1
|
Zhou H, He X, Zhao J, Mei Z, Zhang X, Yuan W, Dong H. A MALDI-TOF mass spectrometry-based method for detection of copy number variations in BRCA1 and BRCA2 genes. Front Mol Biosci 2024; 10:1301652. [PMID: 38274092 PMCID: PMC10808477 DOI: 10.3389/fmolb.2023.1301652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 12/26/2023] [Indexed: 01/27/2024] Open
Abstract
Background: Identifying germline mutations in BRCA1 and BRCA2 genes (BRCAs) would benefit the carriers in multiple aspects. In addition to single-nucleotide variations and small indels, copy number variations (CNVs) is also an indispensable component of identifiable mutations in BRCAs. A sensitive, rapid and throughput-flexible method to detect CNVs would be preferred to meet the rising clinical requirements for BRCAs testing. Methods: We developed a MALDI-TOF-MS-based method (MS assay) which included three steps: first, multiplex end-point PCR followed by a single base extension reaction; second, automated analyte transfer and data acquisition; third, data analysis. We applied MS assay to detect CNVs in BRCAs in 293 Chinese patients with ovarian or pancreatic cancer. All the samples were examined by targeted next-generation sequencing (TS) simultaneously. Samples were further cross-validated by multiplex ligation-dependent probe amplification (MLPA) if the results from MS assay and TS were inconsistent. Long range PCR was then applied to identify the exact breakpoints in BRCAs. Results: MS assay introduced highly multiplexed panels to detect CNVs of BRCAs semi-quantitatively. Simplified on-board data analysis was available for MS assay and no complex bioinformatics was needed. The turnaround time of MS assay was less than 8 hours with a hands-on time of only 40 min. Compared to TS, MS assay exhibited higher sensitivity (100% vs. 75%) and was more flexible in throughput, with the reagent cost per sample remaining constant no matter how many samples were examined per assay. A total of eight CNVs in BRCAs were detected from the 293 samples, and the molecular breakpoints were successfully identified in five samples through long-range PCR followed by Sanger sequencing. Conclusion: Our results suggested that MS assay might be an effective method in primary screening for CNVs in genes such as BRCAs, especially when short turnaround time and/or high sensitivity is a top priority.
Collapse
Affiliation(s)
- Hongjun Zhou
- Nanjing Shenyou Institute of Genome Research, Nanjing, China
| | - Xin He
- Agena Bioscience (Shanghai) Co., Ltd., Shanghai, China
| | - Jiadong Zhao
- Nanjing Shenyou Institute of Genome Research, Nanjing, China
| | - Zhu Mei
- Department of Gastroenterology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiayan Zhang
- Nanjing Shenyou Institute of Genome Research, Nanjing, China
| | - Wen Yuan
- Nanjing Shenyou Institute of Genome Research, Nanjing, China
| | - Hui Dong
- Department of Gastroenterology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| |
Collapse
|
2
|
Chu DT, Vu Ngoc Suong M, Vu Thi H, Vu TD, Nguyen MH, Singh V. The expression and mutation of BRCA1/2 genes in ovarian cancer: a global systematic study. Expert Rev Mol Diagn 2023; 23:53-61. [PMID: 36634123 DOI: 10.1080/14737159.2023.2168190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
INTRODUCTION This systematic review was designed to summarize the findings on expression and mutation of BRCA1/2 genes in ovarian cancer (OC) patients, focusing on mutation detection technology and taking clinical decisions for better treatment. AREAS COVERED We conducted a systematic review by following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses document selection guidelines for the document selection process and the PICOT standard for developing the keywords to search for. A total of 5729 publications were included, and 50 articles were put into the final screening. The results showed that Next-Generation Sequencing was a breakthrough technology in detecting Breast Cancer 1/2 (BRCA1/2) gene mutations because of its efficacy and affordability. Other technologies are also being applied now for mutation detection. The most prominent associations of BRCA1/2 gene mutations were age, heredity, and family history. Furthermore, mutations of BRCA1/2 could improve survival rate and overall survival. There is no sufficient study available to conclude a systematic analysis for the expression of BRCA1/2 gene in OC. EXPERT OPINION Research will continue to develop more diagnostic techniques based on the expression and mutation of BCRA1/2 genes for OC in the near future.
Collapse
Affiliation(s)
- Dinh-Toi Chu
- Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Vietnam.,Faculty of Applied Sciences, International School, Vietnam National University, Hanoi, Vietnam
| | - Mai Vu Ngoc Suong
- Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Vietnam
| | - Hue Vu Thi
- Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Vietnam.,Faculty of Applied Sciences, International School, Vietnam National University, Hanoi, Vietnam
| | - Thuy-Duong Vu
- Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Vietnam
| | - Manh-Hung Nguyen
- Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Vietnam
| | - Vijai Singh
- Department of Biosciences, School of Science, Indrashil University, Mehsana, India
| |
Collapse
|
3
|
Togi S, Ura H, Niida Y. Optimization and Validation of Multimodular, Long-Range PCR-Based Next-Generation Sequencing Assays for Comprehensive Detection of Mutation in Tuberous Sclerosis Complex. J Mol Diagn 2021; 23:424-446. [PMID: 33486073 DOI: 10.1016/j.jmoldx.2020.12.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 10/01/2020] [Accepted: 12/16/2020] [Indexed: 12/17/2022] Open
Abstract
The genetic diagnosis of tuberous sclerosis complex is difficult because of its broad spectrum of mutations. In addition to point mutations in coding regions, intragenic or chromosomal-level large deletions, deep intronic splicing mutations, and mosaic mutations represent a significant proportion of the mutations. In this study, multimodular, long-range PCR-based next-generation sequencing assays were optimized and validated using >100 samples with known TSC1 and TSC2 variants. Multiplex, long-range PCR covering the entire genomic region of both genes detected all 138 known variants; however, it also yielded false-positive results. Intragenic large deletions were detected with accurate breakpoint sequences. Chromosomal-level deletions were estimated by discordant allele segregation in the family and confirmed by DNA microarray. Deep intronic mutations were verified using a combination of long-range DNA PCR and full-length mRNA sequencing. DNA samples were mixed to simulate mosaic mutations, and most variants were detected but could not be distinguished from equivalently detected false-positive results. Repeated false-positive results were classified, and the strategy of selecting the common variants detected in the duplicate analysis and eliminating known false-positive results improved the sensitivity (85.2%) and positive predictive value (96.6%) of a 10% mosaic simulation. Long-range PCRbased next-generation sequencing is a highly versatile genetic test; however, confirmation tests remain necessary for clinical use because false-positive results cannot be completely eliminated from single experiments.
Collapse
Affiliation(s)
- Sumihito Togi
- Center for Clinical Genomics, Kanazawa Medical University, Uchinada, Japan
| | - Hiroki Ura
- Center for Clinical Genomics, Kanazawa Medical University, Uchinada, Japan
| | - Yo Niida
- Division of Genomic Medicine, Department of Advanced Medicine, Medical Research Institute, Kanazawa Medical University, Uchinada, Japan.
| |
Collapse
|
4
|
Zelli V, Compagnoni C, Cannita K, Capelli R, Capalbo C, Di Vito Nolfi M, Alesse E, Zazzeroni F, Tessitore A. Applications of Next Generation Sequencing to the Analysis of Familial Breast/Ovarian Cancer. High Throughput 2020; 9:ht9010001. [PMID: 31936873 PMCID: PMC7151204 DOI: 10.3390/ht9010001] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 01/02/2020] [Accepted: 01/07/2020] [Indexed: 12/24/2022] Open
Abstract
Next generation sequencing (NGS) provides a powerful tool in the field of medical genetics, allowing one to perform multi-gene analysis and to sequence entire exomes (WES), transcriptomes or genomes (WGS). The generated high-throughput data are particularly suitable for enhancing the understanding of the genetic bases of complex, multi-gene diseases, such as cancer. Among the various types of tumors, those with a familial predisposition are of great interest for the isolation of novel genes or gene variants, detectable at the germline level and involved in cancer pathogenesis. The identification of novel genetic factors would have great translational value, helping clinicians in defining risk and prevention strategies. In this regard, it is known that the majority of breast/ovarian cases with familial predisposition, lacking variants in the highly penetrant BRCA1 and BRCA2 genes (non-BRCA), remains unexplained, although several less penetrant genes (e.g., ATM, PALB2) have been identified. In this scenario, NGS technologies offer a powerful tool for the discovery of novel factors involved in familial breast/ovarian cancer. In this review, we summarize and discuss the state of the art applications of NGS gene panels, WES and WGS in the context of familial breast/ovarian cancer.
Collapse
Affiliation(s)
- Veronica Zelli
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, Coppito 2, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (M.D.V.N.); (E.A.); (F.Z.)
