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Personalised medicine and population health: breast and ovarian cancer. Hum Genet 2018; 137:769-778. [DOI: 10.1007/s00439-018-1944-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 10/11/2018] [Indexed: 12/21/2022]
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2
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Li G, Guo X, Chen M, Tang L, Jiang H, Day JX, Xie Y, Peng L, Xu X, Li J, Wang S, Xiao Z, Dai L, Wang J. Prevalence and spectrum of AKT1, PIK3CA, PTEN and TP53 somatic mutations in Chinese breast cancer patients. PLoS One 2018; 13:e0203495. [PMID: 30212483 PMCID: PMC6136723 DOI: 10.1371/journal.pone.0203495] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 07/17/2018] [Indexed: 12/29/2022] Open
Abstract
Breast cancer, one of the most frequently occurring cancers worldwide, is the leading cause of cancer-related death among women. AKT1, PIK3CA, PTEN and TP53 mutations were common observed in breast cancer representing potential clinical biomarkers for cancer classification and treatment. A comprehensive knowledge of AKT1, PIK3CA, PTEN and TP53 mutations in breast cancer was still insufficient in Chinese population. In this study, the complete coding regions and exon-intron boundaries of AKT1, PIK3CA, PTEN and TP53 genes were sequenced in paired breast tumor and normal tissues from 313 Chinese breast cancer patients using microfluidic PCR-based target enrichment and next-generation sequencing technology. Total 120 somatic mutations were identified in 190 of the 313 patients (60.7%), with the mutation frequency of AKT1 as 3.2%, PIK3CA as 36.4%, PTEN as 4.8%, and TP53 as 33.9%. Among these mutations, 1 in PIK3CA (p.I69N), 3 in PTEN (p.K62X, c.635-12_636delTTAACCATGCAGAT and p.N340IfsTer4) and 5 in TP53 (p.Q136AfsTer5, p.K139_P142del, p.Y234dup, p.V274LfsTer31 and p.N310TfsTer35) were novel. Notably, PIK3CA somatic mutations were significantly associated with ER-positive or PR-positive tumors. TP53 somatic mutations were significantly associated with ER-negative, PR-negative, HER2-positive, BRCA1 mutation, Ki67 high expression and basal-like tumors. Our findings provided a comprehensive mutation profiling of AKT1, PIK3CA, PTEN and TP53 genes in Chinese breast cancer patients, which have potential implications in clinical management.
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Affiliation(s)
- Guoli Li
- School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Xinwu Guo
- Sanway Gene Technology Inc., Changsha, Hunan, China
| | - Ming Chen
- Sanway Gene Technology Inc., Changsha, Hunan, China
| | - Lili Tang
- Department of Breast Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Hui Jiang
- School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Julia X. Day
- Sanway Gene Technology Inc., Changsha, Hunan, China
| | - Yueliang Xie
- School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Limin Peng
- Sanway Gene Technology Inc., Changsha, Hunan, China
| | - Xunxun Xu
- Sanway Gene Technology Inc., Changsha, Hunan, China
| | - Jinliang Li
- Sanway Gene Technology Inc., Changsha, Hunan, China
| | - Shouman Wang
- Department of Breast Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Zhi Xiao
- Department of Breast Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Lizhong Dai
- Sanway Gene Technology Inc., Changsha, Hunan, China
- Research Center for Technologies in Nucleic Acid-Based Diagnostics, Changsha, Hunan, China
- Research Center for Technologies in Nucleic Acid-Based Diagnostics and Therapeutics, Changsha, Hunan, China
| | - Jun Wang
- School of Life Sciences, Central South University, Changsha, Hunan, China
- Sanway Gene Technology Inc., Changsha, Hunan, China
- * E-mail:
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3
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Dominguez-Valentin M, Evans DGR, Nakken S, Tubeuf H, Vodak D, Ekstrøm PO, Nissen AM, Morak M, Holinski-Feder E, Martins A, Møller P, Hovig E. Genetic variants of prospectively demonstrated phenocopies in BRCA1/2 kindreds. Hered Cancer Clin Pract 2018; 16:4. [PMID: 29371908 PMCID: PMC5769521 DOI: 10.1186/s13053-018-0086-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 01/10/2018] [Indexed: 01/03/2023] Open
Abstract
