Novartis Research Foundation, San Diego, California, 92121, USA
| | - Matthew Meyerson
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, 02115, USA.,Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Todd R Golub
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA.,Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, 02115, USA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, 02115, USA.,Howard Hughes Medical Institute, Chevy Chase, Maryland, 20815, USA
| | - Michael P Morrissey
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - William R Sellers
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - Robert Schlegel
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA.
| | - Levi A Garraway
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA. .,Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, 02115, USA. .,Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, 02115, USA.
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3
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Wagle N, Helvie K, Lloyd MR, Marini L, Waks AG, Cohen O, Oh C, Sougnez C, Oliver N, Quartey Q, Rotem A, Shah P, Lindeman NI, Krop IE, Garraway LA, Winer EP, Lin NU. A cancer precision medicine platform for multiple simultaneous genomic assays from metastatic biopsies (bx) in ER+ metastatic breast cancer. J Clin Oncol 2016. [DOI: 10.1200/jco.2016.34.15_suppl.11513] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Asaf Rotem
- Dana-Farber Cancer Institute, Boston, MA
| | - Parin Shah
- Dana-Farber Cancer Institute, Boston, MA
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4
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Burger JA, Landau DA, Taylor-Weiner A, Bozic I, Zhang H, Sarosiek K, Wang L, Stewart C, Fan J, Hoellenriegel J, Sivina M, Dubuc AM, Fraser C, Han Y, Li S, Livak KJ, Zou L, Wan Y, Konoplev S, Sougnez C, Brown JR, Abruzzo LV, Carter SL, Keating MJ, Davids MS, Wierda WG, Cibulskis K, Zenz T, Werner L, Cin PD, Kharchencko P, Neuberg D, Kantarjian H, Lander E, Gabriel S, O'Brien S, Letai A, Weitz DA, Nowak MA, Getz G, Wu CJ. Clonal evolution in patients with chronic lymphocytic leukaemia developing resistance to BTK inhibition. Nat Commun 2016; 7:11589. [PMID: 27199251 PMCID: PMC4876453 DOI: 10.1038/ncomms11589] [Citation(s) in RCA: 254] [Impact Index Per Article: 31.8] [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: 09/16/2015] [Accepted: 04/12/2016] [Indexed: 02/06/2023] Open
Abstract
Resistance to the Bruton's tyrosine kinase (BTK) inhibitor ibrutinib has been attributed solely to mutations in BTK and related pathway molecules. Using whole-exome and deep-targeted sequencing, we dissect evolution of ibrutinib resistance in serial samples from five chronic lymphocytic leukaemia patients. In two patients, we detect BTK-C481S mutation or multiple PLCG2 mutations. The other three patients exhibit an expansion of clones harbouring del(8p) with additional driver mutations (EP300, MLL2 and EIF2A), with one patient developing trans-differentiation into CD19-negative histiocytic sarcoma. Using droplet-microfluidic technology and growth kinetic analyses, we demonstrate the presence of ibrutinib-resistant subclones and estimate subclone size before treatment initiation. Haploinsufficiency of TRAIL-R, a consequence of del(8p), results in TRAIL insensitivity, which may contribute to ibrutinib resistance. These findings demonstrate that the ibrutinib therapy favours selection and expansion of rare subclones already present before ibrutinib treatment, and provide insight into the heterogeneity of genetic changes associated with ibrutinib resistance.
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MESH Headings
- Adenine/analogs & derivatives
- Adult
- Agammaglobulinaemia Tyrosine Kinase
- Aged, 80 and over
- Apoptosis
- Cell Transdifferentiation
- Clonal Evolution
- Drug Resistance, Neoplasm/genetics
- Female
- Histiocytic Sarcoma/etiology
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/drug therapy
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Male
- Middle Aged
- Mutation
- Neoplasm Recurrence, Local/genetics
- Piperidines
- Protein-Tyrosine Kinases/antagonists & inhibitors
- Protein-Tyrosine Kinases/genetics
- Pyrazoles/pharmacology
- Pyrazoles/therapeutic use
- Pyrimidines/pharmacology
- Pyrimidines/therapeutic use
- Selection, Genetic
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Affiliation(s)
- Jan A. Burger
- Department of Leukemia, MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Dan A. Landau
- Broad Institute, Cambridge, Massachusetts 02142, USA
- Department of Medicine, Weill Cornell Medicine, New York, New York 10065, USA
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York 10065, USA
- New York Genome Center, New York, New York 10013, USA
| | | | - Ivana Bozic
- Department of Mathematics, Program for Evolutionary Dynamics, Harvard University, Cambridge, Massachusetts 02138, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Huidan Zhang
- Department of Physics, School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, USA
- Department of Cell Biology, Key Laboratory of Cell Biology, Ministry of Public Health, China Medical University, Shenyang 110001, China
- Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University, Shenyang 110001, China
| | - Kristopher Sarosiek
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Lili Wang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Chip Stewart
- Broad Institute, Cambridge, Massachusetts 02142, USA
| | - Jean Fan
- Center for Biomedical Informatics, Harvard Medical School, Boston Massachusetts 02115, USA
| | - Julia Hoellenriegel
- Department of Leukemia, MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Mariela Sivina
- Department of Leukemia, MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Adrian M. Dubuc
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Cameron Fraser
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Yulong Han
- Bioinspired Engineering and Biomechanics Center, Xi'an Jiaotong University, Xi'an 710049, China
| | - Shuqiang Li
- Fluidigm Corporation, South San Francisco, California 94080, USA
| | - Kenneth J. Livak
- Fluidigm Corporation, South San Francisco, California 94080, USA
| | - Lihua Zou
- Broad Institute, Cambridge, Massachusetts 02142, USA
| | - Youzhong Wan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Sergej Konoplev
- Department of Hematopathology, MD Anderson Cancer Center, Houston, Texas 77030, USA
| | | | - Jennifer R. Brown
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Lynne V. Abruzzo
- Department of Hematopathology, MD Anderson Cancer Center, Houston, Texas 77030, USA
| | | | - Michael J. Keating
- Department of Leukemia, MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Matthew S. Davids
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - William G. Wierda
- Department of Leukemia, MD Anderson Cancer Center, Houston, Texas 77030, USA
| | | | - Thorsten Zenz
- National Center for Tumors and German Cancer Research Center (DKFZ), 69121 Heidelberg, Germany
| | - Lillian Werner
- Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Paola Dal Cin
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Peter Kharchencko
- Center for Biomedical Informatics, Harvard Medical School, Boston Massachusetts 02115, USA
| | - Donna Neuberg
- Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Hagop Kantarjian
- Department of Leukemia, MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Eric Lander
- Broad Institute, Cambridge, Massachusetts 02142, USA
| | | | - Susan O'Brien
- Department of Leukemia, MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Anthony Letai
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - David A. Weitz
- Department of Physics, School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Martin A. Nowak
- Department of Mathematics, Program for Evolutionary Dynamics, Harvard University, Cambridge, Massachusetts 02138, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Gad Getz
- Broad Institute, Cambridge, Massachusetts 02142, USA
| | - Catherine J. Wu
- Broad Institute, Cambridge, Massachusetts 02142, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
- Department of Medicine, Brigham & Women's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA
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5
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Shukla SA, Rooney MS, Rajasagi M, Tiao G, Dixon PM, Lawrence MS, Stevens J, Lane WJ, Dellagatta JL, Steelman S, Sougnez C, Cibulskis K, Kiezun A, Hacohen N, Brusic V, Wu CJ, Getz G. Comprehensive analysis of cancer-associated somatic mutations in class I HLA genes. Nat Biotechnol 2016; 33:1152-8. [PMID: 26372948 PMCID: PMC4747795 DOI: 10.1038/nbt.3344] [Citation(s) in RCA: 465] [Impact Index Per Article: 58.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 08/12/2015] [Indexed: 12/17/2022]
Abstract
Detection of somatic mutations in HLA genes using whole-exome sequencing (WES) is hampered by the high polymorphism of the HLA loci, which prevents alignment of sequencing reads to the human reference genome. We describe a computational pipeline that enables accurate inference of germline alleles of class I HLA-A, -B and -C genes and subsequent detection of mutations in these genes using the inferred alleles as a reference. Analysis of WES data from 7,930 pairs of tumor and healthy tissue from the same patient revealed 298 non-silent HLA mutations in tumors from 266 patients. These 298 mutations are enriched for likely functional mutations, including putative loss-of-function events. Recurrence of mutations suggested that these ‘hotspot’ sites were positively selected. Cancers with recurrent somatic HLA mutations were associated with upregulation of signatures of cytolytic activity characteristic of tumor infiltration by effector lymphocytes, supporting immune evasion by altered HLA function as a contributory mechanism in cancer.
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6
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Van Allen EM, Lui VWY, Egloff AM, Goetz EM, Li H, Johnson JT, Duvvuri U, Bauman JE, Stransky N, Zeng Y, Gilbert BR, Pendleton KP, Wang L, Chiosea S, Sougnez C, Wagle N, Zhang F, Du Y, Close D, Johnston PA, McKenna A, Carter SL, Golub TR, Getz G, Mills GB, Garraway LA, Grandis JR. Genomic Correlate of Exceptional Erlotinib Response in Head and Neck Squamous Cell Carcinoma. JAMA Oncol 2016; 1:238-44. [PMID: 26181029 DOI: 10.1001/jamaoncol.2015.34] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
IMPORTANCE Randomized clinical trials demonstrate no benefit for epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors in unselected patients with head and neck squamous cell carcinoma (HNSCC). However, a patient with stage IVA HNSCC received 13 days of neoadjuvant erlotinib and experienced a near-complete histologic response. OBJECTIVE To determine a mechanism of exceptional response to erlotinib therapy in HNSCC. DESIGN, SETTING, AND PARTICIPANTS Single patient with locally advanced HNSCC who received erlotinib monotherapy in a window-of-opportunity clinical trial (patients scheduled to undergo primary cancer surgery are treated briefly with an investigational agent). Whole-exome sequencing of pretreatment tumor and germline patient samples was performed at a quaternary care academic medical center, and a candidate somatic variant was experimentally investigated for mediating erlotinib response. INTERVENTION A brief course of erlotinib monotherapy followed by surgical resection. MAIN OUTCOMES AND MEASURES Identification of pretreatment tumor somatic alterations that may contribute to the exceptional response to erlotinib. Hypotheses were formulated regarding enhanced erlotinib response in preclinical models harboring the patient tumor somatic variant MAPK1 E322K following the identification of tumor somatic variants. RESULTS No EGFR alterations were observed in the pretreatment tumor DNA. Paradoxically, the tumor harbored an activating MAPK1 E322K mutation (allelic fraction 0.13), which predicts ERK activation and erlotinib resistance in EGFR-mutant lung cancer. The HNSCC cells with MAPK1 E322K exhibited enhanced EGFR phosphorylation and erlotinib sensitivity compared with wild-type MAPK1 cells. CONCLUSIONS AND RELEVANCE Selective erlotinib use in HNSCC may be informed by precision oncology approaches.
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Affiliation(s)
- Eliezer M Van Allen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts2Cancer Program, Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge
| | - Vivian W Y Lui
- Department of Pharmacology and Pharmacy, Li-Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong4Department of Biochemistry, Li-Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong5Department of Otolaryngology, University of Pittsb
| | - Ann Marie Egloff
- Department of Otolaryngology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania6Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Eva M Goetz
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Hua Li
- Department of Otolaryngology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Jonas T Johnson
- Department of Otolaryngology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Umamaheswar Duvvuri
- Department of Otolaryngology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Julie E Bauman
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | | | - Yan Zeng
- Department of Otolaryngology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Breean R Gilbert
- Department of Otolaryngology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Kelsey P Pendleton
- Department of Otolaryngology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Lin Wang
- Department of Otolaryngology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Simion Chiosea
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Carrie Sougnez
- Cancer Program, Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge
| | - Nikhil Wagle
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts2Cancer Program, Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge
| | - Fan Zhang
- Department of Systems Biology, University of Texas MD Anderson Cancer Center, Houston
| | - Yu Du
- Department of Otolaryngology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - David Close
- Department of Pharmaceutical Sciences, University of Pittsburgh School of Pharmacy, Pittsburgh, Pennsylvania
| | - Paul A Johnston
- Department of Pharmaceutical Sciences, University of Pittsburgh School of Pharmacy, Pittsburgh, Pennsylvania
| | - Aaron McKenna
- Department of Genome Sciences, University of Washington, Seattle
| | - Scott L Carter
- Cancer Program, Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge
| | - Todd R Golub
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts2Cancer Program, Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge
| | - Gad Getz
- Cancer Program, Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge13Department of Pathology, Massachusetts General Hospital, Boston
| | - Gordon B Mills
- Department of Systems Biology, University of Texas MD Anderson Cancer Center, Houston
| | - Levi A Garraway
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts2Cancer Program, Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge
| | - Jennifer R Grandis
- Department of Otolaryngology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania14Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
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7
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Linehan WM, Spellman PT, Ricketts CJ, Creighton CJ, Fei SS, Davis C, Wheeler DA, Murray BA, Schmidt L, Vocke CD, Peto M, Al Mamun AAM, Shinbrot E, Sethi A, Brooks S, Rathmell WK, Brooks AN, Hoadley KA, Robertson AG, Brooks D, Bowlby R, Sadeghi S, Shen H, Weisenberger DJ, Bootwalla M, Baylin SB, Laird PW, Cherniack AD, Saksena G, Haake S, Li J, Liang H, Lu Y, Mills GB, Akbani R, Leiserson MD, Raphael BJ, Anur P, Bottaro D, Albiges L, Barnabas N, Choueiri TK, Czerniak B, Godwin AK, Hakimi AA, Ho T, Hsieh J, Ittmann M, Kim WY, Krishnan B, Merino MJ, Mills Shaw KR, Reuter VE, Reznik E, Shelley CS, Shuch B, Signoretti S, Srinivasan R, Tamboli P, Thomas G, Tickoo S, Burnett K, Crain D, Gardner J, Lau K, Mallery D, Morris S, Paulauskis JD, Penny RJ, Shelton C, Shelton WT, Sherman M, Thompson E, Yena P, Avedon MT, Bowen J, Gastier-Foster JM, Gerken M, Leraas KM, Lichtenberg TM, Ramirez NC, Santos T, Wise L, Zmuda E, Demchok JA, Felau I, Hutter CM, Sheth M, Sofia HJ, Tarnuzzer R, Wang Z, Yang L, Zenklusen JC, Zhang J(J, Ayala B, Baboud J, Chudamani S, Liu J, Lolla L, Naresh R, Pihl T, Sun Q, Wan Y, Wu Y, Ally A, Balasundaram M, Balu S, Beroukhim R, Bodenheimer T, Buhay C, Butterfield YS, Carlsen R, Carter SL, Chao H, Chuah E, Clarke A, Covington KR, Dahdouli M, Dewal N, Dhalla N, Doddapaneni H, Drummond J, Gabriel SB, Gibbs RA, Guin R, Hale W, Hawes A, Hayes DN, Holt RA, Hoyle AP, Jefferys SR, Jones SJ, Jones CD, Kalra D, Kovar C, Lewis L, Li J, Ma Y, Marra MA, Mayo M, Meng S, Meyerson M, Mieczkowski PA, Moore RA, Morton D, Mose LE, Mungall AJ, Muzny D, Parker JS, Perou CM, Roach J, Schein JE, Schumacher SE, Shi Y, Simons JV, Sipahimalani P, Skelly T, Soloway MG, Sougnez C, Tam A, Tan D, Thiessen N, Veluvolu U, Wang M, Wilkerson MD, Wong T, Wu J, Xi L, Zhou J, Bedford J, Chen F, Fu Y, Gerstein M, Haussler D, Kasaian K, Lai P, Ling S, Radenbaugh A, Van Den Berg D, Weinstein JN, Zhu J, Albert M, Alexopoulou I, Andersen JJ, Auman JT, Bartlett J, Bastacky S, Bergsten J, Blute ML, Boice L, Bollag RJ, Boyd J, Castle E, Chen YB, Cheville JC, Curley E, Davies B, DeVolk A, Dhir R, Dike L, Eckman J, Engel J, Harr J, Hrebinko R, Huang M, Huelsenbeck-Dill L, Iacocca M, Jacobs B, Lobis M, Maranchie JK, McMeekin S, Myers J, Nelson J, Parfitt J, Parwani A, Petrelli N, Rabeno B, Roy S, Salner AL, Slaton J, Stanton M, Thompson RH, Thorne L, Tucker K, Weinberger PM, Winemiller C, Zach LA, Zuna R. Comprehensive Molecular Characterization of Papillary Renal-Cell Carcinoma. N Engl J Med 2016; 374:135-45. [PMID: 26536169 PMCID: PMC4775252 DOI: 10.1056/nejmoa1505917] [Citation(s) in RCA: 887] [Impact Index Per Article: 110.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
BACKGROUND Papillary renal-cell carcinoma, which accounts for 15 to 20% of renal-cell carcinomas, is a heterogeneous disease that consists of various types of renal cancer, including tumors with indolent, multifocal presentation and solitary tumors with an aggressive, highly lethal phenotype. Little is known about the genetic basis of sporadic papillary renal-cell carcinoma, and no effective forms of therapy for advanced disease exist. METHODS We performed comprehensive molecular characterization of 161 primary papillary renal-cell carcinomas, using whole-exome sequencing, copy-number analysis, messenger RNA and microRNA sequencing, DNA-methylation analysis, and proteomic analysis. RESULTS Type 1 and type 2 papillary renal-cell carcinomas were shown to be different types of renal cancer characterized by specific genetic alterations, with type 2 further classified into three individual subgroups on the basis of molecular differences associated with patient survival. Type 1 tumors were associated with MET alterations, whereas type 2 tumors were characterized by CDKN2A silencing, SETD2 mutations, TFE3 fusions, and increased expression of the NRF2-antioxidant response element (ARE) pathway. A CpG island methylator phenotype (CIMP) was observed in a distinct subgroup of type 2 papillary renal-cell carcinomas that was characterized by poor survival and mutation of the gene encoding fumarate hydratase (FH). CONCLUSIONS Type 1 and type 2 papillary renal-cell carcinomas were shown to be clinically and biologically distinct. Alterations in the MET pathway were associated with type 1, and activation of the NRF2-ARE pathway was associated with type 2; CDKN2A loss and CIMP in type 2 conveyed a poor prognosis. Furthermore, type 2 papillary renal-cell carcinoma consisted of at least three subtypes based on molecular and phenotypic features. (Funded by the National Institutes of Health.).