- Center for Molecular Diagnostics and Advanced Therapies, University of L’Aquila, Via Petrini, 67100 L’Aquila, Italy
| | - Chiara Compagnoni
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, Coppito 2, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (M.D.V.N.); (E.A.); (F.Z.)
| | - Katia Cannita
- Medical Oncology Unit, St Salvatore Hospital, Via L. Natali 1, 67100 L’Aquila, Italy;
| | - Roberta Capelli
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, Coppito 2, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (M.D.V.N.); (E.A.); (F.Z.)
| | - Carlo Capalbo
- Department of Molecular Medicine, University of Rome “La Sapienza”, Viale Regina Elena 324, 00161 Rome, Italy;
| | - Mauro Di Vito Nolfi
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, Coppito 2, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (M.D.V.N.); (E.A.); (F.Z.)
| | - Edoardo Alesse
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, Coppito 2, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (M.D.V.N.); (E.A.); (F.Z.)
| | - Francesca Zazzeroni
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, Coppito 2, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (M.D.V.N.); (E.A.); (F.Z.)
| | - Alessandra Tessitore
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, Coppito 2, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (M.D.V.N.); (E.A.); (F.Z.)
- Center for Molecular Diagnostics and Advanced Therapies, University of L’Aquila, Via Petrini, 67100 L’Aquila, Italy
- Correspondence:
| |
Collapse
|
5
|
Ishige T, Itoga S, Kawasaki K, Utsuno E, Beppu M, Sawai S, Nishimura M, Ichikawa T, Nomura F, Matsushita K. Evaluation of analytical factors associated with targeted MEFV gene sequencing using long-range PCR/massively parallel sequencing of whole blood DNA for molecular diagnosis of Familial Mediterranean fever. Clin Chim Acta 2019; 495:562-569. [DOI: 10.1016/j.cca.2019.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 05/27/2019] [Accepted: 06/03/2019] [Indexed: 10/26/2022]
|
6
|
Long-range PCR and high-throughput sequencing of Ostreid herpesvirus 1 indicate high genetic diversity and complex evolution process. Virology 2019; 526:81-90. [DOI: 10.1016/j.virol.2018.09.026] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 09/29/2018] [Accepted: 09/29/2018] [Indexed: 12/11/2022]
|
7
|
Walczak M, Skrzypczak-Zielinska M, Plucinska M, Zakerska-Banaszak O, Marszalek D, Lykowska-Szuber L, Stawczyk-Eder K, Dobrowolska A, Slomski R. Long-range PCR libraries and next-generation sequencing for pharmacogenetic studies of patients treated with anti-TNF drugs. THE PHARMACOGENOMICS JOURNAL 2018; 19:358-367. [PMID: 30293984 DOI: 10.1038/s41397-018-0058-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Revised: 08/06/2018] [Accepted: 08/14/2018] [Indexed: 12/30/2022]
Abstract
Biological therapy with anti-tumor necrosis factor-α (anti-TNF-α) monoclonal antibodies significantly increased the effectiveness of autoimmune disease treatment compared with conventional medicines. However, anti-TNF-α drugs are relatively expensive and a response to the therapy is reported in only 60-70% of patients. Moreover, in up to 5% of patients adverse drug reactions occur. The various effects of biological treatment may be a potential consequence of interindividual genetic variability. Only a few studies have been conducted in this field and which refer to single gene loci. Our aim was to design and optimize a methodology for a broader application of pharmacogenetic studies in patients undergoing anti-TNF-α treatment. Based on the current knowledge, we selected 16 candidate genes: TNFRSF1A, TNFRSF1B, ADAM17, CASP9, FCGR3A, LTA, TNF, FAS, IL1B, IL17A, IL6, MMP1, MMP3, S100A8, S100A9, and S100A12, which are potentially involved in the response to anti-TNF-α therapy. As a research model, three DNA samples from Crohn's disease (CD) patients were used. Targeted genomic regions were amplified in 23 long-range (LR) PCR reactions and after enzymatic fragmentation amplicon libraries were prepared and analyzed by next-generation sequencing (NGS). Our results indicated 592 sequence variations located in all fragments with coverage range of 5-1089. We demonstrate a highly sensitive, flexible, rapid, and economical approach to the pharmacogenetic investigation of anti-TNF-α therapy using amplicon libraries and NGS technology.
Collapse
Affiliation(s)
- Michal Walczak
- Institute of Human Genetics, Polish Academy of Sciences, Strzeszynska 32, 60-479, Poznan, Poland
| | | | - Marianna Plucinska
- Department of Computational Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland
| | - Oliwia Zakerska-Banaszak
- Institute of Human Genetics, Polish Academy of Sciences, Strzeszynska 32, 60-479, Poznan, Poland
| | - Daria Marszalek
- Institute of Human Genetics, Polish Academy of Sciences, Strzeszynska 32, 60-479, Poznan, Poland
| | - Liliana Lykowska-Szuber
- Department of Gastroenterology, Dietetics and Internal Diseases, University of Medical Sciences, Przybyszewskiego 49, 60-355, Poznan, Poland
| | - Kamila Stawczyk-Eder
- Department of Gastroenterology, Dietetics and Internal Diseases, University of Medical Sciences, Przybyszewskiego 49, 60-355, Poznan, Poland
| | - Agnieszka Dobrowolska
- Department of Gastroenterology, Dietetics and Internal Diseases, University of Medical Sciences, Przybyszewskiego 49, 60-355, Poznan, Poland
| | - Ryszard Slomski
- Institute of Human Genetics, Polish Academy of Sciences, Strzeszynska 32, 60-479, Poznan, Poland.,Department of Biochemistry and Biotechnology, University of Life Sciences, Dojazd 11, 60-632, Poznan, Poland
| |
Collapse
|
8
|
Longrange PCR-based next-generation sequencing in pharmacokinetics and pharmacodynamics study of propofol among patients under general anaesthesia. Sci Rep 2017; 7:15399. [PMID: 29133890 PMCID: PMC5684313 DOI: 10.1038/s41598-017-15657-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 10/30/2017] [Indexed: 11/10/2022] Open
Abstract
The individual response of patients to propofol results from the influence of genetic factors. However, the state of knowledge in this matter still remains insufficient. The aim of our study was to determine genetic predictors of variable pharmacokinetics and pharmacodynamics of propofol within selected 9 genes coding for propofol biotransformation enzymes, receptors and transporters. Our studies are the first extensive pharmaocgenetics research of propofol using high throughput sequencing technology. After the design and optimization of long range PCR-based next-generation sequencing experiment, we screened promoter and coding sequences of all genes analyzed among 87 Polish patients undergoing general anaesthesia with propofol. Initially we found that two variants, c.516 G > T in the CYP2B6 gene and c.2677 T > G in the ABCB1 gene, significantly correlate with propofol’s metabolic profile, however after Bonferroni correction the P-values were not statistically significant. Our results suggest, that variants within the CYP2B6 and ABCB1 genes correlate stronger with propofol’s metabolic profile compared to other 7 genes. CYP2B6 and ABCB1 variants can play a potentially important role in response to this anaesthetic and they are promising object for further studies.
Collapse
|
9
|
Yang Z, Sun G. High-frequency, low-coverage "false positives" mutations may be true in GS Junior sequencing studies. Sci Rep 2017; 7:13751. [PMID: 29062110 PMCID: PMC5653793 DOI: 10.1038/s41598-017-13116-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 09/19/2017] [Indexed: 12/29/2022] Open
Abstract
The GS Junior sequencer provides simplified procedures for library preparation and data processing. Errors in pyrosequencing generate some biases during library construction and emulsion PCR amplification. False-positive mutations are identified by related characteristics described in the manufacturer’s manual, and some detected mutations may have ‘borderline’ characteristics when they are detected in few reads or at low frequency. Among these mutations, however, some may be true positives. This study aimed to improve the accuracy of identifying true positives among mutations with borderline false-positive characteristics detected with GS Junior sequencing. Mutations with the borderline features were tested for validity with Sanger sequencing. We examined 10 mutations detected in coverages <20-fold at frequencies >30% (group A) and 16 mutations detected in coverages >20-fold at frequencies < 30% (group B). In group A, two mutations were not confirmed, and two mutations with 100% frequency were confirmed as heterozygous alleles. No mutation in group B was confirmed. The two groups had significantly different false-positive prevalences (p = 0.001). These results suggest that mutations detected at frequencies less than 30% can be confidently identified as false-positives but that mutations detected at frequencies over 30%, despite coverages less than 20-fold, should be verified with Sanger sequencing.