Background In kindreds carrying path_BRCA1/2 variants, some women in these families will develop cancer despite testing negative for the family’s pathogenic variant. These families may have additional genetic variants, which not only may increase the susceptibility of the families’ path_BRCA1/2, but also be capable of causing cancer in the absence of the path_BRCA1/2 variants. We aimed to identify novel genetic variants in prospectively detected breast cancer (BC) or gynecological cancer cases tested negative for their families’ pathogenic BRCA1/2 variant (path_BRCA1 or path_BRCA2). Methods Women with BC or gynecological cancer who had tested negative for path_BRCA1 or path_BRCA2 variants were included. Forty-four cancer susceptibility genes were screened for genetic variation through a targeted amplicon-based sequencing assay. Protein- and RNA splicing-dedicated in silico analyses were performed for all variants of unknown significance (VUS). Variants predicted as the ones most likely affecting pre-mRNA splicing were experimentally analyzed in a minigene assay. Results We identified 48 women who were tested negative for their family’s path_BRCA1 (n = 13) or path_BRCA2 (n = 35) variants. Pathogenic variants in the ATM, BRCA2, MSH6 and MUTYH genes were found in 10% (5/48) of the cases, of whom 15% (2/13) were from path_BRCA1 and 9% (3/35) from path_BRCA2 families. Out of the 26 unique VUS, 3 (12%) were predicted to affect RNA splicing (APC c.721G > A, MAP3K1 c.764A > G and MSH2 c.815C > T). However, by using a minigene, assay we here show that APC c.721G > A does not cause a splicing defect, similarly to what has been recently reported for the MAP3K1 c.764A > G. The MSH2 c.815C > T was previously described as causing partial exon skipping and it was identified in this work together with the path_BRCA2 c.9382C > T (p.R3128X). Conclusion All women in breast or breast/ovarian cancer kindreds would benefit from being offered genetic testing irrespective of which causative genetic variants have been demonstrated in their relatives. Electronic supplementary material The online version of this article (10.1186/s13053-018-0086-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mev Dominguez-Valentin
- 1Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - D Gareth R Evans
- 2Department of Genetic Medicine, The University of Manchester, Manchester Academic Health Science Centre, St. Mary's Hospital, Manchester, UK.,3Genesis Prevention Centre, University Hospital of South Manchester, Southmoor Road, Wythenshawe, UK
| | - Sigve Nakken
- 1Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Hélène Tubeuf
- 4Inserm-U1245, UNIROUEN, Normandie Univ, Normandy Centre for Genomic and Personalized Medicine, Rouen, France.,Interactive Biosoftware, Rouen, France
| | - Daniel Vodak
- 1Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Per Olaf Ekstrøm
- 1Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Anke M Nissen
- 6Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, Ziemssenstr. 1, Munich, Germany.,MGZ-Medizinisch Genetisches Zentrum, Munich, Germany
| | - Monika Morak
- 6Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, Ziemssenstr. 1, Munich, Germany.,MGZ-Medizinisch Genetisches Zentrum, Munich, Germany
| | - Elke Holinski-Feder
- 6Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, Ziemssenstr. 1, Munich, Germany.,MGZ-Medizinisch Genetisches Zentrum, Munich, Germany
| | - Alexandra Martins
- 4Inserm-U1245, UNIROUEN, Normandie Univ, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Pål Møller
- 1Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,8Department of Human Medicine, Universität Witten/Herdecke, Witten, Germany.,9Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Eivind Hovig
- 1Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,10Department of Informatics, University of Oslo, Oslo, Norway.,11Institute of Cancer Genetics and Informatics, Oslo University Hospital, Oslo, Norway
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4
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Lasorsa VA, Formicola D, Pignataro P, Cimmino F, Calabrese FM, Mora J, Esposito MR, Pantile M, Zanon C, De Mariano M, Longo L, Hogarty MD, de Torres C, Tonini GP, Iolascon A, Capasso M. Exome and deep sequencing of clinically aggressive neuroblastoma reveal somatic mutations that affect key pathways involved in cancer progression. Oncotarget 2017; 7:21840-52. [PMID: 27009842 PMCID: PMC5008327 DOI: 10.18632/oncotarget.8187] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 02/09/2016] [Indexed: 02/04/2023] Open
