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Lee NY, Hum M, Amali AA, Lim WK, Wong M, Myint MK, Tay RJ, Ong PY, Samol J, Lim CW, Ang P, Tan MH, Lee SC, Lee ASG. Whole-exome sequencing of BRCA-negative breast cancer patients and case-control analyses identify variants associated with breast cancer susceptibility. Hum Genomics 2022; 16:61. [PMID: 36424660 PMCID: PMC9685974 DOI: 10.1186/s40246-022-00435-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 11/14/2022] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND For the majority of individuals with early-onset or familial breast cancer referred for genetic testing, the genetic basis of their familial breast cancer remains unexplained. To identify novel germline variants associated with breast cancer predisposition, whole-exome sequencing (WES) was performed. METHODS WES on 290 BRCA1/BRCA2-negative Singaporeans with early-onset breast cancer and/or a family history of breast cancer was done. Case-control analysis against the East-Asian subpopulation (EAS) from the Genome Aggregation Database (gnomAD) identified variants enriched in cases, which were further selected by occurrence in cancer gene databases. Variants were further evaluated in repeated case-control analyses using a second case cohort from the database of Genotypes and Phenotypes (dbGaP) comprising 466 early-onset breast cancer patients from the United States, and a Singapore SG10K_Health control cohort. RESULTS Forty-nine breast cancer-associated germline pathogenic variants in 37 genes were identified in Singapore cases versus gnomAD (EAS). Compared against SG10K_Health controls, 13 of 49 variants remain significantly enriched (False Discovery Rate (FDR)-adjusted p < 0.05). Comparing these 49 variants in dbGaP cases against gnomAD (EAS) and SG10K_Health controls revealed 23 concordant variants that were significantly enriched (FDR-adjusted p < 0.05). Fourteen variants were consistently enriched in breast cancer cases across all comparisons (FDR-adjusted p < 0.05). Seven variants in GPRIN2, NRG1, MYO5A, CLIP1, CUX1, GNAS and MGA were confirmed by Sanger sequencing. CONCLUSIONS In conclusion, we have identified pathogenic variants in genes associated with breast cancer predisposition. Importantly, many of these variants were significant in a second case cohort from dbGaP, suggesting that the strategy of using case-control analysis to select variants could potentially be utilized for identifying variants associated with cancer susceptibility.
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Affiliation(s)
- Ning Yuan Lee
- Division of Cellular and Molecular Research, Humphrey Oei Institute of Cancer Research, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore, 169610 Singapore
| | - Melissa Hum
- Division of Cellular and Molecular Research, Humphrey Oei Institute of Cancer Research, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore, 169610 Singapore
| | - Aseervatham Anusha Amali
- Division of Cellular and Molecular Research, Humphrey Oei Institute of Cancer Research, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore, 169610 Singapore
| | - Wei Kiat Lim
- Division of Cellular and Molecular Research, Humphrey Oei Institute of Cancer Research, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore, 169610 Singapore
| | - Matthew Wong
- Division of Cellular and Molecular Research, Humphrey Oei Institute of Cancer Research, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore, 169610 Singapore
| | - Matthew Khine Myint
- Division of Cellular and Molecular Research, Humphrey Oei Institute of Cancer Research, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore, 169610 Singapore
| | - Ru Jin Tay
- Lucence Diagnostics Pte Ltd, 211 Henderson Road, Singapore, 159552 Singapore
| | - Pei-Yi Ong
- Department of Hematology-Oncology, National University Cancer Institute, Singapore (NCIS), National University Health System, 5 Lower Kent Ridge Road, Singapore, 119074 Singapore
| | - Jens Samol
- Medical Oncology Department, Tan Tock Seng Hospital, 11 Jalan Tan Tock Seng, Singapore, 308433 Singapore
- Johns Hopkins University, Baltimore, MD 21218 USA
| | - Chia Wei Lim
- Department of Personalised Medicine, Tan Tock Seng Hospital, 11 Jalan Tan Tock Seng, Singapore, 308433 Singapore
| | - Peter Ang
- Oncocare Cancer Centre, Gleneagles Medical Centre, 6 Napier Road, Singapore, 258499 Singapore
| | - Min-Han Tan
- Lucence Diagnostics Pte Ltd, 211 Henderson Road, Singapore, 159552 Singapore
| | - Soo-Chin Lee
- Department of Hematology-Oncology, National University Cancer Institute, Singapore (NCIS), National University Health System, 5 Lower Kent Ridge Road, Singapore, 119074 Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, 10 Medical Dr, Singapore, 117597 Singapore
- Cancer Science Institute, Singapore (CSI), National University of Singapore, 14 Medical Dr, Singapore, 117599 Singapore
| | - Ann S. G. Lee
- Division of Cellular and Molecular Research, Humphrey Oei Institute of Cancer Research, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore, 169610 Singapore
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, 2 Medical Drive, Singapore, 117593 Singapore
- SingHealth Duke-NUS Oncology Academic Clinical Programme (ONCO ACP), Duke-NUS Graduate Medical School, 8 College Road, Singapore, 169857 Singapore
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Ben Ayed-Guerfali D, Ben Kridis-Rejab W, Ammous-Boukhris N, Ayadi W, Charfi S, Khanfir A, Sellami-Boudawara T, Frikha M, Daoud J, Mokdad-Gargouri R. Novel and recurrent BRCA1/BRCA2 germline mutations in patients with breast/ovarian cancer: a series from the south of Tunisia. J Transl Med 2021; 19:108. [PMID: 33726785 PMCID: PMC7962399 DOI: 10.1186/s12967-021-02772-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 02/26/2021] [Indexed: 12/14/2022] Open
Abstract
Background The incidence of breast cancer (BC) and/or ovarian cancer (OC) is increasing in Tunisia especially in young women and mostly those with family history. However, the spectrum of BRCA mutations remains little explored in Tunisian patients in particular in the southern region. Methods We sequenced the entire coding regions of BRCA1and BRCA2 genes using next generation sequencing (NGS) in 134 selected patients with BC and/or OC. Results Among the 134 patients, 19 (14.17%) carried pathogenic mutations (10 are BRCA1 mutation carriers and 9 are BRCA2 mutation carriers) that are mainly frameshift index (76.9%). Interestingly, 5 out of the 13 variants (38.46%) were found at least twice in unrelated patients, as the c.1310-1313 delAAGA in BRCA2 and the c.5030_5033 delCTAA that has been identified in 4/98 BC patients and in 3/15 OC patients from unrelated families with strong history of cancer. Besides recurrent mutations, 6 variant (4 in BRCA1 and 2 in BRCA2) were not reported previously. Furthermore, 3 unrelated patients carried the VUS c.9976A > T, (K3326*) in BRCA2 exon 27. BRCA carriers correlated significantly with tumor site (p = 0.029) and TNBC cases (p = 0.008). In the groups of patients aged between 31 and 40, and 41–50 years, BRCA1 mutations occurred more frequently in patients with OC than those with BC, and conversely BRCA2 carriers are mostly affected with BC (p = 0.001, and p = 0.044 respectively). Conclusions The overall frequency of the BRCA germline mutations was 14.17% in patients with high risk of breast/ovarian cancer. We identified recurrent mutations as the c.1310_1313 delAAGA in BRCA2 gene and the c.5030_5033 delCTAA in BRCA1 gene that were found in 4% and 20% of familial BC and OC respectively. Our data will contribute in the implementation of genetic counseling and testing for families with high-risk of BC and/or OC.
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Affiliation(s)
- Dorra Ben Ayed-Guerfali
- Center of Biotechnology of Sfax, University of Sfax, Sidi Mansour Street Km 6, BP 1177, 3038, Sfax, Tunisia
| | | | - Nihel Ammous-Boukhris
- Center of Biotechnology of Sfax, University of Sfax, Sidi Mansour Street Km 6, BP 1177, 3038, Sfax, Tunisia
| | - Wajdi Ayadi
- Center of Biotechnology of Sfax, University of Sfax, Sidi Mansour Street Km 6, BP 1177, 3038, Sfax, Tunisia
| | - Slim Charfi
- Department of Anatomo-pathology, Habib Bourguiba Hospital, Sfax, Tunisia
| | - Afef Khanfir
- Department of Oncology, Habib Bourguiba Hospital, Sfax, Tunisia
| | | | - Mounir Frikha
- Department of Oncology, Habib Bourguiba Hospital, Sfax, Tunisia
| | - Jamel Daoud
- Department of Radiotherapy, Habib Bourguiba Hospital, Sfax, Tunisia
| | - Raja Mokdad-Gargouri
- Center of Biotechnology of Sfax, University of Sfax, Sidi Mansour Street Km 6, BP 1177, 3038, Sfax, Tunisia.
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Tariq H, Gul A, Khadim T, Ud-Din H, Tipu HN, Asif M, Ahmed R. Next Generation Sequencing-Based Germline Panel Testing for Breast and Ovarian Cancers in Pakistan. Asian Pac J Cancer Prev 2021; 22:719-724. [PMID: 33773534 PMCID: PMC8286662 DOI: 10.31557/apjcp.2021.22.3.719] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Indexed: 12/16/2022] Open
Abstract
Background: Pathogenic germline mutations in BRCA1/2 constitute the majority of hereditary breast and/or ovarian cancers worldwide. Incidence and mortality rate of breast and ovarian cancers in Pakistani women is high. Thus, to establish the diagnosis for targeted therapy in Pakistan, we conducted Next-generation sequencing-based germline testing for the detection of BRCA1/2 oncogenic variants associated with breast and ovarian cancer subtype. Methods: Peripheral blood of 24 women, diagnosed with breast and epithelial ovarian cancers, was taken from the recruited cases with the consent of performing germline genetic testing. DNA was isolated from the peripheral blood and subjected to indexed BRCA Panel libraries. Targeted NGS was performed for all coding regions and splicing sites of BRCA1 and BRCA2 genes using AmpliSeq for Illumina BRCA Panel and Illumina MiSeq sequencer (placed at AFIP). Analysis of the sequencing results has been done by using Illumina bioinformatics tools. Results: We detected 421 variants having a quality score of 100 in all cases under study. The list of identified variants in BRCA1 and BRCA2 genes was narrowed down after filtering out those which did not pass q30 and those with a minor allele frequency (MAF) > 0.05 based on gnomAD browser. To classify these variants, clinical significance was predicted using external curated databases. As a result, we interpreted (n = 4) 16.7% pathogenic variants in BRCA1 and (n = 6) 25% variants of uncertain significance (VUS) in both genes. Descriptive statistics depicted that the age and BMI of BRCA positive cases are less than BRCA negative cases. Conclusion: Our findings exhibit an initial report for the NGS based cancer genetic testing in Pakistan. This will enable us to pursue screening and diagnosis of hereditary BRCA mutation utilizing the latest state-of-the-art technique locally available in Pakistan ultimately resulting in targeted cancer therapy.