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Affiliation(s)
- W. Marston Linehan
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD
- Corresponding Author: W. Marston Linehan, M.D., Urologic Oncology Branch, National Cancer Institute, Building 10 CRC Room 1-5940, Bethesda, MD 20892-1107 USA, Tel: 301-496-6353, Fax: 301-402-0922,
| | - Paul T. Spellman
- Oregon Health & Science University, Portland, OR
- Corresponding Author: W. Marston Linehan, M.D., Urologic Oncology Branch, National Cancer Institute, Building 10 CRC Room 1-5940, Bethesda, MD 20892-1107 USA, Tel: 301-496-6353, Fax: 301-402-0922,
| | | | | | | | | | | | - Bradley A. Murray
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University Cambridge, MA
| | - Laura Schmidt
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD
| | - Cathy D. Vocke
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD
| | - Myron Peto
- Oregon Health & Science University, Portland, OR
| | | | | | | | - Samira Brooks
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | | | - Angela N. Brooks
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University Cambridge, MA
| | | | - A. Gordon Robertson
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
| | - Denise Brooks
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
| | - Reanne Bowlby
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
| | - Sara Sadeghi
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
| | - Hui Shen
- Van Andel Research Institute, Grand Rapids, MI
| | | | | | | | | | - Andrew D. Cherniack
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University Cambridge, MA
| | - Gordon Saksena
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University Cambridge, MA
| | - Scott Haake
- H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL
| | - Jun Li
- Univ. of Texas MD Anderson Cancer Center, Houston, TX
| | - Han Liang
- Univ. of Texas MD Anderson Cancer Center, Houston, TX
| | - Yiling Lu
- Univ. of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Rehan Akbani
- Univ. of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | - Pavana Anur
- Oregon Health & Science University, Portland, OR
| | - Donald Bottaro
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD
| | | | | | | | | | | | - A. Ari Hakimi
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - James Hsieh
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - William Y. Kim
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | | | - Maria J. Merino
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD
| | | | | | - Ed Reznik
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | | | | | | | | | - Satish Tickoo
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Daniel Crain
- The International Genomics Consortium, Phoenix, AZ
| | | | - Kevin Lau
- The International Genomics Consortium, Phoenix, AZ
| | | | - Scott Morris
- The International Genomics Consortium, Phoenix, AZ
| | | | | | | | | | - Mark Sherman
- The International Genomics Consortium, Phoenix, AZ
| | | | - Peggy Yena
- The International Genomics Consortium, Phoenix, AZ
| | - Melissa T. Avedon
- The Research Institute at Nationwide Children's Hospital, Columbus, OH
| | - Jay Bowen
- The Research Institute at Nationwide Children's Hospital, Columbus, OH
| | | | - Mark Gerken
- The Research Institute at Nationwide Children's Hospital, Columbus, OH
| | - Kristen M. Leraas
- The Research Institute at Nationwide Children's Hospital, Columbus, OH
| | | | - Nilsa C. Ramirez
- The Research Institute at Nationwide Children's Hospital, Columbus, OH
| | - Tracie Santos
- The Research Institute at Nationwide Children's Hospital, Columbus, OH
| | - Lisa Wise
- The Research Institute at Nationwide Children's Hospital, Columbus, OH
| | - Erik Zmuda
- The Research Institute at Nationwide Children's Hospital, Columbus, OH
| | - John A. Demchok
- National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Ina Felau
- National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Carolyn M. Hutter
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Margi Sheth
- National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Heidi J. Sofia
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Roy Tarnuzzer
- National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Zhining Wang
- National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Liming Yang
- National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Jean C. Zenklusen
- National Cancer Institute, National Institutes of Health, Bethesda, MD
| | | | - Brenda Ayala
- SRA International, Inc., 4300 Fair Lakes Court, Fairfax, VA
| | - Julien Baboud
- SRA International, Inc., 4300 Fair Lakes Court, Fairfax, VA
| | - Sudha Chudamani
- Leidos Biomedical Research, Inc. Frederick National Laboratory for Cancer Research, Rockville MD
| | - Jia Liu
- Leidos Biomedical Research, Inc. Frederick National Laboratory for Cancer Research, Rockville MD
| | - Laxmi Lolla
- Leidos Biomedical Research, Inc. Frederick National Laboratory for Cancer Research, Rockville MD
| | - Rashi Naresh
- SRA International, Inc., 4300 Fair Lakes Court, Fairfax, VA
| | - Todd Pihl
- SRA International, Inc., 4300 Fair Lakes Court, Fairfax, VA
| | - Qiang Sun
- SRA International, Inc., 4300 Fair Lakes Court, Fairfax, VA
| | - Yunhu Wan
- SRA International, Inc., 4300 Fair Lakes Court, Fairfax, VA
| | - Ye Wu
- Leidos Biomedical Research, Inc. Frederick National Laboratory for Cancer Research, Rockville MD
| | - Adrian Ally
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
| | - Miruna Balasundaram
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
| | - Saianand Balu
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Rameen Beroukhim
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University Cambridge, MA
| | - Tom Bodenheimer
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | | | | | - Rebecca Carlsen
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
| | - Scott L. Carter
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University Cambridge, MA
| | - Hsu Chao
- Baylor College of Medicine, Houston, TX
| | - Eric Chuah
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
| | - Amanda Clarke
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
| | | | | | | | - Noreen Dhalla
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
| | | | | | - Stacey B. Gabriel
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University Cambridge, MA
| | | | - Ranabir Guin
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
| | | | | | - D. Neil Hayes
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Robert A. Holt
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
| | - Alan P. Hoyle
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | | | - Steven J.M. Jones
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
| | - Corbin D. Jones
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | | | | | | | - Jie Li
- Baylor College of Medicine, Houston, TX
| | - Yussanne Ma
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
| | - Marco A. Marra
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
| | - Michael Mayo
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
| | - Shaowu Meng
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Matthew Meyerson
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University Cambridge, MA
| | | | - Richard A. Moore
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
| | | | - Lisle E. Mose
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Andrew J. Mungall
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
| | | | - Joel S. Parker
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | | | - Jeffrey Roach
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | | | - Steven E. Schumacher
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University Cambridge, MA
| | - Yan Shi
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Janae V. Simons
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Payal Sipahimalani
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
| | - Tara Skelly
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | | | - Carrie Sougnez
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University Cambridge, MA
| | - Angela Tam
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
| | - Donghui Tan
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Nina Thiessen
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
| | | | - Min Wang
- Baylor College of Medicine, Houston, TX
| | | | - Tina Wong
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
| | - Junyuan Wu
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Liu Xi
- Baylor College of Medicine, Houston, TX
| | - Jane Zhou
- Baylor College of Medicine, Houston, TX
| | | | | | - Yao Fu
- Yale University, New Haven, CT
| | | | - David Haussler
- University of California Santa Cruz Genomics Institute, Santa Cruz, CA
| | - Katayoon Kasaian
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
| | - Phillip Lai
- University of Southern California, Los Angeles, CA
| | - Shiyun Ling
- Univ. of Texas MD Anderson Cancer Center, Houston, TX
| | - Amie Radenbaugh
- University of California Santa Cruz Genomics Institute, Santa Cruz, CA
| | | | | | - Jingchun Zhu
- University of California Santa Cruz Genomics Institute, Santa Cruz, CA
| | - Monique Albert
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | | | | | - J. Todd Auman
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - John Bartlett
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Sheldon Bastacky
- University of Pittsburgh Medical Center Presbyterian University Hospital, Pittsburgh, PA
| | - Julie Bergsten
- Penrose-St. Francis Health Services, Colorado Springs, CO
| | | | - Lori Boice
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | | | - Jeff Boyd
- Fox Chase Cancer Center, Philadelphia, PA
| | | | - Ying-Bei Chen
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Erin Curley
- The International Genomics Consortium, Phoenix, AZ
| | - Benjamin Davies
- University of Pittsburgh Medical Center Presbyterian University Hospital, Pittsburgh, PA
| | - April DeVolk
- Penrose-St. Francis Health Services, Colorado Springs, CO
| | - Rajiv Dhir
- University of Pittsburgh Medical Center Presbyterian University Hospital, Pittsburgh, PA
| | | | - John Eckman
- Penrose-St. Francis Health Services, Colorado Springs, CO
| | - Jay Engel
- Kingston General Hospital, Kingston, Ontario, Canada
| | - Jodi Harr
- Penrose-St. Francis Health Services, Colorado Springs, CO
| | - Ronald Hrebinko
- University of Pittsburgh Medical Center Presbyterian University Hospital, Pittsburgh, PA
| | - Mei Huang
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | | | - Mary Iacocca
- Helen F Graham Cancer Center at Christiana Care Health Systems, Newark, DE
| | - Bruce Jacobs
- University of Pittsburgh Medical Center Presbyterian University Hospital, Pittsburgh, PA
| | - Michael Lobis
- Helen F Graham Cancer Center at Christiana Care Health Systems, Newark, DE
| | - Jodi K. Maranchie
- University of Pittsburgh Medical Center Presbyterian University Hospital, Pittsburgh, PA
| | - Scott McMeekin
- University of Oklahoma Health Sciences Center, Oklahoma City, OK
| | - Jerome Myers
- Penrose-St. Francis Health Services, Colorado Springs, CO
| | - Joel Nelson
- University of Pittsburgh Medical Center Presbyterian University Hospital, Pittsburgh, PA
| | | | - Anil Parwani
- University of Pittsburgh Medical Center Presbyterian University Hospital, Pittsburgh, PA
| | - Nicholas Petrelli
- Helen F Graham Cancer Center at Christiana Care Health Systems, Newark, DE
| | - Brenda Rabeno
- Helen F Graham Cancer Center at Christiana Care Health Systems, Newark, DE
| | - Somak Roy
- University of Pittsburgh Medical Center Presbyterian University Hospital, Pittsburgh, PA
| | | | - Joel Slaton
- University of Oklahoma Health Sciences Center, Oklahoma City, OK
| | | | | | - Leigh Thorne
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Kelinda Tucker
- Penrose-St. Francis Health Services, Colorado Springs, CO
| | | | | | | | - Rosemary Zuna
- University of Oklahoma Health Sciences Center, Oklahoma City, OK
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8
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Kasar S, Kim J, Improgo R, Tiao G, Polak P, Haradhvala N, Lawrence MS, Kiezun A, Fernandes SM, Bahl S, Sougnez C, Gabriel S, Lander ES, Kim HT, Getz G, Brown JR. Whole-genome sequencing reveals activation-induced cytidine deaminase signatures during indolent chronic lymphocytic leukaemia evolution. Nat Commun 2015; 6:8866. [PMID: 26638776 PMCID: PMC4686820 DOI: 10.1038/ncomms9866] [Citation(s) in RCA: 177] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 10/08/2015] [Indexed: 12/17/2022] Open
Abstract
Patients with chromosome 13q deletion or normal cytogenetics represent the majority of chronic lymphocytic leukaemia (CLL) cases, yet have relatively few driver mutations. To better understand their genomic landscape, here we perform whole-genome sequencing on a cohort of patients enriched with these cytogenetic characteristics. Mutations in known CLL drivers are seen in only 33% of this cohort, and associated with normal cytogenetics and unmutated IGHV. The most commonly mutated gene in our cohort, IGLL5, shows a mutational pattern suggestive of activation-induced cytidine deaminase (AID) activity. Unsupervised analysis of mutational signatures demonstrates the activities of canonical AID (c-AID), leading to clustered mutations near active transcriptional start sites; non-canonical AID (nc-AID), leading to genome-wide non-clustered mutations, and an ageing signature responsible for most mutations. Using mutation clonality to infer time of onset, we find that while ageing and c-AID activities are ongoing, nc-AID-associated mutations likely occur earlier in tumour evolution. The oncogenic events driving indolent chronic lymphocytic leukaemia are relatively unknown. Here, the authors perform whole genome sequencing on 30 such tumours and identify recurrent mutations in IGLL5 and two activation induced cytidine deaminase signatures that are operative at different stages of CLL evolution.
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Affiliation(s)
- S Kasar
- Department of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA.,Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - J Kim
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - R Improgo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA.,Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - G Tiao
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - P Polak
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - N Haradhvala
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - M S Lawrence
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - A Kiezun
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - S M Fernandes
- Department of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - S Bahl
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - C Sougnez
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - S Gabriel
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - E S Lander
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - H T Kim
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - G Getz
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA.,Department of Pathology and Cancer Center, Massachusetts General Hospital, Boston, Massachusetts 02114, USA.,Department of Pathology, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - J R Brown
- Department of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA.,Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA
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9
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Wang AT, Kim T, Wagner JE, Conti BA, Lach FP, Huang AL, Molina H, Sanborn EM, Zierhut H, Cornes BK, Abhyankar A, Sougnez C, Gabriel SB, Auerbach AD, Kowalczykowski SC, Smogorzewska A. A Dominant Mutation in Human RAD51 Reveals Its Function in DNA Interstrand Crosslink Repair Independent of Homologous Recombination. Mol Cell 2015; 59:478-90. [PMID: 26253028 DOI: 10.1016/j.molcel.2015.07.009] [Citation(s) in RCA: 195] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 05/26/2015] [Accepted: 07/07/2015] [Indexed: 12/17/2022]
Abstract
Repair of DNA interstrand crosslinks requires action of multiple DNA repair pathways, including homologous recombination. Here, we report a de novo heterozygous T131P mutation in RAD51/FANCR, the key recombinase essential for homologous recombination, in a patient with Fanconi anemia-like phenotype. In vitro, RAD51-T131P displays DNA-independent ATPase activity, no DNA pairing capacity, and a co-dominant-negative effect on RAD51 recombinase function. However, the patient cells are homologous recombination proficient due to the low ratio of mutant to wild-type RAD51 in cells. Instead, patient cells are sensitive to crosslinking agents and display hyperphosphorylation of Replication Protein A due to increased activity of DNA2 and WRN at the DNA interstrand crosslinks. Thus, proper RAD51 function is important during DNA interstrand crosslink repair outside of homologous recombination. Our study provides a molecular basis for how RAD51 and its associated factors may operate in a homologous recombination-independent manner to maintain genomic integrity.
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Affiliation(s)
- Anderson T Wang
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY 10065, USA
| | - Taeho Kim
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA 95616, USA
| | - John E Wagner
- Blood and Marrow Transplant Program, Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Brooke A Conti
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY 10065, USA
| | - Francis P Lach
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY 10065, USA
| | - Athena L Huang
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY 10065, USA
| | - Henrik Molina
- Proteomics Resource Center, The Rockefeller University, New York, NY 10065, USA
| | - Erica M Sanborn
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY 10065, USA
| | - Heather Zierhut
- Blood and Marrow Transplant Program, Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA
| | | | | | - Carrie Sougnez
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Arleen D Auerbach
- Human Genetics and Hematology, The Rockefeller University, New York, NY 10065, USA
| | - Stephen C Kowalczykowski
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA 95616, USA
| | - Agata Smogorzewska
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY 10065, USA.
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10
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Brastianos PK, Carter SL, Santagata S, Cahill DP, Taylor-Weiner A, Jones RT, Van Allen EM, Lawrence MS, Horowitz PM, Cibulskis K, Ligon KL, Tabernero J, Seoane J, Martinez-Saez E, Curry WT, Dunn IF, Paek SH, Park SH, McKenna A, Chevalier A, Rosenberg M, Barker FG, Gill CM, Van Hummelen P, Thorner AR, Johnson BE, Hoang MP, Choueiri TK, Signoretti S, Sougnez C, Rabin MS, Lin NU, Winer EP, Stemmer-Rachamimov A, Meyerson M, Garraway L, Gabriel S, Lander ES, Beroukhim R, Batchelor TT, Baselga J, Louis DN, Getz G, Hahn WC. Genomic Characterization of Brain Metastases Reveals Branched Evolution and Potential Therapeutic Targets. Cancer Discov 2015; 5:1164-1177. [PMID: 26410082 PMCID: PMC4916970 DOI: 10.1158/2159-8290.cd-15-0369] [Citation(s) in RCA: 699] [Impact Index Per Article: 77.7] [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: 03/30/2015] [Accepted: 08/11/2015] [Indexed: 12/30/2022]
Abstract
UNLABELLED Brain metastases are associated with a dismal prognosis. Whether brain metastases harbor distinct genetic alterations beyond those observed in primary tumors is unknown. We performed whole-exome sequencing of 86 matched brain metastases, primary tumors, and normal tissue. In all clonally related cancer samples, we observed branched evolution, where all metastatic and primary sites shared a common ancestor yet continued to evolve independently. In 53% of cases, we found potentially clinically informative alterations in the brain metastases not detected in the matched primary-tumor sample. In contrast, spatially and temporally separated brain metastasis sites were genetically homogenous. Distal extracranial and regional lymph node metastases were highly divergent from brain metastases. We detected alterations associated with sensitivity to PI3K/AKT/mTOR, CDK, and HER2/EGFR inhibitors in the brain metastases. Genomic analysis of brain metastases provides an opportunity to identify potentially clinically informative alterations not detected in clinically sampled primary tumors, regional lymph nodes, or extracranial metastases. SIGNIFICANCE Decisions for individualized therapies in patients with brain metastasis are often made from primary-tumor biopsies. We demonstrate that clinically actionable alterations present in brain metastases are frequently not detected in primary biopsies, suggesting that sequencing of primary biopsies alone may miss a substantial number of opportunities for targeted therapy.
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Affiliation(s)
- Priscilla K. Brastianos
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, all in Boston
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, all in Boston
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, all in Boston
- Department of Medical Oncology, Brigham and Women's Hospital, Harvard Medical School - all in Boston
- Broad Institute, Brigham and Women's Hospital, Harvard Medical School - all in Boston
| | - Scott L. Carter
- Joint Center for Cancer Precision Medicine, Brigham and Women's Hospital, Harvard Medical School - all in Boston
- Broad Institute, Brigham and Women's Hospital, Harvard Medical School - all in Boston
| | - Sandro Santagata
- Department of Cancer Biology, Brigham and Women's Hospital, Harvard Medical School - all in Boston
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School - all in Boston
| | - Daniel P. Cahill
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, all in Boston
| | - Amaro Taylor-Weiner
- Broad Institute, Brigham and Women's Hospital, Harvard Medical School - all in Boston
| | - Robert T. Jones
- Department of Medical Oncology, Brigham and Women's Hospital, Harvard Medical School - all in Boston
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School - all in Boston
| | - Eliezer M. Van Allen
- Department of Medical Oncology, Brigham and Women's Hospital, Harvard Medical School - all in Boston
- Broad Institute, Brigham and Women's Hospital, Harvard Medical School - all in Boston
| | - Michael S. Lawrence
- Broad Institute, Brigham and Women's Hospital, Harvard Medical School - all in Boston
| | - Peleg M. Horowitz
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School - all in Boston
| | - Kristian Cibulskis
- Broad Institute, Brigham and Women's Hospital, Harvard Medical School - all in Boston
| | - Keith L. Ligon
- Department of Medical Oncology, Brigham and Women's Hospital, Harvard Medical School - all in Boston
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School - all in Boston
| | - Josep Tabernero
- Department of Medical Oncology, Department of Pathology, Barcelona - all in Spain
| | - Joan Seoane
- Department of Medical Oncology, Department of Pathology, Barcelona - all in Spain
| | - Elena Martinez-Saez
- Vall d'Hebron University Hospital and Institute of Oncology (VHIO), Barcelona - all in Spain
| | - William T. Curry
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, all in Boston
| | - Ian F. Dunn
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School - all in Boston
| | - Sun Ha Paek
- Department of Neurosurgery and Department of Pathology, Seoul National University College of Medicine - all in Korea
| | - Sung-Hye Park
- Department of Neurosurgery and Department of Pathology, Seoul National University College of Medicine - all in Korea
| | - Aaron McKenna
- Broad Institute, Brigham and Women's Hospital, Harvard Medical School - all in Boston
| | - Aaron Chevalier
- Broad Institute, Brigham and Women's Hospital, Harvard Medical School - all in Boston
| | - Mara Rosenberg
- Broad Institute, Brigham and Women's Hospital, Harvard Medical School - all in Boston
| | - Frederick G. Barker
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, all in Boston
| | - Corey M. Gill
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, all in Boston
| | - Paul Van Hummelen
- Department of Medical Oncology, Brigham and Women's Hospital, Harvard Medical School - all in Boston
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School - all in Boston
| | - Aaron R. Thorner
- Department of Medical Oncology, Brigham and Women's Hospital, Harvard Medical School - all in Boston
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School - all in Boston
| | - Bruce E. Johnson
- Department of Medical Oncology, Brigham and Women's Hospital, Harvard Medical School - all in Boston
| | - Mai P. Hoang
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, all in Boston
| | - Toni K. Choueiri
- Department of Medical Oncology, Brigham and Women's Hospital, Harvard Medical School - all in Boston
| | - Sabina Signoretti
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School - all in Boston
| | - Carrie Sougnez
- Broad Institute, Brigham and Women's Hospital, Harvard Medical School - all in Boston
| | - Michael S. Rabin
- Department of Medical Oncology, Brigham and Women's Hospital, Harvard Medical School - all in Boston
| | - Nancy U. Lin
- Department of Medical Oncology, Brigham and Women's Hospital, Harvard Medical School - all in Boston
| | - Eric P. Winer
- Department of Medical Oncology, Brigham and Women's Hospital, Harvard Medical School - all in Boston
| | - Anat Stemmer-Rachamimov
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, all in Boston
| | - Matthew Meyerson
- Department of Medical Oncology, Brigham and Women's Hospital, Harvard Medical School - all in Boston
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School - all in Boston
- Broad Institute, Brigham and Women's Hospital, Harvard Medical School - all in Boston
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School - all in Boston
| | - Levi Garraway
- Department of Medical Oncology, Brigham and Women's Hospital, Harvard Medical School - all in Boston
- Joint Center for Cancer Precision Medicine, Brigham and Women's Hospital, Harvard Medical School - all in Boston
- Broad Institute, Brigham and Women's Hospital, Harvard Medical School - all in Boston
| | - Stacey Gabriel
- Broad Institute, Brigham and Women's Hospital, Harvard Medical School - all in Boston
| | - Eric S. Lander
- Broad Institute, Brigham and Women's Hospital, Harvard Medical School - all in Boston
| | - Rameen Beroukhim
- Department of Medical Oncology, Brigham and Women's Hospital, Harvard Medical School - all in Boston
- Department of Cancer Biology, Brigham and Women's Hospital, Harvard Medical School - all in Boston
- Broad Institute, Brigham and Women's Hospital, Harvard Medical School - all in Boston
| | - Tracy T. Batchelor
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, all in Boston
| | - Jose Baselga
- Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York City
| | - David N. Louis
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, all in Boston
| | - Gad Getz
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, all in Boston
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, all in Boston
- Broad Institute, Brigham and Women's Hospital, Harvard Medical School - all in Boston
| | - William C. Hahn
- Department of Medical Oncology, Brigham and Women's Hospital, Harvard Medical School - all in Boston
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School - all in Boston
- Broad Institute, Brigham and Women's Hospital, Harvard Medical School - all in Boston
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11
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Shukla SA, Rajasagi M, Dixon P, Tiao G, Lawrence MS, Sougnez C, Brusic V, Cibulskis K, Kiezun A, Wu CJ, Getz G. Abstract 1093: Sensitive detection of somatic mutations in class I HLA genes reveals enrichment for functional events in cancer. Cancer Res 2015. [DOI: 10.1158/1538-7445.am2015-1093] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [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
Abstract
Recent studies have revealed enhanced somatic mutation rate in HLA genes in several tumor types and has strongly implicated HLA dysfunction as a possible mediator of immune evasion. Mutation detection in this highly polymorphic and GC-rich locus, however, is complicated by suboptimal alignment to the canonical reference genome and lowered capture efficiency. To address this challenge, we developed the POLYSOLVER (POLYmorphic loci reSOLVER) algorithm for accurate inference of class I HLA-A, -B and -C alleles from whole exome sequencing (WES) data, which can then be used for more sensitive and specific mutation detection. POLYSOLVER comprises two broad steps: alignment optimization and subsequent inference of the alleles using a Bayesian classifier. When applied to 133 HapMap samples of known HLA type, POLYSOLVER outperformed other publicly available tools with an overall protein-level accuracy of 97% and was particularly more powerful at low sequencing depths with an overall accuracy of 96%.
To accurately detect HLA mutations in tumor samples, we performed HLA typing by applying POLYSOLVER to the paired germline sample, re-aligned the HLA reads from both tumor and normal to the inferred HLA alleles while filtering out likely erroneous alignments, and then applied standard tools (MuTect and Strelka) to detect somatic mutations by comparing the re-aligned tumor and normal HLA reads. Based on orthogonal RNA-Seq validation, we estimate an improvement in sensitivity from 57.1% to 94.3% and specificity from 43.8% to 81.3% over standard methods.
Pan-cancer analysis of TCGA data from 3,608 tumor/normal pairs by POLYSOLVER across 12 tumor types revealed 147 non-silent HLA mutations in 121 patients. We identified colon adenocarcinoma to be significantly affected by somatic mutation in class I HLA genes, further supporting HLA mutation as a common oncogenic mechanism. By contrast, HLA mutations were not detected in chronic lymphocytic leukemia (n = 129). Alterations likely to have a functional effect, including loss-of-function, were significantly enriched in HLA mutations compared to non-HLA mutations (P < 2.2×10-16). We also observed that 70 of the 147 total HLA mutations (47.6%) fell in 23 recurrent sites suggesting positive selection at these positions. Finally, we determined that the majority of the detected mutations mapped to regions critical for antigen presentation.