Abstract
The spectrum of somatic mutation of the most aggressive forms of neuroblastoma is not completely determined. We sought to identify potential cancer drivers in clinically aggressive neuroblastoma. Whole exome sequencing was conducted on 17 germline and tumor DNA samples from high-risk patients with adverse events within 36 months from diagnosis (HR-Event3) to identify somatic mutations and deep targeted sequencing of 134 genes selected from the initial screening in additional 48 germline and tumor pairs (62.5% HR-Event3 and high-risk patients), 17 HR-Event3 tumors and 17 human-derived neuroblastoma cell lines. We revealed 22 significantly mutated genes, many of which implicated in cancer progression. Fifteen genes (68.2%) were highly expressed in neuroblastoma supporting their involvement in the disease. CHD9, a cancer driver gene, was the most significantly altered (4.0% of cases) after ALK. Other genes (PTK2, NAV3, NAV1, FZD1 and ATRX), expressed in neuroblastoma and involved in cell invasion and migration were mutated at frequency ranged from 4% to 2%. Focal adhesion and regulation of actin cytoskeleton pathways, were frequently disrupted (14.1% of cases) thus suggesting potential novel therapeutic strategies to prevent disease progression. Notably BARD1, CHEK2 and AXIN2 were enriched in rare, potentially pathogenic, germline variants. In summary, whole exome and deep targeted sequencing identified novel cancer genes of clinically aggressive neuroblastoma. Our analyses show pathway-level implications of infrequently mutated genes in leading neuroblastoma progression.
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Affiliation(s)
- Vito Alessandro Lasorsa
- University of Naples Federico II, Department of Molecular Medicine and Medical Biotechnology, Naples, Italy.,CEINGE Biotecnolgie Avanzate, Naples, Italy
| | - Daniela Formicola
- University of Naples Federico II, Department of Molecular Medicine and Medical Biotechnology, Naples, Italy.,CEINGE Biotecnolgie Avanzate, Naples, Italy
| | - Piero Pignataro
- University of Naples Federico II, Department of Molecular Medicine and Medical Biotechnology, Naples, Italy.,CEINGE Biotecnolgie Avanzate, Naples, Italy
| | - Flora Cimmino
- University of Naples Federico II, Department of Molecular Medicine and Medical Biotechnology, Naples, Italy.,CEINGE Biotecnolgie Avanzate, Naples, Italy
| | | | - Jaume Mora
- Hospital Sant Joan de Déu, Developmental Tumor Biology Laboratory and Department of Oncology, Esplugues de Llobregat, Barcelona, Spain
| | - Maria Rosaria Esposito
- Pediatric Research Institute (IRP), Fondazione Città della Speranza, Neuroblastoma Laboratory, Padua, Italy
| | - Marcella Pantile
- Pediatric Research Institute (IRP), Fondazione Città della Speranza, Neuroblastoma Laboratory, Padua, Italy
| | - Carlo Zanon
- Pediatric Research Institute (IRP), Fondazione Città della Speranza, Neuroblastoma Laboratory, Padua, Italy
| | - Marilena De Mariano
- U.O.C. Bioterapie, IRCCS AOU San Martino-IST, National Cancer Research Institute, Genoa, Italy
| | - Luca Longo
- U.O.C. Bioterapie, IRCCS AOU San Martino-IST, National Cancer Research Institute, Genoa, Italy
| | - Michael D Hogarty
- Children's Hospital of Philadelphia, Division of Oncology, Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States of America
| | - Carmen de Torres
- Hospital Sant Joan de Déu, Developmental Tumor Biology Laboratory and Department of Oncology, Esplugues de Llobregat, Barcelona, Spain
| | - Gian Paolo Tonini
- Pediatric Research Institute (IRP), Fondazione Città della Speranza, Neuroblastoma Laboratory, Padua, Italy
| | - Achille Iolascon
- University of Naples Federico II, Department of Molecular Medicine and Medical Biotechnology, Naples, Italy.,CEINGE Biotecnolgie Avanzate, Naples, Italy
| | - Mario Capasso
- University of Naples Federico II, Department of Molecular Medicine and Medical Biotechnology, Naples, Italy.,CEINGE Biotecnolgie Avanzate, Naples, Italy.,IRCCS SDN, Istituto di Ricerca Diagnostica e Nucleare, Naples, Italy
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5
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Thompson LL, Jeusset LMP, Lepage CC, McManus KJ. Evolving Therapeutic Strategies to Exploit Chromosome Instability in Cancer. Cancers (Basel) 2017; 9:cancers9110151. [PMID: 29104272 PMCID: PMC5704169 DOI: 10.3390/cancers9110151] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Revised: 10/27/2017] [Accepted: 10/31/2017] [Indexed: 12/12/2022] Open