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Affiliation(s)
- Hassan Tariq
- Department of Histopathology, Armed Forces Institute of Pathology, Rawalpindi, Pakistan
| | - Asma Gul
- Department of Histopathology, Armed Forces Institute of Pathology, Rawalpindi, Pakistan
| | - Tahir Khadim
- Department of Histopathology, Armed Forces Institute of Pathology, Rawalpindi, Pakistan
| | - Hafeez Ud-Din
- Department of Histopathology, Armed Forces Institute of Pathology, Rawalpindi, Pakistan
| | - Hamid Nawaz Tipu
- Department of Immunology, Armed Forces Institute of Pathology, Rawalpindi, Pakistan
| | - Muhammad Asif
- Department of Histopathology, Armed Forces Institute of Pathology, Rawalpindi, Pakistan
| | - Rabia Ahmed
- Department of Histopathology, PNS Shifa Hospital, Karachi, Pakistan
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Lemeshko VA, Teptsova TS, Ratushnyak SS, Musina NZ. Assessing the Relevance of Molecular Genetic Testing for Mutations in BRCA Genes of Patients with Ovarian and Breast Cancer. RUSS J GENET+ 2021. [DOI: 10.1134/s1022795420100075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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5
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Jung SM, Ryu JM, Park HS, Park JS, Kang E, Lee S, Lee HB, Youn HJ, Yoo TK, Kim J, Lee JE, Han SA, Kim D, Kim SW. Trends in Risk-Reducing Mastectomy and Risk-Reducing Salpingo-Oophorectomy in Korean Carriers of the BRCA1/2 Mutation. J Breast Cancer 2020; 23:647-655. [PMID: 33408890 PMCID: PMC7779723 DOI: 10.4048/jbc.2020.23.e61] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 11/24/2020] [Indexed: 12/13/2022] Open
Abstract
Purpose BRCA1/2 mutations are associated with risks of breast and ovarian cancer. In Korea, incidences of BRCA1/2 genetic testing and risk-reducing surgery (RRS) have increased with insurance coverage and the Angelina Jolie effect. The aim of this study was to identify trends in RRS performed in Korean women with the BRCA1/2 mutation. Methods We retrospectively reviewed the medical records of BRCA1/2 mutation carriers with (affected carriers) and without (unaffected carriers) breast cancer until August 2018 from 25 Korean Hereditary Breast Cancer (KOHBRA)-affiliated hospitals. Results The numbers of contralateral risk-reducing mastectomy (RRM) and risk-reducing bilateral salpingo-oophorectomy (RRBSO) in affected carriers have increased 5.8- and 3.6-fold, respectively, since 2013. The numbers of RRBSO in unaffected carriers has increased 8-fold since 2013. The number of institutions that perform RRS has increased gradually. The number of hospitals that perform contralateral RRM on affected carriers increased from 3 in 2012 to 11 in 2018, and that of those that perform RRBSO increased from 7 to 17. The number of hospitals that perform bilateral RRM on unaffected carriers increased from 1 in 2012 to 2 in 2018, and that of those that perform RRBSO increased from 1 to 8. However, the hospitals showed differences in the rates of RRM or RRBSO performed. Conclusion The incidence of RRS increased each year throughout the study period. However, in Korea, the rate of RRS procedures depended on the hospital.
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Affiliation(s)
- Sung Mi Jung
- Division of Breast Surgery, Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jai Min Ryu
- Division of Breast Surgery, Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Hyung Seok Park
- Department of Surgery, Yonsei University College of Medicine, Seoul, Korea
| | - Ji Soo Park
- Division of Medical Oncology, Department of Internal Medicine, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Korea
| | - Eunyoung Kang
- Department of Surgery, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Seeyoun Lee
- Department of Surgery, National Cancer Center, Goyang, Korea
| | - Han-Byoel Lee
- Department of Surgery, Seoul National University College of Medicine, Seoul, Korea
| | - Hyun Jo Youn
- Division of Breast Thyroid Surgery, Department of Surgery, Jeonbuk National University Medical School, Jeonju, Korea
| | - Tae-Kyung Yoo
- Division of Breast Surgery, Department of Surgery, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Jisun Kim
- Division of Breast Surgery, Department of Surgery, University of Ulsan College of Medicine, Asan Medical Center, Seoul, Korea
| | - Jeong Eon Lee
- Division of Breast Surgery, Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Sang Ah Han
- Department of Surgery, School of Medicine, Kyung Hee University, Seoul, Korea
| | - Dongwon Kim
- Department of Surgery, Daerim St. Mary's Hospital, Seoul, Korea
| | - Sung-Won Kim
- Department of Surgery, Daerim St. Mary's Hospital, Seoul, Korea
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Rivera D, Paudice M, Gismondi V, Anselmi G, Vellone VG, Varesco L. Implementing NGS-based BRCA tumour tissue testing in FFPE ovarian carcinoma specimens: hints from a real-life experience within the framework of expert recommendations. J Clin Pathol 2020; 74:596-603. [PMID: 32895300 DOI: 10.1136/jclinpath-2020-206840] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 08/05/2020] [Accepted: 08/06/2020] [Indexed: 12/19/2022]
Abstract
AIMS Next Generation Sequencing (NGS)-based BRCA tumour tissue testing poses several challenges. As a first step of its implementation within a regional health service network, an in-house validation study was compared with published recommendations. METHODS Epithelial ovarian cancer (EOC) formalin-fixed paraffin-embedded specimens stored in the archives of the eight regional pathology units were selected from a consecutive series of patients with known BRCA germline status. Two expert pathologists evaluated tumour cell content for manual macrodissection. DNA extraction, library preparation and NGS analyses were performed blinded to the germinal status. Parameters used in the study were confronted with guidelines for the validation of NGS-based oncology panels and for BRCA tumour tissue testing. RESULTS NGS analyses were successful in 66 of 67 EOC specimens, with good quality metrics and high reproducibility among different runs. In all, 19 BRCA pathogenic variants were identified: 12 were germline and 7 were somatic. A 100% concordance with blood tests was detected for germline variants. A BRCA1 variant showed a controversial classification. In different areas of two early stage EOCs showing somatic variants, intratumour heterogeneity not relevant for test results (variant allele frequency >5%) was observed. Compared with expert recommendations, main limitations of the study were absence of controls with known somatic BRCA status and exclusion from the validation of BRCA copy number variations (CNV). CONCLUSIONS A close collaboration between pathology and genetics units provides advantages in the implementation of BRCA tumour tissue testing. The development of tools for designing and interpreting complex testing in-house validation could improve process quality.
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Affiliation(s)
- Daniela Rivera
- Hereditary Cancer Unit, IRCCS Ospedale Policlinico San Martino, Genova, Liguria, Italy
| | - Michele Paudice
- Department of Surgical Sciences and Integrated Diagnostics (DISC), Univeristy of Genoa, Genova, Liguria, Italy
| | - Viviana Gismondi
- Hereditary Cancer Unit, IRCCS Ospedale Policlinico San Martino, Genova, Liguria, Italy
| | - Giorgia Anselmi
- Anatomic Pathology University Unit, IRCCS Ospedale Policlinico San Martino, Genova, Liguria, Italy
| | - Valerio Gaetano Vellone
- Department of Surgical Sciences and Integrated Diagnostics (DISC), Univeristy of Genoa, Genova, Liguria, Italy .,Anatomic Pathology University Unit, IRCCS Ospedale Policlinico San Martino, Genova, Liguria, Italy
| | - Liliana Varesco
- Hereditary Cancer Unit, IRCCS Ospedale Policlinico San Martino, Genova, Liguria, Italy
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Siu RHP, Liu Y, Chan KHY, Ridzewski C, Slaughter LS, Wu AR. Optimization of on-bead emulsion polymerase chain reaction based on single particle analysis. Talanta 2020; 221:121593. [PMID: 33076127 DOI: 10.1016/j.talanta.2020.121593] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 08/20/2020] [Accepted: 08/26/2020] [Indexed: 10/23/2022]
Abstract
Emulsion polymerase chain reaction (ePCR) enables parallel amplification of millions of different DNA molecules while avoiding bias and chimeric byproducts, essential criteria for applications including next generation sequencing, aptamer selection, and protein-DNA interaction studies. Despite these advantages, ePCR remains underused due to the lack of optimal starting conditions, straightforward methods to evaluate success, and guidelines for tuning the reaction. This knowledge has been elusive for bulk emulsion generation methods, such as stirring and vortexing, the only methods that can emulsify libraries of ≥108 sequences within minutes, because these emulsions have not been characterized in ways that preserve the heterogeneity that defines successful ePCR. Our study quantifies the outcome of ePCR from conditions specified in the literature using single particle analysis, which preserves this heterogeneity. We combine ePCR with magnetic microbeads and quantify the amplification yield via qPCR and the proportion of clonal and saturated beads via flow cytometry. Our single particle level analysis of thousands of beads resolves two key criteria that define the success of ePCR: 1) whether the target fraction of 20% clonal beads predicted by the Poisson distribution is achieved, and 2) whether those beads are partially or maximally covered by amplified DNA. We found that among the two concentrations of polymerase tested, only the higher one, which is 20-fold more than the concentration recommended for conventional PCR, could yield sufficient PCR products. Dramatic increases in the concentrations of reverse primer and nucleotides recommended in literature gave no measurable change in outcome. We thus provide evidence-based starting conditions for effective and economical ePCR for real DNA libraries and a straightforward workflow for evaluating the success of tuning ePCR prior to downstream applications.
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Affiliation(s)
- Ryan H P Siu
- Division of Life Science, Hong Kong University of Science and Technology, Hong Kong
| | - Yang Liu
- Division of Life Science, Hong Kong University of Science and Technology, Hong Kong
| | - Kaitlin H Y Chan
- Division of Life Science, Hong Kong University of Science and Technology, Hong Kong
| | - Clara Ridzewski
- Natural and Environmental Sciences, Zittau/Görlitz University of Applied Sciences, Germany
| | - Liane Siu Slaughter
- Division of Life Science, Hong Kong University of Science and Technology, Hong Kong.
| | - Angela R Wu
- Division of Life Science, Hong Kong University of Science and Technology, Hong Kong; Department of Chemical and Biological Engineering, Hong Kong University of Science and Technology, Hong Kong.