In addition to enabling better detection of HLA mutations, accurate HLA typing by POLYSOLVER can also be used to study germline associations of HLA alleles in diseases, and in donor screening for organ transplantation. It may be extended to extracting typing and mutation information from whole genome or RNA sequencing data and from other polymorphic regions in the genome such as MHC class II, TAP1 and TAP2 genes, and MIC-A and MIC-B ligands. POLYSOLVER hence is a generally applicable analysis framework to address these otherwise challenging loci.
Citation Format: Sachet A. Shukla, Mohini Rajasagi, Philip Dixon, Grace Tiao, Michael S. Lawrence, Carrie Sougnez, Vladimir Brusic, Kristian Cibulskis, Adam Kiezun, Catherine J. Wu, Gad Getz. Sensitive detection of somatic mutations in class I HLA genes reveals enrichment for functional events in cancer. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 1093. doi:10.1158/1538-7445.AM2015-1093
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12
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Robinson D, Van Allen EM, Wu YM, Schultz N, Lonigro RJ, Mosquera JM, Montgomery B, Taplin ME, Pritchard CC, Attard G, Beltran H, Abida W, Bradley RK, Vinson J, Cao X, Vats P, Kunju LP, Hussain M, Feng FY, Tomlins SA, Cooney KA, Smith DC, Brennan C, Siddiqui J, Mehra R, Chen Y, Rathkopf DE, Morris MJ, Solomon SB, Durack JC, Reuter VE, Gopalan A, Gao J, Loda M, Lis RT, Bowden M, Balk SP, Gaviola G, Sougnez C, Gupta M, Yu EY, Mostaghel EA, Cheng HH, Mulcahy H, True LD, Plymate SR, Dvinge H, Ferraldeschi R, Flohr P, Miranda S, Zafeiriou Z, Tunariu N, Mateo J, Perez-Lopez R, Demichelis F, Robinson BD, Schiffman M, Nanus DM, Tagawa ST, Sigaras A, Eng KW, Elemento O, Sboner A, Heath EI, Scher HI, Pienta KJ, Kantoff P, de Bono JS, Rubin MA, Nelson PS, Garraway LA, Sawyers CL, Chinnaiyan AM. Integrative clinical genomics of advanced prostate cancer. Cell 2015; 161:1215-1228. [PMID: 26000489 DOI: 10.1016/j.cell.2015.05.001] [Citation(s) in RCA: 2219] [Impact Index Per Article: 246.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Revised: 04/06/2015] [Accepted: 04/27/2015] [Indexed: 12/15/2022]
Abstract
Toward development of a precision medicine framework for metastatic, castration-resistant prostate cancer (mCRPC), we established a multi-institutional clinical sequencing infrastructure to conduct prospective whole-exome and transcriptome sequencing of bone or soft tissue tumor biopsies from a cohort of 150 mCRPC affected individuals. Aberrations of AR, ETS genes, TP53, and PTEN were frequent (40%-60% of cases), with TP53 and AR alterations enriched in mCRPC compared to primary prostate cancer. We identified new genomic alterations in PIK3CA/B, R-spondin, BRAF/RAF1, APC, β-catenin, and ZBTB16/PLZF. Moreover, aberrations of BRCA2, BRCA1, and ATM were observed at substantially higher frequencies (19.3% overall) compared to those in primary prostate cancers. 89% of affected individuals harbored a clinically actionable aberration, including 62.7% with aberrations in AR, 65% in other cancer-related genes, and 8% with actionable pathogenic germline alterations. This cohort study provides clinically actionable information that could impact treatment decisions for these affected individuals.
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Affiliation(s)
- Dan Robinson
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Eliezer M Van Allen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Yi-Mi Wu
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Nikolaus Schultz
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Robert J Lonigro
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Juan-Miguel Mosquera
- Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, New York, NY 10021, USA; Institute for Precision Medicine, Weill Medical College of Cornell University, New York, NY 10021, USA; New York Presbyterian Hospital, New York, NY 10021, USA; Meyer Cancer, Weill Medical College of Cornell University, New York, NY 10021, USA
| | - Bruce Montgomery
- Computational Biology Program, Public Health Sciences Division and Basic Science Division, Fred Hutchinson Cancer Center, University of Washington, Seattle, WA 98109, USA; Department of Medicine and VAPSHCS, University of Washington, Seattle, WA 98109, USA
| | - Mary-Ellen Taplin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Colin C Pritchard
- Department of Laboratory Medicine, University of Washington, Seattle, WA 98195, USA
| | - Gerhardt Attard
- Cancer Biomarkers Team, Division of Clinical Studies, The Institute of Cancer Research, London SM2 5NG, UK; Prostate Cancer Targeted Therapy Group and Drug Development Unit, The Royal Marsden NHS Foundation Trust, London SM2 5NG, UK
| | - Himisha Beltran
- Institute for Precision Medicine, Weill Medical College of Cornell University, New York, NY 10021, USA; New York Presbyterian Hospital, New York, NY 10021, USA; Department of Medicine, Weill Medical College of Cornell University, New York, NY 10021, USA; Meyer Cancer, Weill Medical College of Cornell University, New York, NY 10021, USA
| | - Wassim Abida
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Genitourinary Oncology Service, Department of Medicine, Sidney Kimmel Center for Prostate and Urologic Cancers, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Robert K Bradley
- Computational Biology Program, Public Health Sciences Division and Basic Science Division, Fred Hutchinson Cancer Center, University of Washington, Seattle, WA 98109, USA
| | - Jake Vinson
- Prostate Cancer Clinical Trials Consortium, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Xuhong Cao
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Pankaj Vats
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Lakshmi P Kunju
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Maha Hussain
- Department of Internal Medicine, Division of Hematology Oncology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Urology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Felix Y Feng
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Radiation Oncology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Scott A Tomlins
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Urology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Kathleen A Cooney
- Department of Internal Medicine, Division of Hematology Oncology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Urology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - David C Smith
- Department of Internal Medicine, Division of Hematology Oncology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Urology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Christine Brennan
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Javed Siddiqui
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Rohit Mehra
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Yu Chen
- Department of Medicine, Weill Medical College of Cornell University, New York, NY 10021, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Genitourinary Oncology Service, Department of Medicine, Sidney Kimmel Center for Prostate and Urologic Cancers, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Dana E Rathkopf
- Department of Medicine, Weill Medical College of Cornell University, New York, NY 10021, USA; Genitourinary Oncology Service, Department of Medicine, Sidney Kimmel Center for Prostate and Urologic Cancers, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Michael J Morris
- Department of Medicine, Weill Medical College of Cornell University, New York, NY 10021, USA; Genitourinary Oncology Service, Department of Medicine, Sidney Kimmel Center for Prostate and Urologic Cancers, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Stephen B Solomon
- Interventional Radiology, Department of Radiology Service, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Jeremy C Durack
- Interventional Radiology, Department of Radiology Service, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Victor E Reuter
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Anuradha Gopalan
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Jianjiong Gao
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Massimo Loda
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA; Center for Molecular Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Pathology, Brigham & Women's Hospital, Boston, MA 02115, USA
| | - Rosina T Lis
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Molecular Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Michaela Bowden
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Molecular Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Pathology, Brigham & Women's Hospital, Boston, MA 02115, USA
| | - Stephen P Balk
- Division of Hematology-Oncology, Department of Medicine, Beth Israel Deaconess Cancer Center, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Glenn Gaviola
- Department of Musculoskeletal Radiology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Carrie Sougnez
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Manaswi Gupta
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Evan Y Yu
- Department of Medicine and VAPSHCS, University of Washington, Seattle, WA 98109, USA
| | - Elahe A Mostaghel
- Computational Biology Program, Public Health Sciences Division and Basic Science Division, Fred Hutchinson Cancer Center, University of Washington, Seattle, WA 98109, USA; Department of Medicine and VAPSHCS, University of Washington, Seattle, WA 98109, USA
| | - Heather H Cheng
- Computational Biology Program, Public Health Sciences Division and Basic Science Division, Fred Hutchinson Cancer Center, University of Washington, Seattle, WA 98109, USA; Department of Medicine and VAPSHCS, University of Washington, Seattle, WA 98109, USA
| | - Hyojeong Mulcahy
- Department of Radiology, University of Washington, Seattle, WA 98109, USA
| | - Lawrence D True
- Department of Pathology, University of Washington Medical Center, Seattle, WA 98109, USA
| | - Stephen R Plymate
- Department of Medicine and VAPSHCS, University of Washington, Seattle, WA 98109, USA
| | - Heidi Dvinge
- Computational Biology Program, Public Health Sciences Division and Basic Science Division, Fred Hutchinson Cancer Center, University of Washington, Seattle, WA 98109, USA
| | - Roberta Ferraldeschi
- Cancer Biomarkers Team, Division of Clinical Studies, The Institute of Cancer Research, London SM2 5NG, UK; Prostate Cancer Targeted Therapy Group and Drug Development Unit, The Royal Marsden NHS Foundation Trust, London SM2 5NG, UK
| | - Penny Flohr
- Cancer Biomarkers Team, Division of Clinical Studies, The Institute of Cancer Research, London SM2 5NG, UK; Prostate Cancer Targeted Therapy Group and Drug Development Unit, The Royal Marsden NHS Foundation Trust, London SM2 5NG, UK
| | - Susana Miranda
- Cancer Biomarkers Team, Division of Clinical Studies, The Institute of Cancer Research, London SM2 5NG, UK; Prostate Cancer Targeted Therapy Group and Drug Development Unit, The Royal Marsden NHS Foundation Trust, London SM2 5NG, UK
| | - Zafeiris Zafeiriou
- Cancer Biomarkers Team, Division of Clinical Studies, The Institute of Cancer Research, London SM2 5NG, UK; Prostate Cancer Targeted Therapy Group and Drug Development Unit, The Royal Marsden NHS Foundation Trust, London SM2 5NG, UK
| | - Nina Tunariu
- Cancer Biomarkers Team, Division of Clinical Studies, The Institute of Cancer Research, London SM2 5NG, UK; Prostate Cancer Targeted Therapy Group and Drug Development Unit, The Royal Marsden NHS Foundation Trust, London SM2 5NG, UK
| | - Joaquin Mateo
- Cancer Biomarkers Team, Division of Clinical Studies, The Institute of Cancer Research, London SM2 5NG, UK; Prostate Cancer Targeted Therapy Group and Drug Development Unit, The Royal Marsden NHS Foundation Trust, London SM2 5NG, UK
| | - Raquel Perez-Lopez
- Cancer Biomarkers Team, Division of Clinical Studies, The Institute of Cancer Research, London SM2 5NG, UK; Prostate Cancer Targeted Therapy Group and Drug Development Unit, The Royal Marsden NHS Foundation Trust, London SM2 5NG, UK
| | - Francesca Demichelis
- Institute for Precision Medicine, Weill Medical College of Cornell University, New York, NY 10021, USA; Laboratory of Computational Oncology, CIBIO, Centre for Integrative Biology, University of Trento, 38123 Mattarello TN, Italy
| | - Brian D Robinson
- Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, New York, NY 10021, USA; Institute for Precision Medicine, Weill Medical College of Cornell University, New York, NY 10021, USA; New York Presbyterian Hospital, New York, NY 10021, USA; Meyer Cancer, Weill Medical College of Cornell University, New York, NY 10021, USA
| | - Marc Schiffman
- Institute for Precision Medicine, Weill Medical College of Cornell University, New York, NY 10021, USA; Division of Interventional Radiology, Department of Radiology, New York-Presbyterian Hospital/Weill Cornell Medical Center, New York, NY 10021, USA; Meyer Cancer, Weill Medical College of Cornell University, New York, NY 10021, USA
| | - David M Nanus
- Institute for Precision Medicine, Weill Medical College of Cornell University, New York, NY 10021, USA; New York Presbyterian Hospital, New York, NY 10021, USA; Department of Medicine, Weill Medical College of Cornell University, New York, NY 10021, USA; Meyer Cancer, Weill Medical College of Cornell University, New York, NY 10021, USA
| | - Scott T Tagawa
- Institute for Precision Medicine, Weill Medical College of Cornell University, New York, NY 10021, USA; New York Presbyterian Hospital, New York, NY 10021, USA; Department of Medicine, Weill Medical College of Cornell University, New York, NY 10021, USA; Meyer Cancer, Weill Medical College of Cornell University, New York, NY 10021, USA
| | - Alexandros Sigaras
- Institute for Precision Medicine, Weill Medical College of Cornell University, New York, NY 10021, USA; Institute for Computational Biomedicine, Department of Physiology and Biophysics, Weill Medical College of Cornell University, New York, NY 10021, USA; Department of Physiology & Biophysics, Weill Medical College of Cornell University, New York, NY 10021, USA
| | - Kenneth W Eng
- Institute for Precision Medicine, Weill Medical College of Cornell University, New York, NY 10021, USA; Institute for Computational Biomedicine, Department of Physiology and Biophysics, Weill Medical College of Cornell University, New York, NY 10021, USA; Department of Physiology & Biophysics, Weill Medical College of Cornell University, New York, NY 10021, USA
| | - Olivier Elemento
- Institute for Computational Biomedicine, Department of Physiology and Biophysics, Weill Medical College of Cornell University, New York, NY 10021, USA
| | - Andrea Sboner
- Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, New York, NY 10021, USA; Institute for Precision Medicine, Weill Medical College of Cornell University, New York, NY 10021, USA; Institute for Computational Biomedicine, Department of Physiology and Biophysics, Weill Medical College of Cornell University, New York, NY 10021, USA; Meyer Cancer, Weill Medical College of Cornell University, New York, NY 10021, USA
| | - Elisabeth I Heath
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI 48201, USA; Molecular Therapeutics Program, Barbara Ann Karmanos Cancer Institute, Detroit, MI 48201, USA
| | - Howard I Scher
- Department of Medicine, Weill Medical College of Cornell University, New York, NY 10021, USA; Genitourinary Oncology Service, Department of Medicine, Sidney Kimmel Center for Prostate and Urologic Cancers, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Kenneth J Pienta
- The James Buchanan Brady Urological Institute and Department of Urology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Philip Kantoff
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Johann S de Bono
- Cancer Biomarkers Team, Division of Clinical Studies, The Institute of Cancer Research, London SM2 5NG, UK; Prostate Cancer Targeted Therapy Group and Drug Development Unit, The Royal Marsden NHS Foundation Trust, London SM2 5NG, UK
| | - Mark A Rubin
- Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, New York, NY 10021, USA; Institute for Precision Medicine, Weill Medical College of Cornell University, New York, NY 10021, USA; New York Presbyterian Hospital, New York, NY 10021, USA; Meyer Cancer, Weill Medical College of Cornell University, New York, NY 10021, USA
| | - Peter S Nelson
- Department of Medicine and VAPSHCS, University of Washington, Seattle, WA 98109, USA; Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Division of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Meyer Cancer, Weill Medical College of Cornell University, New York, NY 10021, USA
| | - Levi A Garraway
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Charles L Sawyers
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
| | - Arul M Chinnaiyan
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Urology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI 48109, USA.
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Robinson D, Van Allen EM, Wu YM, Schultz N, Lonigro RJ, Mosquera JM, Montgomery B, Taplin ME, Pritchard CC, Attard G, Beltran H, Abida W, Bradley RK, Vinson J, Cao X, Vats P, Kunju LP, Hussain M, Feng FY, Tomlins SA, Cooney KA, Smith DC, Brennan C, Siddiqui J, Mehra R, Chen Y, Rathkopf DE, Morris MJ, Solomon SB, Durack JC, Reuter VE, Gopalan A, Gao J, Loda M, Lis RT, Bowden M, Balk SP, Gaviola G, Sougnez C, Gupta M, Yu EY, Mostaghel EA, Cheng HH, Mulcahy H, True LD, Plymate SR, Dvinge H, Ferraldeschi R, Flohr P, Miranda S, Zafeiriou Z, Tunariu N, Mateo J, Perez-Lopez R, Demichelis F, Robinson BD, Sboner A, Schiffman M, Nanus DM, Tagawa ST, Sigaras A, Eng KW, Elemento O, Sboner A, Heath EI, Scher HI, Pienta KJ, Kantoff P, de Bono JS, Rubin MA, Nelson PS, Garraway LA, Sawyers CL, Chinnaiyan AM. Integrative Clinical Genomics of Advanced Prostate Cancer. Cell 2015; 162:454. [PMID: 28843286 DOI: 10.1016/j.cell.2015.06.053] [Citation(s) in RCA: 370] [Impact Index Per Article: 41.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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14
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Brat DJ, Verhaak RGW, Aldape KD, Yung WKA, Salama SR, Cooper LAD, Rheinbay E, Miller CR, Vitucci M, Morozova O, Robertson AG, Noushmehr H, Laird PW, Cherniack AD, Akbani R, Huse JT, Ciriello G, Poisson LM, Barnholtz-Sloan JS, Berger MS, Brennan C, Colen RR, Colman H, Flanders AE, Giannini C, Grifford M, Iavarone A, Jain R, Joseph I, Kim J, Kasaian K, Mikkelsen T, Murray BA, O'Neill BP, Pachter L, Parsons DW, Sougnez C, Sulman EP, Vandenberg SR, Van Meir EG, von Deimling A, Zhang H, Crain D, Lau K, Mallery D, Morris S, Paulauskis J, Penny R, Shelton T, Sherman M, Yena P, Black A, Bowen J, Dicostanzo K, Gastier-Foster J, Leraas KM, Lichtenberg TM, Pierson CR, Ramirez NC, Taylor C, Weaver S, Wise L, Zmuda E, Davidsen T, Demchok JA, Eley G, Ferguson ML, Hutter CM, Mills Shaw KR, Ozenberger BA, Sheth M, Sofia HJ, Tarnuzzer R, Wang Z, Yang L, Zenklusen JC, Ayala B, Baboud J, Chudamani S, Jensen MA, Liu J, Pihl T, Raman R, Wan Y, Wu Y, Ally A, Auman JT, Balasundaram M, Balu S, Baylin SB, Beroukhim R, Bootwalla MS, Bowlby R, Bristow CA, Brooks D, Butterfield Y, Carlsen R, Carter S, Chin L, Chu A, Chuah E, Cibulskis K, Clarke A, Coetzee SG, Dhalla N, Fennell T, Fisher S, Gabriel S, Getz G, Gibbs R, Guin R, Hadjipanayis A, Hayes DN, Hinoue T, Hoadley K, Holt RA, Hoyle AP, Jefferys SR, Jones S, Jones CD, Kucherlapati R, Lai PH, Lander E, Lee S, Lichtenstein L, Ma Y, Maglinte DT, Mahadeshwar HS, Marra MA, Mayo M, Meng S, Meyerson ML, Mieczkowski PA, Moore RA, Mose LE, Mungall AJ, Pantazi A, Parfenov M, Park PJ, Parker JS, Perou CM, Protopopov A, Ren X, Roach J, Sabedot TS, Schein J, Schumacher SE, Seidman JG, Seth S, Shen H, Simons JV, Sipahimalani P, Soloway MG, Song X, Sun H, Tabak B, Tam A, Tan D, Tang J, Thiessen N, Triche T, Van Den Berg DJ, Veluvolu U, Waring S, Weisenberger DJ, Wilkerson MD, Wong T, Wu J, Xi L, Xu AW, Yang L, Zack TI, Zhang J, Aksoy BA, Arachchi H, Benz C, Bernard B, Carlin D, Cho J, DiCara D, Frazer S, Fuller GN, Gao J, Gehlenborg N, Haussler D, Heiman DI, Iype L, Jacobsen A, Ju Z, Katzman S, Kim H, Knijnenburg T, Kreisberg RB, Lawrence MS, Lee W, Leinonen K, Lin P, Ling S, Liu W, Liu Y, Liu Y, Lu Y, Mills G, Ng S, Noble MS, Paull E, Rao A, Reynolds S, Saksena G, Sanborn Z, Sander C, Schultz N, Senbabaoglu Y, Shen R, Shmulevich I, Sinha R, Stuart J, Sumer SO, Sun Y, Tasman N, Taylor BS, Voet D, Weinhold N, Weinstein JN, Yang D, Yoshihara K, Zheng S, Zhang W, Zou L, Abel T, Sadeghi S, Cohen ML, Eschbacher J, Hattab EM, Raghunathan A, Schniederjan MJ, Aziz D, Barnett G, Barrett W, Bigner DD, Boice L, Brewer C, Calatozzolo C, Campos B, Carlotti CG, Chan TA, Cuppini L, Curley E, Cuzzubbo S, Devine K, DiMeco F, Duell R, Elder JB, Fehrenbach A, Finocchiaro G, Friedman W, Fulop J, Gardner J, Hermes B, Herold-Mende C, Jungk C, Kendler A, Lehman NL, Lipp E, Liu O, Mandt R, McGraw M, Mclendon R, McPherson C, Neder L, Nguyen P, Noss A, Nunziata R, Ostrom QT, Palmer C, Perin A, Pollo B, Potapov A, Potapova O, Rathmell WK, Rotin D, Scarpace L, Schilero C, Senecal K, Shimmel K, Shurkhay V, Sifri S, Singh R, Sloan AE, Smolenski K, Staugaitis SM, Steele R, Thorne L, Tirapelli DPC, Unterberg A, Vallurupalli M, Wang Y, Warnick R, Williams F, Wolinsky Y, Bell S, Rosenberg M, Stewart C, Huang F, Grimsby JL, Radenbaugh AJ, Zhang J. Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas. N Engl J Med 2015; 372:2481-98. [PMID: 26061751 PMCID: PMC4530011 DOI: 10.1056/nejmoa1402121] [Citation(s) in RCA: 2118] [Impact Index Per Article: 235.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
BACKGROUND Diffuse low-grade and intermediate-grade gliomas (which together make up the lower-grade gliomas, World Health Organization grades II and III) have highly variable clinical behavior that is not adequately predicted on the basis of histologic class. Some are indolent; others quickly progress to glioblastoma. The uncertainty is compounded by interobserver variability in histologic diagnosis. Mutations in IDH, TP53, and ATRX and codeletion of chromosome arms 1p and 19q (1p/19q codeletion) have been implicated as clinically relevant markers of lower-grade gliomas. METHODS We performed genomewide analyses of 293 lower-grade gliomas from adults, incorporating exome sequence, DNA copy number, DNA methylation, messenger RNA expression, microRNA expression, and targeted protein expression. These data were integrated and tested for correlation with clinical outcomes. RESULTS Unsupervised clustering of mutations and data from RNA, DNA-copy-number, and DNA-methylation platforms uncovered concordant classification of three robust, nonoverlapping, prognostically significant subtypes of lower-grade glioma that were captured more accurately by IDH, 1p/19q, and TP53 status than by histologic class. Patients who had lower-grade gliomas with an IDH mutation and 1p/19q codeletion had the most favorable clinical outcomes. Their gliomas harbored mutations in CIC, FUBP1, NOTCH1, and the TERT promoter. Nearly all lower-grade gliomas with IDH mutations and no 1p/19q codeletion had mutations in TP53 (94%) and ATRX inactivation (86%). The large majority of lower-grade gliomas without an IDH mutation had genomic aberrations and clinical behavior strikingly similar to those found in primary glioblastoma. CONCLUSIONS The integration of genomewide data from multiple platforms delineated three molecular classes of lower-grade gliomas that were more concordant with IDH, 1p/19q, and TP53 status than with histologic class. Lower-grade gliomas with an IDH mutation either had 1p/19q codeletion or carried a TP53 mutation. Most lower-grade gliomas without an IDH mutation were molecularly and clinically similar to glioblastoma. (Funded by the National Institutes of Health.).