Abstract
Cancer is a devastating disease that claims over 8 million lives each year. Understanding the molecular etiology of the disease is critical to identify and develop new therapeutic strategies and targets. Chromosome instability (CIN) is an abnormal phenotype, characterized by progressive numerical and/or structural chromosomal changes, which is observed in virtually all cancer types. CIN generates intratumoral heterogeneity, drives cancer development, and promotes metastatic progression, and thus, it is associated with highly aggressive, drug-resistant tumors and poor patient prognosis. As CIN is observed in both primary and metastatic lesions, innovative strategies that exploit CIN may offer therapeutic benefits and better outcomes for cancer patients. Unfortunately, exploiting CIN remains a significant challenge, as the aberrant mechanisms driving CIN and their causative roles in cancer have yet to be fully elucidated. The development and utilization of CIN-exploiting therapies is further complicated by the associated risks for off-target effects and secondary cancers. Accordingly, this review will assess the strengths and limitations of current CIN-exploiting therapies, and discuss emerging strategies designed to overcome these challenges to improve outcomes and survival for patients diagnosed with cancer.
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Affiliation(s)
- Laura L Thompson
- Department of Biochemistry & Medical Genetics, University of Manitoba, Winnipeg, MB R3T 2N2, Canada.
- Research Institute in Oncology and Hematology, CancerCare Manitoba, Winnipeg, MB R3E 0V9, Canada.
| | - Lucile M-P Jeusset
- Department of Biochemistry & Medical Genetics, University of Manitoba, Winnipeg, MB R3T 2N2, Canada.
- Research Institute in Oncology and Hematology, CancerCare Manitoba, Winnipeg, MB R3E 0V9, Canada.
| | - Chloe C Lepage
- Department of Biochemistry & Medical Genetics, University of Manitoba, Winnipeg, MB R3T 2N2, Canada.
- Research Institute in Oncology and Hematology, CancerCare Manitoba, Winnipeg, MB R3E 0V9, Canada.
| | - Kirk J McManus
- Department of Biochemistry & Medical Genetics, University of Manitoba, Winnipeg, MB R3T 2N2, Canada.
- Research Institute in Oncology and Hematology, CancerCare Manitoba, Winnipeg, MB R3E 0V9, Canada.
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6
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D Antonio M, Weghorn D, D Antonio-Chronowska A, Coulet F, Olson KM, DeBoever C, Drees F, Arias A, Alakus H, Richardson AL, Schwab RB, Farley EK, Sunyaev SR, Frazer KA. Identifying DNase I hypersensitive sites as driver distal regulatory elements in breast cancer. Nat Commun 2017; 8:436. [PMID: 28874753 PMCID: PMC5585396 DOI: 10.1038/s41467-017-00100-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 06/01/2017] [Indexed: 12/03/2022] Open
Abstract
Efforts to identify driver mutations in cancer have largely focused on genes, whereas non-coding sequences remain relatively unexplored. Here we develop a statistical method based on characteristics known to influence local mutation rate and a series of enrichment filters in order to identify distal regulatory elements harboring putative driver mutations in breast cancer. We identify ten DNase I hypersensitive sites that are significantly mutated in breast cancers and associated with the aberrant expression of neighboring genes. A pan-cancer analysis shows that three of these elements are significantly mutated across multiple cancer types and have mutation densities similar to protein-coding driver genes. Functional characterization of the most highly mutated DNase I hypersensitive sites in breast cancer (using in silico and experimental approaches) confirms that they are regulatory elements and affect the expression of cancer genes. Our study suggests that mutations of regulatory elements in tumors likely play an important role in cancer development. Cancer driver mutations can occur within noncoding genomic sequences. Here, the authors develop a statistical approach to identify candidate noncoding driver mutations in DNase I hypersensitive sites in breast cancer and experimentally demonstrate they are regulatory elements of known cancer genes.