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Qu S, Chen Q, Yi Y, Shao K, Zhang W, Wang Y, Bai J, Li X, Liu Z, Wang X, Jing R, Guan Y, Yi X, Yan M, Cao B, Chen F, Zhu S, Yang X, Wu Y, Huang J. A Reference System for BRCA Mutation Detection Based on Next-Generation Sequencing in the Chinese Population. J Mol Diagn 2019; 21:677-686. [DOI: 10.1016/j.jmoldx.2019.03.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 01/17/2019] [Accepted: 03/13/2019] [Indexed: 12/12/2022] Open
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Nicolussi A, Belardinilli F, Mahdavian Y, Colicchia V, D'Inzeo S, Petroni M, Zani M, Ferraro S, Valentini V, Ottini L, Giannini G, Capalbo C, Coppa A. Next-generation sequencing of BRCA1 and BRCA2 genes for rapid detection of germline mutations in hereditary breast/ovarian cancer. PeerJ 2019; 7:e6661. [PMID: 31065452 PMCID: PMC6482939 DOI: 10.7717/peerj.6661] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 02/19/2019] [Indexed: 12/12/2022] Open
Abstract
Background Conventional methods used to identify BRCA1 and BRCA2 germline mutations in hereditary cancers, such as Sanger sequencing/multiplex ligation-dependent probe amplification (MLPA), are time-consuming and expensive, due to the large size of the genes. The recent introduction of next-generation sequencing (NGS) benchtop platforms offered a powerful alternative for mutation detection, dramatically improving the speed and the efficiency of DNA testing. Here we tested the performance of the Ion Torrent PGM platform with the Ion AmpliSeq BRCA1 and BRCA2 Panel in our clinical routine of breast/ovarian hereditary cancer syndrome assessment. Methods We first tested the NGS approach in a cohort of 11 patients (training set) who had previously undergone genetic diagnosis in our laboratory by conventional methods. Then, we applied the optimized pipeline to the consecutive cohort of 136 uncharacterized probands (validation set). Results By minimal adjustments in the analytical pipeline of Torrent Suite Software we obtained a 100% concordance with Sanger results regarding the identification of single nucleotide alterations, insertions, and deletions with the exception of three large genomic rearrangements (LGRs) contained in the training set. The optimized pipeline applied to the validation set (VS), identified pathogenic and polymorphic variants, including a novel BRCA2 pathogenic variant at exon 3, 100% of which were confirmed by Sanger in their correct zygosity status. To identify LGRs, all negative samples of the VS were subjected to MLPA analysis. Discussion Our experience strongly supports that the Ion Torrent PGM technology in BRCA1 and BRCA2 germline variant identification, combined with MLPA analysis, is highly sensitive, easy to use, faster, and cheaper than traditional (Sanger sequencing/MLPA) approaches.
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Affiliation(s)
- Arianna Nicolussi
- Department of Experimental Medicine, University of Roma "La Sapienza", Roma, Italy
| | | | - Yasaman Mahdavian
- Department of Molecular Medicine, University of Roma "La Sapienza", Roma, Italy
| | - Valeria Colicchia
- Department of Molecular Medicine, University of Roma "La Sapienza", Roma, Italy
| | - Sonia D'Inzeo
- Department of Experimental Medicine, University of Roma "La Sapienza", Roma, Italy.,U.O.C. Microbiology and Virology Laboratory, A.O. San Camillo Forlanini, Roma, Italy
| | - Marialaura Petroni
- Istituto Italiano di Tecnologia, Center for Life Nano Science@Sapienza, Roma, Italy
| | - Massimo Zani
- Department of Molecular Medicine, University of Roma "La Sapienza", Roma, Italy
| | - Sergio Ferraro
- Department of Molecular Medicine, University of Roma "La Sapienza", Roma, Italy
| | - Virginia Valentini
- Department of Molecular Medicine, University of Roma "La Sapienza", Roma, Italy
| | - Laura Ottini
- Department of Molecular Medicine, University of Roma "La Sapienza", Roma, Italy
| | - Giuseppe Giannini
- Department of Molecular Medicine, University of Roma "La Sapienza", Roma, Italy.,Istituto Pasteur-Fondazione Cenci Bolognetti, Roma, Italy
| | - Carlo Capalbo
- Department of Molecular Medicine, University of Roma "La Sapienza", Roma, Italy
| | - Anna Coppa
- Department of Experimental Medicine, University of Roma "La Sapienza", Roma, Italy
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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]
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11
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Liang Y, Yang X, Li H, Zhu A, Guo Z, Li M. Prevalence and Spectrum of BRCA1/2 Germline Mutations in Women with Breast Cancer in China Based on Next-Generation Sequencing. Med Sci Monit 2018; 24:2465-2475. [PMID: 29681614 PMCID: PMC5936051 DOI: 10.12659/msm.905812] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Background BRCA1 and BRCA2 (BRCA1/2) play important roles in the development of breast cancer, but information regarding BRCA1/2 mutations in Chinese females remains limited. The aim of this study was to investigate the prevalence and spectrum of BRCA1/2 mutations in China. Material/Methods In total, 595 breast cancer patients in China were screened with an amplicon-based panel for the detection of BRCA1/2 mutations in coding regions using next-generation sequencing (NGS) with a Personal Genome Machine. Every pathogenic mutation detected was confirmed by Sanger sequencing. The disease-causing potential of variants of uncertain significance (VUS) was predicted using PolyPhen-2, SIFT, PhyloP, and Grantham. Results The prevalence of BRCA1/2 mutations was 8.07% in the Chinese population. Forty-two pathogenic mutations were identified in 48 cases (17 BRCA1 cases and 31 BRCA2 cases), including 19 novel mutations. Nine VUS were predicted to be deleterious by PolyPhen-2 and SIFT and subsequently predicted by PhyloP and Grantham for the evolutionary conservation. Conclusions These results suggest that NGS is useful as a rapid, high-throughput, and cost-effective screening tool for the analysis of BRCA1/2 mutations. Based on this panel, we found that BRCA1/2 germline mutations in China exhibit distinct characteristics compared to those in Western populations.
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Affiliation(s)
- Yi Liang
- School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, Guangdong, China (mainland)
| | - Xuexi Yang
- School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, Guangdong, China (mainland)
| | - Hong Li
- School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, Guangdong, China (mainland)
| | - Anna Zhu
- Guangzhou Darui Biotechnology Co. Ltd., Guangzhou, Guangdong, China (mainland)
| | - Zhiwei Guo
- School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, Guangdong, China (mainland)
| | - Ming Li
- School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, Guangdong, China (mainland)
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12
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Pop LA, Cojocneanu-Petric RM, Pileczki V, Morar-Bolba G, Irimie A, Lazar V, Lombardo C, Paradiso A, Berindan-Neagoe I. Genetic alterations in sporadic triple negative breast cancer. Breast 2018; 38:30-38. [DOI: 10.1016/j.breast.2017.11.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 10/10/2017] [Accepted: 11/09/2017] [Indexed: 02/07/2023] Open
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13
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Enyedi MZ, Jaksa G, Pintér L, Sükösd F, Gyuris Z, Hajdu A, Határvölgyi E, Priskin K, Haracska L. Simultaneous detection of BRCA mutations and large genomic rearrangements in germline DNA and FFPE tumor samples. Oncotarget 2018; 7:61845-61859. [PMID: 27533253 PMCID: PMC5308695 DOI: 10.18632/oncotarget.11259] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 07/19/2016] [Indexed: 11/25/2022] Open
Abstract
The development of breast and ovarian cancer is strongly connected to the inactivation of the BRCA1 and BRCA2 genes by different germline and somatic alterations, and their diagnosis has great significance in targeted tumor therapy, since recently approved PARP inhibitors show high efficiency in the treatment of BRCA-deficient tumors. This raises the need for new diagnostic methods that are capable of performing an integrative mutation analysis of the BRCA genes not only from germline DNA but also from formalin-fixed and paraffin-embedded (FFPE) tumor samples. Here we describe the development of such a methodology based on next-generation sequencing and a new bioinformatics software for data analysis. The diagnostic method was initially developed on an Illumina MiSeq NGS platform using germline-mutated stem cell lines and then adapted for the Ion Torrent PGM NGS platform as well. We also investigated the usability of NGS coverage data for the detection of copy number variations and exon deletions as a replacement of the conventional MLPA technique. Finally, we tested the developed workflow on FFPE samples from breast and ovarian cancer patients. Our method meets the sensitivity and specificity requirements for the genetic diagnosis of breast and ovarian cancers both from germline and FFPE samples.
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Affiliation(s)
- Márton Zsolt Enyedi
- Institute of Genetics, Biological Research Centre of the Hungarian Academy of Sciences, Szeged 6726, Hungary
| | | | | | - Farkas Sükösd
- Department of Pathology, Faculty of Medicine, University of Szeged, Szeged 6720, Hungary
| | | | - Adrienn Hajdu
- Delta Bio 2000 Ltd., Szeged 6726, Hungary.,Department of Pathology, Faculty of Medicine, University of Szeged, Szeged 6720, Hungary
| | | | | | - Lajos Haracska
- Institute of Genetics, Biological Research Centre of the Hungarian Academy of Sciences, Szeged 6726, Hungary
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14
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Apessos A, Agiannitopoulos K, Pepe G, Tsaousis GN, Papadopoulou E, Metaxa-Mariatou V, Tsirigoti A, Efstathiadou C, Markopoulos C, Xepapadakis G, Venizelos V, Tsiftsoglou A, Natsiopoulos I, Nasioulas G. Comprehensive BRCA mutation analysis in the Greek population. Experience from a single clinical diagnostic center. Cancer Genet 2018; 220:1-12. [DOI: 10.1016/j.cancergen.2017.10.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 10/09/2017] [Accepted: 10/12/2017] [Indexed: 12/28/2022]
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15
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Goodwin S, McPherson JD, McCombie WR. Coming of age: ten years of next-generation sequencing technologies. Nat Rev Genet 2017; 17:333-51. [PMID: 27184599 PMCID: PMC10373632 DOI: 10.1038/nrg.2016.49] [Citation(s) in RCA: 2147] [Impact Index Per Article: 306.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Since the completion of the human genome project in 2003, extraordinary progress has been made in genome sequencing technologies, which has led to a decreased cost per megabase and an increase in the number and diversity of sequenced genomes. An astonishing complexity of genome architecture has been revealed, bringing these sequencing technologies to even greater advancements. Some approaches maximize the number of bases sequenced in the least amount of time, generating a wealth of data that can be used to understand increasingly complex phenotypes. Alternatively, other approaches now aim to sequence longer contiguous pieces of DNA, which are essential for resolving structurally complex regions. These and other strategies are providing researchers and clinicians a variety of tools to probe genomes in greater depth, leading to an enhanced understanding of how genome sequence variants underlie phenotype and disease.
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Affiliation(s)
- Sara Goodwin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - John D McPherson
- Department of Biochemistry and Molecular Medicine; and the Comprehensive Cancer Center, University of California, Davis, California 95817, USA
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16
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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.
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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
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17
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Chakravorty S, Hegde M. Gene and Variant Annotation for Mendelian Disorders in the Era of Advanced Sequencing Technologies. Annu Rev Genomics Hum Genet 2017; 18:229-256. [PMID: 28415856 DOI: 10.1146/annurev-genom-083115-022545] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Comprehensive annotations of genetic and noncoding regions and corresponding accurate variant classification for Mendelian diseases are the next big challenge in the new genomic era of personalized medicine. Progress in the development of faster and more accurate pipelines for genome annotation and variant classification will lead to the discovery of more novel disease associations and candidate therapeutic targets. This ultimately will facilitate better patient recruitment in clinical trials. In this review, we describe the trends in research at the intersection of basic and clinical genomics that aims to increase understanding of overall genomic complexity, complex inheritance patterns of disease, and patient-phenotype-specific genomic associations. We describe the emerging field of translational functional genomics, which integrates other functional "-omics" approaches that support next-generation sequencing genomic data in order to facilitate personalized diagnostics, disease management, biomarker discovery, and medicine. We also discuss the utility of this integrated approach for diagnostic clinics and medical databases and its role in the future of personalized medicine.