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Rickman KA, Lach FP, Abhyankar A, Donovan FX, Sanborn EM, Kennedy JA, Sougnez C, Gabriel SB, Elemento O, Chandrasekharappa SC, Schindler D, Auerbach AD, Smogorzewska A. Deficiency of UBE2T, the E2 Ubiquitin Ligase Necessary for FANCD2 and FANCI Ubiquitination, Causes FA-T Subtype of Fanconi Anemia. Cell Rep 2015; 12:35-41. [PMID: 26119737 DOI: 10.1016/j.celrep.2015.06.014] [Citation(s) in RCA: 98] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Revised: 05/28/2015] [Accepted: 06/03/2015] [Indexed: 02/03/2023] Open
Abstract
Fanconi anemia (FA) is a rare bone marrow failure and cancer predisposition syndrome resulting from pathogenic mutations in genes encoding proteins participating in the repair of DNA interstrand crosslinks (ICLs). Mutations in 17 genes (FANCA-FANCS) have been identified in FA patients, defining 17 complementation groups. Here, we describe an individual presenting with typical FA features who is deficient for the ubiquitin-conjugating enzyme (E2), UBE2T. UBE2T is known to interact with FANCL, the E3 ubiquitin-ligase component of the multiprotein FA core complex, and is necessary for the monoubiquitination of FANCD2 and FANCI. Proband fibroblasts do not display FANCD2 and FANCI monoubiquitination, do not form FANCD2 foci following treatment with mitomycin C, and are hypersensitive to crosslinking agents. These cellular defects are complemented by expression of wild-type UBE2T, demonstrating that deficiency of the protein UBE2T can lead to Fanconi anemia. UBE2T gene gains an alias of FANCT.
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Affiliation(s)
- Kimberly A Rickman
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY 10065, USA
| | - Francis P Lach
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY 10065, USA
| | | | - Frank X Donovan
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Erica M Sanborn
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY 10065, USA
| | - Jennifer A Kennedy
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY 10065, USA
| | - Carrie Sougnez
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Olivier Elemento
- Institute for Computational Biomedicine, Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10021, USA
| | - Settara C Chandrasekharappa
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Detlev Schindler
- Institute for Human Genetics, Biozentrum, Universität Würzburg, 97074 Würzburg, Germany
| | - Arleen D Auerbach
- Human Genetics and Hematology, The Rockefeller University, New York, NY 10065, USA
| | - Agata Smogorzewska
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY 10065, USA.
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16
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Kim H, Zheng S, Amini SS, Virk SM, Mikkelsen T, Brat DJ, Grimsby J, Sougnez C, Muller F, Hu J, Sloan AE, Cohen ML, Van Meir EG, Scarpace L, Laird PW, Weinstein JN, Lander ES, Gabriel S, Getz G, Meyerson M, Chin L, Barnholtz-Sloan JS, Verhaak RGW. Whole-genome and multisector exome sequencing of primary and post-treatment glioblastoma reveals patterns of tumor evolution. Genome Res 2015; 25:316-27. [PMID: 25650244 PMCID: PMC4352879 DOI: 10.1101/gr.180612.114] [Citation(s) in RCA: 285] [Impact Index Per Article: 31.7] [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] [Indexed: 02/07/2023]
Abstract
Glioblastoma (GBM) is a prototypical heterogeneous brain tumor refractory to conventional therapy. A small residual population of cells escapes surgery and chemoradiation, resulting in a typically fatal tumor recurrence ∼7 mo after diagnosis. Understanding the molecular architecture of this residual population is critical for the development of successful therapies. We used whole-genome sequencing and whole-exome sequencing of multiple sectors from primary and paired recurrent GBM tumors to reconstruct the genomic profile of residual, therapy resistant tumor initiating cells. We found that genetic alteration of the p53 pathway is a primary molecular event predictive of a high number of subclonal mutations in glioblastoma. The genomic road leading to recurrence is highly idiosyncratic but can be broadly classified into linear recurrences that share extensive genetic similarity with the primary tumor and can be directly traced to one of its specific sectors, and divergent recurrences that share few genetic alterations with the primary tumor and originate from cells that branched off early during tumorigenesis. Our study provides mechanistic insights into how genetic alterations in primary tumors impact the ensuing evolution of tumor cells and the emergence of subclonal heterogeneity.
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Affiliation(s)
- Hoon Kim
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Siyuan Zheng
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA; Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Seyed S Amini
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Selene M Virk
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, USA
| | - Tom Mikkelsen
- Departments of Neurology and Neurosurgery, Henry Ford Hospital, Detroit, Michigan 48202, USA
| | - Daniel J Brat
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | - Jonna Grimsby
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Carrie Sougnez
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Florian Muller
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Jian Hu
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Andrew E Sloan
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, USA; Brain Tumor and Neuro-oncology Center, Department of Neurosurgery, University Hospitals Case Medical Center, Case Western Reserve School of Medicine, Cleveland, Ohio 44106, USA
| | - Mark L Cohen
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, USA; Department of Pathology, University Hospitals Case Medical Center, Cleveland, Ohio 44106, USA
| | - Erwin G Van Meir
- Department of Neurosurgery and Hematology and Medical Oncology, Winship Cancer Institute and School of Medicine, Emory University, Atlanta, Georgia 30322, USA
| | - Lisa Scarpace
- Departments of Neurology and Neurosurgery, Henry Ford Hospital, Detroit, Michigan 48202, USA
| | - Peter W Laird
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, Michigan 49503, USA
| | - John N Weinstein
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Eric S Lander
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Stacey Gabriel
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Gad Getz
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Matthew Meyerson
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA
| | - Lynda Chin
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Jill S Barnholtz-Sloan
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, USA
| | - Roel G W Verhaak
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA; Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA;
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17
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Landau DA, Clement K, Ziller MJ, Boyle P, Fan J, Gu H, Stevenson K, Sougnez C, Wang L, Li S, Kotliar D, Zhang W, Ghandi M, Garraway L, Fernandes SM, Livak KJ, Gabriel S, Gnirke A, Lander ES, Brown JR, Neuberg D, Kharchenko PV, Hacohen N, Getz G, Meissner A, Wu CJ. Locally disordered methylation forms the basis of intratumor methylome variation in chronic lymphocytic leukemia. Cancer Cell 2014; 26:813-825. [PMID: 25490447 PMCID: PMC4302418 DOI: 10.1016/j.ccell.2014.10.012] [Citation(s) in RCA: 266] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Revised: 09/16/2014] [Accepted: 10/24/2014] [Indexed: 01/01/2023]
Abstract
Intratumoral heterogeneity plays a critical role in tumor evolution. To define the contribution of DNA methylation to heterogeneity within tumors, we performed genome-scale bisulfite sequencing of 104 primary chronic lymphocytic leukemias (CLLs). Compared with 26 normal B cell samples, CLLs consistently displayed higher intrasample variability of DNA methylation patterns across the genome, which appears to arise from stochastically disordered methylation in malignant cells. Transcriptome analysis of bulk and single CLL cells revealed that methylation disorder was linked to low-level expression. Disordered methylation was further associated with adverse clinical outcome. We therefore propose that disordered methylation plays a similar role to that of genetic instability, enhancing the ability of cancer cells to search for superior evolutionary trajectories.
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MESH Headings
- B-Lymphocytes/metabolism
- CpG Islands
- DNA Methylation
- Epigenesis, Genetic
- Gene Expression Regulation, Leukemic
- Genetic Variation
- Genome, Human
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/pathology
- Molecular Sequence Data
- Sequence Analysis, DNA
- Sulfites/chemistry
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Affiliation(s)
- Dan A Landau
- Cancer Vaccine Center, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Broad Institute, Cambridge, MA 02139, USA
| | - Kendell Clement
- Broad Institute, Cambridge, MA 02139, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA 02139, USA
| | - Michael J Ziller
- Broad Institute, Cambridge, MA 02139, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | | | - Jean Fan
- Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | | | - Kristen Stevenson
- Department of Biostatistics and Computational Biology, Dana Farber Cancer Institute, Boston, MA 02115, USA
| | | | - Lili Wang
- Cancer Vaccine Center, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Shuqiang Li
- Fluidigm, South San Francisco, CA 94080, USA
| | - Dylan Kotliar
- Cancer Vaccine Center, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Wandi Zhang
- Cancer Vaccine Center, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | | | - Levi Garraway
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Broad Institute, Cambridge, MA 02139, USA
| | - Stacey M Fernandes
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | | | | | | | | | - Jennifer R Brown
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Donna Neuberg
- Department of Biostatistics and Computational Biology, Dana Farber Cancer Institute, Boston, MA 02115, USA
| | - Peter V Kharchenko
- Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA; Division of Hematology/Oncology, Children's Hospital, Boston, MA 02115, USA
| | - Nir Hacohen
- Broad Institute, Cambridge, MA 02139, USA; Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Gad Getz
- Broad Institute, Cambridge, MA 02139, USA; Cancer Center and Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Alexander Meissner
- Broad Institute, Cambridge, MA 02139, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA.
| | - Catherine J Wu
- Cancer Vaccine Center, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Division of Hematology/Oncology, Children's Hospital, Boston, MA 02115, USA.
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18
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Kim H, Zheng S, Amini S, Virk S, Mikkelsen T, Brat D, Sougnez C, Muller F, Hu J, Sloan A, Cohen M, Van Meir E, Scarpace L, Lander E, Gabriel S, Getz G, Meyerson M, Chin L, Barnholtz-Sloan J, Verhaak R. GE-17 * ALTERATION OF THE p53 PATHWAY AND ANCESTRAL PROGENITORS ARE ASSOCIATED WITH TUMOR RECURRENCE IN GLIOBLASTOMA. Neuro Oncol 2014. [DOI: 10.1093/neuonc/nou256.17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Adalsteinsson VA, Lohr JG, Cibulskis K, Choudhury AD, Rosenberg M, Cruz-Gordillo P, Francis J, Zhang C, Shalek AK, Satija R, Trombetta JT, Lu D, Tallapragada N, Tahirova NT, Kim S, Blumenstiel B, Sougnez C, Auclair D, Allen EMV, Nakabayashi M, Lis RT, Lee GSM, Li T, Chabot MS, Taplin ME, Clancy TE, Loda M, Regev A, Meyerson M, Hahn WC, Kantoff PW, Golub TR, Getz G, Boehm JS, Love JC. Abstract 993: Whole exome sequencing of CTCs as a window into metastatic cancer. Cancer Res 2014. [DOI: 10.1158/1538-7445.am2014-993] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [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
Abstract
Comprehensive analysis of cancer genomes in clinical settings holds the promise to inform prognoses and guide the deployment of precise cancer treatments. A major barrier, however, is the inaccessibility of adequate metastatic tissue for accurate genomic analysis. The recognition that circulating tumor cells (CTCs) are present in many advanced cancer patients suggests an exciting opportunity to overcome this challenge. For instance, if CTCs could be comprehensively sequenced, it would be possible to obtain an orthogonal sample of the tumor burden_including subsets of transiting cells bound for metastatic colonization_potentially yielding new insights to complement the static sampling of resected or biopsied lesions.
We report an integrated process to isolate, qualify, and sequence whole exomes of CTCs with high fidelity, using a census-based sequencing strategy. We isolated CTCs by magnetic bead purification (Illumina MagSweeper) from the blood of patients with prostate cancer, and integrated a nanowell platform to automatically image and recover candidate single CTCs. We then developed a strategy to qualify individual CTC-derived libraries for DNA sequencing after whole genome amplification, and established an analytical framework for accurate calling of mutations using census-based sequencing and MuTect. Whole exome sequencing was performed on 20 single CTCs, obtained from a patient with advanced prostate cancer. We validated our sequencing process by comparing CTC-derived mutations to mutations found in a lymph node metastasis and nine separate cores of the primary tumor. 51 of 73 CTC mutations (70%) were observed in the metastasis or the primary tumor. Moreover, we identified 9 early trunk mutations and 56 metastatic trunk mutations in the non-CTC tumor samples and found 100% and 73% of these, respectively, in CTC exomes. Our work demonstrates the feasibility of CTC sequencing and the ability to confidently call somatic mutations. CTCs may therefore represent a non-invasive window into the mutational landscape of metastatic cancer, and may have utility for genomics in clinical practice.
Citation Format: Viktor A. Adalsteinsson, Jens G. Lohr, Kristian Cibulskis, Atish D. Choudhury, Mara Rosenberg, Peter Cruz-Gordillo, Joshua Francis, ChengZhong Zhang, Alexander K. Shalek, Rahul Satija, John T. Trombetta, Diana Lu, Naren Tallapragada, Narmin T. Tahirova, Sora Kim, Brendan Blumenstiel, Carrie Sougnez, Daniel Auclair, Eliezer M. Van Allen, Mari Nakabayashi, Rosina T. Lis, Gwo-Shu M. Lee, Tiantian Li, Matthew S. Chabot, Mary-Ellen Taplin, Thomas E. Clancy, Massimo Loda, Aviv Regev, Matthew Meyerson, William C. Hahn, Philip W. Kantoff, Todd R. Golub, Gad Getz, Jesse S. Boehm, J Christopher Love. Whole exome sequencing of CTCs as a window into metastatic cancer. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 993. doi:10.1158/1538-7445.AM2014-993
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Kim H, Zheng S, Amini SS, Virk SM, Mikkelsen T, Brat DJ, Grimsby J, Sougnez C, Sloan AE, Cohen ML, Meir EGV, Scarpace L, Laird PW, Weinstein JN, Lander E, Gabriel S, Getz G, Meyerson M, Chin L, Barnholtz-Sloan JS, Verhaak RG. Abstract 984: Alteration of the p53 pathway is associated with subclonal tumor progression in glioblastoma. Cancer Res 2014. [DOI: 10.1158/1538-7445.am2014-984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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
Abstract
To evaluate evolutionary patterns in progression and therapy-resistance of GBM, we analyzed the genomic profiles of 252 GBM samples from The Cancer Genome Atlas (TCGA)1, including 48 multi-sector and recurrent tumor biopsies taken from 17 pairs of pre- and post-treatment GBMs, to understand 1) the intratumoral heterogeneity of GBM and 2) how GBM responds to therapeutic intervention.
We integrated variant allele fraction, DNA copy number and genotype information to determine clonality of all mutations and found that 69.5% of mutations (median across samples 70.1% ± 19.6%) were classified as clonal and 30.5% as subclonal. To verify our classification approach, we classified mutations detected in two non-overlapping biopsies from 11 tumors into clonal and subclonal categories. Of mutations detected in both tumor sectors 86.2% were classified as clonal and 45.2% of sample-private mutations were categorized as clonal, which was a strongly significant difference (P = 1.8×10-87).
Separating patients into discrete age groups by an interval of 10 years, we found a significant linear correlation between clonal mutations and age (P < 0.001). This observation supports the notion that clonal mutations predominantly accumulated over the life span of the cell population that gave rise to the cell of origin before neoplastic onset2. No correlation with age was found for subclonal mutations. In contrast, the frequency of subclonal mutations was strongly correlated with the presence of alterations related to the p53 pathway (P < 0.001), particularly TP53 point mutation or amplification of MDM2. This observation raises the possibility that p53 pathway alterations stimulate subclonal evolution, possibly by providing greater tolerance to DNA damage and/or suppression of apoptosis3.
To evaluate the effects of clonal heterogeneity on disease recurrence, we analyzed matched pairs of primary and recurrent GBM, including five pairs with mutated TP53 and nine pairs with wildtype TP53. Recurrent TP53 mutant GBM showed a further and significant increase in the subclonal mutation frequency. In contrast, TP53 wildtype tumors showed an increase in the frequency of clonal mutations compared to their matched primary tumor. These data suggest that TP53 mutant GBM became increasingly clonally complex at time of recurrence, whereas TP53 wildtype GBM showed a reduced level of intratumoral heterogeneity. We observed an ultramutator phenotype in three recurrent tumors, associated with temozolomide treatment.
Our results suggest that mutations in the p53 pathway affect the response to therapy by supporting greater intratumoral heterogeneity. Paradoxically we observe a trend towards improved event free survival in samples with high subclonal mutation frequency. Further research is needed to assess whether the level of intratumoral heterogeneity is a reflection of the molecular portrait of GBM progression.
Citation Format: Hoon Kim, Siyuan Zheng, Seyed S. Amini, Selene M. Virk, Tom Mikkelsen, Daniel J. Brat, Jonna Grimsby, Carrie Sougnez, Andrew E. Sloan, Mark L. Cohen, Erwin G. Van Meir, Lisa Scarpace, The Cancer Genome Research Network, Peter W. Laird, John N. Weinstein, Eric Lander, Stacey Gabriel, Gad Getz, Matthew Meyerson, Lynda Chin, Jill S. Barnholtz-Sloan, Roel G.w. Verhaak. Alteration of the p53 pathway is associated with subclonal tumor progression in glioblastoma. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 984. doi:10.1158/1538-7445.AM2014-984
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Affiliation(s)
- Hoon Kim
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Siyuan Zheng
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Seyed S. Amini
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | | | - Jonna Grimsby
- 5The Broad Institute of MIT and Harvard, Cambridge, MA
| | | | | | | | | | | | | | | | - Eric Lander
- 5The Broad Institute of MIT and Harvard, Cambridge, MA
| | | | - Gad Getz
- 5The Broad Institute of MIT and Harvard, Cambridge, MA
| | | | - Lynda Chin
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
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Verhaak RGW, Kim H, Zheng S, Amini SS, Virk SM, Mikkelsen T, Brat DJ, Grimsby J, Sougnez C, Muller F, Hu J, Sloan AE, Cohen ML, Van Meir EG, Scarpace L, Laird PW, Weinstein JN, Lander E, Gabriel S, Getz G, Meyerson M, Chin L, Barnholtz-Sloan JS. THE P53 PATHWAY AND ANCESTRAL PROGENITORS ARE ASSOCIATED WITH TUMOR RECURRENCE IN GLIOBLASTOMA. Neuro Oncol 2014. [DOI: 10.1093/neuonc/nou206.10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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22
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Cho J, Bass AJ, Lawrence MS, Cibulskis K, Cho A, Lee SN, Yamauchi M, Wagle N, Pochanard P, Kim N, Park AK, Won J, Hur HS, Greulich H, Ogino S, Sougnez C, Voet D, Tabernero J, Jimenez J, Baselga J, Gabriel SB, Lander ES, Getz G, Eck MJ, Park WY, Meyerson M. Colon cancer-derived oncogenic EGFR G724S mutant identified by whole genome sequence analysis is dependent on asymmetric dimerization and sensitive to cetuximab. Mol Cancer 2014; 13:141. [PMID: 24894453 PMCID: PMC4072491 DOI: 10.1186/1476-4598-13-141] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [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: 02/07/2014] [Accepted: 05/23/2014] [Indexed: 12/19/2022] Open
Abstract
Background Inhibition of the activated epidermal growth factor receptor (EGFR) with either enzymatic kinase inhibitors or anti-EGFR antibodies such as cetuximab, is an effective modality of treatment for multiple human cancers. Enzymatic EGFR inhibitors are effective for lung adenocarcinomas with somatic kinase domain EGFR mutations while, paradoxically, anti-EGFR antibodies are more effective in colon and head and neck cancers where EGFR mutations occur less frequently. In colorectal cancer, anti-EGFR antibodies are routinely used as second-line therapy of KRAS wild-type tumors. However, detailed mechanisms and genomic predictors for pharmacological response to these antibodies in colon cancer remain unclear. Findings We describe a case of colorectal adenocarcinoma, which was found to harbor a kinase domain mutation, G724S, in EGFR through whole genome sequencing. We show that G724S mutant EGFR is oncogenic and that it differs from classic lung cancer derived EGFR mutants in that it is cetuximab responsive in vitro, yet relatively insensitive to small molecule kinase inhibitors. Through biochemical and cellular pharmacologic studies, we have determined that cells harboring the colon cancer-derived G719S and G724S mutants are responsive to cetuximab therapy in vitro and found that the requirement for asymmetric dimerization of these mutant EGFR to promote cellular transformation may explain their greater inhibition by cetuximab than small-molecule kinase inhibitors. Conclusion The colon-cancer derived G719S and G724S mutants are oncogenic and sensitive in vitro to cetuximab. These data suggest that patients with these mutations may benefit from the use of anti-EGFR antibodies as part of the first-line therapy.