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Affiliation(s)
- Matteo D Antonio
- Moores Cancer Center, University of California, La Jolla, San Diego, CA, 92093, USA
| | - Donate Weghorn
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | | | - Florence Coulet
- Department of Pediatrics, University of California, La Jolla, San Diego, CA, 92093, USA.,Department of Genetics, Pitie-Salpetriere Hospital, Pierre and Marie Curie University, Paris, 75013, France
| | - Katrina M Olson
- Department of Medicine, Division of Cardiology, University of California, La Jolla, San Diego, CA, 92093, USA.,Division of Biological Sciences, Section of Molecular Biology, University of California, La Jolla, San Diego, CA, 92093, USA
| | - Christopher DeBoever
- Bioinformatics and Systems Biology, University of California, La Jolla, San Diego, CA, 92093, USA
| | - Frauke Drees
- Department of Pediatrics, University of California, La Jolla, San Diego, CA, 92093, USA
| | - Angelo Arias
- Department of Pediatrics, University of California, La Jolla, San Diego, CA, 92093, USA
| | - Hakan Alakus
- Department of Pediatrics, University of California, La Jolla, San Diego, CA, 92093, USA.,Department of General, Visceral and Cancer Surgery, University of Cologne, Cologne, 50937, Germany
| | - Andrea L Richardson
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA.,The Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Richard B Schwab
- Moores Cancer Center, University of California, La Jolla, San Diego, CA, 92093, USA.,Department of Medicine, School of Medicine, University of California, La Jolla, San Diego, CA, 92093, USA
| | - Emma K Farley
- Department of Medicine, Division of Cardiology, University of California, La Jolla, San Diego, CA, 92093, USA. .,Division of Biological Sciences, Section of Molecular Biology, University of California, La Jolla, San Diego, CA, 92093, USA.
| | - Shamil R Sunyaev
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
| | - Kelly A Frazer
- Moores Cancer Center, University of California, La Jolla, San Diego, CA, 92093, USA. .,Institute for Genomic Medicine, University of California, La Jolla, San Diego, CA, 92093, USA. .,Department of Pediatrics, University of California, La Jolla, San Diego, CA, 92093, USA.
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7
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Abstract
BACKGROUND Targeted gene sequencing (TGS) and whole exome sequencing (WES) are being used in clinical testing in laboratories. We compared the performances of TGS and WES using the same DNA samples. METHODS DNA was extracted from 10 endometrial tumor tissue specimens. Sequencing were performed with an Illumina HiSeq 2000. We randomly selected variants to confirm through Sanger sequencing or mutant-enriched PCR with Sanger sequencing. RESULTS We found that the variants identified in both TGS and WES were true positives (47/47), regardless of the sequencing depth. Most variants found in TGS only were true positives (34/40), and most of the variants found by WES only were false positives (8/18). From these results, we suggest that the sequencing depth may not play important role in the accuracy of NGS-based methods. After analysis, we found that WES had a sensitivity of 72.70%, specificity of 96.27%, precision of 99.44%, and accuracy of 75.03%. CONCLUSIONS The results of NGS-based methods must currently be validated, especially for important reported variants regardless of the methods used, and for the use of WES in cancers a higher false negative rate must be considered. More sensitive methods should be used to confirm the NGS results in uneven cancer tissues.