Collapse
Affiliation(s)
- Zhiliang Yang
- Department of Pediatrics, the First Hospital of China Medical University, Shenyang, 110001, China.
| | - Guilian Sun
- Department of Pediatrics, the First Hospital of China Medical University, Shenyang, 110001, China
| |
Collapse
|
10
|
Rath M, Jenssen SE, Schwefel K, Spiegler S, Kleimeier D, Sperling C, Kaderali L, Felbor U. High-throughput sequencing of the entire genomic regions of CCM1/KRIT1 , CCM2 and CCM3/PDCD10 to search for pathogenic deep-intronic splice mutations in cerebral cavernous malformations. Eur J Med Genet 2017. [DOI: 10.1016/j.ejmg.2017.06.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
|
11
|
Schmidt AY, Hansen TVO, Ahlborn LB, Jønson L, Yde CW, Nielsen FC. Next-Generation Sequencing-Based Detection of Germline Copy Number Variations in BRCA1/BRCA2: Validation of a One-Step Diagnostic Workflow. J Mol Diagn 2017; 19:809-816. [PMID: 28822785 DOI: 10.1016/j.jmoldx.2017.07.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 06/23/2017] [Accepted: 07/12/2017] [Indexed: 12/19/2022] Open
Abstract
Genetic testing of BRCA1/2 includes screening for single nucleotide variants and small insertions/deletions and for larger copy number variations (CNVs), primarily by Sanger sequencing and multiplex ligation-dependent probe amplification (MLPA). With the advent of next-generation sequencing (NGS), it has become feasible to provide CNV information and sequence data using a single platform. We report the use of NGS gene panel sequencing on the Illumina MiSeq platform and JSI SeqPilot SeqNext software to call germline CNVs in BRCA1 and BRCA2. For validation 18 different BRCA1/BRCA2 CNVs previously identified by MLPA in 48 Danish breast and/or ovarian cancer families were analyzed. Moreover, 120 patient samples previously determined as negative for BRCA1/BRCA2 CNVs by MLPA were included in the analysis. Comparison of the NGS data with the data from MLPA revealed that the sensitivity was 100%, whereas the specificity was 95%. Taken together, this study validates a one-step bioinformatics work-flow to call germline BRCA1/2 CNVs using data obtained by NGS of a breast cancer gene panel. The work-flow represents a robust and easy-to-use method for full BRCA1/2 screening, which can be easily implemented in routine diagnostic testing and adapted to genes other than BRCA1/2.
Collapse
Affiliation(s)
- Ane Y Schmidt
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Thomas V O Hansen
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Lise B Ahlborn
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Lars Jønson
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Christina W Yde
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Finn C Nielsen
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark.
| |
Collapse
|
12
|
Najm J, Rath M, Schröder W, Felbor U. Diagnostic single gene analyses beyond Sanger. Hamostaseologie 2017; 38:158-165. [DOI: 10.5482/hamo-17-01-0008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
|
13
|
Paulo P, Pinto P, Peixoto A, Santos C, Pinto C, Rocha P, Veiga I, Soares G, Machado C, Ramos F, Teixeira MR. Validation of a Next-Generation Sequencing Pipeline for the Molecular Diagnosis of Multiple Inherited Cancer Predisposing Syndromes. J Mol Diagn 2017; 19:502-513. [PMID: 28529006 DOI: 10.1016/j.jmoldx.2017.05.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Despite the growing knowledge of the genetic background behind the cancers that occur in a context of hereditary predisposition, personal or family cancer history may not be clear enough to support directional gene testing. Defined targeted next-generation sequencing gene panels allow identification of the causative disease mutations of multigene syndromes and differential diagnosis for syndromes with phenotypically overlapping characteristics. Herein, we established a next-generation sequencing analysis pipeline for the molecular diagnosis of multiple inherited cancer predisposing syndromes using the commercially available target sequencing panel TruSight Cancer. To establish the analysis pipeline, we included 22 control samples with deleterious mutations covering all genes currently analyzed at our institution by standard Sanger sequencing. We tested the pipeline using 51 samples from patients with a clinical diagnosis of neurofibromatosis type 1 (NF1), 10 of which without previous molecular characterization of the causative NF1 mutations. We propose a thoroughly validated analysis pipeline that combines Isaac Enrichment, Burrows-Wheeler Aligner Enrichment, and NextGENe for the alignment and variant calling, and GeneticistAssistant for variant annotation and prioritization. This pipeline allowed the identification of disease-causing mutations in all 73 patients, including a large duplication of 37 bp in NF1. We show that high sensitivity and specificity can be achieved by using multiple bioinformatic tools for alignment and variant calling and careful variant filtering, having in mind the clinical question.
Collapse
Affiliation(s)
- Paula Paulo
- Cancer Genetics Group, Portuguese Oncology Institute of Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto, Porto, Portugal
| | - Pedro Pinto
- Cancer Genetics Group, Portuguese Oncology Institute of Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto, Porto, Portugal
| | - Ana Peixoto
- Department of Genetics, Portuguese Oncology Institute of Porto, Porto, Portugal
| | - Catarina Santos
- Department of Genetics, Portuguese Oncology Institute of Porto, Porto, Portugal
| | - Carla Pinto
- Department of Genetics, Portuguese Oncology Institute of Porto, Porto, Portugal
| | - Patrícia Rocha
- Department of Genetics, Portuguese Oncology Institute of Porto, Porto, Portugal
| | - Isabel Veiga
- Department of Genetics, Portuguese Oncology Institute of Porto, Porto, Portugal
| | - Gabriela Soares
- Jacinto de Magalhães Medical Genetics Center, Centro Hospitalar do Porto, Porto, Portugal
| | - Catarina Machado
- Department of Genetics, Hospital de Santa Maria, Centro Hospitalar Lisboa Norte, Lisboa, Portugal
| | - Fabiana Ramos
- Department of Genetics, Hospital Pediátrico Carmona da Mota, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Manuel R Teixeira
- Cancer Genetics Group, Portuguese Oncology Institute of Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto, Porto, Portugal; Department of Genetics, Portuguese Oncology Institute of Porto, Porto, Portugal; Biomedical Sciences Institute, University of Porto, Porto, Portugal.
| |
Collapse
|
14
|
Minucci A, De Paolis E, Concolino P, De Bonis M, Rizza R, Canu G, Scaglione GL, Mignone F, Scambia G, Zuppi C, Capoluongo E. Competitive PCR-High Resolution Melting Analysis (C-PCR-HRMA) for large genomic rearrangements (LGRs) detection: A new approach to assess quantitative status of BRCA1 gene in a reference laboratory. Clin Chim Acta 2017; 470:83-92. [PMID: 28465148 DOI: 10.1016/j.cca.2017.04.026] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Revised: 04/28/2017] [Accepted: 04/28/2017] [Indexed: 11/15/2022]
Abstract
AIM OF THE STUDY Evaluation of copy number variation (CNV) in BRCA1/2 genes, due to large genomic rearrangements (LGRs), is a mandatory analysis in hereditary breast and ovarian cancers families, if no pathogenic variants are found by sequencing. LGRs cannot be detected by conventional methods and several alternative methods have been developed. Since these approaches are expensive and time consuming, identification of alternative screening methods for LGRs detection is needed in order to reduce and optimize the diagnostic procedure. The aim of this study was to investigate a Competitive PCR-High Resolution Melting Analysis (C-PCR-HRMA) as molecular tool to detect recurrent BRCA1 LGRs. MATERIAL AND METHODS C-PCR-HRMA was performed on exons 3, 14, 18, 19, 20 and 21 of the BRCA1 gene; exons 4, 6 and 7 of the ALB gene were used as reference fragments. RESULTS This study showed that it is possible to identify recurrent BRCA1 LGRs, by melting peak height ratio between target (BRCA1) and reference (ALB) fragments. Furthermore, we underline that a peculiar amplicon-melting profile is associated to a specific BRCA1 LGR. All C-PCR-HRMA results were confirmed by Multiplex ligation-dependent probe amplification. CONCLUSIONS C-PCR-HRMA has proved to be an innovative, efficient and fast method for BRCA1 LGRs detection. Given the sensitivity, specificity and ease of use, c-PCR-HRMA can be considered an attractive and powerful alternative to other methods for BRCA1 CNVs screening, improving molecular strategies for BRCA testing in the context of Massive Parallel Sequencing.
Collapse
Affiliation(s)
- Angelo Minucci
- Laboratory of Clinical Molecular and Personalized Diagnostics, Institute of Biochemistry and Clinical Biochemistry, Teaching and Research Hospital "Agostino Gemelli" Foundation, Rome, Italy.
| | - Elisa De Paolis
- Laboratory of Clinical Molecular and Personalized Diagnostics, Institute of Biochemistry and Clinical Biochemistry, Teaching and Research Hospital "Agostino Gemelli" Foundation, Rome, Italy
| | - Paola Concolino
- Laboratory of Clinical Molecular and Personalized Diagnostics, Institute of Biochemistry and Clinical Biochemistry, Teaching and Research Hospital "Agostino Gemelli" Foundation, Rome, Italy
| | - Maria De Bonis
- Laboratory of Clinical Molecular and Personalized Diagnostics, Institute of Biochemistry and Clinical Biochemistry, Teaching and Research Hospital "Agostino Gemelli" Foundation, Rome, Italy
| | - Roberta Rizza
- Laboratory of Clinical Molecular and Personalized Diagnostics, Institute of Biochemistry and Clinical Biochemistry, Teaching and Research Hospital "Agostino Gemelli" Foundation, Rome, Italy
| | - Giulia Canu
- Laboratory of Clinical Molecular and Personalized Diagnostics, Institute of Biochemistry and Clinical Biochemistry, Teaching and Research Hospital "Agostino Gemelli" Foundation, Rome, Italy
| | - Giovanni Luca Scaglione
- Laboratory of Clinical Molecular and Personalized Diagnostics, Institute of Biochemistry and Clinical Biochemistry, Teaching and Research Hospital "Agostino Gemelli" Foundation, Rome, Italy
| | - Flavio Mignone
- Department of Science and Innovation Technology (DISIT), University of Piemonte Orientale, Alessandria, Italy
| | - Giovanni Scambia
- Department of Obstetrics and Gynecology, Division of Gynecologic Oncology, Teaching and Research Hospital "Agostino Gemelli" Foundation, Rome, Italy
| | - Cecilia Zuppi
- Laboratory of Clinical Molecular and Personalized Diagnostics, Institute of Biochemistry and Clinical Biochemistry, Teaching and Research Hospital "Agostino Gemelli" Foundation, Rome, Italy
| | - Ettore Capoluongo
- Laboratory of Clinical Molecular and Personalized Diagnostics, Institute of Biochemistry and Clinical Biochemistry, Teaching and Research Hospital "Agostino Gemelli" Foundation, Rome, Italy.