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Affiliation(s)
- Jeonghee Cho
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston MA 02115, USA.
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23
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McFadden DG, Papagiannakopoulos T, Taylor-Weiner A, Stewart C, Carter SL, Cibulskis K, Bhutkar A, McKenna A, Dooley A, Vernon A, Sougnez C, Malstrom S, Heimann M, Park J, Chen F, Farago AF, Dayton T, Shefler E, Gabriel S, Getz G, Jacks T. Genetic and clonal dissection of murine small cell lung carcinoma progression by genome sequencing. Cell 2014; 156:1298-1311. [PMID: 24630729 DOI: 10.1016/j.cell.2014.02.031] [Citation(s) in RCA: 204] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2013] [Revised: 11/27/2013] [Accepted: 02/12/2014] [Indexed: 12/14/2022]
Abstract
Small cell lung carcinoma (SCLC) is a highly lethal, smoking-associated cancer with few known targetable genetic alterations. Using genome sequencing, we characterized the somatic evolution of a genetically engineered mouse model (GEMM) of SCLC initiated by loss of Trp53 and Rb1. We identified alterations in DNA copy number and complex genomic rearrangements and demonstrated a low somatic point mutation frequency in the absence of tobacco mutagens. Alterations targeting the tumor suppressor Pten occurred in the majority of murine SCLC studied, and engineered Pten deletion accelerated murine SCLC and abrogated loss of Chr19 in Trp53; Rb1; Pten compound mutant tumors. Finally, we found evidence for polyclonal and sequential metastatic spread of murine SCLC by comparative sequencing of families of related primary tumors and metastases. We propose a temporal model of SCLC tumorigenesis with implications for human SCLC therapeutics and the nature of cancer-genome evolution in GEMMs.
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Affiliation(s)
- David G McFadden
- Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Thales Papagiannakopoulos
- Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Amaro Taylor-Weiner
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Chip Stewart
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Scott L Carter
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kristian Cibulskis
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Arjun Bhutkar
- Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Aaron McKenna
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Alison Dooley
- Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Amanda Vernon
- Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Carrie Sougnez
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Scott Malstrom
- Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Megan Heimann
- Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Jennifer Park
- Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Frances Chen
- Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Anna F Farago
- Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Talya Dayton
- Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Erica Shefler
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Stacey Gabriel
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Gad Getz
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Cancer Center and Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA.
| | - Tyler Jacks
- Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
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Helman E, Lawrence MS, Stewart C, Sougnez C, Getz G, Meyerson M. Somatic retrotransposition in human cancer revealed by whole-genome and exome sequencing. Genome Res 2014; 24:1053-63. [PMID: 24823667 PMCID: PMC4079962 DOI: 10.1101/gr.163659.113] [Citation(s) in RCA: 158] [Impact Index Per Article: 15.8] [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] [Indexed: 01/27/2023]
Abstract
Retrotransposons constitute a major source of genetic variation, and somatic retrotransposon insertions have been reported in cancer. Here, we applied TranspoSeq, a computational framework that identifies retrotransposon insertions from sequencing data, to whole genomes from 200 tumor/normal pairs across 11 tumor types as part of The Cancer Genome Atlas (TCGA) Pan-Cancer Project. In addition to novel germline polymorphisms, we find 810 somatic retrotransposon insertions primarily in lung squamous, head and neck, colorectal, and endometrial carcinomas. Many somatic retrotransposon insertions occur in known cancer genes. We find that high somatic retrotransposition rates in tumors are associated with high rates of genomic rearrangement and somatic mutation. Finally, we developed TranspoSeq-Exome to interrogate an additional 767 tumor samples with hybrid-capture exome data and discovered 35 novel somatic retrotransposon insertions into exonic regions, including an insertion into an exon of the PTEN tumor suppressor gene. The results of this large-scale, comprehensive analysis of retrotransposon movement across tumor types suggest that somatic retrotransposon insertions may represent an important class of structural variation in cancer.
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Affiliation(s)
- Elena Helman
- Harvard-MIT Division of Health Sciences & Technology, Cambridge, Massachusetts 02139, USA; Broad Institute of MIT and Harvard, Cambridge, Masachusetts 02142, USA
| | | | - Chip Stewart
- Broad Institute of MIT and Harvard, Cambridge, Masachusetts 02142, USA
| | - Carrie Sougnez
- Broad Institute of MIT and Harvard, Cambridge, Masachusetts 02142, USA
| | - Gad Getz
- Broad Institute of MIT and Harvard, Cambridge, Masachusetts 02142, USA; Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - Matthew Meyerson
- Harvard-MIT Division of Health Sciences & Technology, Cambridge, Massachusetts 02139, USA; Broad Institute of MIT and Harvard, Cambridge, Masachusetts 02142, USA; Center for Cancer Genome Discovery and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA; Department of Pathology, Brigham & Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
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25
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Lohr JG, Adalsteinsson VA, Cibulskis K, Choudhury AD, Rosenberg M, Cruz-Gordillo P, Francis JM, Zhang CZ, Shalek AK, Satija R, Trombetta JJ, Lu D, Tallapragada N, Tahirova N, Kim S, Blumenstiel B, Sougnez C, Lowe A, Wong B, Auclair D, Van Allen EM, Nakabayashi M, Lis RT, Lee GSM, Li T, Chabot MS, Ly A, Taplin ME, Clancy TE, Loda M, Regev A, Meyerson M, Hahn WC, Kantoff PW, Golub TR, Getz G, Boehm JS, Love JC. Whole-exome sequencing of circulating tumor cells provides a window into metastatic prostate cancer. Nat Biotechnol 2014; 32:479-84. [PMID: 24752078 PMCID: PMC4034575 DOI: 10.1038/nbt.2892] [Citation(s) in RCA: 429] [Impact Index Per Article: 42.9] [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: 10/25/2013] [Accepted: 03/30/2014] [Indexed: 02/06/2023]
Abstract
Comprehensive analyses of cancer genomes promise to inform prognoses and precise cancer treatments. A major barrier, however, is inaccessibility of metastatic tissue. A potential solution is to characterize circulating tumor cells (CTCs), but this requires overcoming the challenges of isolating rare cells and sequencing low-input material. Here we report an integrated process to isolate, qualify and sequence whole exomes of CTCs with high fidelity using a census-based sequencing strategy. Power calculations suggest that mapping of >99.995% of the standard exome is possible in CTCs. We validated our process in two patients with prostate cancer, including one for whom we sequenced CTCs, a lymph node metastasis and nine cores of the primary tumor. Fifty-one of 73 CTC mutations (70%) were present in matched tissue. Moreover, we identified 10 early trunk and 56 metastatic trunk mutations in the non-CTC tumor samples and found 90% and 73% of these mutations, respectively, in CTC exomes. This study establishes a foundation for CTC genomics in the clinic.
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Affiliation(s)
- Jens G Lohr
- 1] The Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA. [2] Dana-Farber Cancer Institute, Boston, Massachusetts, USA. [3] Harvard Medical School, Boston, Massachusetts, USA. [4]
| | - Viktor A Adalsteinsson
- 1] The Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA. [2] Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA. [3]
| | - Kristian Cibulskis
- 1] The Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA. [2]
| | - Atish D Choudhury
- 1] The Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA. [2] Dana-Farber Cancer Institute, Boston, Massachusetts, USA. [3] Harvard Medical School, Boston, Massachusetts, USA
| | - Mara Rosenberg
- The Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Peter Cruz-Gordillo
- The Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Joshua M Francis
- 1] The Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA. [2] Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Cheng-Zhong Zhang
- 1] The Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA. [2] Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Alex K Shalek
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Rahul Satija
- The Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - John J Trombetta
- The Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Diana Lu
- The Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Naren Tallapragada
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Narmin Tahirova
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Sora Kim
- The Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Brendan Blumenstiel
- The Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Carrie Sougnez
- The Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Alarice Lowe
- Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Bang Wong
- The Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Daniel Auclair
- The Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Eliezer M Van Allen
- 1] The Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA. [2] Dana-Farber Cancer Institute, Boston, Massachusetts, USA. [3] Harvard Medical School, Boston, Massachusetts, USA
| | - Mari Nakabayashi
- 1] Dana-Farber Cancer Institute, Boston, Massachusetts, USA. [2] Harvard Medical School, Boston, Massachusetts, USA
| | - Rosina T Lis
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Gwo-Shu M Lee
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Tiantian Li
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | | | - Amy Ly
- Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Mary-Ellen Taplin
- 1] Dana-Farber Cancer Institute, Boston, Massachusetts, USA. [2] Harvard Medical School, Boston, Massachusetts, USA
| | - Thomas E Clancy
- 1] Dana-Farber Cancer Institute, Boston, Massachusetts, USA. [2] Harvard Medical School, Boston, Massachusetts, USA. [3] Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Massimo Loda
- 1] The Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA. [2] Dana-Farber Cancer Institute, Boston, Massachusetts, USA. [3] Harvard Medical School, Boston, Massachusetts, USA. [4] Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Aviv Regev
- 1] The Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA. [2] Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA. [3] Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
| | - Matthew Meyerson
- 1] The Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA. [2] Dana-Farber Cancer Institute, Boston, Massachusetts, USA. [3] Harvard Medical School, Boston, Massachusetts, USA
| | - William C Hahn
- 1] The Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA. [2] Dana-Farber Cancer Institute, Boston, Massachusetts, USA. [3] Harvard Medical School, Boston, Massachusetts, USA. [4] Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Philip W Kantoff
- 1] Dana-Farber Cancer Institute, Boston, Massachusetts, USA. [2] Harvard Medical School, Boston, Massachusetts, USA
| | - Todd R Golub
- 1] The Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA. [2] Dana-Farber Cancer Institute, Boston, Massachusetts, USA. [3] Harvard Medical School, Boston, Massachusetts, USA. [4] Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
| | - Gad Getz
- 1] The Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA. [2] Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Jesse S Boehm
- The Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - J Christopher Love
- 1] The Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA. [2] Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA. [3] Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
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Brennan C, Verhaak R, McKenna A, Campos B, Noushmehr H, Salama S, Zheng S, Chakravarty D, Sanborn J, Berman S, Beroukhim R, Bernard B, Wu CJ, Genovese G, Shmulevich I, Barnholtz-Sloan J, Zou L, Vegesna R, Shukla S, Ciriello G, Yung W, Zhang W, Sougnez C, Mikkelsen T, Aldape K, Bigner D, Van Meir E, Prados M, Sloan A, Black K, Eschbacher J, Finocchiaro G, Friedman W, Andrews D, Guha A, Iacocca M, O’Neill B, Foltz G, Myers J, Weisenberger D, Penny R, Kucherlapati R, Perou C, Hayes D, Gibbs R, Marra M, Mills G, Lander E, Spellman P, Wilson R, Sander C, Weinstein J, Meyerson M, Gabriel S, Laird P, Haussler D, Getz G, Chin L. The Somatic Genomic Landscape of Glioblastoma. Cell 2014. [DOI: 10.1016/j.cell.2014.04.004] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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27
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Rosenberg JE, Kim J, Cherniack A, Sougnez C, Meyerson M, Getz G, Weinstein JN, Lerner SP, Kwiatkowski DJ. Somatic genomic alterations in urothelial cancer: Results of the Cancer Genome Atlas (TCGA) bladder cancer (BC) analysis. J Clin Oncol 2014. [DOI: 10.1200/jco.2014.32.4_suppl.285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
285 Background: We report here an integrated analysis of mutation and somatic copy number alterations (SCNAs) in 131 BCs to provide a comprehensive landscape of molecular alterations. Methods: Exon capture, whole exome sequencing (WES), and SNP arrays were performed on 131 MIBCs with no prior chemotherapy treatment, analyzed using the Cancer Genome Atlas Firehose Pipeline, and validated using orthogonal methods. Significantly mutated genes (SMGs) were determined by MutSig v1.5. Recurrent SCNAs were identified via GISTIC 2.0. Consensus non-negative matrix factorization (CNMF) was used to identify SCNA and SMG clusters. Results: 32 genes showed statistically significant levels of recurrent somatic mutation. Known druggable SMGs included FGFR3 (12%), PIK3CA (20%), TSC1 (8%), and ERBB3 (11%). CDKN1A (14%), ERCC2 (12%), RXRA (9%), ELF3 (8%), KLF5 (8%), FOXQ1 (5%), RHOB (5%), PAIP1 (5%), and BTG2 (5%) were not previously reported as SMGs in any other TCGA cancer type. Truncating mutations in 4 SMGs involved in epigenetic regulation (MLL2, ARID1A, KDM6A, and EP300) were significantly enriched. Clustering of both SMGs and focal SNCAs in 125 samples identified three distinct groups. Group A is highly enriched in focal SCNAs in several genes, as well as mutations in MLL2. Group B is enriched in papillary histology, loss of CDKN2A, and alterations in FGFR3. Group C has TP53 mutations, enrichment with RB1 mutations, and amplifications of E2F3 and CCNE1. There were no statistically significant associations between smoking status and the mutational spectrum, frequency of mutation in any SMG, focal SCNAs, or CNMF subtype. Conclusions: Analyses identified potential therapeutic targets in 69% of BCs, including 42% with targets in the PI3K/AKT/mTOR pathway and 45% with targets (including ERBB2) in the RTK/MAPK pathway. Clustering reveals 3 groups with differences in pattern of genomic alteration suggesting the possibility of different pathogenic mechanisms of BC development. Epigenetic regulatory genes were more frequently mutated in urothelial carcinoma than in any common cancer studied to date, suggesting the future possibility of targeted therapy for chromatin abnormalities.
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Affiliation(s)
| | - Jaegil Kim
- Broad Institute of Harvard and MIT, Cambridge, MA
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28
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Lohr JG, Stojanov P, Carter SL, Cruz-Gordillo P, Lawrence MS, Auclair D, Sougnez C, Knoechel B, Gould J, Saksena G, Cibulskis K, McKenna A, Chapman MA, Straussman R, Levy J, Perkins LM, Keats JJ, Schumacher SE, Rosenberg M, Getz G, Golub TR. Widespread genetic heterogeneity in multiple myeloma: implications for targeted therapy. Cancer Cell 2014; 25:91-101. [PMID: 24434212 PMCID: PMC4241387 DOI: 10.1016/j.ccr.2013.12.015] [Citation(s) in RCA: 741] [Impact Index Per Article: 74.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2013] [Revised: 10/09/2013] [Accepted: 12/23/2013] [Indexed: 01/17/2023]
Abstract
We performed massively parallel sequencing of paired tumor/normal samples from 203 multiple myeloma (MM) patients and identified significantly mutated genes and copy number alterations and discovered putative tumor suppressor genes by determining homozygous deletions and loss of heterozygosity. We observed frequent mutations in KRAS (particularly in previously treated patients), NRAS, BRAF, FAM46C, TP53, and DIS3 (particularly in nonhyperdiploid MM). Mutations were often present in subclonal populations, and multiple mutations within the same pathway (e.g., KRAS, NRAS, and BRAF) were observed in the same patient. In vitro modeling predicts only partial treatment efficacy of targeting subclonal mutations, and even growth promotion of nonmutated subclones in some cases. These results emphasize the importance of heterogeneity analysis for treatment decisions.
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Affiliation(s)
- Jens G Lohr
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02412, USA; Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Petar Stojanov
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02412, USA; Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Scott L Carter
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02412, USA
| | - Peter Cruz-Gordillo
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02412, USA
| | - Michael S Lawrence
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02412, USA
| | - Daniel Auclair
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02412, USA
| | - Carrie Sougnez
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02412, USA
| | - Birgit Knoechel
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02412, USA; Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Boston Children's Hospital, 350 Longwood Avenue, Boston, MA 02115, USA
| | - Joshua Gould
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02412, USA
| | - Gordon Saksena
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02412, USA
| | - Kristian Cibulskis
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02412, USA
| | - Aaron McKenna
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02412, USA
| | - Michael A Chapman
- Cambridge Institute for Medical Research, Addenbrooke's Hospital, Hills Road, Cambridge CB2 0XY, UK
| | - Ravid Straussman
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02412, USA
| | - Joan Levy
- The Multiple Myeloma Research Foundation, 383 Main Avenue, Fifth Floor, Norwalk, CT 06581, USA
| | - Louise M Perkins
- The Multiple Myeloma Research Foundation, 383 Main Avenue, Fifth Floor, Norwalk, CT 06581, USA
| | - Jonathan J Keats
- Translational Genomics Research Institute (TGen), 445 N. Fifth Street, Phoenix, AZ 85004, USA
| | - Steven E Schumacher
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02412, USA; Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Mara Rosenberg
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02412, USA
| | | | - Gad Getz
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02412, USA; Massachusetts General Hospital Cancer Center and Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Todd R Golub
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02412, USA; Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
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Brennan CW, Verhaak RGW, McKenna A, Campos B, Noushmehr H, Salama SR, Zheng S, Chakravarty D, Sanborn JZ, Berman SH, Beroukhim R, Bernard B, Wu CJ, Genovese G, Shmulevich I, Barnholtz-Sloan J, Zou L, Vegesna R, Shukla SA, Ciriello G, Yung WK, Zhang W, Sougnez C, Mikkelsen T, Aldape K, Bigner DD, Van Meir EG, Prados M, Sloan A, Black KL, Eschbacher J, Finocchiaro G, Friedman W, Andrews DW, Guha A, Iacocca M, O'Neill BP, Foltz G, Myers J, Weisenberger DJ, Penny R, Kucherlapati R, Perou CM, Hayes DN, Gibbs R, Marra M, Mills GB, Lander E, Spellman P, Wilson R, Sander C, Weinstein J, Meyerson M, Gabriel S, Laird PW, Haussler D, Getz G, Chin L. The somatic genomic landscape of glioblastoma. Cell 2013; 155:462-77. [PMID: 24120142 DOI: 10.1016/j.cell.2013.09.034] [Citation(s) in RCA: 3374] [Impact Index Per Article: 306.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Revised: 07/28/2013] [Accepted: 09/17/2013] [Indexed: 12/12/2022]
Abstract
We describe the landscape of somatic genomic alterations based on multidimensional and comprehensive characterization of more than 500 glioblastoma tumors (GBMs). We identify several novel mutated genes as well as complex rearrangements of signature receptors, including EGFR and PDGFRA. TERT promoter mutations are shown to correlate with elevated mRNA expression, supporting a role in telomerase reactivation. Correlative analyses confirm that the survival advantage of the proneural subtype is conferred by the G-CIMP phenotype, and MGMT DNA methylation may be a predictive biomarker for treatment response only in classical subtype GBM. Integrative analysis of genomic and proteomic profiles challenges the notion of therapeutic inhibition of a pathway as an alternative to inhibition of the target itself. These data will facilitate the discovery of therapeutic and diagnostic target candidates, the validation of research and clinical observations and the generation of unanticipated hypotheses that can advance our molecular understanding of this lethal cancer.
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Affiliation(s)
- Cameron W Brennan
- Human Oncology and Pathogenesis Program, Brain Tumor Center, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA; Department of Neurosurgery, Memorial Sloan-Kettering Cancer Center, Department of Neurological Surgery, Weill Cornell Medical Center, New York, NY 10065, USA.
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30
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Francis JM, Kiezun A, Ramos AH, Serra S, Pedamallu CS, Qian ZR, Banck MS, Kanwar R, Kulkarni AA, Karpathakis A, Manzo V, Contractor T, Philips J, Nickerson E, Pho N, Hooshmand SM, Brais LK, Lawrence MS, Pugh T, McKenna A, Sivachenko A, Cibulskis K, Carter SL, Ojesina AI, Freeman S, Jones RT, Voet D, Saksena G, Auclair D, Onofrio R, Shefler E, Sougnez C, Grimsby J, Green L, Lennon N, Meyer T, Caplin M, Chung DC, Beutler AS, Ogino S, Thirlwell C, Shivdasani R, Asa SL, Harris CR, Getz G, Kulke M, Meyerson M. Somatic mutation of CDKN1B in small intestine neuroendocrine tumors. Nat Genet 2013; 45:1483-6. [PMID: 24185511 DOI: 10.1038/ng.2821] [Citation(s) in RCA: 236] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Accepted: 10/10/2013] [Indexed: 12/11/2022]
Abstract
The diagnosed incidence of small intestine neuroendocrine tumors (SI-NETs) is increasing, and the underlying genomic mechanisms have not yet been defined. Using exome- and genome-sequence analysis of SI-NETs, we identified recurrent somatic mutations and deletions in CDKN1B, the cyclin-dependent kinase inhibitor gene, which encodes p27. We observed frameshift mutations of CDKN1B in 14 of 180 SI-NETs, and we detected hemizygous deletions encompassing CDKN1B in 7 out of 50 SI-NETs, nominating p27 as a tumor suppressor and implicating cell cycle dysregulation in the etiology of SI-NETs.
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Affiliation(s)
- Joshua M Francis
- 1] Broad Institute, Cambridge, Massachusetts, USA. [2] Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA. [3]
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31
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Kim H, Zheng S, Amini SS, Virk S, Mikkelsen T, Brat DJ, Grimsby J, Sougnez C, Sloan AE, Cohen ML, Van Meir EG, Scarpace L, Laird PW, Weinstein JN, Lander ES, Gabriel S, Getz G, Meyerson M, Chin L, Barnholtz-Sloan JS, Verhaak RGW. Abstract B130: The intratumoral heterogeneity of glioblastoma suggests a pivotal role for clonal evolution. Mol Cancer Ther 2013. [DOI: 10.1158/1535-7163.targ-13-b130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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
Abstract
To investigate therapy induced evolutionary patterns in glioblastoma (GBM), we completed whole exome sequencing of all samples, as well as transcriptome sequencing, DNA copy number, DNA methylation, and mRNA from at least one primary sample, and one (post-therapy) recurrent sample. Sample collection was enabled through The Cancer Genome Atlas Research Network (TCGA). Multiple spatially distinct samples were available for five primary and six recurrent cases, allowing the integration of intratumoral heterogeneity with the evolutionary processes that shape the tumor recurrence after therapeutic intervention.