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Affiliation(s)
- Samya Chakravorty
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia 30322;
| | - Madhuri Hegde
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia 30322;
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18
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Hwang SM, Lee KC, Lee MS, Park KU. Comparison of Ion Personal Genome Machine Platforms for the Detection of Variants in BRCA1 and BRCA2. Cancer Res Treat 2017; 50:255-264. [PMID: 28392550 PMCID: PMC5784618 DOI: 10.4143/crt.2017.062] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 04/03/2017] [Indexed: 11/26/2022] Open
Abstract
Purpose Transition to next generation sequencing (NGS) for BRCA1/BRCA2 analysis in clinical laboratories is ongoing but different platforms and/or data analysis pipelines give different results resulting in difficulties in implementation. We have evaluated the Ion Personal Genome Machine (PGM) Platforms (Ion PGM, Ion PGM Dx, Thermo Fisher Scientific) for the analysis of BRCA1/2. Materials and Methods The results of Ion PGM with OTG-snpcaller, a pipeline based on Torrent mapping alignment program and Genome Analysis Toolkit, from 75 clinical samples and 14 reference DNA samples were compared with Sanger sequencing for BRCA1/BRCA2. Ten clinical samples and 14 reference DNA samples were additionally sequenced by Ion PGM Dx with Torrent Suite. Results Fifty types of variants including 18 pathogenic or variants of unknown significance were identified from 75 clinical samples and known variants of the reference samples were confirmed by Sanger sequencing and/or NGS. One false-negative results were present for Ion PGM/OTG-snpcaller for an indel variant misidentified as a single nucleotide variant. However, eight discordant results were present for Ion PGM Dx/Torrent Suite with both false-positive and -negative results. A 40-bp deletion, a 4-bp deletion and a 1-bp deletion variant was not called and a false-positive deletion was identified. Four other variants were misidentified as another variant. Conclusion Ion PGM/OTG-snpcaller showed acceptable performance with good concordance with Sanger sequencing. However, Ion PGM Dx/Torrent Suite showed many discrepant results not suitable for use in a clinical laboratory, requiring further optimization of the data analysis for calling variants.
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Affiliation(s)
- Sang Mee Hwang
- Department of Laboratory Medicine, Seoul National University Bundang Hospital, Seongnam, Korea.,Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Ki Chan Lee
- Eone-Diagnomics Genome Center, Incheon, Korea
| | | | - Kyoung Un Park
- Department of Laboratory Medicine, Seoul National University Bundang Hospital, Seongnam, Korea.,Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Korea
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19
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De Summa S, Malerba G, Pinto R, Mori A, Mijatovic V, Tommasi S. GATK hard filtering: tunable parameters to improve variant calling for next generation sequencing targeted gene panel data. BMC Bioinformatics 2017; 18:119. [PMID: 28361668 PMCID: PMC5374681 DOI: 10.1186/s12859-017-1537-8] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND NGS technology represents a powerful alternative to the standard Sanger sequencing in the context of clinical setting. The proprietary software that are generally used for variant calling often depend on preset parameters that may not fit in a satisfactory manner for different genes. GATK, which is widely used in the academic world, is rich in parameters for variant calling. However the self-adjusting parameter calibration of GATK requires data from a large number of exomes. When these are not available, which is the standard condition of a diagnostic laboratory, the parameters must be set by the operator (hard filtering). The aim of the present paper was to set up a procedure to assess the best parameters to be used in the hard filtering of GATK. This was pursued by using classification trees on true and false variants from simulated sequences of a real dataset data. RESULTS We simulated two datasets, with different coverages, including all the sequence alterations identified in a real dataset according to their observed frequencies. Simulated sequences were aligned with standard protocols and then regression trees were built up to identify the most reliable parameters and cutoff values to discriminate true and false variant calls. Moreover, we analyzed flanking sequences of region presenting a high rate of false positive calls observing that such sequences present a low complexity make up. CONCLUSIONS Our results showed that GATK hard filtering parameter values can be tailored through a simulation study based-on the DNA region of interest to ameliorate the accuracy of the variant calling.
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Affiliation(s)
- Simona De Summa
- IRCCS-Istituto Tumori "Giovanni Paolo II", Molecular Genetics Laboratory, viale Orazio Flacco, 65, 70124, Bari, Italy
| | - Giovanni Malerba
- Department of Neuroscience, Biomedicine and Movement Sciences, Section of Biology and Genetics, University of Verona, Strada Le Grazie 8, 37135, Verona, Italy.
| | - Rosamaria Pinto
- IRCCS-Istituto Tumori "Giovanni Paolo II", Molecular Genetics Laboratory, viale Orazio Flacco, 65, 70124, Bari, Italy
| | - Antonio Mori
- Department of Neuroscience, Biomedicine and Movement Sciences, Section of Biology and Genetics, University of Verona, Strada Le Grazie 8, 37135, Verona, Italy
| | - Vladan Mijatovic
- Department of Neuroscience, Biomedicine and Movement Sciences, Section of Biology and Genetics, University of Verona, Strada Le Grazie 8, 37135, Verona, Italy
| | - Stefania Tommasi
- IRCCS-Istituto Tumori "Giovanni Paolo II", Molecular Genetics Laboratory, viale Orazio Flacco, 65, 70124, Bari, Italy
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20
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Sequence specific sorting of DNA molecules with FACS using 3dPCR. Sci Rep 2017; 7:39385. [PMID: 28051104 PMCID: PMC5209659 DOI: 10.1038/srep39385] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 11/22/2016] [Indexed: 12/04/2022] Open
Abstract
Genetic heterogeneity is an important feature of many biological systems, but introduces technical challenges to their characterization. Even with the best modern instruments, only a small fraction of DNA molecules present in a sample can be read, and they are recovered in the form of short, hundred-base reads. In this paper, we introduce 3dPCR, a method to sort DNA molecules with sequence specificity. 3dPCR allows heterogeneous populations of DNA to be sorted to recover long targets for deep sequencing. It is valuable whenever a target sequence is rare in a mixed population, such as for characterizing mutations in heterogeneous cancer cell populations or identifying cells containing a specific genetic sequence or infected with a target virus.
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21
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Abstract
Increased demand for BRCA testing is placing pressures on diagnostic laboratories to raise their mutation screening capacity and handle the challenges associated with classifying BRCA sequence variants for clinical significance, for example interpretation of pathogenic mutations or variants of unknown significance, accurate determination of large genomic rearrangements and detection of somatic mutations in DNA extracted from formalin-fixed, paraffin-embedded tumour samples. Many diagnostic laboratories are adopting next-generation sequencing (NGS) technology to increase their screening capacity and reduce processing time and unit costs. However, migration to NGS introduces complexities arising from choice of components of the BRCA testing workflow, such as NGS platform, enrichment method and bioinformatics analysis process. An efficient, cost-effective accurate mutation detection strategy and a standardised, systematic approach to the reporting of BRCA test results is imperative for diagnostic laboratories. This review covers the challenges of BRCA testing from the perspective of a diagnostics laboratory.
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Affiliation(s)
- Andrew J Wallace
- Genomic Diagnostics Laboratory, Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester, UK
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22
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Improved Efficiency and Reliability of NGS Amplicon Sequencing Data Analysis for Genetic Diagnostic Procedures Using AGSA Software. BIOMED RESEARCH INTERNATIONAL 2016; 2016:5623089. [PMID: 27656653 PMCID: PMC5021467 DOI: 10.1155/2016/5623089] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 06/28/2016] [Indexed: 11/23/2022]
Abstract
Screening for BRCA mutations in women with familial risk of breast or ovarian cancer is an ideal situation for high-throughput sequencing, providing large amounts of low cost data. However, 454, Roche, and Ion Torrent, Thermo Fisher, technologies produce homopolymer-associated indel errors, complicating their use in routine diagnostics. We developed software, named AGSA, which helps to detect false positive mutations in homopolymeric sequences. Seventy-two familial breast cancer cases were analysed in parallel by amplicon 454 pyrosequencing and Sanger dideoxy sequencing for genetic variations of the BRCA genes. All 565 variants detected by dideoxy sequencing were also detected by pyrosequencing. Furthermore, pyrosequencing detected 42 variants that were missed with Sanger technique. Six amplicons contained homopolymer tracts in the coding sequence that were systematically misread by the software supplied by Roche. Read data plotted as histograms by AGSA software aided the analysis considerably and allowed validation of the majority of homopolymers. As an optimisation, additional 250 patients were analysed using microfluidic amplification of regions of interest (Access Array Fluidigm) of the BRCA genes, followed by 454 sequencing and AGSA analysis. AGSA complements a complete line of high-throughput diagnostic sequence analysis, reducing time and costs while increasing reliability, notably for homopolymer tracts.
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23
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Cragun D, Scherr C, Camperlengo L, Vadaparampil ST, Pal T. Evolution of Hereditary Breast Cancer Genetic Services: Are Changes Reflected in the Knowledge and Clinical Practices of Florida Providers? Genet Test Mol Biomarkers 2016; 20:569-578. [PMID: 27525501 DOI: 10.1089/gtmb.2016.0113] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
AIMS We describe practitioner knowledge and practices related to hereditary breast and ovarian cancer (HBOC) in an evolving landscape of genetic testing. METHODS A survey was mailed in late 2013 to Florida providers who order HBOC testing. Descriptive statistics were conducted to characterize participants' responses. RESULTS Of 101 respondents, 66% indicated either no genetics education or education through a commercial laboratory. Although 79% of respondents were aware of the Supreme Court ruling resulting in the loss of Myriad Genetics' BRCA gene patent, only 19% had ordered testing from a different laboratory. With regard to pretest counseling, 78% of respondents indicated they usually discuss 11 of 14 nationally recommended elements for informed consent. Pretest discussion times varied from 3 to 120 min, with approximately half spending <20 min. Elements not routinely covered by >40% of respondents included (1) possibility of a variant of uncertain significance (VUS) and (2) issues related to life/disability insurance. With regard to genetic testing for HBOC, 88% would test an unaffected sister of a breast cancer patient identified with a BRCA VUS. CONCLUSIONS Results highlight the need to identify whether variability in hereditary cancer service delivery impacts patient outcomes. Findings also reveal opportunities to facilitate ongoing outreach and education.