| |
Collapse
|
15
|
Park HS, Park SJ, Kim JY, Kim S, Ryu J, Sohn J, Park S, Kim GM, Hwang IS, Choi JR, Kim SI. Next-generation sequencing of BRCA1/2 in breast cancer patients: potential effects on clinical decision-making using rapid, high-accuracy genetic results. Ann Surg Treat Res 2017; 92:331-339. [PMID: 28480178 PMCID: PMC5416916 DOI: 10.4174/astr.2017.92.5.331] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 11/14/2016] [Accepted: 11/29/2016] [Indexed: 12/16/2022] Open
Abstract
Purpose We evaluated the clinical role of rapid next-generation sequencing (NGS) for identifying BRCA1/2 mutations compared to traditional Sanger sequencing. Methods Twenty-four paired samples from 12 patients were analyzed in this prospective study to compare the performance of NGS to the Sanger method. Both NGS and Sanger sequencing were performed in 2 different laboratories using blood samples from patients with breast cancer. We then analyzed the accuracy of NGS in terms of variant calling and determining concordance rates of BRCA1/2 mutation detection. Results The overall concordance rate of BRCA1/2 mutation identification was 100%. Variants of unknown significance (VUS) were reported in two cases of BRCA1 and 3 cases of BRCA2 after Sanger sequencing, whereas NGS reported only 1 case of BRCA1 VUS, likely due to differences in reference databases used for mutation identification. The median turnaround time of Sanger sequencing was 22 days (range, 14–26 days), while the median time of NGS was only 6 days (range, 3–21 days). Conclusion NGS yielded comparably accurate results to Sanger sequencing and in a much shorter time with respect to BRCA1/2 mutation identification. The shorter turnaround time and higher accuracy of NGS may help clinicians make more timely and informed decisions regarding surgery or neoadjuvant chemotherapy in patients with breast cancer.
Collapse
Affiliation(s)
- Hyung Seok Park
- Department of Surgery, Yonsei University College of Medicine, Seoul, Korea
| | - Seo-Jin Park
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Jee Ye Kim
- Department of Surgery, Yonsei University College of Medicine, Seoul, Korea
| | - Sanghwa Kim
- Department of Surgery, Yonsei University College of Medicine, Seoul, Korea
| | - Jaegyu Ryu
- Department of Surgery, Yonsei University College of Medicine, Seoul, Korea
| | - Joohyuk Sohn
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Seho Park
- Department of Surgery, Yonsei University College of Medicine, Seoul, Korea
| | - Gun Min Kim
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - In Sik Hwang
- Brain Korea 21 PLUS Project for Medical Science, Yonsei University, Seoul, Korea
| | - Jong-Rak Choi
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Korea.,Brain Korea 21 PLUS Project for Medical Science, Yonsei University, Seoul, Korea
| | - Seung Il Kim
- Department of Surgery, Yonsei University College of Medicine, Seoul, Korea
| |
Collapse
|
16
|
Neveling K, Mensenkamp AR, Derks R, Kwint M, Ouchene H, Steehouwer M, van Lier B, Bosgoed E, Rikken A, Tychon M, Zafeiropoulou D, Castelein S, Hehir-Kwa J, Tjwan Thung D, Hofste T, Lelieveld SH, Bertens SMM, Adan IBJF, Eijkelenboom A, Tops BB, Yntema H, Stokowy T, Knappskog PM, Høberg-Vetti H, Steen VM, Boyle E, Martin B, Ligtenberg MJL, Shendure J, Nelen MR, Hoischen A. BRCA Testing by Single-Molecule Molecular Inversion Probes. Clin Chem 2016; 63:503-512. [PMID: 27974384 DOI: 10.1373/clinchem.2016.263897] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 09/29/2016] [Indexed: 12/16/2022]
Abstract
BACKGROUND Despite advances in next generation DNA sequencing (NGS), NGS-based single gene tests for diagnostic purposes require improvements in terms of completeness, quality, speed, and cost. Single-molecule molecular inversion probes (smMIPs) are a technology with unrealized potential in the area of clinical genetic testing. In this proof-of-concept study, we selected 2 frequently requested gene tests, those for the breast cancer genes BRCA1 and BRCA2, and developed an automated work flow based on smMIPs. METHODS The BRCA1 and BRCA2 smMIPs were validated using 166 human genomic DNA samples with known variant status. A generic automated work flow was built to perform smMIP-based enrichment and sequencing for BRCA1, BRCA2, and the checkpoint kinase 2 (CHEK2) c.1100del variant. RESULTS Pathogenic and benign variants were analyzed in a subset of 152 previously BRCA-genotyped samples, yielding an analytical sensitivity and specificity of 100%. Following automation, blind analysis of 65 in-house samples and 267 Norwegian samples correctly identified all true-positive variants (>3000), with no false positives. Consequent to process optimization, turnaround times were reduced by 60% to currently 10-15 days. Copy number variants were detected with an analytical sensitivity of 100% and an analytical specificity of 88%. CONCLUSIONS smMIP-based genetic testing enables automated and reliable analysis of the coding sequences of BRCA1 and BRCA2. The use of single-molecule tags, double-tiled targeted enrichment, and capturing and sequencing in duplo, in combination with automated library preparation and data analysis, results in a robust process and reduces routine turnaround times. Furthermore, smMIP-based copy number variation analysis could make independent copy number variation tools like multiplex ligation-dependent probes amplification dispensable.
Collapse
Affiliation(s)
- Kornelia Neveling
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Arjen R Mensenkamp
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Ronny Derks
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Michael Kwint
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Hicham Ouchene
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Marloes Steehouwer
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Bart van Lier
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Ermanno Bosgoed
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Alwin Rikken
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Marloes Tychon
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Dimitra Zafeiropoulou
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Steven Castelein
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Jayne Hehir-Kwa
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Djie Tjwan Thung
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Tom Hofste
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Stefan H Lelieveld
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Stijn M M Bertens
- Department of Mechanical Engineering, Eindhoven University of Technology, Eindhoven, the Netherlands
| | - Ivo B J F Adan
- Department of Mechanical Engineering, Eindhoven University of Technology, Eindhoven, the Netherlands
| | - Astrid Eijkelenboom
- Department of Pathology, Radboud university medical center, Nijmegen, the Netherlands
| | - Bastiaan B Tops
- Department of Pathology, Radboud university medical center, Nijmegen, the Netherlands
| | - Helger Yntema
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Tomasz Stokowy
- Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway.,Western Norway Familial Cancer Center, Haukeland University Hospital, Bergen, Norway
| | - Per M Knappskog
- Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway
| | - Hildegunn Høberg-Vetti
- Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway.,Western Norway Familial Cancer Center, Haukeland University Hospital, Bergen, Norway
| | - Vidar M Steen
- Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway.,Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Evan Boyle
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Beth Martin
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Marjolijn J L Ligtenberg
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands.,Department of Pathology, Radboud university medical center, Nijmegen, the Netherlands
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Marcel R Nelen
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands;
| | - Alexander Hoischen
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands.,Donders Centre for Neuroscience, Radboud University Nijmegen, Nijmegen, the Netherlands
| |
Collapse
|
17
|
Clinical Applications of Next-Generation Sequencing in Cancer Diagnosis. Pathol Oncol Res 2016; 23:225-234. [PMID: 27722982 DOI: 10.1007/s12253-016-0124-z] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/01/2016] [Accepted: 10/04/2016] [Indexed: 12/22/2022]
Abstract
With the advancement and improvement of new sequencing technology, next-generation sequencing (NGS) has been applied increasingly in cancer genomics research fields. More recently, NGS has been adopted in clinical oncology to advance personalized treatment of cancer. NGS is utilized to novel diagnostic and rare cancer mutations, detection of translocations, inversions, insertions and deletions, detection of copy number variants, detect familial cancer mutation carriers, provide the molecular rationale for appropriate targeted, therapeutic and prognostic. NGS holds many advantages, such as the ability to fully sequence all types of mutations for a large number of genes (hundreds to thousands) and the sensitivity, speed in a single test at a relatively low cost compared to be other sequencing modalities. Here we described the technology, methods and applications that can be immediately considered and some of the challenges that lie ahead.