Sample unique mutations were common, but most of the somatic variants in driver genes (like TP53 and EGFR) were preserved across the tumor and after therapy. We found that the therapeutic bottleneck resulted in proportionally higher numbers of (mostly clonal) mutations, reduced clonal complexity and changes in the mutation spectrum. GBM recurrence could be grouped into two categories, characterized by drastically different clonal evolution patterns. Our findings suggest that multi-sector sequencing sharpens the analysis but is not essential for precise delineation of the tumor progression process. Projecting our results on genomic data from 253 primary GBMs, we observed that the number of clonal, but not subclonal, mutations increased with age at diagnosis, and the two categories differed in their mutation spectrum.
This study represents an important advance toward comprehensive characterization of the genomic alterations of GBM before and after cytotoxic treatment and surgery. Our analysis of spatially and temporally distinct samples provides new insights into the relevance of intratumoral heterogeneity on disease progression in GBM.
Acknowledgements:
This work is supported by Award Numbers 5 P50 CA127001 and 5 P50 CA083639-12 from the National Cancer Institute (NCI) to RGWV. H.K. is supported in part by the Odyssey Program and Theodore N. Law Endowment for Scientific Achievement at The University of Texas MD Anderson Cancer Center. The results published here are in whole or part based upon data generated by The Cancer Genome Atlas project established by the NCI and NHGRI.
Citation Information: Mol Cancer Ther 2013;12(11 Suppl):B130.
Citation Format: Hoon Kim, Siyuan Zheng, Seyed S. Amini, Selene Virk, Tom Mikkelsen, Daniel J. Brat, Jonna Grimsby, Carrie Sougnez, Andrew E. Sloan, Mark L. Cohen, Erwin G. Van Meir, Lisa Scarpace, Peter W. Laird, John N. Weinstein, Eric S. Lander, Stacey Gabriel, Gaddy Getz, Matthew Meyerson, Lynda Chin, Jill S. Barnholtz-Sloan, Roeland GW Verhaak. The intratumoral heterogeneity of glioblastoma suggests a pivotal role for clonal evolution. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2013 Oct 19-23; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(11 Suppl):Abstract nr B130.
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Affiliation(s)
- Hoon Kim
- 1Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Siyuan Zheng
- 1Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Seyed S. Amini
- 1Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Selene Virk
- 2Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH
| | - Tom Mikkelsen
- 3Departments of Neurology and Neurosurgery, Henry Ford Hospital, Detroit, MI
| | - Daniel J. Brat
- 4Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA
| | - Jonna Grimsby
- 5The Broad Institute of MIT and Harvard, Cambridge, MA
| | | | - Andrew E. Sloan
- 2Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH
| | - Mark L. Cohen
- 2Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH
| | - Erwin G. Van Meir
- 4Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA
| | - Lisa Scarpace
- 3Departments of Neurology and Neurosurgery, Henry Ford Hospital, Detroit, MI
| | - Peter W. Laird
- 6USC Epigenome Center, University of Southern California, Los Angeles, CA
| | - John N. Weinstein
- 1Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | - Gaddy Getz
- 5The Broad Institute of MIT and Harvard, Cambridge, MA
| | | | - Lynda Chin
- 7Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Jill S. Barnholtz-Sloan
- 2Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH
| | - Roeland GW Verhaak
- 1Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX
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Adachi K, Sasaki H, Nagahisa S, Yoshida K, Hattori N, Nishiyama Y, Kawase T, Hasegawa M, Abe M, Hirose Y, Alentorn A, Marie Y, Poggioli S, Alshehhi H, Boisselier B, Carpentier C, Mokhtari K, Capelle L, Figarella-Branger D, Hoang-Xuan K, Sanson M, Delattre JY, Idbaih A, Yust-Katz S, Anderson M, Olar A, Eterovic A, Ezzeddine N, Chen K, Zhao H, Fuller G, Aldape K, de Groot J, Andor N, Harness J, Lopez SG, Fung TL, Mewes HW, Petritsch C, Arivazhagan A, Somasundaram K, Thennarasu K, Pandey P, Anandh B, Santosh V, Chandramouli B, Hegde A, Kondaiah P, Rao M, Bell R, Kang R, Hong C, Song J, Costello J, Bell R, Nagarajan R, Zhang B, Diaz A, Wang T, Song J, Costello J, Bie L, Li Y, Li Y, Liu H, Luyo WFC, Carnero MH, Iruegas MEP, Morell AR, Figueiras MC, Lopez RL, Valverde CF, Chan AKY, Pang JCS, Chung NYF, Li KKW, Poon WS, Chan DTM, Wang Y, Ng HAK, Chaumeil M, Larson P, Yoshihara H, Vigneron D, Nelson S, Pieper R, Phillips J, Ronen S, Clark V, Omay ZE, Serin A, Gunel J, Omay B, Grady C, Youngblood M, Bilguvar K, Baehring J, Piepmeier J, Gutin P, Vortmeyer A, Brennan C, Pamir MN, Kilic T, Krischek B, Simon M, Yasuno K, Gunel M, Cohen AL, Sato M, Aldape KD, Mason C, Diefes K, Heathcock L, Abegglen L, Shrieve D, Couldwell W, Schiffman JD, Colman H, D'Alessandris QG, Cenci T, Martini M, Ricci-Vitiani L, De Maria R, Larocca LM, Pallini R, de Groot J, Theeler B, Aldape K, Lang F, Rao G, Gilbert M, Sulman E, Luthra R, Eterovic K, Chen K, Routbort M, Verhaak R, Mills G, Mendelsohn J, Meric-Bernstam F, Yung A, MacArthur K, Hahn S, Kao G, Lustig R, Alonso-Basanta M, Chandrasekaran S, Wileyto EP, Reyes E, Dorsey J, Fujii K, Kurozumi K, Ichikawa T, Onishi M, Ishida J, Shimazu Y, Kaur B, Chiocca EA, Date I, Geisenberger C, Mock A, Warta R, Schwager C, Hartmann C, von Deimling A, Abdollahi A, Herold-Mende C, Gevaert O, Achrol A, Gholamin S, Mitra S, Westbroek E, Loya J, Mitchell L, Chang S, Steinberg G, Plevritis S, Cheshier S, Gevaert O, Mitchell L, Achrol A, Xu J, Steinberg G, Cheshier S, Napel S, Zaharchuk G, Plevritis S, Gevaert O, Achrol A, Chang S, Harsh G, Steinberg G, Cheshier S, Plevritis S, Gutman D, Holder C, Colen R, Dunn W, Jain R, Cooper L, Hwang S, Flanders A, Brat D, Hayes J, Droop A, Thygesen H, Boissinot M, Westhead D, Short S, Lawler S, Bady P, Kurscheid S, Delorenzi M, Hegi ME, Crosby C, Faulkner C, Smye-Rumsby T, Kurian K, Williams M, Hopkins K, Faulkner C, Palmer A, Williams H, Wragg C, Haynes HR, Williams M, Hopkins K, Kurian KM, Haynes HR, Crosby C, Williams H, White P, Hopkins K, Williams M, Kurian KM, Ishida J, Kurozumi K, Ichikawa T, Onishi M, Fujii K, Shimazu Y, Oka T, Date I, Jalbert L, Elkhaled A, Phillips J, Chang S, Nelson S, Jensen R, Salzman K, Schabel M, Gillespie D, Mumert M, Johnson B, Mazor T, Hong C, Barnes M, Yamamoto S, Ueda H, Tatsuno K, Aihara K, Jalbert L, Nelson S, Bollen A, Hirst M, Marra M, Mukasa A, Saito N, Aburatani H, Berger M, Chang S, Taylor B, Costello J, Popov S, Mackay A, Ingram W, Burford A, Jury A, Vinci M, Jones C, Jones DTW, Hovestadt V, Picelli S, Wang W, Northcott PA, Kool M, Reifenberger G, Pietsch T, Sultan M, Lehrach H, Yaspo ML, Borkhardt A, Landgraf P, Eils R, Korshunov A, Zapatka M, Radlwimmer B, Pfister SM, Lichter P, Joy A, Smirnov I, Reiser M, Shapiro W, Mills G, Kim S, Feuerstein B, Jungk C, Mock A, Geisenberger C, Warta R, Friauf S, Unterberg A, Herold-Mende C, Juratli TA, McElroy J, Meng W, Huebner A, Geiger KD, Krex D, Schackert G, Chakravarti A, Lautenschlaeger T, Kim BY, Jiang W, Beiko J, Prabhu S, DeMonte F, Lang F, Gilbert M, Aldape K, Sawaya R, Cahill D, McCutcheon I, Lau C, Wang L, Terashima K, Yamaguchi S, Burstein M, Sun J, Suzuki T, Nishikawa R, Nakamura H, Natsume A, Terasaka S, Ng HK, Muzny D, Gibbs R, Wheeler D, Lautenschlaeger T, Juratli TA, McElroy J, Meng W, Huebner A, Geiger KD, Krex D, Schackert G, Chakravarti A, Zhang XQ, Sun S, Lam KF, Kiang KMY, Pu JKS, Ho ASW, Leung GKK, Loebel F, Curry WT, Barker FG, Lelic N, Chi AS, Cahill DP, Lu D, Yin J, Teo C, McDonald K, Madhankumar A, Weston C, Slagle-Webb B, Sheehan J, Patel A, Glantz M, Connor J, Maire C, Francis J, Zhang CZ, Jung J, Manzo V, Adalsteinsson V, Homer H, Blumenstiel B, Pedamallu CS, Nickerson E, Ligon A, Love C, Meyerson M, Ligon K, Mazor T, Johnson B, Hong C, Barnes M, Jalbert LE, Nelson SJ, Bollen AW, Smirnov IV, Song JS, Olshen AB, Berger MS, Chang SM, Taylor BS, Costello JF, Mehta S, Armstrong B, Peng S, Bapat A, Berens M, Melendez B, Mollejo M, Mur P, Hernandez-Iglesias T, Fiano C, Ruiz J, Rey JA, Mock A, Stadler V, Schulte A, Lamszus K, Schichor C, Westphal M, Tonn JC, Unterberg A, Herold-Mende C, Morozova O, Katzman S, Grifford M, Salama S, Haussler D, Nagarajan R, Zhang B, Johnson B, Bell R, Olshen A, Fouse S, Diaz A, Smirnov I, Kang R, Wang T, Costello J, Nakamizo S, Sasayama T, Tanaka H, Tanaka K, Mizukawa K, Yoshida M, Kohmura E, Northcott P, Hovestadt V, Jones D, Kool M, Korshunov A, Lichter P, Pfister S, Otani R, Mukasa A, Takayanagi S, Saito K, Tanaka S, Shin M, Saito N, Ozawa T, Riester M, Cheng YK, Huse J, Helmy K, Charles N, Squatrito M, Michor F, Holland E, Perrech M, Dreher L, Rohn G, Goldbrunner R, Timmer M, Pollo B, Palumbo V, Calatozzolo C, Patane M, Nunziata R, Farinotti M, Silvani A, Lodrini S, Finocchiaro G, Lopez E, Rioscovian A, Ruiz R, Siordia G, de Leon AP, Rostomily C, Rostomily R, Silbergeld D, Kolstoe D, Chamberlain M, Silber J, Roth P, Keller A, Hoheisel J, Codo P, Bauer A, Backes C, Leidinger P, Meese E, Thiel E, Korfel A, Weller M, Saito K, Mukasa A, Nagae G, Nagane M, Aihara K, Takayanagi S, Tanaka S, Aburatani H, Saito N, Salama S, Sanborn JZ, Grifford M, Brennan C, Mikkelsen T, Jhanwar S, Chin L, Haussler D, Sasayama T, Tanaka K, Nakamizo S, Nishihara M, Tanaka H, Mizukawa K, Kohmura E, Schliesser M, Grimm C, Weiss E, Claus R, Weichenhan D, Weiler M, Hielscher T, Sahm F, Wiestler B, Klein AC, Blaes J, Weller M, Plass C, Wick W, Stragliotto G, Rahbar A, Soderberg-Naucler C, Sulman E, Won M, Ezhilarasan R, Sun P, Blumenthal D, Vogelbaum M, Colman H, Jenkins R, Chakravarti A, Jeraj R, Brown P, Jaeckle K, Schiff D, Dignam J, Atkins J, Brachman D, Werner-Wasik M, Gilbert M, Mehta M, Aldape K, Terashima K, Shen J, Luan J, Yu A, Suzuki T, Nishikawa R, Matsutani M, Liang Y, Man TK, Lau C, Trister A, Tokita M, Mikheeva S, Mikheev A, Friend S, Rostomily R, van den Bent M, Erdem L, Gorlia T, Taphoorn M, Kros J, Wesseling P, Dubbink H, Ibdaih A, Sanson M, French P, van Thuijl H, Mazor T, Johnson B, Fouse S, Heimans J, Wesseling P, Ylstra B, Reijneveld J, Taylor B, Berger M, Chang S, Costello J, Prabowo A, van Thuijl H, Scheinin I, van Essen H, Spliet W, Ferrier C, van Rijen P, Veersema T, Thom M, Meeteren ASV, Reijneveld J, Ylstra B, Wesseling P, Aronica E, Kim H, Zheng S, Mikkelsen T, Brat DJ, Virk S, Amini S, Sougnez C, Chin L, Barnholtz-Sloan J, Verhaak RGW, Watts C, Sottoriva A, Spiteri I, Piccirillo S, Touloumis A, Collins P, Marioni J, Curtis C, Tavare S, Weiss E, Grimm C, Schliesser M, Hielscher T, Claus R, Sahm F, Wiestler B, Klein AC, Blaes J, Tews B, Weiler M, Weichenhan D, Hartmann C, Weller M, Plass C, Wick W, Yeung TPC, Al-Khazraji B, Morrison L, Hoffman L, Jackson D, Lee TY, Yartsev S, Bauman G, Zheng S, Fu J, Vegesna R, Mao Y, Heathcock LE, Torres-Garcia W, Ezhilarasan R, Wang S, McKenna A, Chin L, Brennan CW, Yung WKA, Weinstein JN, Aldape KD, Sulman EP, Chen K, Koul D, Verhaak RGW. OMICS AND PROGNSTIC MARKERS. Neuro Oncol 2013; 15:iii136-iii155. [PMCID: PMC3823898 DOI: 10.1093/neuonc/not183] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/21/2023] Open
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Zack TI, Schumacher SE, Carter SL, Cherniack AD, Saksena G, Tabak B, Lawrence MS, Zhsng CZ, Wala J, Mermel CH, Sougnez C, Gabriel SB, Hernandez B, Shen H, Laird PW, Getz G, Meyerson M, Beroukhim R. Pan-cancer patterns of somatic copy number alteration. Nat Genet 2013; 45:1134-40. [PMID: 24071852 PMCID: PMC3966983 DOI: 10.1038/ng.2760] [Citation(s) in RCA: 1281] [Impact Index Per Article: 116.5] [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] [Indexed: 02/07/2023]
Abstract
Determining how somatic copy number alterations (SCNAs) promote cancer is an important goal. We characterized SCNA patterns in 4,934 cancers from The Cancer Genome Atlas Pan-Cancer data set. Whole-genome doubling, observed in 37% of cancers, was associated with higher rates of every other type of SCNA, TP53 mutations, CCNE1 amplifications and alterations of the PPP2R complex. SCNAs that were internal to chromosomes tended to be shorter than telomere-bounded SCNAs, suggesting different mechanisms underlying their generation. Significantly recurrent focal SCNAs were observed in 140 regions, including 102 without known oncogene or tumor suppressor gene targets and 50 with significantly mutated genes. Amplified regions without known oncogenes were enriched for genes involved in epigenetic regulation. When levels of genomic disruption were accounted for, 7% of region pairs were anticorrelated, and these regions tended to encompass genes whose proteins physically interact, suggesting related functions. These results provide insights into mechanisms of generation and functional consequences of cancer-related SCNAs.
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Affiliation(s)
- Travis I Zack
- Broad Institute, Cambridge, Massachusetts, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA; Biophysics Program, Harvard University, Boston, Massachusetts, USA
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Lawrence MS, Stojanov P, Polak P, Kryukov GV, Cibulskis K, Sivachenko A, Carter SL, Stewart C, Mermel CH, Roberts SA, Kiezun A, Hammerman PS, McKenna A, Drier Y, Zou L, Ramos AH, Pugh TJ, Stransky N, Helman E, Kim J, Sougnez C, Ambrogio L, Nickerson E, Shefler E, Cortés ML, Auclair D, Saksena G, Voet D, Noble M, DiCara D, Lin P, Lichtenstein L, Heiman DI, Fennell T, Imielinski M, Hernandez B, Hodis E, Baca S, Dulak AM, Lohr J, Landau DA, Wu CJ, Melendez-Zajgla J, Hidalgo-Miranda A, Koren A, McCarroll SA, Mora J, Crompton B, Onofrio R, Parkin M, Winckler W, Ardlie K, Gabriel SB, Roberts CWM, Biegel JA, Stegmaier K, Bass AJ, Garraway LA, Meyerson M, Golub TR, Gordenin DA, Sunyaev S, Lander ES, Getz G. Mutational heterogeneity in cancer and the search for new cancer-associated genes. Nature 2013. [PMID: 23770567 DOI: 10.1038/nature12213.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Major international projects are underway that are aimed at creating a comprehensive catalogue of all the genes responsible for the initiation and progression of cancer. These studies involve the sequencing of matched tumour-normal samples followed by mathematical analysis to identify those genes in which mutations occur more frequently than expected by random chance. Here we describe a fundamental problem with cancer genome studies: as the sample size increases, the list of putatively significant genes produced by current analytical methods burgeons into the hundreds. The list includes many implausible genes (such as those encoding olfactory receptors and the muscle protein titin), suggesting extensive false-positive findings that overshadow true driver events. We show that this problem stems largely from mutational heterogeneity and provide a novel analytical methodology, MutSigCV, for resolving the problem. We apply MutSigCV to exome sequences from 3,083 tumour-normal pairs and discover extraordinary variation in mutation frequency and spectrum within cancer types, which sheds light on mutational processes and disease aetiology, and in mutation frequency across the genome, which is strongly correlated with DNA replication timing and also with transcriptional activity. By incorporating mutational heterogeneity into the analyses, MutSigCV is able to eliminate most of the apparent artefactual findings and enable the identification of genes truly associated with cancer.
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Affiliation(s)
| | - Petar Stojanov
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Paz Polak
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Harvard Medical School, Boston, MA, 02115, USA.,Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Gregory V Kryukov
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Harvard Medical School, Boston, MA, 02115, USA.,Brigham and Women's Hospital, Boston, MA, 02115, USA
| | | | | | - Scott L Carter
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Chip Stewart
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Craig H Mermel
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Steven A Roberts
- Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, NIH, DHHS, Durham, NC 27709, USA
| | - Adam Kiezun
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Peter S Hammerman
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Aaron McKenna
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Genome Sciences, University of Washington, Seattle, WA 98195
| | - Yotam Drier
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Harvard Medical School, Boston, MA, 02115, USA.,Massachusetts General Hospital, Boston, MA, 02114, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA.,Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Lihua Zou
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Alex H Ramos
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Trevor J Pugh
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Harvard Medical School, Boston, MA, 02115, USA
| | - Nicolas Stransky
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Elena Helman
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Jaegil Kim
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Carrie Sougnez
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Lauren Ambrogio
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | | | - Erica Shefler
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Maria L Cortés
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Daniel Auclair
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Gordon Saksena
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Douglas Voet
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Michael Noble
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Daniel DiCara
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Pei Lin
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Lee Lichtenstein
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - David I Heiman
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Timothy Fennell
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Marcin Imielinski
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Bryan Hernandez
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Eran Hodis
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Sylvan Baca
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Austin M Dulak
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Jens Lohr
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Dan-Avi Landau
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Yale Cancer Center, Department of Hematology, New Haven, CT
| | - Catherine J Wu
- Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Harvard Medical School, Boston, MA, 02115, USA
| | | | | | - Amnon Koren
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Harvard Medical School, Boston, MA, 02115, USA
| | - Steven A McCarroll
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Harvard Medical School, Boston, MA, 02115, USA
| | - Jaume Mora
- Department of Pediatric Oncology, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Brian Crompton
- Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Boston Children's Hospital, Boston, MA, 02115, USA
| | - Robert Onofrio
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Melissa Parkin
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Wendy Winckler
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Kristin Ardlie
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Stacey B Gabriel
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Charles W M Roberts
- Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Harvard Medical School, Boston, MA, 02115, USA.,Boston Children's Hospital, Boston, MA, 02115, USA
| | | | - Kimberly Stegmaier
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Boston Children's Hospital, Boston, MA, 02115, USA
| | - Adam J Bass
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Harvard Medical School, Boston, MA, 02115, USA
| | - Levi A Garraway
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Harvard Medical School, Boston, MA, 02115, USA
| | - Matthew Meyerson
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Harvard Medical School, Boston, MA, 02115, USA
| | - Todd R Golub
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Harvard Medical School, Boston, MA, 02115, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA
| | - Dmitry A Gordenin
- Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, NIH, DHHS, Durham, NC 27709, USA
| | - Shamil Sunyaev
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Harvard Medical School, Boston, MA, 02115, USA.,Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Eric S Lander
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Harvard Medical School, Boston, MA, 02115, USA.,Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Gad Getz
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Massachusetts General Hospital, Boston, MA, 02114, USA
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Ley TJ, Miller C, Ding L, Raphael BJ, Mungall AJ, Robertson AG, Hoadley K, Triche TJ, Laird PW, Baty JD, Fulton LL, Fulton R, Heath SE, Kalicki-Veizer J, Kandoth C, Klco JM, Koboldt DC, Kanchi KL, Kulkarni S, Lamprecht TL, Larson DE, Lin L, Lu C, McLellan MD, McMichael JF, Payton J, Schmidt H, Spencer DH, Tomasson MH, Wallis JW, Wartman LD, Watson MA, Welch J, Wendl MC, Ally A, Balasundaram M, Birol I, Butterfield Y, Chiu R, Chu A, Chuah E, Chun HJ, Corbett R, Dhalla N, Guin R, He A, Hirst C, Hirst M, Holt RA, Jones S, Karsan A, Lee D, Li HI, Marra MA, Mayo M, Moore RA, Mungall K, Parker J, Pleasance E, Plettner P, Schein J, Stoll D, Swanson L, Tam A, Thiessen N, Varhol R, Wye N, Zhao Y, Gabriel S, Getz G, Sougnez C, Zou L, Leiserson MDM, Vandin F, Wu HT, Applebaum F, Baylin SB, Akbani R, Broom BM, Chen K, Motter TC, Nguyen K, Weinstein JN, Zhang N, Ferguson ML, Adams C, Black A, Bowen J, Gastier-Foster J, Grossman T, Lichtenberg T, Wise L, Davidsen T, Demchok JA, Shaw KRM, Sheth M, Sofia HJ, Yang L, Downing JR, Eley G. Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia. N Engl J Med 2013; 368:2059-74. [PMID: 23634996 PMCID: PMC3767041 DOI: 10.1056/nejmoa1301689] [Citation(s) in RCA: 3565] [Impact Index Per Article: 324.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
BACKGROUND Many mutations that contribute to the pathogenesis of acute myeloid leukemia (AML) are undefined. The relationships between patterns of mutations and epigenetic phenotypes are not yet clear. METHODS We analyzed the genomes of 200 clinically annotated adult cases of de novo AML, using either whole-genome sequencing (50 cases) or whole-exome sequencing (150 cases), along with RNA and microRNA sequencing and DNA-methylation analysis. RESULTS AML genomes have fewer mutations than most other adult cancers, with an average of only 13 mutations found in genes. Of these, an average of 5 are in genes that are recurrently mutated in AML. A total of 23 genes were significantly mutated, and another 237 were mutated in two or more samples. Nearly all samples had at least 1 nonsynonymous mutation in one of nine categories of genes that are almost certainly relevant for pathogenesis, including transcription-factor fusions (18% of cases), the gene encoding nucleophosmin (NPM1) (27%), tumor-suppressor genes (16%), DNA-methylation-related genes (44%), signaling genes (59%), chromatin-modifying genes (30%), myeloid transcription-factor genes (22%), cohesin-complex genes (13%), and spliceosome-complex genes (14%). Patterns of cooperation and mutual exclusivity suggested strong biologic relationships among several of the genes and categories. CONCLUSIONS We identified at least one potential driver mutation in nearly all AML samples and found that a complex interplay of genetic events contributes to AML pathogenesis in individual patients. The databases from this study are widely available to serve as a foundation for further investigations of AML pathogenesis, classification, and risk stratification. (Funded by the National Institutes of Health.).