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Affiliation(s)
- Deborah Cragun
- 1 Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute , Tampa, Florida.,2 Department of Global Health, University of South Florida , Tampa, Florida
| | - Courtney Scherr
- 3 Department of Communication Studies, Northwestern University , Chicago, Illinois
| | - Lucia Camperlengo
- 1 Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute , Tampa, Florida
| | - Susan T Vadaparampil
- 1 Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute , Tampa, Florida
| | - Tuya Pal
- 1 Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute , Tampa, Florida
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24
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Evaluation of an amplicon-based next-generation sequencing panel for detection of BRCA1 and BRCA2 genetic variants. Breast Cancer Res Treat 2016; 158:433-40. [PMID: 27383479 DOI: 10.1007/s10549-016-3891-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 06/27/2016] [Indexed: 01/15/2023]
Abstract
The recent advances in the next-generation sequencing (NGS) technology have enabled fast, accurate, and cost-effective genetic testing. Here, we evaluated the performance of a targeted NGS panel for BRCA1/2 sequencing and confirmed its applicability in routine clinical diagnostics. We tested samples from 88 patients using the TruSeq custom panel (Illumina Inc, USA) and a MiSeq sequencer (Illumina) and compared the results to the outcomes of conventional Sanger sequencing. All 1015 sequence variations identified by Sanger sequencing were detected by NGS, except for one missense variant that might have been missed due to a rare mutation on a primer-binding site. One deletion variation, c.1909 + 12delT of BRCA2, was falsely called in all samples due to a homopolymer error. In addition, seven different single-nucleotide substitutions with low variant frequencies (range: 16.2-33.3 %) were falsely called by NGS. In a separate batch, 10 different false-positive variations were found in five samples. The overall sensitivity and positive predictive value of NGS were estimated to be 99.9 and 87.5 %, respectively. The false-positive results could be excluded by setting quality and alternative allele ratio filters and/or by visual inspection using the IGV software. Targeted NGS panel for BRCA1 and BRCA2 showed an excellent agreement with Sanger sequencing results. We therefore conclude that this NGS panel can be used for routine diagnostic method in a clinical genetic laboratory.
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25
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Pilato B, Pinto R, De Summa S, Petriella D, Lacalamita R, Danza K, Paradiso A, Tommasi S. BRCA1-2 diagnostic workflow from next-generation sequencing technologies to variant identification and final report. Genes Chromosomes Cancer 2016; 55:803-13. [PMID: 27225819 DOI: 10.1002/gcc.22383] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 05/23/2016] [Accepted: 05/23/2016] [Indexed: 12/14/2022] Open
Abstract
The BRCA1-BRCA2 genes predispose to hereditary breast and ovarian cancer, and the germline and mutational status of these genes defines a target population that can benefit from PARP inhibitor treatments. To respond to the increasing number of BRCA1-BRCA2 tests, it is necessary to shift to high-throughput technologies that are reliable and less time consuming. Different methodological platforms are dedicated to this purpose with different approaches and algorithms for analysis. Our aim was to set up a cost-effective and low time-consuming BRCA1-BRCA2 mutation detection workflow using the Ion Torrent PGM technology. A retrospective cohort of 40 patients with familial breast/ovarian cancer previously tested by Sanger sequencing and a prospective cohort of 72 patients (validation set) were analyzed. The validation set included 64 patients affected by familial breast/ovarian cancer and eight sporadic ovarian cancer cases, who are potential candidates for PARPi treatments. A complete and standardized workflow easily usable and suitable in a certified laboratory has been proved and validated. This includes all steps from library preparation to the final report. The use of next-generation sequencing will be of benefit for patients enrolled in the genetic counseling process and, moreover, will enhance the process of selecting patients eligible for personalized treatments. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Brunella Pilato
- Molecular Genetics Laboratory, IRCCS Istituto Tumori "Giovanni Paolo II,", Bari, Italy
| | - Rosamaria Pinto
- Molecular Genetics Laboratory, IRCCS Istituto Tumori "Giovanni Paolo II,", Bari, Italy
| | - Simona De Summa
- Molecular Genetics Laboratory, IRCCS Istituto Tumori "Giovanni Paolo II,", Bari, Italy
| | - Daniela Petriella
- Molecular Genetics Laboratory, IRCCS Istituto Tumori "Giovanni Paolo II,", Bari, Italy
| | - Rosanna Lacalamita
- Molecular Genetics Laboratory, IRCCS Istituto Tumori "Giovanni Paolo II,", Bari, Italy
| | - Katia Danza
- Molecular Genetics Laboratory, IRCCS Istituto Tumori "Giovanni Paolo II,", Bari, Italy
| | - Angelo Paradiso
- Experimental Medical Oncology Unit, IRCCS Istituto Tumori "Giovanni Paolo II,", Bari, Italy
| | - Stefania Tommasi
- Molecular Genetics Laboratory, IRCCS Istituto Tumori "Giovanni Paolo II,", Bari, Italy
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26
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Schenkel LC, Kerkhof J, Stuart A, Reilly J, Eng B, Woodside C, Levstik A, Howlett CJ, Rupar AC, Knoll JHM, Ainsworth P, Waye JS, Sadikovic B. Clinical Next-Generation Sequencing Pipeline Outperforms a Combined Approach Using Sanger Sequencing and Multiplex Ligation-Dependent Probe Amplification in Targeted Gene Panel Analysis. J Mol Diagn 2016; 18:657-667. [PMID: 27376475 DOI: 10.1016/j.jmoldx.2016.04.002] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 03/07/2016] [Accepted: 04/19/2016] [Indexed: 01/17/2023] Open
Abstract
Advances in next-generation sequencing (NGS) have facilitated parallel analysis of multiple genes enabling the implementation of cost-effective, rapid, and high-throughput methods for the molecular diagnosis of multiple genetic conditions, including the identification of BRCA1 and BRCA2 mutations in high-risk patients for hereditary breast and ovarian cancer. We clinically validated a NGS pipeline designed to replace Sanger sequencing and multiplex ligation-dependent probe amplification analysis and to facilitate detection of sequence and copy number alterations in a single test focusing on a BRCA1/BRCA2 gene analysis panel. Our custom capture library covers 46 exons, including BRCA1 exons 2, 3, and 5 to 24 and BRCA2 exons 2 to 27, with 20 nucleotides of intronic regions both 5' and 3' of each exon. We analyzed 402 retrospective patients, with previous Sanger sequencing and multiplex ligation-dependent probe amplification results, and 240 clinical prospective patients. One-hundred eighty-three unique variants, including sequence and copy number variants, were detected in the retrospective (n = 95) and prospective (n = 88) cohorts. This standardized NGS pipeline demonstrated 100% sensitivity and 100% specificity, uniformity, and high-depth nucleotide coverage per sample (approximately 7000 reads per nucleotide). Subsequently, the NGS pipeline was applied to the analysis of larger gene panels, which have shown similar uniformity, sample-to-sample reproducibility in coverage distribution, and sensitivity and specificity for detection of sequence and copy number variants.
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Affiliation(s)
- Laila C Schenkel
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
| | - Jennifer Kerkhof
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, Children's Health Research Institute, London, Ontario, Canada
| | - Alan Stuart
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, Children's Health Research Institute, London, Ontario, Canada
| | - Jack Reilly
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, Children's Health Research Institute, London, Ontario, Canada
| | - Barry Eng
- Department of Pathology and Laboratory Medicine, Hamilton Regional Laboratory Medicine Program, Hamilton Health Sciences, Hamilton, Ontario, Canada
| | - Crystal Woodside
- Department of Pathology and Laboratory Medicine, Hamilton Regional Laboratory Medicine Program, Hamilton Health Sciences, Hamilton, Ontario, Canada
| | - Alexander Levstik
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, Children's Health Research Institute, London, Ontario, Canada
| | - Christopher J Howlett
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
| | - Anthony C Rupar
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada; Biochemical Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, Ontario, Canada
| | - Joan H M Knoll
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada; Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, Children's Health Research Institute, London, Ontario, Canada
| | - Peter Ainsworth
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada; Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, Children's Health Research Institute, London, Ontario, Canada
| | - John S Waye
- Department of Pathology and Laboratory Medicine, Hamilton Regional Laboratory Medicine Program, Hamilton Health Sciences, Hamilton, Ontario, Canada
| | - Bekim Sadikovic
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada; Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, Children's Health Research Institute, London, Ontario, Canada.
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Jouali F, Laarabi FZ, Marchoudi N, Ratbi I, Elalaoui SC, Rhaissi H, Fekkak J, Sefiani A. First application of next-generation sequencing in Moroccan breast/ovarian cancer families and report of a novel frameshift mutation of the BRCA1 gene. Oncol Lett 2016; 12:1192-1196. [PMID: 27446417 DOI: 10.3892/ol.2016.4739] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 05/24/2016] [Indexed: 11/05/2022] Open
Abstract
At present, breast cancer is the most common type of cancer in females. The majority of cases are sporadic, but 5-10% are due to an inherited predisposition to develop breast and ovarian cancers, which are transmitted as an autosomal dominant form with incomplete penetrance. The beneficial effects of clinical genetic testing, including next generation sequencing (NGS) for BRCA1/2 mutations, is major; in particular, it benefits the care of patients and the counseling of relatives that are at risk of breast cancer, in order to reduce breast cancer mortality. BRCA genetic testing was performed in 15 patients with breast cancer and a family with positivity for the heterozygous c.6428C>A mutation of the BRCA2 gene. Informed consent was obtained from all the subjects. Genomic DNAs were extracted and the NGS for genes was performed using the Ion Torrent Personal Genome Machine (PGM) with a 316 chip. The reads were aligned with the human reference HG19 genome to elucidate variants in the BRCA1 and BRCA2 genes. Mutations detected by the PGM platform were confirmed by target direct Sanger sequencing on a second patient DNA sample. In total, 4 BRCA variants were identified in 6 families by NGS. Of these, 3 mutations had been previously reported: c.2126insA of BRCA1, and c.1310_1313delAAGA and c.7235insG of BRCA2. The fourth variant, c.3453delT in BRCA1, has, to the best of our knowledge, never been previously reported. The present study is the first to apply NGS of the BRCA1 and BRCA2 genes to a Moroccan population, prompting additional investigation into local founder mutations and variant characteristics in the region. The variants with no clear clinical significance may present a diagnostic challenge when performing targeted resequencing. These results confirm that an NGS approach based on Ampliseq libraries and PGM sequencing is a highly efficient, speedy and high-throughput mutation detection method, which may be preferable in lower income countries.