Collapse
|
18
|
Lim D, Ngeow J. Evaluation of the methods to identify patients who may benefit from PARP inhibitor use. Endocr Relat Cancer 2016; 23:R267-85. [PMID: 27226207 DOI: 10.1530/erc-16-0116] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Accepted: 05/23/2016] [Indexed: 12/17/2022]
Abstract
The effectiveness of poly (ADP-ribose) polymerase inhibitors (PARPi) in treating cancers associated with BRCA1/2 mutations hinges upon the concept of synthetic lethality and exemplifies the principles of precision medicine. Currently, most clinical trials are recruiting patients based on pathological subtypes or have included BRCA mutation analysis (germ line and/or somatic) as part of the selection criteria. Mounting evidence, however, suggests that these drugs may also be efficacious in tumors with defects in other genes involved in the homologous recombination repair pathway. Advances in molecular profiling techniques together with increased research efforts have led to a better understanding of the molecular aberrations underlying this BRCA-like phenotype and helped broaden the concept of BRCAness. Hence, it is likely that the list of predictive biomarkers for PARPi therapy will increase in future. There is currently no gold standard method of testing for PARPi response and no universal guidelines are in place on how to incorporate biomarker testing into routine clinical diagnostics. In this review, we explore the concept of BRCAness and highlight the different methods that have been used to identify patients who may benefit from the use of these anticancer agents. The identification of predictive biomarkers is crucial in improving patient selection and expanding the clinical applications of PARPi therapy.
Collapse
Affiliation(s)
- Diana Lim
- Department of PathologyNational University Health System, Singapore, Singapore
| | - Joanne Ngeow
- Lee Kong Chian School of MedicineNanyang Technological University, Singapore, Singapore Cancer Genetics ServiceDivision of Medical Oncology, National Cancer Centre, Singapore, Singapore
| |
Collapse
|
19
|
Ermolenko NA, Boyarskikh UA, Kechin AA, Mazitova AM, Khrapov EA, Petrova VD, Lazarev AF, Kushlinskii NE, Filipenko ML. Massive Parallel Sequencing for Diagnostic Genetic Testing of BRCA Genes - a Single Center Experience. Asian Pac J Cancer Prev 2015; 16:7935-41. [DOI: 10.7314/apjcp.2015.16.17.7935] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
|
20
|
Cracking the Code of Human Diseases Using Next-Generation Sequencing: Applications, Challenges, and Perspectives. BIOMED RESEARCH INTERNATIONAL 2015; 2015:161648. [PMID: 26665001 PMCID: PMC4668301 DOI: 10.1155/2015/161648] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/06/2015] [Revised: 09/30/2015] [Accepted: 10/18/2015] [Indexed: 02/07/2023]
Abstract
Next-generation sequencing (NGS) technologies have greatly impacted on every field of molecular research mainly because they reduce costs and increase throughput of DNA sequencing. These features, together with the technology's flexibility, have opened the way to a variety of applications including the study of the molecular basis of human diseases. Several analytical approaches have been developed to selectively enrich regions of interest from the whole genome in order to identify germinal and/or somatic sequence variants and to study DNA methylation. These approaches are now widely used in research, and they are already being used in routine molecular diagnostics. However, some issues are still controversial, namely, standardization of methods, data analysis and storage, and ethical aspects. Besides providing an overview of the NGS-based approaches most frequently used to study the molecular basis of human diseases at DNA level, we discuss the principal challenges and applications of NGS in the field of human genomics.
Collapse
|
21
|
Arsenic R, Treue D, Lehmann A, Hummel M, Dietel M, Denkert C, Budczies J. Comparison of targeted next-generation sequencing and Sanger sequencing for the detection of PIK3CA mutations in breast cancer. BMC Clin Pathol 2015; 15:20. [PMID: 26587011 PMCID: PMC4652376 DOI: 10.1186/s12907-015-0020-6] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 11/12/2015] [Indexed: 01/04/2023] Open
Abstract
Background Phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha, PIK3CA, is one of the most frequently mutated genes in breast cancer, and the mutation status of PIK3CA has clinical relevance related to response to therapy. The aim of our study was to investigate the mutation status of PIK3CA gene and to evaluate the concordance between NGS and SGS for the most important hotspot regions in exon 9 and 20, to investigate additional hotspots outside of these exons using NGS, and to correlate the PIK3CA mutation status with the clinicopathological characteristics of the cohort. Methods In the current study, next-generation sequencing (NGS) and Sanger Sequencing (SGS) was used for the mutational analysis of PIK3CA in 186 breast carcinomas. Results Altogether, 64 tumors had PIK3CA mutations, 55 of these mutations occurred in exons 9 and 20. Out of these 55 mutations, 52 could also be detected by Sanger sequencing resulting in a concordance of 98.4 % between the two sequencing methods. The three mutations missed by SGS had low variant frequencies below 10 %. Additionally, 4.8 % of the tumors had mutations in exons 1, 4, 7, and 13 of PIK3CA that were not detected by SGS. PIK3CA mutation status was significantly associated with hormone receptor-positivity, HER2-negativity, tumor grade, and lymph node involvement. However, there was no statistically significant association between the PIK3CA mutation status and overall survival. Conclusions Based on our study, NGS is recommended as follows: 1) for correctly assessing the mutation status of PIK3CA in breast cancer, especially for cases with low tumor content, 2) for the detection of subclonal mutations, and 3) for simultaneous mutation detection in multiple exons. Electronic supplementary material The online version of this article (doi:10.1186/s12907-015-0020-6) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Ruza Arsenic
- Institute of Pathology, Charité University Hospital Berlin, Berlin, Germany
| | - Denise Treue
- Institute of Pathology, Charité University Hospital Berlin, Berlin, Germany
| | - Annika Lehmann
- Institute of Pathology, Charité University Hospital Berlin, Berlin, Germany
| | - Michael Hummel
- Institute of Pathology, Charité University Hospital Berlin, Berlin, Germany
| | - Manfred Dietel
- Institute of Pathology, Charité University Hospital Berlin, Berlin, Germany
| | - Carsten Denkert
- Institute of Pathology, Charité University Hospital Berlin, Berlin, Germany
| | - Jan Budczies
- Institute of Pathology, Charité University Hospital Berlin, Berlin, Germany
| |
Collapse
|
22
|
Minucci A, Scambia G, Santonocito C, Concolino P, Canu G, Mignone F, Saggese I, Guarino D, Costella A, Molinario R, De Bonis M, Ferrandina G, Petrillo M, Scaglione GL, Capoluongo E. Clinical impact on ovarian cancer patients of massive parallel sequencing forBRCAmutation detection: the experience at Gemelli hospital and a literature review. Expert Rev Mol Diagn 2015; 15:1383-403. [DOI: 10.1586/14737159.2015.1081059] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
|
23
|
Md. SSG, Diego-Álvarez D, Buades C, Romera-López A, Pérez-Cabornero L, Valero-Hervás D, Cantalapiedra D, Bioinformatics, Felipe-Ponce V, Hernández-Poveda G, José Roca M, Casañs C, Fernández-Pedrosa V, M. CC, C. ÁA, P. JCT, C. ÓR, Marco G, Gil M, Miñambres R, Ballester A. DIAGNÓSTICO MOLECULAR DE ENFERMEDADES GENÉTICAS: DEL DIAGNÓSTICO GENÉTICO AL DIAGNÓSTICO GENÓMICO CON LA SECUENCIACIÓN MASIVA. REVISTA MÉDICA CLÍNICA LAS CONDES 2015. [DOI: 10.1016/j.rmclc.2015.07.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
|
24
|
D'Argenio V, Esposito MV, Telese A, Precone V, Starnone F, Nunziato M, Cantiello P, Iorio M, Evangelista E, D'Aiuto M, Calabrese A, Frisso G, D'Aiuto G, Salvatore F. The molecular analysis of BRCA1 and BRCA2: Next-generation sequencing supersedes conventional approaches. Clin Chim Acta 2015; 446:221-5. [PMID: 25896959 DOI: 10.1016/j.cca.2015.03.045] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Revised: 03/31/2015] [Accepted: 03/31/2015] [Indexed: 12/14/2022]
Abstract
BACKGROUND Accurate and sensitive detection of BRCA1/2 germ-line mutations is crucial for the clinical management of women affected by breast cancer, for prevention and, notably, also for the identification of at-risk healthy relatives. The most widely used methods for BRCA1/2 molecular analysis are Sanger sequencing, and denaturing high performance liquid chromatography (dHPLC) followed by the Sanger method. However, recent findings suggest that next-generation sequencing (NGS)-based approaches may be an efficient tool for diagnostic purposes. In this context, we evaluated the effectiveness of NGS for BRCA gene analysis compared with dHPLC/Sanger sequencing. METHODS Seventy women were screened for BRCA1/2 mutations by both dHPLC/Sanger sequencing and NGS, and the data were analyzed using a bioinformatic pipeline. RESULTS Sequence data analysis showed that NGS is more sensitive in detecting BRCA1/2 variants than the conventional procedure, namely, dHPLC/Sanger. CONCLUSION Next-generation sequencing is more sensitive, faster, easier to use and less expensive than the conventional Sanger method. Consequently, it is a reliable procedure for the routine molecular screening of the BRCA1/2 genes.