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36
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Dulak AM, Stojanov P, Peng S, Lawrence MS, Fox C, Stewart C, Bandla S, Imamura Y, Schumacher SE, Shefler E, McKenna A, Cibulskis K, Sivachenko A, Carter SL, Saksena G, Voet D, Ramos AH, Auclair D, Thompson K, Sougnez C, Onofrio RC, Guiducci C, Beroukhim R, Zhou D, Lin L, Lin J, Reddy R, Chang A, Luketich JD, Pennathur A, Ogino S, Golub TR, Gabriel SB, Lander ES, Beer DG, Godfrey TE, Getz G, Bass AJ. Exome and whole-genome sequencing of esophageal adenocarcinoma identifies recurrent driver events and mutational complexity. Nat Genet 2013; 45:478-86. [PMID: 23525077 PMCID: PMC3678719 DOI: 10.1038/ng.2591] [Citation(s) in RCA: 566] [Impact Index Per Article: 51.5] [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: 11/26/2012] [Accepted: 03/01/2013] [Indexed: 12/11/2022]
Abstract
The incidence of esophageal adenocarcinoma (EAC) has risen 600% over the last 30 years. With a 5-year survival rate of ~15%, the identification of new therapeutic targets for EAC is greatly important. We analyze the mutation spectra from whole-exome sequencing of 149 EAC tumor-normal pairs, 15 of which have also been subjected to whole-genome sequencing. We identify a mutational signature defined by a high prevalence of A>C transversions at AA dinucleotides. Statistical analysis of exome data identified 26 significantly mutated genes. Of these genes, five (TP53, CDKN2A, SMAD4, ARID1A and PIK3CA) have previously been implicated in EAC. The new significantly mutated genes include chromatin-modifying factors and candidate contributors SPG20, TLR4, ELMO1 and DOCK2. Functional analyses of EAC-derived mutations in ELMO1 identifies increased cellular invasion. Therefore, we suggest the potential activation of the RAC1 pathway as a contributor to EAC tumorigenesis.
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Affiliation(s)
- Austin M. Dulak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Petar Stojanov
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Shouyong Peng
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Michael S. Lawrence
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Cameron Fox
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Chip Stewart
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Santhoshi Bandla
- Department of Surgery, University of Rochester, Rochester, NY 14642, USA
| | - Yu Imamura
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Steven E. Schumacher
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Erica Shefler
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Aaron McKenna
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kristian Cibulskis
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Andrey Sivachenko
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Scott L. Carter
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Gordon Saksena
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Douglas Voet
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Alex H. Ramos
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Daniel Auclair
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kristin Thompson
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Carrie Sougnez
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Robert C. Onofrio
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Candace Guiducci
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Rameen Beroukhim
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Brigham and Women’s Hospital, Boston, MA, 02115, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - David Zhou
- Department of Surgery, University of Rochester, Rochester, NY 14642, USA
| | - Lin Lin
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jules Lin
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Rishindra Reddy
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Andrew Chang
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - James D. Luketich
- Department of Cardiothoracic Surgery, University of Pittsburgh Medical Center, Pittsburgh, PA 15206, USA
| | - Arjun Pennathur
- Department of Cardiothoracic Surgery, University of Pittsburgh Medical Center, Pittsburgh, PA 15206, USA
| | - Shuji Ogino
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Brigham and Women’s Hospital, Boston, MA, 02115, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
- Department of Epidemiology, Harvard School of Public Health, Boston, MA 02115, USA
| | - Todd R. Golub
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA
| | - Stacey B. Gabriel
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Eric S. Lander
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - David G. Beer
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Tony E. Godfrey
- Department of Surgery, University of Rochester, Rochester, NY 14642, USA
| | - Gad Getz
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Adam J. Bass
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Brigham and Women’s Hospital, Boston, MA, 02115, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
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Puffenberger EG, Jinks RN, Wang H, Xin B, Fiorentini C, Sherman EA, Degrazio D, Shaw C, Sougnez C, Cibulskis K, Gabriel S, Kelley RI, Morton DH, Strauss KA. A homozygous missense mutation in HERC2 associated with global developmental delay and autism spectrum disorder. Hum Mutat 2013; 33:1639-46. [PMID: 23065719 DOI: 10.1002/humu.22237] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
We studied a unique phenotype of cognitive delay, autistic behavior, and gait instability segregating in three separate sibships. We initiated genome-wide mapping in two sibships using Affymetrix 10K SNP Mapping Arrays and identified a homozygous 8.2 Mb region on chromosome 15 common to five affected children. We used exome sequencing of two affected children to assess coding sequence variants within the mapped interval. Four novel homozygous exome variants were shared between the two patients; however, only two variants localized to the mapped interval on chromosome 15. A third sibship in an Ohio Amish deme narrowed the mapped interval to 2.6 Mb and excluded one of the two novel homozygous exome variants. The remaining variant, a missense change in HERC2 (c.1781C>T, p.Pro594Leu), occurs in a highly conserved proline residue within an RCC1-like functional domain. Functional studies of truncated HERC2 in adherent retinal pigment epithelium cells suggest that the p.Pro594Leu variant induces protein aggregation and leads to decreased HERC2 abundance. The phenotypic correlation with the mouse Herc1 and Herc2 mutants as well as the phenotypic overlap with Angelman syndrome provide further evidence that pathogenic changes in HERC2 are associated with nonsyndromic intellectual disability, autism, and gait disturbance. Hum Mutat 33:1639-1646, 2012. © 2012 Wiley Periodicals, Inc.
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Stojanov P, Carter SL, Rosshandler II, Sivachenko A, Salido Guadarrama A, Vazquez K, Cordoba SR, Cibulskis K, Sougnez C, Voet D, Saksena G, Lichtenstein L, Zou L, Frazer S, Stewart C, Beroukhim R, Meyerson M, Lawrence MS, Getz G. Abstract 5135: Analysis of formalin-fixed paraffin-embedded (FFPE) samples. Cancer Res 2013. [DOI: 10.1158/1538-7445.am2013-5135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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
Abstract
The availability of large numbers of formalin-fixed, paraffin-embedded (FFPE) tumor DNA samples, together with accurate and specific clinical annotations, can be a great resource for in-depth analysis of correlations of somatic and germline DNA alterations with clinical outcome. However, the effects of this tissue preservation technique on next-generation DNA sequencing technologies and downstream analyses are still being investigated. Furthermore, usually the archives of such FFPE samples do not include matched normal tissue, which complicates the process of identifying somatic alterations. We are in the process of analyzing lung adenocarcinoma, colorectal and prostate patient datasets, which contain both an FFPE and a fresh-frozen tumor together with a matched blood normal sample. The availability of both a frozen and an FFPE tumor sample enables us to compare the detected somatic point mutations and indels, taking into account the fact that these pairs are produced from different aliquots of DNA. This analysis includes calculating the power to detect variants in the FFPE sample given that they have been observed in the fresh frozen tumor, as well as the validation rate of clonal SNVs between the two samples. We are also developing a method for classification of SNVs as germline or somatic without a paired normal sample by taking advantage of the fact that most tumor samples contain a substantial fraction of normal cells. Because stromal contamination has a different effect on the allelic fraction of somatic vs. germline SNVs, we can apply algorithms to estimate tumor purity and absolute somatic copy numbers in order to distinguish the two types of events. We present preliminary results from these analyses.
Citation Format: Petar Stojanov, Scott L. Carter, Ivan Imaz Rosshandler, Andrey Sivachenko, Alberto Salido Guadarrama, Karla Vazquez, Sandra Romero Cordoba, Kristian Cibulskis, Carrie Sougnez, Douglas Voet, Gordon Saksena, Lee Lichtenstein, Lihua Zou, Scott Frazer, Chip Stewart, Rameen Beroukhim, Matthew Meyerson, Michael S. Lawrence, Gad Getz. Analysis of formalin-fixed paraffin-embedded (FFPE) samples. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 5135. doi:10.1158/1538-7445.AM2013-5135
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Chmielecki J, Rosenberg M, Imielinski M, Hernandez B, Lawrence M, Sivachenko A, Cibulskis K, Voet D, Sougnez C, Gabriel S, Getz G, Meyerson M. Abstract 1112: Whole exome and whole genome sequence analysis of lung adenocarcinoma. Cancer Res 2013. [DOI: 10.1158/1538-7445.am2013-1112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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
Abstract
Lung adenocarcinoma is the leading cause of cancer-related death worldwide. Recent molecular characterization of this disease through large-scale sequencing efforts has identified distinct subsets driven by mutant oncogenes or kinase fusion proteins, many of which can be inhibited with targeted therapies. Despite these advances, almost half of all lung cancers still lack an identifiable driver. Here, we describe the genomic profiling of 230 normal-paired lung adenocarcinoma samples included as part of The Cancer Genome Atlas (TCGA) effort. All samples were subjected to whole exome analysis, copy number profiling and a subset were also subjected to whole genome sequencing. Mutation calling was performed with the MuTect algorithm. To identify significantly mutated genes, we used the MutSig CV algorithm, a statistically rigorous analysis that takes into account nucleotide context, gene-expression, replication time, and somatic background mutation rate. Mutation rate in lung adenocarcinoma was quite high with an average of 242 mutations/tumor observed (median: 161, range: 11-1328). In total, we identified mutations in over 13,500 genes of which 10 genes reached statistical significance (q<0.1). One significant gene was excluded from further analyses as it was not expressed in RNA-seq data. In addition to mutant genes with established roles in lung adenocarcinoma (e.g. TP53, KRAS, STK11, EGFR, RB1, KEAP1, and BRAF), we also identified other statistically significant mutant genes whose role in lung tumorigenesis is presently unclear. These included mutations in the RNA-binding protein RBM10, and the integrin protein ITGAL. Although statistically insignificant by a small degree, we also identified mutations in the splicing factor U2AF1, and the SWI/SNF complex proteins SMARCA4 and ARID1A. We are currently analyzing whole genome sequences to confirm these events, and identify known and novel fusion events that may be contributing to tumorigenesis. In conclusion, we have analyzed the exomes of 230 lung adenocarcinoma samples and identified known and unknown mutations in this disease. Ultimately, these data will be integrated with ongoing expression, methylation, pathway, miRNA, and proteomic analyses. At its conclusion, this effort will represent the most comprehensive profiling of lung adenocarcinoma samples to date, and will provide a detailed integrative picture of the molecular mechanisms contributing to this disease.
Citation Format: Juliann Chmielecki, Mara Rosenberg, Marcin Imielinski, Bryan Hernandez, Michael Lawrence, Andrey Sivachenko, Kristian Cibulskis, Douglas Voet, Carrie Sougnez, Stacey Gabriel, Gad Getz, Matthew Meyerson, The Cancer Genome Atlas Research Network. Whole exome and whole genome sequence analysis of lung adenocarcinoma. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1112. doi:10.1158/1538-7445.AM2013-1112
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40
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McFadden DG, Papagiannakopoulos T, Cibulskis K, Stewart C, Carter S, Taylor-Weiner A, Bhutkar A, Sougnez C, Dooley A, Shefler E, Lander E, Gabriel S, Getz G, Jacks T. Abstract 1084: Comprehensive genomic analysis of murine small cell lung carcinoma uncovers recurrent Pten alterations that drive tumor progression and alter tumor genome evolution. Cancer Res 2013. [DOI: 10.1158/1538-7445.am2013-1084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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
Abstract
Small cell lung carcinoma (SCLC) is a highly lethal tumor for which few targetable genetic alterations have been identified. SCLC is tightly associated with an extended history of tobacco use, and recent DNA sequencing studies have revealed highly mutated SCLC cancer genomes. Interestingly, two studies analyzing the human SCLC genome report distinct sets of putative driver mutations, highlighting the challenge of identifying functional events in highly mutated cancers. In the absence of environmental mutagens, a previously established genetically engineered mouse model of SCLC initiated by combined loss of Trp53 and Rb1 recapitulates the salient clinical features of human SCLC including tumor histologic progression and frequent distant metastases. This model has been shown to acquire DNA copy number alterations shared with human SCLC, suggesting that cross-species cancer genomics may identify a subset of driver events in human cancers.
In order to characterize the spectrum of acquired events in murine SCLC and identify evolutionarily conserved drivers of SCLC progression, we define the somatic genome and transcriptome of a large panel of murine SCLC at single nucleotide resolution using exome, genome and RNA sequencing. We uncover complex subclonality in primary murine SCLC tumors and detect evidence for clonal selection during metastatic spread. As expected in the absence of environmental mutagens, we demonstrate a low somatic mutation frequency in murine SCLC. Using integrative genomic analyses we uncover alterations in chromatin remodeling enzymes and identify Pten as a critical tumor suppressor in this model. Engineered Pten deletion in murine SCLC dramatically accelerates tumorigenesis and fundamentally alters the genomic evolution of these tumors. This work represents the first large-scale comprehensive genomic characterization of a genetically engineered mouse cancer model at single nucleotide resolution, has implications for the nature of tumor evolution in mouse cancer models and identifies a potential therapeutic target in a subset of human SCLC.
Citation Format: David G. McFadden, Thales Papagiannakopoulos, Kristian Cibulskis, Chip Stewart, Scott Carter, Amaro Taylor-Weiner, Arjun Bhutkar, Carrie Sougnez, Alison Dooley, Erica Shefler, Eric Lander, Stacey Gabriel, Gad Getz, Tyler Jacks. Comprehensive genomic analysis of murine small cell lung carcinoma uncovers recurrent Pten alterations that drive tumor progression and alter tumor genome evolution. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1084. doi:10.1158/1538-7445.AM2013-1084
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Affiliation(s)
| | | | | | - Chip Stewart
- 2Broad Institute of MIT and Harvard, Cambridge, MA
| | - Scott Carter
- 2Broad Institute of MIT and Harvard, Cambridge, MA
| | | | - Arjun Bhutkar
- 1MIT Koch Institute for Integrative Cancer Research, Cambridge, MA
| | | | - Alison Dooley
- 1MIT Koch Institute for Integrative Cancer Research, Cambridge, MA
| | | | - Eric Lander
- 2Broad Institute of MIT and Harvard, Cambridge, MA
| | | | - Gad Getz
- 2Broad Institute of MIT and Harvard, Cambridge, MA
| | - Tyler Jacks
- 1MIT Koch Institute for Integrative Cancer Research, Cambridge, MA
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Brooks AN, Wan Y, Choi P, Jing R, DeLuca DS, Sougnez C, Chmielecki J, Imielinski M, Getz G, Wu CJ, Meyerson M. Abstract 3150: Characterizing the effects of somatic mutations in splice factors on the transcriptome. Cancer Res 2013. [DOI: 10.1158/1538-7445.am2013-3150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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
Abstract
Recent studies have identified recurrent somatic mutations in splice factors, including SF3B1 and U2AF1, in myelodysplastic syndromes, chronic lymphocytic leukemias, breast cancer, and lung adenocarcinoma. In one study, 91 tumor and matched normal whole-exomes were sequenced from patients with CLL and the second most frequently mutated gene was SF3B1. Analysis of 187 whole-exomes in lung adenocarcinoma and matched normals revealed recurrent somatic mutations in the splice factor U2AF1 in 3% of cases. In addition to U2AF1 mutations, recurrent truncating mutations were observed in a putative splice factor, RBM10, in 4% of lung adenocarcinomas. The recurrence of somatic mutations in splice factors in multiple tumor types suggests that alterations in RNA splicing may play an important role in tumorigenesis.
Although these mutations have been identified in cancer genomes, the effect on the cancer transcriptome has yet to be fully explored; therefore, we do not understand how mutations in splice factors can contribute to tumorigenesis. We hypothesize that somatic mutations in splice factors cause alterations in mRNA splicing of important cancer genes.
We are using a computational tool called JuncBASE to identify alternative splicing in tumor transcriptomes from RNA-Seq data. We are then associating somatic mutations in splice factors, found from whole-exome sequencing, with splicing signatures identified through RNA-Seq.
Preliminary results on the identification of splice events associated with SF3B1 mutations in CLL reveal novel isoforms of multiple genes specifically expressed in SF3B1 mutant samples. Additionally, we examined the effects of SF3B1, U2AF1, and RBM10 mutations on tumor transcriptomes using RNA-Seq data from The Cancer Genome Atlas.
Citation Format: Angela N. Brooks, Youzhong Wan, Peter Choi, Rui Jing, David S. DeLuca, Carrie Sougnez, Juliann Chmielecki, Marcin Imielinski, Gad Getz, Catherine J. Wu, Matthew Meyerson. Characterizing the effects of somatic mutations in splice factors on the transcriptome. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 3150. doi:10.1158/1538-7445.AM2013-3150
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Affiliation(s)
| | | | - Peter Choi
- 1Dana-Farber Cancer Institute, Boston, MA
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Pugh TJ, Morozova O, Attiyeh EF, Asgharzadeh S, Wei JS, Auclair D, Carter SL, Cibulskis K, Hanna M, Kiezun A, Kim J, Lawrence MS, Lichenstein L, McKenna A, Pedamallu CS, Ramos AH, Shefler E, Sivachenko A, Sougnez C, Stewart C, Ally A, Birol I, Chiu R, Corbett RD, Hirst M, Jackman SD, Kamoh B, Khodabakshi AH, Krzywinski M, Lo A, Moore RA, Mungall KL, Qian J, Tam A, Thiessen N, Zhao Y, Cole KA, Diamond M, Diskin SJ, Mosse YP, Wood AC, Ji L, Sposto R, Badgett T, London WB, Moyer Y, Gastier-Foster JM, Smith MA, Guidry Auvil JM, Gerhard DS, Hogarty MD, Jones SJM, Lander ES, Gabriel SB, Getz G, Seeger RC, Khan J, Marra MA, Meyerson M, Maris JM. The genetic landscape of high-risk neuroblastoma. Nat Genet 2013; 45:279-84. [PMID: 23334666 PMCID: PMC3682833 DOI: 10.1038/ng.2529] [Citation(s) in RCA: 813] [Impact Index Per Article: 73.9] [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: 09/27/2012] [Accepted: 12/20/2012] [Indexed: 12/11/2022]
Abstract
Neuroblastoma is a malignancy of the developing sympathetic nervous system that often presents with widespread metastatic disease, resulting in survival rates of less than 50%1. To determine the spectrum of somatic mutation in high-risk neuroblastoma, we studied 240 cases using a combination of whole exome, genome and transcriptome sequencing as part of the Therapeutically Applicable Research to Generate Effective Treatments (TARGET) initiative. Here we report a low median exonic mutation frequency of 0.60 per megabase (0.48 non-silent), and remarkably few recurrently mutated genes in these tumors. Genes with significant somatic mutation frequencies included ALK (9.2% of cases), PTPN11 (2.9%), ATRX (2.5%, an additional 7.1% had focal deletions), MYCN (1.7%, a recurrent p.Pro44Leu alteration), and NRAS (0.83%). Rare, potentially pathogenic germline variants were significantly enriched in ALK, CHEK2, PINK1, and BARD1. The relative paucity of recurrent somatic mutations in neuroblastoma challenges current therapeutic strategies reliant upon frequently altered oncogenic drivers.