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Affiliation(s)
- Farah Jouali
- Anoual Laboratory of Radio-Immuno Analysis, Casablanca 20360, Morocco; Laboratory of Pathophysiology and Molecular Genetics, Ben M'Sik Faculty of Science, Casablanca 7955, Morocco
| | - Fatima-Zahra Laarabi
- Department of Medical Genetics, National Institute of Health, Rabat 769, Morocco
| | - Nabila Marchoudi
- Anoual Laboratory of Radio-Immuno Analysis, Casablanca 20360, Morocco
| | - Ilham Ratbi
- Department of Medical Genetics, National Institute of Health, Rabat 769, Morocco; Human Genome Center, Faculty of Medicine and Pharmacy, Mohammed V University, Rabat 8007, Morocco
| | - Siham Chafai Elalaoui
- Department of Medical Genetics, National Institute of Health, Rabat 769, Morocco; Human Genome Center, Faculty of Medicine and Pharmacy, Mohammed V University, Rabat 8007, Morocco
| | - Houria Rhaissi
- Laboratory of Pathophysiology and Molecular Genetics, Ben M'Sik Faculty of Science, Casablanca 7955, Morocco
| | - Jamal Fekkak
- Anoual Laboratory of Radio-Immuno Analysis, Casablanca 20360, Morocco
| | - Abdelaziz Sefiani
- Department of Medical Genetics, National Institute of Health, Rabat 769, Morocco; Human Genome Center, Faculty of Medicine and Pharmacy, Mohammed V University, Rabat 8007, Morocco
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Kwong A, Shin VY, Au CH, Law FBF, Ho DN, Ip BK, Wong ATC, Lau SS, To RMY, Choy G, Ford JM, Ma ESK, Chan TL. Detection of Germline Mutation in Hereditary Breast and/or Ovarian Cancers by Next-Generation Sequencing on a Four-Gene Panel. J Mol Diagn 2016; 18:580-94. [PMID: 27157322 DOI: 10.1016/j.jmoldx.2016.03.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Revised: 03/01/2016] [Accepted: 03/21/2016] [Indexed: 10/21/2022] Open
Abstract
Mutation in BRCA1/BRCA2 genes accounts for 20% of familial breast cancers, 5% to 10% of which may be due to other less penetrant genes which are still incompletely studied. Herein, a four-gene panel was used to examine the prevalence of BRCA1, BRCA2, TP53, and PTEN in hereditary breast and ovarian cancers in Southern Chinese population. In this cohort, 948 high-risk breast and/or ovarian patients were recruited for genetic screening by next-generation sequencing (NGS). The performance of our NGS pipeline was evaluated with 80 Sanger-validated known mutations and eight negative cases. With appropriate bioinformatics analysis pipeline, the detection sensitivity of NGS is comparable with Sanger sequencing. The prevalence of BRCA1/BRCA2 germline mutations was 9.4% in our Chinese cohort, of which 48.8% of the mutations arose from hotspot mutations. With the use of a tailor-made algorithm, HomopolymerQZ, more mutations were detected compared with single mutation detection algorithm. The frequencies of PTEN and TP53 were 0.21% and 0.53%, respectively, in the Southern Chinese patients with breast and/or ovarian cancers. High-throughput NGS approach allows the incorporation of control cohort that provides an ethnicity-specific data for polymorphic variants. Our data suggest that hotspot mutations screening such as SNaPshot could be an effective preliminary screening alternative adopted in a standard clinical laboratory without NGS setup.
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Affiliation(s)
- Ava Kwong
- Department of Surgery, The University of Hong Kong, Hong Kong, People's Republic of China; Department of Surgery, Hong Kong Sanatorium & Hospital, Hong Kong, People's Republic of China; Hong Kong Hereditary Breast Cancer Family Registry, Hong Kong, People's Republic of China.
| | - Vivian Y Shin
- Department of Surgery, The University of Hong Kong, Hong Kong, People's Republic of China
| | - Chun H Au
- Department of Molecular Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, People's Republic of China
| | - Fian B F Law
- Hong Kong Hereditary Breast Cancer Family Registry, Hong Kong, People's Republic of China; Department of Molecular Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, People's Republic of China
| | - Dona N Ho
- Department of Molecular Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, People's Republic of China
| | - Bui K Ip
- Department of Molecular Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, People's Republic of China
| | - Anthony T C Wong
- Department of Molecular Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, People's Republic of China
| | - Silvia S Lau
- Department of Medical Physics and Research, Hong Kong Sanatorium & Hospital, Hong Kong, People's Republic of China
| | - Rene M Y To
- Department of Molecular Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, People's Republic of China
| | - Gigi Choy
- Department of Molecular Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, People's Republic of China
| | - James M Ford
- Department of Medicine (Oncology), Stanford University School of Medicine, Stanford, California
| | - Edmond S K Ma
- Hong Kong Hereditary Breast Cancer Family Registry, Hong Kong, People's Republic of China; Department of Molecular Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, People's Republic of China
| | - Tsun L Chan
- Hong Kong Hereditary Breast Cancer Family Registry, Hong Kong, People's Republic of China; Department of Molecular Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, People's Republic of China
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Inherited breast cancer predisposition in Asians: multigene panel testing outcomes from Singapore. NPJ Genom Med 2016; 1:15003. [PMID: 29263802 PMCID: PMC5685290 DOI: 10.1038/npjgenmed.2015.3] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 10/12/2015] [Accepted: 10/14/2015] [Indexed: 12/20/2022] Open
Abstract
Genetic testing for germline mutations in breast cancer predisposition genes can potentially identify individuals at a high risk of developing breast and/or ovarian cancer. There is a paucity of such mutational information for Asians. Panel testing of 25 cancer susceptibility genes and BRCA1/2 deletion/duplication analysis was performed for 220 Asian breast cancer patients or their family members referred for genetics risk assessment. All 220 participants had at least one high-risk feature: having a family history of breast and/or ovarian cancer in first- and/or second-degree relatives; having breast and ovarian cancer in the same individual or bilateral breast cancer; having early-onset breast cancer or ovarian cancer (⩽40 years of age). We identified 67 pathogenic variants in 66 (30.0%) patients. Of these, 19 (28.3%) occurred in BRCA1, 16 (23.9%) in BRCA2, 7 (10.4%) in PALB2, 6 (9.0%) in TP53, 2 (3.0%) in PTEN, 2 (3.0%) in CDH1 and 15 (22.4%) in other predisposition genes. Notably, 47.8% of pathogenic variants were in non-BRCA1/2 genes. Of the 66 patients with pathogenic mutations, 63.6% (42/66) were under the age of 40 years. Family history of breast and/or ovarian cancer is enriched in patients with BRCA1/2 pathogenic variants but less predictive for non-BRCA1/2 related pathogenic variations. We detected a median of three variants of unknown significance (VUS) per gene (range 0–21). Custom gene panel testing is feasible and useful for the detection of pathogenic mutations and should be done in the setting of a formal clinical cancer genetics service given the rate of VUS.
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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
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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.
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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
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Dean M, Boland J, Yeager M, Im KM, Garland L, Rodriguez-Herrera M, Perez M, Mitchell J, Roberson D, Jones K, Lee HJ, Eggebeen R, Sawitzke J, Bass S, Zhang X, Robles V, Hollis C, Barajas C, Rath E, Arentz C, Figueroa JA, Nguyen DD, Nahleh Z. Addressing health disparities in Hispanic breast cancer: accurate and inexpensive sequencing of BRCA1 and BRCA2. Gigascience 2015; 4:50. [PMID: 26543556 PMCID: PMC4634732 DOI: 10.1186/s13742-015-0088-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 08/13/2015] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Germline mutations in the BRCA1 and BRCA2 genes account for 20-25 % of inherited breast cancers and about 10 % of all breast cancer cases. Detection of BRCA mutation carriers can lead to therapeutic interventions such as mastectomy, oophorectomy, hormonal prevention therapy, improved screening, and targeted therapies such as PARP-inhibition. We estimate that African Americans and Hispanics are 4-5 times less likely to receive BRCA screening, despite having similar mutation frequencies as non-Jewish Caucasians, who have higher breast cancer mortality. To begin addressing this health disparity, we initiated a nationwide trial of BRCA testing of Latin American women with breast cancer. Patients were recruited through community organizations, clinics, public events, and by mail and Internet. Subjects completed the consent process and questionnaire, and provided a saliva sample by mail or in person. DNA from 120 subjects was used to sequence the entirety of BRCA1 and BRCA2 coding regions and splice sites, and validate pathogenic mutations, with a total material cost of $85/subject. Subjects ranged in age from 23 to 81 years (mean age, 51 years), 6 % had bilateral disease, 57 % were ER/PR+, 23 % HER2+, and 17 % had triple-negative disease. RESULTS A total of seven different predicted deleterious mutations were identified, one newly described and the rest rare. In addition, four variants of unknown effect were found. CONCLUSIONS Application of this strategy on a larger scale could lead to improved cancer care of minority and underserved populations.
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Affiliation(s)
- Michael Dean
- Laboratory of Experimental Immunology, National Cancer Institute, Frederick, MD 21702 USA
| | - Joseph Boland
- Cancer Genetics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Gaithersburg, MD USA
| | - Meredith Yeager
- Cancer Genetics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Gaithersburg, MD USA
| | - Kate M. Im
- Laboratory of Experimental Immunology, National Cancer Institute, Frederick, MD 21702 USA
| | - Lisa Garland
- Laboratory of Experimental Immunology, National Cancer Institute, Frederick, MD 21702 USA
| | | | - Mylen Perez
- Laboratory of Experimental Immunology, National Cancer Institute, Frederick, MD 21702 USA
| | - Jason Mitchell
- Cancer Genetics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Gaithersburg, MD USA
| | - David Roberson
- Cancer Genetics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Gaithersburg, MD USA
| | - Kristine Jones
- Cancer Genetics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Gaithersburg, MD USA
| | - Hyo Jung Lee
- Cancer Genetics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Gaithersburg, MD USA
| | - Rebecca Eggebeen
- Cancer Genetics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Gaithersburg, MD USA
| | - Julie Sawitzke
- Basic Science Program, Leidos Biomedical Research, Inc., Frederick, MD USA
| | - Sara Bass
- Cancer Genetics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Gaithersburg, MD USA
| | - Xijun Zhang
- Cancer Genetics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Gaithersburg, MD USA
| | | | - Celia Hollis
- Latino Community Development Agency, Oklahoma City, OK USA
| | | | - Edna Rath
- Texas Tech University Health Sciences Center, El Paso, TX USA
| | - Candy Arentz
- Texas Tech University Health Sciences Center, Lubbock, TX USA
| | | | - Diane D. Nguyen
- Texas Tech University Health Sciences Center, Lubbock, TX USA
| | - Zeina Nahleh
- Texas Tech University Health Sciences Center, El Paso, TX USA
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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]
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Crona J, Ljungström V, Welin S, Walz MK, Hellman P, Björklund P. Bioinformatic Challenges in Clinical Diagnostic Application of Targeted Next Generation Sequencing: Experience from Pheochromocytoma. PLoS One 2015; 10:e0133210. [PMID: 26230854 PMCID: PMC4521794 DOI: 10.1371/journal.pone.0133210] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Accepted: 06/24/2015] [Indexed: 11/28/2022] Open
Abstract
Background Recent studies have demonstrated equal quality of targeted next generation sequencing (NGS) compared to Sanger Sequencing. Whereas these novel sequencing processes have a validated robust performance, choice of enrichment method and different available bioinformatic software as reliable analysis tool needs to be further investigated in a diagnostic setting. Methods DNA from 21 patients with genetic variants in SDHB, VHL, EPAS1, RET, (n=17) or clinical criteria of NF1 syndrome (n=4) were included. Targeted NGS was performed using Truseq custom amplicon enrichment sequenced on an Illumina MiSEQ instrument. Results were analysed in parallel using three different bioinformatics pipelines; (1) Commercially available MiSEQ Reporter, fully automatized and integrated software, (2) CLC Genomics Workbench, graphical interface based software, also commercially available, and ICP (3) an in-house scripted custom bioinformatic tool. Results A tenfold read coverage was achieved in between 95-98% of targeted bases. All workflows had alignment of reads to SDHA and NF1 pseudogenes. Compared to Sanger sequencing, variant calling revealed a sensitivity ranging from 83 to 100% and a specificity of 99.9-100%. Only MiSEQ reporter identified all pathogenic variants in both sequencing runs. Conclusions We conclude that targeted next generation sequencing have equal quality compared to Sanger sequencing. Enrichment specificity and the bioinformatic performance need to be carefully assessed in a diagnostic setting. As acceptable accuracy was noted for a fully automated bioinformatic workflow, we suggest that processing of NGS data could be performed without expert bioinformatics skills utilizing already existing commercially available bioinformatics tools.