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8
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Merino GA, Murua YA, Fresno C, Sendoya JM, Golubicki M, Iseas S, Coraglio M, Podhajcer OL, Llera AS, Fernández EA. TarSeqQC: Quality control on targeted sequencing experiments in R. Hum Mutat 2017; 38:494-502. [DOI: 10.1002/humu.23204] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 02/06/2017] [Accepted: 02/19/2017] [Indexed: 01/15/2023]
Affiliation(s)
- Gabriela A. Merino
- Ua Area Cs. Agr. Ing. Bio. Y S, Conicet; Universidad Católica de Córdoba; Córdoba Argentina
- Facultad de Ciencias Exactas; Físicas y Naturales; Universidad Nacional de Córdoba; Córdoba Argentina
| | - Yanina A. Murua
- Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires-CONICET; Buenos Aires Argentina
| | - Cristóbal Fresno
- Ua Area Cs. Agr. Ing. Bio. Y S, Conicet; Universidad Católica de Córdoba; Córdoba Argentina
| | - Juan M. Sendoya
- Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires-CONICET; Buenos Aires Argentina
| | - Mariano Golubicki
- Intergrupo Argentino para el Tratamiento de los Tumores Gastrointestinales; Buenos Aires Argentina
| | - Soledad Iseas
- Hospital de Gastroenterología “Dr. Carlos Bonorino Udaondo”; Buenos Aires Argentina
| | - Mariana Coraglio
- Hospital de Gastroenterología “Dr. Carlos Bonorino Udaondo”; Buenos Aires Argentina
| | - Osvaldo L. Podhajcer
- Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires-CONICET; Buenos Aires Argentina
| | - Andrea S. Llera
- Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires-CONICET; Buenos Aires Argentina
| | - Elmer A. Fernández
- Ua Area Cs. Agr. Ing. Bio. Y S, Conicet; Universidad Católica de Córdoba; Córdoba Argentina
- Facultad de Ciencias Exactas; Físicas y Naturales; Universidad Nacional de Córdoba; Córdoba Argentina
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9
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Peng CH, Liao CT, Ng KP, Tai AS, Peng SC, Yeh JP, Chen SJ, Tsao KC, Yen TC, Hsieh WP. Somatic copy number alterations detected by ultra-deep targeted sequencing predict prognosis in oral cavity squamous cell carcinoma. Oncotarget 2016; 6:19891-906. [PMID: 26087196 PMCID: PMC4637328 DOI: 10.18632/oncotarget.4336] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 05/23/2015] [Indexed: 12/20/2022] Open
Abstract
Background Ultra-deep targeted sequencing (UDT-Seq) has advanced our knowledge on the incidence and functional significance of somatic mutations. However, the utility of UDT-Seq in detecting copy number alterations (CNAs) remains unclear. With the goal of improving molecular prognostication and identifying new therapeutic targets, we designed this study to assess whether UDT-Seq may be useful for detecting CNA in oral cavity squamous cell carcinoma (OSCC). Methods We sequenced a panel of clinically actionable cancer mutations in 310 formalin-fixed paraffin-embedded OSCC specimens. A linear model was developed to overcome uneven coverage across target regions and multiple samples. The 5-year rates of secondary primary tumors, local recurrence, neck recurrence, distant metastases, and survival served as the outcome measures. We confirmed the prognostic significance of the CNA signatures in an independent sample of 105 primary OSCC specimens. Results The CNA burden across 10 targeted genes was found to predict prognosis in two independent cohorts. FGFR1 and PIK3CAamplifications were associated with prognosis independent of clinical risk factors. Genes exhibiting CNA were clustered in the proteoglycan metabolism, the FOXO signaling, and the PI3K-AKT signaling pathways, for which targeted drugs are already available or currently under development. Conclusions UDT-Seq is clinically useful to identify CNA, which significantly improve the prognostic information provided by traditional clinicopathological risk factors in OSCC patients.
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Affiliation(s)
- Chien-Hua Peng
- Departments of Resource Center for Clinical Research, Chang Gung Memorial Hospital, Taoyuan, Taiwan, R.O.C
| | - Chun-Ta Liao
- Otorhinolaryngology, Head and Neck Surgery, Chang Gung Memorial Hospital, Taoyuan, Taiwan, R.O.C.,Head and Neck Oncology Group, Chang Gung Memorial Hospital, Taoyuan, Taiwan, R.O.C
| | - Ka-Pou Ng
- Institute of Statistics, National Tsing Hua University, Hsinchu, Taiwan, R.O.C
| | - An-Shun Tai
- Institute of Statistics, National Tsing Hua University, Hsinchu, Taiwan, R.O.C
| | - Shih-Chi Peng
- Department of Nuclear Medicine and Molecular Imaging Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan, R.O.C
| | - Jen-Pao Yeh