Collapse
Affiliation(s)
- Valeria D'Argenio
- CEINGE-Biotecnologie Avanzate, via G. Salvatore 486, 80145 Naples, Italy; Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Via Pansini 5, 80131 Naples, Italy
| | | | - Antonella Telese
- CEINGE-Biotecnologie Avanzate, via G. Salvatore 486, 80145 Naples, Italy
| | - Vincenza Precone
- CEINGE-Biotecnologie Avanzate, via G. Salvatore 486, 80145 Naples, Italy; Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Via Pansini 5, 80131 Naples, Italy
| | - Flavio Starnone
- CEINGE-Biotecnologie Avanzate, via G. Salvatore 486, 80145 Naples, Italy
| | - Marcella Nunziato
- CEINGE-Biotecnologie Avanzate, via G. Salvatore 486, 80145 Naples, Italy; Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Via Pansini 5, 80131 Naples, Italy
| | | | - Mariangela Iorio
- CEINGE-Biotecnologie Avanzate, via G. Salvatore 486, 80145 Naples, Italy
| | - Eloisa Evangelista
- CEINGE-Biotecnologie Avanzate, via G. Salvatore 486, 80145 Naples, Italy
| | - Massimiliano D'Aiuto
- Department of Senology, Istituto Nazionale Tumori - IRCCS Fondazione Pascale, Naples, Italy
| | - Alessandra Calabrese
- Department of Senology, Istituto Nazionale Tumori - IRCCS Fondazione Pascale, Naples, Italy
| | - Giulia Frisso
- CEINGE-Biotecnologie Avanzate, via G. Salvatore 486, 80145 Naples, Italy; Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Via Pansini 5, 80131 Naples, Italy
| | - Giuseppe D'Aiuto
- Department of Senology, Istituto Nazionale Tumori - IRCCS Fondazione Pascale, Naples, Italy
| | - Francesco Salvatore
- CEINGE-Biotecnologie Avanzate, via G. Salvatore 486, 80145 Naples, Italy; Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Via Pansini 5, 80131 Naples, Italy; IRCCS-Fondazione SDN, Naples, Italy.
| |
Collapse
|
25
|
Ellison G, Huang S, Carr H, Wallace A, Ahdesmaki M, Bhaskar S, Mills J. A reliable method for the detection of BRCA1 and BRCA2 mutations in fixed tumour tissue utilising multiplex PCR-based targeted next generation sequencing. BMC Clin Pathol 2015; 15:5. [PMID: 25859162 PMCID: PMC4391122 DOI: 10.1186/s12907-015-0004-6] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 02/23/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Germline mutations in BRCA1 or BRCA2 lead to a high lifetime probability of developing ovarian or breast cancer. These genes can also be involved in the development of non-hereditary tumours as somatic BRCA1/2 pathogenic variants are found in some of these cancers. Since patients with somatic BRCA pathogenic variants may benefit from treatment with poly ADP ribose polymerase inhibitors, it is important to be able to test for somatic changes in routinely available tumour samples. Such samples are typically formalin-fixed paraffin-embedded (FFPE) tissue, where the extracted DNA tends to be highly fragmented and of limited quantity, making analysis of large genes such as BRCA1 and BRCA2 challenging. This is made more difficult as somatic changes may be evident in only part of the sample, due to the presence of normal tissue. METHODS We examined the feasibility of analysing DNA extracted from FFPE ovarian and breast tumour tissue to identify significant DNA variants in BRCA1/ BRCA2 using next generation sequencing methods that were sensitive enough to detect low level mutations, multiplexed to reduce the amount of DNA required and had short amplicon design. The utility of two GeneRead DNAseq Targeted Exon Enrichment Panels with different designs targeting only BRCA1/2 exons, and the Ion AmpliSeq BRCA community panel, followed by library preparation and adaptor ligation using the TruSeq DNA PCR-Free HT Sample Preparation Kit and NGS analysis on the MiSeq were investigated. RESULTS Using the GeneRead method, we successfully analysed over 76% of samples, with >95% coverage of BRCA1/2 coding regions and a mean average read depth of >1000-fold. All mutations identified were confirmed where possible by Sanger sequencing or replication to eliminate the risk of false positive results due to artefacts within FFPE material. Admixture experiments demonstrated that BRCA1/2 variants could be detected if present in >10% of the sample. A sample subset was evaluated using the Ion AmpliSeq BRCA panel, achieving >99% coverage and sufficient read depth for a proportion of the samples. CONCLUSIONS Detection of BRCA1/2 variants in fixed tissue is feasible, and could be performed prospectively to facilitate optimum treatment decisions for ovarian or breast cancer patients.
Collapse
Affiliation(s)
- Gillian Ellison
- Personalised HealthCare and Biomarkers, Innovative Medicines and Early Development, AstraZeneca, Alderley Park, Macclesfield, SK10 4TG UK
| | - Shuwen Huang
- Genomic Diagnostics Laboratory, Manchester Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, Saint Mary's Hospital, Oxford Road, Manchester, M13 9WL UK
| | - Hedley Carr
- Translational Science, Oncology Innovative Medicines Unit, AstraZeneca, Alderley Park, Macclesfield, SK10 4TG UK
| | - Andrew Wallace
- Genomic Diagnostics Laboratory, Manchester Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, Saint Mary's Hospital, Oxford Road, Manchester, M13 9WL UK
| | - Miika Ahdesmaki
- R&D Information, AstraZeneca, Alderley Park, Macclesfield, SK10 4TG UK
| | - Sanjeev Bhaskar
- Genomic Diagnostics Laboratory, Manchester Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, Saint Mary's Hospital, Oxford Road, Manchester, M13 9WL UK
| | - John Mills
- Personalised HealthCare and Biomarkers, Innovative Medicines and Early Development, AstraZeneca, Alderley Park, Macclesfield, SK10 4TG UK
| |
Collapse
|
26
|
Two novel frameshift mutations in BRCA2 gene detected by next generation sequencing in a survey of Spanish patients of breast cancer. Clin Transl Oncol 2015; 17:576-80. [DOI: 10.1007/s12094-014-1271-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Accepted: 12/22/2014] [Indexed: 01/07/2023]
|
27
|
Banu M, Simion M, Ratiu AC, Popescu M, Romanitan C, Danila M, Radoi A, Ecovoiu AA, Kusko M. Enhanced nucleotide mismatch detection based on a 3D silicon nanowire microarray. RSC Adv 2015. [DOI: 10.1039/c5ra14442f] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
|
28
|
Trujillano D, Weiss MER, Schneider J, Köster J, Papachristos EB, Saviouk V, Zakharkina T, Nahavandi N, Kovacevic L, Rolfs A. Next-generation sequencing of the BRCA1 and BRCA2 genes for the genetic diagnostics of hereditary breast and/or ovarian cancer. J Mol Diagn 2014; 17:162-70. [PMID: 25556971 DOI: 10.1016/j.jmoldx.2014.11.004] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2014] [Revised: 11/23/2014] [Accepted: 11/25/2014] [Indexed: 01/01/2023] Open
Abstract
Genetic testing for hereditary breast and/or ovarian cancer mostly relies on laborious molecular tools that use Sanger sequencing to scan for mutations in the BRCA1 and BRCA2 genes. We explored a more efficient genetic screening strategy based on next-generation sequencing of the BRCA1 and BRCA2 genes in 210 hereditary breast and/or ovarian cancer patients. We first validated this approach in a cohort of 115 samples with previously known BRCA1 and BRCA2 mutations and polymorphisms. Genomic DNA was amplified using the Ion AmpliSeq BRCA1 and BRCA2 panel. The DNA Libraries were pooled, barcoded, and sequenced using an Ion Torrent Personal Genome Machine sequencer. The combination of different robust bioinformatics tools allowed detection of all previously known pathogenic mutations and polymorphisms in the 115 samples, without detecting spurious pathogenic calls. We then used the same assay in a discovery cohort of 95 uncharacterized hereditary breast and/or ovarian cancer patients for BRCA1 and BRCA2. In addition, we describe the allelic frequencies across 210 hereditary breast and/or ovarian cancer patients of 74 unique definitely and likely pathogenic and uncertain BRCA1 and BRCA2 variants, some of which have not been previously annotated in the public databases. Targeted next-generation sequencing is ready to substitute classic molecular methods to perform genetic testing on the BRCA1 and BRCA2 genes and provides a greater opportunity for more comprehensive testing of at-risk patients.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | - Arndt Rolfs
- Centogene AG, Rostock, Germany; Albrecht-Kossel-Institute for Neuroregeneration, Medical University Rostock, Rostock, Germany
| |
Collapse
|
29
|
Chevrier S, Boidot R. gDNA enrichment by a transposase-based technology for NGS analysis of the whole sequence of BRCA1, BRCA2, and 9 genes involved in DNA damage repair. J Vis Exp 2014:e51902. [PMID: 25350069 DOI: 10.3791/51902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
The widespread use of Next Generation Sequencing has opened up new avenues for cancer research and diagnosis. NGS will bring huge amounts of new data on cancer, and especially cancer genetics. Current knowledge and future discoveries will make it necessary to study a huge number of genes that could be involved in a genetic predisposition to cancer. In this regard, we developed a Nextera design to study 11 complete genes involved in DNA damage repair. This protocol was developed to safely study 11 genes (ATM, BARD1, BRCA1, BRCA2, BRIP1, CHEK2, PALB2, RAD50, RAD51C, RAD80, and TP53) from promoter to 3'-UTR in 24 patients simultaneously. This protocol, based on transposase technology and gDNA enrichment, gives a great advantage in terms of time for the genetic diagnosis thanks to sample multiplexing. This protocol can be safely used with blood gDNA.