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Affiliation(s)
- Joakim Crona
- Department of Surgical Sciences, Uppsala University, SE-75185, Uppsala, Sweden
- * E-mail:
| | - Viktor Ljungström
- Department of Immunology, Genetics and Pathology, Uppsala University, SE-75185, Uppsala, Sweden
| | - Staffan Welin
- Departments of Medical Sciences, Uppsala University, SE-75185, Uppsala, Sweden
| | - Martin K. Walz
- Department for Surgery and Centre of Minimal Invasive Surgery, Kliniken Essen-Mitte, Academic Teaching Hospital of the University of Duisburg-Essen, DE-45136 Essen, Germany
| | - Per Hellman
- Department of Surgical Sciences, Uppsala University, SE-75185, Uppsala, Sweden
| | - Peyman Björklund
- Department of Surgical Sciences, Uppsala University, SE-75185, Uppsala, Sweden
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Abstract
Purpose The National Comprehensive Cancer Network (NCCN) has proposed guidelines for the genetic testing of the BRCA1 and BRCA2 genes, based on studies in western populations. This current study assessed potential predictive factors for BRCA mutation probability, in an Asian population. Methods A total of 359 breast cancer patients, who presented with either a family history (FH) of breast and/or ovarian cancer or early onset breast cancer, were accrued at the National Cancer Center Singapore (NCCS). The relationships between clinico-pathological features and mutational status were calculated using the Chi-squared test and binary logistic regression analysis. Results Of 359 patients, 45 (12.5%) had deleterious or damaging missense mutations in BRCA1 and/or BRCA2. BRCA1 mutations were more likely to be found in ER-negative than ER-positive breast cancer patients (P=0.01). Moreover, ER-negative patients with BRCA mutations were diagnosed at an earlier age (40 vs. 48 years, P=0.008). Similarly, triple-negative breast cancer (TNBC) patients were more likely to have BRCA1 mutations (P=0.001) and that these patients were diagnosed at a relatively younger age than non-TNBC patients (38 vs. 46 years, P=0.028). Our analysis has confirmed that ER-negative status, TNBC status and a FH of hereditary breast and ovarian cancer (HBOC) are strong factors predicting the likelihood of having BRCA mutations. Conclusions Our study provides evidence that TNBC or ER-negative patients may benefit from BRCA genetic testing, particularly younger patients (<40 years) or those with a strong FH of HBOC, in Asian patients.
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Oliveira TG, Mitne-Neto M, Cerdeira LT, Marsiglia JD, Arteaga-Fernandez E, Krieger JE, Pereira AC. A Variant Detection Pipeline for Inherited Cardiomyopathy–Associated Genes Using Next-Generation Sequencing. J Mol Diagn 2015; 17:420-30. [DOI: 10.1016/j.jmoldx.2015.02.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Revised: 02/11/2015] [Accepted: 02/26/2015] [Indexed: 01/26/2023] Open
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Kluska A, Balabas A, Paziewska A, Kulecka M, Nowakowska D, Mikula M, Ostrowski J. New recurrent BRCA1/2 mutations in Polish patients with familial breast/ovarian cancer detected by next generation sequencing. BMC Med Genomics 2015; 8:19. [PMID: 25948282 PMCID: PMC4429836 DOI: 10.1186/s12920-015-0092-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2015] [Accepted: 04/23/2015] [Indexed: 12/19/2022] Open
Abstract
Background Targeted PCR-based genetic testing for BRCA1 and BRCA2 can be performed at a lower cost than full gene testing; however, it may overlook mutations responsible for familial breast and/or ovarian cancers. In the present study, we report the utility of next generation sequencing (NGS) to identify new pathogenic variants of BRCA1/2. Methods BRCA1 and BRCA2 exons were amplified using the Ion AmpliSeq BRCA1/2 Panel and sequenced on the Ion Torrent PGM sequencer in 512 women with familial and/or only early onset breast and/or ovarian cancers who were negative for selected BRCA1/2 mutations. Results 146 single nucleotide variants (SNVs) and 32 indels were identified. Of them, 14 SNVs and 17 indels were considered as pathogenic or likely pathogenic. One and 18 pathogenic mutations had been detected previously in the Polish and other populations, respectively, and 12 deleterious mutations were previously unknown. Eight mutations were recurrent; Q563X (BRCA1), N3124I (BRCA2) and c.4516delG (BRCA1) were found in eight, six and four patients, respectively, and two other mutations (c.9118-2A > G and c.7249delCA in BRCA2) were detected in three patients each. Altogether, BRCA1/2 pathogenic mutations were identified in 52 out of 512 (10%) patients. Conclusions NGS substantially improved the detection rates of a wide spectrum of mutations in Polish patients with familial breast and/or ovarian cancer. Although targeted screening for specific BRCA1 mutations can be offered to all Polish breast or ovarian cancer patients, NGS-based testing is justified in patients with breast or ovarian cancer likely related to BRCA1/2 who test negative for the selected BRCA1/2 pathogenic mutations. Electronic supplementary material The online version of this article (doi:10.1186/s12920-015-0092-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Anna Kluska
- Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, 02-781, Warsaw, Poland.
| | - Aneta Balabas
- Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, 02-781, Warsaw, Poland.
| | - Agnieszka Paziewska
- Department of Gastroenterology, Hepatology and Clinical Oncology, Medical Center for Postgraduate Education, 01-813, Warsaw, Poland.
| | - Maria Kulecka
- Department of Gastroenterology, Hepatology and Clinical Oncology, Medical Center for Postgraduate Education, 01-813, Warsaw, Poland.
| | - Dorota Nowakowska
- Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, 02-781, Warsaw, Poland.
| | - Michal Mikula
- Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, 02-781, Warsaw, Poland.
| | - Jerzy Ostrowski
- Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, 02-781, Warsaw, Poland. .,Department of Gastroenterology, Hepatology and Clinical Oncology, Medical Center for Postgraduate Education, 01-813, Warsaw, Poland.
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Trujillano D, Weiss MER, Köster J, Papachristos EB, Werber M, Kandaswamy KK, Marais A, Eichler S, Creed J, Baysal E, Jaber IY, Mehaney DA, Farra C, Rolfs A. Validation of a semiconductor next-generation sequencing assay for the clinical genetic screening of CFTR. Mol Genet Genomic Med 2015; 3:396-403. [PMID: 26436105 PMCID: PMC4585447 DOI: 10.1002/mgg3.149] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2015] [Revised: 03/17/2015] [Accepted: 03/24/2015] [Indexed: 12/13/2022] Open
Abstract
Genetic testing for cystic fibrosis and CFTR-related disorders mostly relies on laborious molecular tools that use Sanger sequencing to scan for mutations in the CFTR gene. We have explored a more efficient genetic screening strategy based on next-generation sequencing (NGS) of the CFTR gene. We validated this approach in a cohort of 177 patients with previously known CFTR mutations and polymorphisms. Genomic DNA was amplified using the Ion AmpliSeq™ CFTR panel. The DNA libraries were pooled, barcoded, and sequenced using an Ion Torrent PGM sequencer. The combination of different robust bioinformatics tools allowed us to detect previously known pathogenic mutations and polymorphisms in the 177 samples, without detecting spurious pathogenic calls. In summary, the assay achieves a sensitivity of 94.45% (95% CI: 92% to 96.9%), with a specificity of detecting nonvariant sites from the CFTR reference sequence of 100% (95% CI: 100% to 100%), a positive predictive value of 100% (95% CI: 100% to 100%), and a negative predictive value of 99.99% (95% CI: 99.99% to 100%). In addition, we describe the observed allelic frequencies of 94 unique definitely and likely pathogenic, uncertain, and neutral CFTR variants, some of them not previously annotated in the public databases. Strikingly, a seven exon spanning deletion as well as several more technically challenging variants such as pathogenic poly-thymidine-guanine and poly-thymidine (poly-TG-T) tracts were also detected. Targeted NGS is ready to substitute classical molecular methods to perform genetic testing on the CFTR gene.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Erol Baysal
- Pathology and Genetics Department, Dubai Genetic and Thalassemia Center, Dubai Health Authority Dubai, United Arab Emirates
| | - Iqbal Yousuf Jaber
- Pathology and Genetics Department, Dubai Genetic and Thalassemia Center, Dubai Health Authority Dubai, United Arab Emirates
| | - Dina Ahmed Mehaney
- Clinical and Chemical Pathology Department, Faculty of Medicine, Cairo University Cairo, Egypt
| | - Chantal Farra
- Department of Pathology & Laboratory Medicine, American University of Beirut Medical Center Beirut, Lebanon
| | - Arndt Rolfs
- Centogene AG Rostock, Germany ; Albrecht-Kossel-Institute for Neuroregeneration, Medical University Rostock Rostock, Germany
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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.
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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
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Galindo-González L, Pinzón-Latorre D, Bergen EA, Jensen DC, Deyholos MK. Ion Torrent sequencing as a tool for mutation discovery in the flax (Linum usitatissimum L.) genome. PLANT METHODS 2015; 11:19. [PMID: 25788971 PMCID: PMC4363359 DOI: 10.1186/s13007-015-0062-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2014] [Accepted: 03/02/2015] [Indexed: 05/29/2023]
Abstract
BACKGROUND Detection of induced mutations is valuable for inferring gene function and for developing novel germplasm for crop improvement. Many reverse genetics approaches have been developed to identify mutations in genes of interest within a mutagenized population, including some approaches that rely on next-generation sequencing (e.g. exome capture, whole genome resequencing). As an alternative to these genome or exome-scale methods, we sought to develop a scalable and efficient method for detection of induced mutations that could be applied to a small number of target genes, using Ion Torrent technology. We developed this method in flax (Linum usitatissimum), to demonstrate its utility in a crop species. RESULTS We used an amplicon-based approach in which DNA samples from an ethyl methanesulfonate (EMS)-mutagenized population were pooled and used as template in PCR reactions to amplify a region of each gene of interest. Barcodes were incorporated during PCR, and the pooled amplicons were sequenced using an Ion Torrent PGM. A pilot experiment with known SNPs showed that they could be detected at a frequency > 0.3% within the pools. We then selected eight genes for which we wanted to discover novel mutations, and applied our approach to screen 768 individuals from the EMS population, using either the Ion 314 or Ion 316 chips. Out of 29 potential mutations identified after processing the NGS reads, 16 mutations were confirmed using Sanger sequencing. CONCLUSIONS The methodology presented here demonstrates the utility of Ion Torrent technology in detecting mutation variants in specific genome regions for large populations of a species such as flax. The methodology could be scaled-up to test >100 genes using the higher capacity chips now available from Ion Torrent.