- Institute of Statistics, National Tsing Hua University, Hsinchu, Taiwan, R.O.C
| | - Shu-Jen Chen
- Department of Biomedical Sciences, School of Medicine, Chang Gung University, Taoyuan, Taiwan, R.O.C
| | - Kuo-Chien Tsao
- Medical Biotechnology and Laboratory Science, Research Center for Emerging Viral Infections, Chang Gung Memorial Hospital, Taoyuan, Taiwan, R.O.C.,Laboratory Medicine, Chang Gung Memorial Hospital, Taoyuan, Taiwan, R.O.C
| | - Tzu-Chen Yen
- Department of Nuclear Medicine and Molecular Imaging Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan, R.O.C
| | - Wen-Ping Hsieh
- Otorhinolaryngology, Head and Neck Surgery, Chang Gung Memorial Hospital, Taoyuan, Taiwan, R.O.C
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10
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Lai Z, Markovets A, Ahdesmaki M, Chapman B, Hofmann O, McEwen R, Johnson J, Dougherty B, Barrett JC, Dry JR. VarDict: a novel and versatile variant caller for next-generation sequencing in cancer research. Nucleic Acids Res 2016; 44:e108. [PMID: 27060149 PMCID: PMC4914105 DOI: 10.1093/nar/gkw227] [Citation(s) in RCA: 531] [Impact Index Per Article: 66.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2015] [Accepted: 03/22/2016] [Indexed: 12/22/2022] Open
Abstract
Accurate variant calling in next generation sequencing (NGS) is critical to understand cancer genomes better. Here we present VarDict, a novel and versatile variant caller for both DNA- and RNA-sequencing data. VarDict simultaneously calls SNV, MNV, InDels, complex and structural variants, expanding the detected genetic driver landscape of tumors. It performs local realignments on the fly for more accurate allele frequency estimation. VarDict performance scales linearly to sequencing depth, enabling ultra-deep sequencing used to explore tumor evolution or detect tumor DNA circulating in blood. In addition, VarDict performs amplicon aware variant calling for polymerase chain reaction (PCR)-based targeted sequencing often used in diagnostic settings, and is able to detect PCR artifacts. Finally, VarDict also detects differences in somatic and loss of heterozygosity variants between paired samples. VarDict reprocessing of The Cancer Genome Atlas (TCGA) Lung Adenocarcinoma dataset called known driver mutations in KRAS, EGFR, BRAF, PIK3CA and MET in 16% more patients than previously published variant calls. We believe VarDict will greatly facilitate application of NGS in clinical cancer research.
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Affiliation(s)
- Zhongwu Lai
- Oncology iMed, AstraZeneca, Waltham, MA 02451, USA
| | | | | | - Brad Chapman
- Bioinformatics Core, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Oliver Hofmann
- Bioinformatics Core, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Bearsden Glasgow, G61 1QH, UK
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11
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Contini E, Paganini I, Sestini R, Candita L, Capone GL, Barbetti L, Falconi S, Frusconi S, Giotti I, Giuliani C, Torricelli F, Benelli M, Papi L. A Systematic Assessment of Accuracy in Detecting Somatic Mosaic Variants by Deep Amplicon Sequencing: Application to NF2 Gene. PLoS One 2015; 10:e0129099. [PMID: 26066488 PMCID: PMC4466335 DOI: 10.1371/journal.pone.0129099] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 05/05/2015] [Indexed: 11/18/2022] Open
Abstract
The accurate detection of low-allelic variants is still challenging, particularly for the identification of somatic mosaicism, where matched control sample is not available. High throughput sequencing, by the simultaneous and independent analysis of thousands of different DNA fragments, might overcome many of the limits of traditional methods, greatly increasing the sensitivity. However, it is necessary to take into account the high number of false positives that may arise due to the lack of matched control samples. Here, we applied deep amplicon sequencing to the analysis of samples with known genotype and variant allele fraction (VAF) followed by a tailored statistical analysis. This method allowed to define a minimum value of VAF for detecting mosaic variants with high accuracy. Then, we exploited the estimated VAF to select candidate alterations in NF2 gene in 34 samples with unknown genotype (30 blood and 4 tumor DNAs), demonstrating the suitability of our method. The strategy we propose optimizes the use of deep amplicon sequencing for the identification of low abundance variants. Moreover, our method can be applied to different high throughput sequencing approaches to estimate the background noise and define the accuracy of the experimental design.