Collapse
Affiliation(s)
- Sandy Chevrier
- Department of Biology and Pathology of Tumors, Unit of Molecular Biology, Platform of Immunomonitoring and Genetics, Centre Georges-François Leclerc
| | - Romain Boidot
- Department of Biology and Pathology of Tumors, Unit of Molecular Biology, Platform of Immunomonitoring and Genetics, Centre Georges-François Leclerc;
| |
Collapse
|
30
|
Guan Y, Hu H, Peng Y, Gong Y, Yi Y, Shao L, Liu T, Li G, Wang R, Dai P, Bignon YJ, Xiao Z, Yang L, Mu F, Xiao L, Xie Z, Yan W, Xu N, Zhou D, Yi X. Detection of inherited mutations for hereditary cancer using target enrichment and next generation sequencing. Fam Cancer 2014; 14:9-18. [DOI: 10.1007/s10689-014-9749-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
|
31
|
Concolino P, Costella A, Minucci A, Scaglione GL, Santonocito C, Salutari V, Scambia G, Zuppi C, Capoluongo E. A preliminary Quality Control (QC) for next generation sequencing (NGS) library evaluation turns out to be a very useful tool for a rapid detection of BRCA1/2 deleterious mutations. Clin Chim Acta 2014; 437:72-7. [PMID: 25007954 DOI: 10.1016/j.cca.2014.06.026] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Revised: 06/27/2014] [Accepted: 06/27/2014] [Indexed: 12/11/2022]
Abstract
BACKGROUND Recent advances in next generation sequencing (NGS) technology have enabled comprehensive and accurate screening of the entire genomic region of BRCA1/2 genes and, to date, many studies report the effectiveness of these technologies. Here we show that Gene Scan (GS) labeling Quality Control (QC), performed before massive parallel pyrosequencing, coupled with Multiple Amplicon Quantification software (MAQ-S) analysis is a rapid and powerful tool in the detection of deleterious BRCA mutations carried by different patients. METHODS GS labeling QC assay was performed according to the manufacturers' instructions and MAQ-S software was employed for analysis results. RESULTS GS labeling QC was able to detect 14 different BRCA frameshift mutations in our patients. In addition, two novel BRCA mutations (c.1893_1894insTTAAGCCCACAAAT in BRCA1 gene and c.9413_9414insT in BRCA2 gene) were identified. CONCLUSION We prove that a simple QC step may represent a valid and useful tool for a rapid detection of frameshift mutations in BRCA genes. For this reason, we recommend using this approach before massive parallel sequencing.
Collapse
Affiliation(s)
- Paola Concolino
- Laboratory of Molecular Biology, Institute of Biochemistry and Clinical Biochemistry, Catholic University of Sacred Heart, Largo A. Gemelli 8, 00168 Rome, Italy.
| | - Alessandra Costella
- Laboratory of Molecular Biology, Institute of Biochemistry and Clinical Biochemistry, Catholic University of Sacred Heart, Largo A. Gemelli 8, 00168 Rome, Italy
| | - Angelo Minucci
- Laboratory of Molecular Biology, Institute of Biochemistry and Clinical Biochemistry, Catholic University of Sacred Heart, Largo A. Gemelli 8, 00168 Rome, Italy
| | - Giovanni Luca Scaglione
- Laboratory of Molecular Biology, Institute of Biochemistry and Clinical Biochemistry, Catholic University of Sacred Heart, Largo A. Gemelli 8, 00168 Rome, Italy
| | - Concetta Santonocito
- Laboratory of Molecular Biology, Institute of Biochemistry and Clinical Biochemistry, Catholic University of Sacred Heart, Largo A. Gemelli 8, 00168 Rome, Italy
| | - Vanda Salutari
- Department of Obstetrics and Gynecology, Catholic University of Sacred Heart, Largo A. Gemelli 8, 00168 Rome, Italy
| | - Giovanni Scambia
- Department of Obstetrics and Gynecology, Catholic University of Sacred Heart, Largo A. Gemelli 8, 00168 Rome, Italy
| | - Cecilia Zuppi
- Laboratory of Molecular Biology, Institute of Biochemistry and Clinical Biochemistry, Catholic University of Sacred Heart, Largo A. Gemelli 8, 00168 Rome, Italy
| | - Ettore Capoluongo
- Laboratory of Molecular Biology, Institute of Biochemistry and Clinical Biochemistry, Catholic University of Sacred Heart, Largo A. Gemelli 8, 00168 Rome, Italy.
| |
Collapse
|
32
|
Genetic testing in hereditary breast and ovarian cancer using massive parallel sequencing. BIOMED RESEARCH INTERNATIONAL 2014; 2014:542541. [PMID: 25136594 PMCID: PMC4098986 DOI: 10.1155/2014/542541] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 06/05/2014] [Indexed: 01/18/2023]
Abstract
High throughput methods such as next generation sequencing are increasingly used in molecular diagnosis. The aim of this study was to develop a workflow for the detection of BRCA1 and BRCA2 mutations using massive parallel sequencing in a 454 GS Junior bench top sequencer. Our approach was first validated in a panel of 23 patients containing 62 unique variants that had been previously Sanger sequenced. Subsequently, 101 patients with familial breast and ovarian cancer were studied. BRCA1 and BRCA2 exon enrichment has been performed by PCR amplification using the BRCA MASTR kit (Multiplicom). Bioinformatic analysis of reads is performed with the AVA software v2.7 (Roche). In total, all 62 variants were detected resulting in a sensitivity of 100%. 71 false positives were called resulting in a specificity of 97.35%. All of them correspond to deletions located in homopolymeric stretches. The analysis of the homopolymers stretches of 6 bp or longer using the BRCA HP kit (Multiplicom) increased the specificity of the detection of BRCA1 and BRCA2 mutations to 99.99%. We show here that massive parallel pyrosequencing can be used as a diagnostic strategy to test for BRCA1 and BRCA2 mutations meeting very stringent sensitivity and specificity parameters replacing traditional Sanger sequencing with a lower cost.
Collapse
|
33
|
Hansen MF, Neckmann U, Lavik LAS, Vold T, Gilde B, Toft RK, Sjursen W. A massive parallel sequencing workflow for diagnostic genetic testing of mismatch repair genes. Mol Genet Genomic Med 2014; 2:186-200. [PMID: 24689082 PMCID: PMC3960061 DOI: 10.1002/mgg3.62] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Revised: 11/21/2013] [Accepted: 12/02/2013] [Indexed: 11/11/2022] Open
Abstract
The purpose of this study was to develop a massive parallel sequencing (MPS) workflow for diagnostic analysis of mismatch repair (MMR) genes using the GS Junior system (Roche). A pathogenic variant in one of four MMR genes, (MLH1, PMS2, MSH6, and MSH2), is the cause of Lynch Syndrome (LS), which mainly predispose to colorectal cancer. We used an amplicon-based sequencing method allowing specific and preferential amplification of the MMR genes including PMS2, of which several pseudogenes exist. The amplicons were pooled at different ratios to obtain coverage uniformity and maximize the throughput of a single-GS Junior run. In total, 60 previously identified and distinct variants (substitutions and indels), were sequenced by MPS and successfully detected. The heterozygote detection range was from 19% to 63% and dependent on sequence context and coverage. We were able to distinguish between false-positive and true-positive calls in homopolymeric regions by cross-sample comparison and evaluation of flow signal distributions. In addition, we filtered variants according to a predefined status, which facilitated variant annotation. Our study shows that implementation of MPS in routine diagnostics of LS can accelerate sample throughput and reduce costs without compromising sensitivity, compared to Sanger sequencing.