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Affiliation(s)
- Trevor J Pugh
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
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43
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Verhaak RGW, Tamayo P, Yang JY, Hubbard D, Zhang H, Creighton CJ, Fereday S, Lawrence M, Carter SL, Mermel CH, Kostic AD, Etemadmoghadam D, Saksena G, Cibulskis K, Duraisamy S, Levanon K, Sougnez C, Tsherniak A, Gomez S, Onofrio R, Gabriel S, Chin L, Zhang N, Spellman PT, Zhang Y, Akbani R, Hoadley KA, Kahn A, Köbel M, Huntsman D, Soslow RA, Defazio A, Birrer MJ, Gray JW, Weinstein JN, Bowtell DD, Drapkin R, Mesirov JP, Getz G, Levine DA, Meyerson M. Prognostically relevant gene signatures of high-grade serous ovarian carcinoma. J Clin Invest 2012; 123:517-25. [PMID: 23257362 DOI: 10.1172/jci65833] [Citation(s) in RCA: 319] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Accepted: 10/24/2012] [Indexed: 12/26/2022] Open
Abstract
Because of the high risk of recurrence in high-grade serous ovarian carcinoma (HGS-OvCa), the development of outcome predictors could be valuable for patient stratification. Using the catalog of The Cancer Genome Atlas (TCGA), we developed subtype and survival gene expression signatures, which, when combined, provide a prognostic model of HGS-OvCa classification, named "Classification of Ovarian Cancer" (CLOVAR). We validated CLOVAR on an independent dataset consisting of 879 HGS-OvCa expression profiles. The worst outcome group, accounting for 23% of all cases, was associated with a median survival of 23 months and a platinum resistance rate of 63%, versus a median survival of 46 months and platinum resistance rate of 23% in other cases. Associating the outcome prediction model with BRCA1/BRCA2 mutation status, residual disease after surgery, and disease stage further optimized outcome classification. Ovarian cancer is a disease in urgent need of more effective therapies. The spectrum of outcomes observed here and their association with CLOVAR signatures suggests variations in underlying tumor biology. Prospective validation of the CLOVAR model in the context of additional prognostic variables may provide a rationale for optimal combination of patient and treatment regimens.
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Affiliation(s)
- Roel G W Verhaak
- Department of Bioinformatics and Computational Biology, MD Anderson Cancer Center, Houston, Texas 77030, USA.
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Barretina J, Caponigro G, Stransky N, Venkatesan K, Margolin AA, Kim S, J.Wilson C, Lehár J, Kryukov GV, Sonkin D, Reddy A, Liu M, Murray L, Berger MF, Monahan JE, Morais P, Meltzer J, Korejwa A, Jané-Valbuena J, Mapa FA, Thibault J, Bric-Furlong E, Raman P, Shipway A, Engels IH, Cheng J, Yu GK, Yu J, Aspesi P, de Silva M, Jagtap K, Jones MD, Wang L, Hatton C, Palescandolo E, Gupta S, Mahan S, Sougnez C, Onofrio RC, Liefeld T, MacConaill L, Winckler W, Reich M, Li N, Mesirov JP, Gabriel SB, Getz G, Ardlie K, Chan V, Myer VE, Weber BL, Porter J, Warmuth M, Finan P, Harris JL, Meyerson M, Golub TR, Morrissey MP, Sellers WR, Schlegel R, Garraway LA. Addendum: The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature 2012. [DOI: 10.1038/nature11735] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Imielinski M, Berger AH, Hammerman PS, Hernandez B, Pugh TJ, Hodis E, Cho J, Suh J, Capelletti M, Sivachenko A, Sougnez C, Auclair D, Lawrence MS, Stojanov P, Cibulskis K, Choi K, de Waal L, Sharifnia T, Brooks A, Greulich H, Banerji S, Zander T, Seidel D, Leenders F, Ansén S, Ludwig C, Engel-Riedel W, Stoelben E, Wolf J, Goparju C, Thompson K, Winckler W, Kwiatkowski D, Johnson BE, Jänne PA, Miller VA, Pao W, Travis WD, Pass HI, Gabriel SB, Lander ES, Thomas RK, Garraway LA, Getz G, Meyerson M. Mapping the hallmarks of lung adenocarcinoma with massively parallel sequencing. Cell 2012; 150:1107-20. [PMID: 22980975 DOI: 10.1016/j.cell.2012.08.029] [Citation(s) in RCA: 1379] [Impact Index Per Article: 114.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Revised: 07/27/2012] [Accepted: 08/27/2012] [Indexed: 01/03/2023]
Abstract
Lung adenocarcinoma, the most common subtype of non-small cell lung cancer, is responsible for more than 500,000 deaths per year worldwide. Here, we report exome and genome sequences of 183 lung adenocarcinoma tumor/normal DNA pairs. These analyses revealed a mean exonic somatic mutation rate of 12.0 events/megabase and identified the majority of genes previously reported as significantly mutated in lung adenocarcinoma. In addition, we identified statistically recurrent somatic mutations in the splicing factor gene U2AF1 and truncating mutations affecting RBM10 and ARID1A. Analysis of nucleotide context-specific mutation signatures grouped the sample set into distinct clusters that correlated with smoking history and alterations of reported lung adenocarcinoma genes. Whole-genome sequence analysis revealed frequent structural rearrangements, including in-frame exonic alterations within EGFR and SIK2 kinases. The candidate genes identified in this study are attractive targets for biological characterization and therapeutic targeting of lung adenocarcinoma.
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Affiliation(s)
- Marcin Imielinski
- Broad Institute of Harvard and MIT, 7 Cambridge Center, Cambridge, MA 02142, USA
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Dixon-Salazar TJ, Silhavy JL, Udpa N, Schroth J, Bielas S, Schaffer AE, Olvera J, Bafna V, Zaki MS, Abdel-Salam GH, Mansour LA, Selim L, Abdel-Hadi S, Marzouki N, Ben-Omran T, Al-Saana NA, Sonmez FM, Celep F, Azam M, Hill KJ, Collazo A, Fenstermaker AG, Novarino G, Akizu N, Garimella KV, Sougnez C, Russ C, Gabriel SB, Gleeson JG. Exome sequencing can improve diagnosis and alter patient management. Sci Transl Med 2012; 4:138ra78. [PMID: 22700954 DOI: 10.1126/scitranslmed.3003544] [Citation(s) in RCA: 194] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The translation of "next-generation" sequencing directly to the clinic is still being assessed but has the potential for genetic diseases to reduce costs, advance accuracy, and point to unsuspected yet treatable conditions. To study its capability in the clinic, we performed whole-exome sequencing in 118 probands with a diagnosis of a pediatric-onset neurodevelopmental disease in which most known causes had been excluded. Twenty-two genes not previously identified as disease-causing were identified in this study (19% of cohort), further establishing exome sequencing as a useful tool for gene discovery. New genes identified included EXOC8 in Joubert syndrome and GFM2 in a patient with microcephaly, simplified gyral pattern, and insulin-dependent diabetes. Exome sequencing uncovered 10 probands (8% of cohort) with mutations in genes known to cause a disease different from the initial diagnosis. Upon further medical evaluation, these mutations were found to account for each proband's disease, leading to a change in diagnosis, some of which led to changes in patient management. Our data provide proof of principle that genomic strategies are useful in clarifying diagnosis in a proportion of patients with neurodevelopmental disorders.
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Affiliation(s)
- Tracy J Dixon-Salazar
- Howard Hughes Medical Institute, Institute for Genomic Medicine, Rady Children's Hospital, University of California, San Diego, San Diego, CA 92093, USA
| | - Jennifer L Silhavy
- Howard Hughes Medical Institute, Institute for Genomic Medicine, Rady Children's Hospital, University of California, San Diego, San Diego, CA 92093, USA
| | - Nitin Udpa
- Department of Computer Sciences, School of Engineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jana Schroth
- Howard Hughes Medical Institute, Institute for Genomic Medicine, Rady Children's Hospital, University of California, San Diego, San Diego, CA 92093, USA
| | - Stephanie Bielas
- Howard Hughes Medical Institute, Institute for Genomic Medicine, Rady Children's Hospital, University of California, San Diego, San Diego, CA 92093, USA
| | - Ashleigh E Schaffer
- Howard Hughes Medical Institute, Institute for Genomic Medicine, Rady Children's Hospital, University of California, San Diego, San Diego, CA 92093, USA
| | - Jesus Olvera
- Howard Hughes Medical Institute, Institute for Genomic Medicine, Rady Children's Hospital, University of California, San Diego, San Diego, CA 92093, USA
| | - Vineet Bafna
- Department of Computer Sciences, School of Engineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Maha S Zaki
- Clinical Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo 12311, Egypt
| | - Ghada H Abdel-Salam
- Clinical Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo 12311, Egypt
| | | | - Laila Selim
- Cairo University Children's Hospital, Cairo 406, Egypt
| | | | - Naima Marzouki
- Laboratoire Génétique Moléculaire, El Razi University Hospital, Marrakech 2360, Morocco
| | - Tawfeg Ben-Omran
- Clinical and Metabolic Genetics Division, Department of Pediatrics, Hamad Medical Corporation, Doha 3050, Qatar
| | - Nouriya A Al-Saana
- Department of Pediatrics, Dhahran Health Center, Saudi Aramco Corporation, Dhahran 31311, KSA
| | - F Müjgan Sonmez
- Child Neurology Department, Medical School of Karadeniz Technical University, Trabzon 61080, Turkey
| | - Figen Celep
- Medical Biology Department, Medical School of Karadeniz Technical University, Trabzon 61080, Turkey
| | - Matloob Azam
- Department of Paediatrics and Child Neurology, Wah Medical College, Wah Cantt, Pakistan
| | - Kiley J Hill
- Howard Hughes Medical Institute, Institute for Genomic Medicine, Rady Children's Hospital, University of California, San Diego, San Diego, CA 92093, USA
| | - Adrienne Collazo
- Howard Hughes Medical Institute, Institute for Genomic Medicine, Rady Children's Hospital, University of California, San Diego, San Diego, CA 92093, USA
| | - Ali G Fenstermaker
- Howard Hughes Medical Institute, Institute for Genomic Medicine, Rady Children's Hospital, University of California, San Diego, San Diego, CA 92093, USA
| | - Gaia Novarino
- Howard Hughes Medical Institute, Institute for Genomic Medicine, Rady Children's Hospital, University of California, San Diego, San Diego, CA 92093, USA
| | - Naiara Akizu
- Howard Hughes Medical Institute, Institute for Genomic Medicine, Rady Children's Hospital, University of California, San Diego, San Diego, CA 92093, USA
| | - Kiran V Garimella
- The Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Carrie Sougnez
- The Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Carsten Russ
- The Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Stacey B Gabriel
- The Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Joseph G Gleeson
- Howard Hughes Medical Institute, Institute for Genomic Medicine, Rady Children's Hospital, University of California, San Diego, San Diego, CA 92093, USA
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Banerji S, Cibulskis K, Rangel-Escareño C, Brown KK, Carter SL, Frederick AM, Lawrence MS, Sivachenko AY, Sougnez C, Zou L, Cortes ML, Fernandez-Lopez JC, Peng S, Ardlie KG, Auclair D, Bautista-Piña V, Duke F, Francis J, Jung J, Maffuz-Aziz A, Onofrio RC, Parkin M, Pho NH, Quintanar-Jurado V, Ramos AH, Rebollar-Vega R, Rodríguez-Cuevas SA, Romero-Cordoba SL, Schumacher SE, Stransky N, Thompson KM, Uribe-Figueroa L, Baselga J, Beroukhim R, Polyak K, Sgroi DC, Richardson AL, Jimenez-Sánchez G, Lander ES, Gabriel SB, Garraway LA, Golub TR, Meléndez-Zajgla J, Toker A, Getz G, Meyerson M, Hidalgo-Miranda A. Abstract PL07-01: Molecular profiling of breast cancer in Mexico: Identification of novel therapeutic targets through whole genome sequencing analysis. Cancer Epidemiol Biomarkers Prev 2012. [DOI: 10.1158/1055-9965.disp12-pl07-01] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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] Open
Abstract
Abstract
Today, more than 55% of the world's breast cancer cases are diagnosed in low and middle-income countries and in 2020, more that 70% of the cases will come from the developing nations. In Mexico, breast cancer-specific mortality doubled during the past 20 years, representing the second-leading cause of death in women between 30 and 59 years and the leading cause of cancer related death in the female population. According to statistics, in Mexico a woman dies due to breast cancer every two hours. Even though breast cancer represents a major public health problem in the developing world, knowledge about the genetic and genomic structure of breast tumors in Mexican or Latin American populations is very limited. In the past four years, we have participated in the Slim Initiative of Genomic Medicine (SIGMA) Project, a collaboration between the Carlos Slim Institute of Health, the Broad Institute, and the National Institute of Genomic Medicine in Mexico city. The goal of the SIGMA project is to characterize the genomic basis of common diseases, including several types of cancer. This effort has focused on the application of whole genome and whole exome sequencing of human tumors. In the case of breast cancer, we have analyzed the whole genomes of 22 tumor/normal tissue pairs and the whole exomes of 103 tumor/normal tissues from Mexican and Vietnamese patients. Sequence analysis led to the novel identification of potential loss of function mutations of the CBFB transcription factor, and deletions of its partner RUNX1, an event which has never been previously reported in breast tumors or in any other epithelial tumor. Of clinical relevance, we also identified a somatic translocation involving MAGI3 and AKT3 in a triple negative breast tumor. Ectopic expression of the fusion transcrip leads to constitutive phosphorylation of downstream GSK and loss of contact inhibition. Most importantly, the activity of the fusion protein can be abrogated by an ATP-competitive small molecule inhibitor of AKT, potentially representing a new therapeutic avenue for these patients. In parallel with sequencing, we have also been working on the analysis of somatic DNA copy number aberrations, messenger RNA expression, and microRNA expression patterns in tumors from Mexican patients. Intrinsic breast cancer sub-typing in 125 tumors from Mexican patients showed that 13.6% of the tumors were basal-like, 16.8% were Her2-enriched, 24.8% Luminal A, 34.4% Luminal B and 10.4 normal-like. With microRNA expression, we have identified a group of microRNAs whose role in breast cancer has not been previously described and are currently analyzing differential microRNA expression across tumor sub-types, in particular triple negative tumors, where we have been able to identify at least three different tumor sub-groups based on microRNA expression patterns.
Citation Format: Shantanu Banerji, Kristian Cibulskis, Claudia Rangel-Escareño, Kristin K. Brown, Scott L. Carter, Abbie M. Frederick, Michael S. Lawrence, Andrey Y. Sivachenko, Carrie Sougnez, Lihua Zou, Maria L. Cortes, Juan C. Fernandez-Lopez, Shouyong Peng, Kristin G. Ardlie, Daniel Auclair, Veronica Bautista-Piña, Fujiko Duke, Joshua Francis, Joonil Jung, Antonio Maffuz-Aziz, Robert C. Onofrio, Melissa Parkin, Nam H. Pho, Valeria Quintanar-Jurado, Alex H. Ramos, Rosa Rebollar-Vega, Sergio A. Rodríguez-Cuevas, Sandra L. Romero-Cordoba, Steven E. Schumacher, Nicolas Stransky, Kristin M. Thompson, Laura Uribe-Figueroa, Jose Baselga, Rameen Beroukhim, Kornelia Polyak, Dennis C. Sgroi, Andrea L. Richardson, Gerardo Jimenez-Sánchez, Eric S. Lander, Stacey B. Gabriel, Levi A. Garraway, Todd R. Golub, Jorge Meléndez-Zajgla, Alex Toker, Gad Getz, Matthew Meyerson, Alfredo Hidalgo-Miranda. Molecular profiling of breast cancer in Mexico: Identification of novel therapeutic targets through whole genome sequencing analysis. [abstract]. In: Proceedings of the Fifth AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2012 Oct 27-30; San Diego, CA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2012;21(10 Suppl):Abstract nr PL07-01.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Lihua Zou
- 1The Broad Institute of MIT and Harvard, Cambridge, MA,
| | | | | | | | | | | | | | - Fujiko Duke
- 1The Broad Institute of MIT and Harvard, Cambridge, MA,
| | | | - Joonil Jung
- 1The Broad Institute of MIT and Harvard, Cambridge, MA,
| | | | | | | | - Nam H. Pho
- 1The Broad Institute of MIT and Harvard, Cambridge, MA,
| | | | - Alex H. Ramos
- 1The Broad Institute of MIT and Harvard, Cambridge, MA,
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Todd R. Golub
- 1The Broad Institute of MIT and Harvard, Cambridge, MA,
| | | | - Alex Toker
- 3Beth Israel Deaconess Medical Center, Boston, MA,
| | - Gad Getz
- 1The Broad Institute of MIT and Harvard, Cambridge, MA,
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48
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Lee RS, Stewart C, Carter SL, Ambrogio L, Cibulskis K, Sougnez C, Lawrence MS, Auclair D, Mora J, Golub TR, Biegel JA, Getz G, Roberts CWM. A remarkably simple genome underlies highly malignant pediatric rhabdoid cancers. J Clin Invest 2012; 122:2983-8. [PMID: 22797305 DOI: 10.1172/jci64400] [Citation(s) in RCA: 303] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2012] [Accepted: 06/07/2012] [Indexed: 01/07/2023] Open
Abstract
Cancer is principally considered a genetic disease, and numerous mutations are thought essential to drive its growth. However, the existence of genomically stable cancers and the emergence of mutations in genes that encode chromatin remodelers raise the possibility that perturbation of chromatin structure and epigenetic regulation are capable of driving cancer formation. Here we sequenced the exomes of 35 rhabdoid tumors, highly aggressive cancers of early childhood characterized by biallelic loss of SMARCB1, a subunit of the SWI/SNF chromatin remodeling complex. We identified an extremely low rate of mutation, with loss of SMARCB1 being essentially the sole recurrent event. Indeed, in 2 of the cancers there were no other identified mutations. Our results demonstrate that high mutation rates are dispensable for the genesis of cancers driven by mutation of a chromatin remodeling complex. Consequently, cancer can be a remarkably genetically simple disease.
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Affiliation(s)
- Ryan S Lee
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
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Berger MF, Hodis E, Heffernan TP, Deribe YL, Lawrence MS, Protopopov A, Ivanova E, Watson IR, Nickerson E, Ghosh P, Zhang H, Zeid R, Ren X, Cibulskis K, Sivachenko AY, Wagle N, Sucker A, Sougnez C, Onofrio R, Ambrogio L, Auclair D, Fennell T, Carter SL, Drier Y, Stojanov P, Singer MA, Voet D, Jing R, Saksena G, Barretina J, Ramos AH, Pugh TJ, Stransky N, Parkin M, Winckler W, Mahan S, Ardlie K, Baldwin J, Wargo J, Schadendorf D, Meyerson M, Gabriel SB, Golub TR, Wagner SN, Lander ES, Getz G, Chin L, Garraway LA. Melanoma genome sequencing reveals frequent PREX2 mutations. Nature 2012; 485:502-6. [PMID: 22622578 PMCID: PMC3367798 DOI: 10.1038/nature11071] [Citation(s) in RCA: 552] [Impact Index Per Article: 46.0] [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: 09/07/2010] [Accepted: 03/09/2012] [Indexed: 12/31/2022]
Abstract
Melanoma is notable for its metastatic propensity, lethality in the advanced setting, and association with ultraviolet (UV) exposure early in life1. To obtain a comprehensive genomic view of melanoma, we sequenced the genomes of 25 metastatic melanomas and matched germline DNA. A wide range of point mutation rates was observed: lowest in melanomas whose primaries arose on non-UV exposed hairless skin of the extremities (3 and 14 per Mb genome), intermediate in those originating from hair-bearing skin of the trunk (range = 5 to 55 per Mb), and highest in a patient with a documented history of chronic sun exposure (111 per Mb). Analysis of whole-genome sequence data identified PREX2 - a PTEN-interacting protein and negative regulator of PTEN in breast cancer2 - as a significantly mutated gene with a mutation frequency of approximately 14% in an independent extension cohort of 107 human melanomas. PREX2 mutations are biologically relevant, as ectopic expression of mutant PREX2 accelerated tumor formation of immortalized human melanocytes in vivo. Thus, whole-genome sequencing of human melanoma tumors revealed genomic evidence of UV pathogenesis and discovered a new recurrently mutated gene in melanoma.
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Affiliation(s)
- Michael F Berger
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
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50
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Cibulskis K, Sivachenko A, Hammerman P, Imaz I, Pugh T, Sougnez C, Winckler W, Gabriel S, Getz G. Abstract 3960: Rapid and efficient large-scale somatic mutation validation approaches for cancer genome sequencing. Cancer Res 2012. [DOI: 10.1158/1538-7445.am2012-3960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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
Abstract
The landscape of somatic alterations in cancer is being rapidly uncovered by large-scale cancer genome sequencing projects in individual laboratories as well as consortia such as The Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC). The decreasing cost of sequencing has resulted in an increase in the number of cancer genomes that are being sequenced, and thus the numbers of candidate somatic mutations being identified are rapidly expanding. A single cancer genome from a cancer with an average mutation background rate, such as ovarian or breast cancer, will have 3000-6000 mutations. A high mutation rate cancer such as melanoma or colon cancer can have as many as 100,000 mutations/genome. Multiplying these numbers by the dozens of sequenced genomes and hundreds of sequenced exomes across a wide spectrum of tumor types yields a staggering number of candidate mutations. However, approaches for rapidly validating these findings at scale have been lagging behind. Current approaches, such as custom designed hybrid capture arrays followed by sequencing, can take months to complete and cannot begin until the initial sequencing is complete and mutations are called. This can lead to long delays in the interpretation and publication of biological findings. Here we describe the results of several approaches for rapid and efficient validation on large-scale projects, such as TCGA. We will share our approach and results using Fluidigm and PacBio sequencing for validation and sample extension at a small scale with rapid turnaround where we have validated PIK3CA and TP53 mutations in breast cancer samples of varying purity as well as significantly mutated genes in medulloblastoma. Ideally one could validate mutations and gene fusions concurrent with their discovery. To that end, we will also describe our validation results using RNA-Seq data, commonly produced concurrently with genome and exome sequencing, in lung squamous and renal cancer. Finally, we will explore an approach for instant-validation through simultaneous sequencing of barcoded discovery and cross-validation libraries.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 3960. doi:1538-7445.AM2012-3960
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Affiliation(s)
| | | | | | - Ivan Imaz
- 3Instituto Nacional de Medicina Genomica, Mexico City, Mexico
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