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Affiliation(s)
- Elisa Contini
- Diagnostic Genetics Unit, Careggi University Hospital, Florence, Italy
| | - Irene Paganini
- Department of Biomedical Experimental and Clinical Sciences, Medical Genetics, University of Florence, Florence, Italy
| | - Roberta Sestini
- Department of Biomedical Experimental and Clinical Sciences, Medical Genetics, University of Florence, Florence, Italy
| | - Luisa Candita
- Department of Biomedical Experimental and Clinical Sciences, Medical Genetics, University of Florence, Florence, Italy
| | - Gabriele Lorenzo Capone
- Department of Biomedical Experimental and Clinical Sciences, Medical Genetics, University of Florence, Florence, Italy
| | - Lorenzo Barbetti
- Department of Biomedical Experimental and Clinical Sciences, Medical Genetics, University of Florence, Florence, Italy
| | - Serena Falconi
- Diagnostic Genetics Unit, Careggi University Hospital, Florence, Italy
| | - Sabrina Frusconi
- Diagnostic Genetics Unit, Careggi University Hospital, Florence, Italy
| | - Irene Giotti
- Diagnostic Genetics Unit, Careggi University Hospital, Florence, Italy
| | - Costanza Giuliani
- Diagnostic Genetics Unit, Careggi University Hospital, Florence, Italy
| | | | - Matteo Benelli
- Diagnostic Genetics Unit, Careggi University Hospital, Florence, Italy
- * E-mail:
| | - Laura Papi
- Department of Biomedical Experimental and Clinical Sciences, Medical Genetics, University of Florence, Florence, Italy
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12
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Smith EN, Jepsen K, Khosroheidari M, Rassenti LZ, D'Antonio M, Ghia EM, Carson DA, Jamieson CH, Kipps TJ, Frazer KA. Biased estimates of clonal evolution and subclonal heterogeneity can arise from PCR duplicates in deep sequencing experiments. Genome Biol 2014; 15:420. [PMID: 25103687 PMCID: PMC4165357 DOI: 10.1186/s13059-014-0420-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Accepted: 08/07/2014] [Indexed: 11/17/2022] Open
Abstract
Accurate allele frequencies are important for measuring subclonal heterogeneity and clonal evolution. Deep-targeted sequencing data can contain PCR duplicates, inflating perceived read depth. Here we adapted the Illumina TruSeq Custom Amplicon kit to include single molecule tagging (SMT) and show that SMT-identified duplicates arise from PCR. We demonstrate that retention of PCR duplicate reads can imply clonal evolution when none exists, while their removal effectively controls the false positive rate. Additionally, PCR duplicates alter estimates of subclonal heterogeneity in tumor samples. Our method simplifies PCR duplicate identification and emphasizes their removal in studies of tumor heterogeneity and clonal evolution.
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13
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Yu Z, Cao K, Tischler T, Stolle CA, Santani AB. Mung bean nuclease treatment increases capture specificity of microdroplet-PCR based targeted DNA enrichment. PLoS One 2014; 9:e103491. [PMID: 25058678 PMCID: PMC4110027 DOI: 10.1371/journal.pone.0103491] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Accepted: 07/01/2014] [Indexed: 12/04/2022] Open
Abstract
Targeted DNA enrichment coupled with next generation sequencing has been increasingly used for interrogation of select sub-genomic regions at high depth of coverage in a cost effective manner. Specificity measured by on-target efficiency is a key performance metric for target enrichment. Non-specific capture leads to off-target reads, resulting in waste of sequencing throughput on irrelevant regions. Microdroplet-PCR allows simultaneous amplification of up to thousands of regions in the genome and is among the most commonly used strategies for target enrichment. Here we show that carryover of single-stranded template genomic DNA from microdroplet-PCR constitutes a major contributing factor for off-target reads in the resultant libraries. Moreover, treatment of microdroplet-PCR enrichment products with a nuclease specific to single-stranded DNA alleviates off-target load and improves enrichment specificity. We propose that nuclease treatment of enrichment products should be incorporated in the workflow of targeted sequencing using microdroplet-PCR for target capture. These findings may have a broad impact on other PCR based applications for which removal of template DNA is beneficial.
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Affiliation(s)
- Zhenming Yu
- Division of Genomic Diagnostics and Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- * E-mail: (ZY) (ZY); (ABS) (AS)
| | - Kajia Cao
- Division of Genomic Diagnostics and Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Tanya Tischler
- Division of Genomic Diagnostics and Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Catherine A. Stolle
- Division of Genomic Diagnostics and Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Avni B. Santani
- Division of Genomic Diagnostics and Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- * E-mail: (ZY) (ZY); (ABS) (AS)
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