Collapse
Affiliation(s)
- Maren F Hansen
- Department of Laboratory Medicine, Children and Women's Health, Faculty of Medicine, Norwegian University of Science and Technology Trondheim, Norway
| | - Ulrike Neckmann
- Department of Laboratory Medicine, Children and Women's Health, Faculty of Medicine, Norwegian University of Science and Technology Trondheim, Norway
| | - Liss A S Lavik
- Department of Pathology and Medical Genetics, St. Olavs Hospital Trondheim, Norway
| | - Trine Vold
- Department of Pathology and Medical Genetics, St. Olavs Hospital Trondheim, Norway
| | - Bodil Gilde
- Department of Pathology and Medical Genetics, St. Olavs Hospital Trondheim, Norway
| | - Ragnhild K Toft
- Department of Laboratory Medicine, Children and Women's Health, Faculty of Medicine, Norwegian University of Science and Technology Trondheim, Norway
| | - Wenche Sjursen
- Department of Laboratory Medicine, Children and Women's Health, Faculty of Medicine, Norwegian University of Science and Technology Trondheim, Norway ; Department of Pathology and Medical Genetics, St. Olavs Hospital Trondheim, Norway
| |
Collapse
|
34
|
Drouilhet L, Mansanet C, Sarry J, Tabet K, Bardou P, Woloszyn F, Lluch J, Harichaux G, Viguié C, Monniaux D, Bodin L, Mulsant P, Fabre S. The highly prolific phenotype of Lacaune sheep is associated with an ectopic expression of the B4GALNT2 gene within the ovary. PLoS Genet 2013; 9:e1003809. [PMID: 24086150 PMCID: PMC3784507 DOI: 10.1371/journal.pgen.1003809] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Accepted: 08/06/2013] [Indexed: 12/31/2022] Open
Abstract
Prolific sheep have proven to be a valuable model to identify genes and mutations implicated in female fertility. In the Lacaune sheep breed, large variation in litter size is genetically determined by the segregation of a fecundity major gene influencing ovulation rate, named FecL and its prolific allele FecL(L) . Our previous work localized FecL on sheep chromosome 11 within a locus of 1.1 Mb encompassing 20 genes. With the aim to identify the FecL gene, we developed a high throughput sequencing strategy of long-range PCR fragments spanning the locus of FecL(L) carrier and non-carrier ewes. Resulting informative markers defined a new 194.6 kb minimal interval. The reduced FecL locus contained only two genes, insulin-like growth factor 2 mRNA binding protein 1 (IGF2BP1) and beta-1,4-N-acetyl-galactosaminyl transferase 2 (B4GALNT2), and we identified two SNP in complete linkage disequilibrium with FecL(L) . B4GALNT2 appeared as the best positional and expressional candidate for FecL, since it showed an ectopic expression in the ovarian follicles of FecL(L) /FecL(L) ewes at mRNA and protein levels. In FecL(L) carrier ewes only, B4GALNT2 transferase activity was localized in granulosa cells and specifically glycosylated proteins were detected in granulosa cell extracts and follicular fluids. The identification of these glycoproteins by mass spectrometry revealed at least 10 proteins, including inhibin alpha and betaA subunits, as potential targets of B4GALNT2 activity. Specific ovarian protein glycosylation by B4GALNT2 is proposed as a new mechanism of ovulation rate regulation in sheep, and could contribute to open new fields of investigation to understand female infertility pathogenesis.
Collapse
Affiliation(s)
- Laurence Drouilhet
- INRA-ENVT, UMR 444, Laboratoire de Génétique Cellulaire, Castanet-Tolosan, France
| | - Camille Mansanet
- INRA UMR 85, CNRS UMR 7247, Université de Tours, IFCE, Physiologie de la Reproduction et des Comportements, Nouzilly, France
| | - Julien Sarry
- INRA-ENVT, UMR 444, Laboratoire de Génétique Cellulaire, Castanet-Tolosan, France
| | - Kamila Tabet
- INRA-ENVT, UMR 444, Laboratoire de Génétique Cellulaire, Castanet-Tolosan, France
| | - Philippe Bardou
- INRA, SIGENAE, Laboratoire de Génétique Cellulaire, Castanet-Tolosan, France
| | - Florent Woloszyn
- INRA-ENVT, UMR 444, Laboratoire de Génétique Cellulaire, Castanet-Tolosan, France
| | - Jérome Lluch
- INRA, GeT-PlaGe Genotoul, Castanet-Tolosan, France
| | - Grégoire Harichaux
- INRA UMR 85, CNRS UMR 7247, Université de Tours, IFCE, Physiologie de la Reproduction et des Comportements, Nouzilly, France
- INRA, Plate-forme d'Analyse Intégrative des Biomolécules, Laboratoire de Spectrométrie de Masse, Nouzilly, France
| | - Catherine Viguié
- UMR 1331 INRA-ENVT-EIP-INPT-UPS, Toxicologie Alimentaire, Toulouse, France
| | - Danielle Monniaux
- INRA UMR 85, CNRS UMR 7247, Université de Tours, IFCE, Physiologie de la Reproduction et des Comportements, Nouzilly, France
| | - Loys Bodin
- INRA, UR 631, Station d'Amélioration Génétique des Animaux, Castanet-Tolosan, France
| | - Philippe Mulsant
- INRA-ENVT, UMR 444, Laboratoire de Génétique Cellulaire, Castanet-Tolosan, France
| | - Stéphane Fabre
- INRA-ENVT, UMR 444, Laboratoire de Génétique Cellulaire, Castanet-Tolosan, France
- INRA UMR 85, CNRS UMR 7247, Université de Tours, IFCE, Physiologie de la Reproduction et des Comportements, Nouzilly, France
| |
Collapse
|
35
|
De Brakeleer S, De Grève J, Lissens W, Teugels E. Systematic detection of pathogenic alu element insertions in NGS-based diagnostic screens: the BRCA1/BRCA2 example. Hum Mutat 2013; 34:785-91. [PMID: 23420552 DOI: 10.1002/humu.22297] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2012] [Accepted: 02/06/2013] [Indexed: 12/24/2022]
Abstract
Pathogenic Alu element insertions are rarely reported, whereas their occurrence is expected to be much higher. Alu containing alleles are usually out-competed during the PCR process and consequently undetectable with the classical screening methods. However, with the introduction of the next generation sequencing (NGS) technology in the diagnostic field, new opportunities are emerging. NGS data for a particular genomic region can be seen as the summation of all the individual sequences (reads) obtained for that region and no longer as the mean of this sum as it is the case for traditional Sanger sequencing. Because each single read covering that region is expected to be generated from a different template molecule, the presence of one single mutant read must theoretically be sufficient to identify the mutation. However, generation and identification of mutant reads bearing Alu insertions remains challenging and several wet/dry bench parameters need to be optimized. Hereby we present the proof of principle of a NGS-based mutation screening procedure allowing the detection of inherited Alu insertions within any predefined sequence by investigating 2 cases: c.1739_1740insAlu in BRCA1 and c.156_157insAlu in BRCA2.
Collapse
Affiliation(s)
- Sylvia De Brakeleer
- Laboratory of Molecular and Medical Oncology, Vrije Universiteit Brussel, Belgium
| | | | | | | |
Collapse
|
36
|
Affiliation(s)
- Shuko Harada
- University of Alabama at Birmingham Birmingham Alabama
| | - Bruce R. Korf
- University of Alabama at Birmingham Birmingham Alabama
| |
Collapse
|
37
|
Next-generation sequencing meets genetic diagnostics: development of a comprehensive workflow for the analysis of BRCA1 and BRCA2 genes. Eur J Hum Genet 2012; 21:864-70. [PMID: 23249957 DOI: 10.1038/ejhg.2012.270] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Revised: 09/28/2012] [Accepted: 11/13/2012] [Indexed: 11/08/2022] Open
Abstract
Next-generation sequencing (NGS) is changing genetic diagnosis due to its huge sequencing capacity and cost-effectiveness. The aim of this study was to develop an NGS-based workflow for routine diagnostics for hereditary breast and ovarian cancer syndrome (HBOCS), to improve genetic testing for BRCA1 and BRCA2. A NGS-based workflow was designed using BRCA MASTR kit amplicon libraries followed by GS Junior pyrosequencing. Data analysis combined Variant Identification Pipeline freely available software and ad hoc R scripts, including a cascade of filters to generate coverage and variant calling reports. A BRCA homopolymer assay was performed in parallel. A research scheme was designed in two parts. A Training Set of 28 DNA samples containing 23 unique pathogenic mutations and 213 other variants (33 unique) was used. The workflow was validated in a set of 14 samples from HBOCS families in parallel with the current diagnostic workflow (Validation Set). The NGS-based workflow developed permitted the identification of all pathogenic mutations and genetic variants, including those located in or close to homopolymers. The use of NGS for detecting copy-number alterations was also investigated. The workflow meets the sensitivity and specificity requirements for the genetic diagnosis of HBOCS and improves on the cost-effectiveness of current approaches.
Collapse
|
38
|
Guan YF, Li GR, Wang RJ, Yi YT, Yang L, Jiang D, Zhang XP, Peng Y. Application of next-generation sequencing in clinical oncology to advance personalized treatment of cancer. CHINESE JOURNAL OF CANCER 2012; 31:463-70. [PMID: 22980418 PMCID: PMC3777453 DOI: 10.5732/cjc.012.10216] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
With the development and improvement of new sequencing technology, next-generation sequencing (NGS) has been applied increasingly in cancer genomics research over the past decade. More recently, NGS has been adopted in clinical oncology to advance personalized treatment of cancer. NGS is used to identify novel and rare cancer mutations, detect familial cancer mutation carriers, and provide molecular rationale for appropriate targeted therapy. Compared to traditional sequencing, NGS holds many advantages, such as the ability to fully sequence all types of mutations for a large number of genes (hundreds to thousands) in a single test at a relatively low cost. However, significant challenges, particularly with respect to the requirement for simpler assays, more flexible throughput, shorter turnaround time, and most importantly, easier data analysis and interpretation, will have to be overcome to translate NGS to the bedside of cancer patients. Overall, continuous dedication to apply NGS in clinical oncology practice will enable us to be one step closer to personalized medicine.
Collapse
Affiliation(s)
- Yan-Fang Guan
- Shenzhen Clinical Molecular Diagnostic Engineering Laboratory, BGI-Shenzhen, Shenzhen, Guangdong, People's Republic of China
| | | | | | | | | | | | | | | |
Collapse
|