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Affiliation(s)
| | - David Pinzón-Latorre
- />Department of Biological Sciences, University of Alberta, Edmonton, AB Canada T6G 2E9
| | - Erik A Bergen
- />Department of Biological Sciences, University of Alberta, Edmonton, AB Canada T6G 2E9
| | - Dustin C Jensen
- />Department of Computing Sciences, Kings University College, Edmonton, AB Canada T6B 2H3
| | - Michael K Deyholos
- />IK Barber School of Arts & Sciences, University of British Columbia, Okanagan campus, Kelowna, BC Canada V1V 1 V7
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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]
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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.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Arndt Rolfs
- Centogene AG, Rostock, Germany; Albrecht-Kossel-Institute for Neuroregeneration, Medical University Rostock, Rostock, Germany
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Cao YY, Qu YJ, Song F, Zhang T, Bai JL, Jin YW, Wang H. Fast clinical molecular diagnosis of hyperphenylalaninemia using next-generation sequencing-based on a custom AmpliSeq™ panel and Ion Torrent PGM sequencing. Mol Genet Metab 2014; 113:261-6. [PMID: 25456745 DOI: 10.1016/j.ymgme.2014.10.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Revised: 10/05/2014] [Accepted: 10/05/2014] [Indexed: 12/15/2022]
Abstract
Hyperphenylalaninemia (HPA) can be classified into phenylketonuria (PKU) and tetrahydrobiopterin deficiency (BH4D), according to the defect of enzyme activity, both of which vary substantially in severity, treatment, and prognosis of the disease. To set up a fast and comprehensive assay in order to achieve early etiological diagnosis and differential diagnosis for children with HPA, we designed a custom AmpliSeq™ panel for the sequencing of coding DNA sequence (CDS), flanking introns, 5' untranslated region (UTR) and 3' UTR from five HPA-causing genes (PAH, PTS, QDPR, GCH1, and PCBD1) using the Ion Torrent Personal Genome Machine (PGM) Sequencer. A standard group of 15 samples with previously known DNA sequences and a test group of 37 HPA patients with unknown mutations were used for assay validation and application, respectively. All variations were confirmed by Sanger sequencing. In the standard group, all the known mutations were detected and were consistent with the results of previous Sanger sequencing. In the test group, we identified mutations in 71 of 74 alleles, with a mutation detection rate of 95.9%. We also found a frame shift deletion p.Ile25Metfs*13 in PAH that was previously unreported. In addition, 1 of 37 in the test group was inconsistent with either the molecular diagnosis or clinical diagnosis by traditional differential methods. In conclusion, our comprehensive assay based on a custom AmpliSeq™ panel and Ion Torrent PGM sequencing has wider coverage, higher throughput, is much faster, and more efficient when compared with the traditional molecular detection method for HPA patients, which could meet the medical need for individualized diagnosis and treatment.
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Affiliation(s)
- Yan-yan Cao
- Department of Medical Genetics, Capital Institute of Pediatrics, Beijing 100020, China.
| | - Yu-jin Qu
- Department of Medical Genetics, Capital Institute of Pediatrics, Beijing 100020, China.
| | - Fang Song
- Department of Medical Genetics, Capital Institute of Pediatrics, Beijing 100020, China.
| | - Ting Zhang
- Department of Medical Genetics, Capital Institute of Pediatrics, Beijing 100020, China.
| | - Jin-li Bai
- Department of Medical Genetics, Capital Institute of Pediatrics, Beijing 100020, China.
| | - Yu-wei Jin
- Department of Medical Genetics, Capital Institute of Pediatrics, Beijing 100020, China.
| | - Hong Wang
- Department of Medical Genetics, Capital Institute of Pediatrics, Beijing 100020, China.
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de Koning TJ, Jongbloed JDH, Sikkema-Raddatz B, Sinke RJ. Targeted next-generation sequencing panels for monogenetic disorders in clinical diagnostics: the opportunities and challenges. Expert Rev Mol Diagn 2014; 15:61-70. [PMID: 25367078 DOI: 10.1586/14737159.2015.976555] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Next-generation sequencing (NGS) will soon be used for clinically heterogeneous, inherited disorders and the increasing number of disease-causing genes reported. Diagnostic laboratories therefore need to decide which NGS methods they are going to invest in and how to implement them. We discuss here the challenges and opportunities of using targeted resequencing (TRS) panels for diagnosing monogenetic disorders. Of the different NGS approaches available, TRS panels offer the opportunity to sequence and analyze a limited set of predetermined target genes. At present, TRS panels offer better base-pair coverage, running times, costs and dataset handling than other NGS applications such as whole genome sequencing and whole exome sequencing. However, working with TRS panels also poses new challenges in variant interpretation, data handling and bioinformatic analyses. To optimize the analyses, TRS panel testing should be performed by bioinformaticians, clinicians and laboratory staff in close collaboration.
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Affiliation(s)
- Tom J de Koning
- University of Groningen, University Medical Center Groningen, Department of Genetics, CB 50, PO Box 30.001, 9700 RB Groningen, The Netherlands
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Gréen A, Gréen H, Rehnberg M, Svensson A, Gunnarsson C, Jonasson J. Assessment of HaloPlex amplification for sequence capture and massively parallel sequencing of arrhythmogenic right ventricular cardiomyopathy-associated genes. J Mol Diagn 2014; 17:31-42. [PMID: 25445213 DOI: 10.1016/j.jmoldx.2014.09.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Revised: 08/12/2014] [Accepted: 09/03/2014] [Indexed: 12/30/2022] Open
Abstract
The genetic basis of arrhythmogenic right ventricular cardiomyopathy (ARVC) is complex. Mutations in genes encoding components of the cardiac desmosomes have been implicated as being causally related to ARVC. Next-generation sequencing allows parallel sequencing and duplication/deletion analysis of many genes simultaneously, which is appropriate for screening of mutations in disorders with heterogeneous genetic backgrounds. We designed and validated a next-generation sequencing test panel for ARVC using HaloPlex. We used SureDesign to prepare a HaloPlex enrichment system for sequencing of DES, DSC2, DSG2, DSP, JUP, PKP2, RYR2, TGFB3, TMEM43, and TTN from patients with ARVC using a MiSeq instrument. Performance characteristics were determined by comparison with Sanger, as the gold standard, and TruSeq Custom Amplicon sequencing of DSC2, DSG2, DSP, JUP, and PKP2. All the samples were successfully sequenced after HaloPlex capture, with >99% of targeted nucleotides covered by >20×. The sequences were of high quality, although one problematic area due to a presumptive context-specific sequencing error-causing motif located in exon 1 of the DSP gene was detected. The mutations found by Sanger sequencing were also found using the HaloPlex technique. Depending on the bioinformatics pipeline, sensitivity varied from 99.3% to 100%, and specificity varied from 99.9% to 100%. Three variant positions found by Sanger and HaloPlex sequencing were missed by TruSeq Custom Amplicon owing to loss of coverage.
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Affiliation(s)
- Anna Gréen
- Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden; Department of Clinical Genetics, County Council of Östergötland, Linköping, Sweden.
| | - Henrik Gréen
- Department of Forensic Genetics and Forensic Toxicology, National Board of Forensic Medicine, Linköping, Sweden; Division of Drug Research, Department of Medical and Health Sciences, Linköping University, Linköping, Sweden; Science for Life Laboratory, School of Biotechnology, Division of Gene Technology, Royal Institute of Technology, Stockholm, Sweden
| | - Malin Rehnberg
- Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden; Department of Clinical Genetics, County Council of Östergötland, Linköping, Sweden
| | - Anneli Svensson
- Department of Medicine and Health Science, Linköping University, Linköping, Sweden; Department of Cardiology, County Council of Östergötland, Linköping, Sweden
| | - Cecilia Gunnarsson
- Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden; Department of Clinical Genetics, County Council of Östergötland, Linköping, Sweden
| | - Jon Jonasson
- Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden; Department of Clinical Genetics, County Council of Östergötland, Linköping, Sweden
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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]
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Motoike IN, Matsumoto M, Danjoh I, Katsuoka F, Kojima K, Nariai N, Sato Y, Yamaguchi-Kabata Y, Ito S, Kudo H, Nishijima I, Nishikawa S, Pan X, Saito R, Saito S, Saito T, Shirota M, Tsuda K, Yokozawa J, Igarashi K, Minegishi N, Tanabe O, Fuse N, Nagasaki M, Kinoshita K, Yasuda J, Yamamoto M. Validation of multiple single nucleotide variation calls by additional exome analysis with a semiconductor sequencer to supplement data of whole-genome sequencing of a human population. BMC Genomics 2014; 15:673. [PMID: 25109789 PMCID: PMC4138778 DOI: 10.1186/1471-2164-15-673] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Accepted: 08/01/2014] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Validation of single nucleotide variations in whole-genome sequencing is critical for studying disease-related variations in large populations. A combination of different types of next-generation sequencers for analyzing individual genomes may be an efficient means of validating multiple single nucleotide variations calls simultaneously. RESULTS Here, we analyzed 12 independent Japanese genomes using two next-generation sequencing platforms: the Illumina HiSeq 2500 platform for whole-genome sequencing (average depth 32.4×), and the Ion Proton semiconductor sequencer for whole exome sequencing (average depth 109×). Single nucleotide polymorphism (SNP) calls based on the Illumina Human Omni 2.5-8 SNP chip data were used as the reference. We compared the variant calls for the 12 samples, and found that the concordance between the two next-generation sequencing platforms varied between 83% and 97%. CONCLUSIONS Our results show the versatility and usefulness of the combination of exome sequencing with whole-genome sequencing in studies of human population genetics and demonstrate that combining data from multiple sequencing platforms is an efficient approach to validate and supplement SNP calls.
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Affiliation(s)
- Ikuko N Motoike
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Mitsuyo Matsumoto
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
- />Department of Biochemistry, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Aoba-ku, Sendai, 980-8575 Japan
| | - Inaho Danjoh
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Fumiki Katsuoka
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
- />Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Aoba-ku, Sendai, 980-8575 Japan
| | - Kaname Kojima
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Naoki Nariai
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Yukuto Sato
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Yumi Yamaguchi-Kabata
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Shin Ito
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Hisaaki Kudo
- />Department of Biobank, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Ichiko Nishijima
- />Department of Biobank, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Satoshi Nishikawa
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Xiaoqing Pan
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Rumiko Saito
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Sakae Saito
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Tomo Saito
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Matsuyuki Shirota
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
- />Department of Applied Information Sciences, Graduate School of Information Sciences, Tohoku University, 6-6-05 Aramaki Aza Aoba, Aoba-ku, Sendai, Miyagi, 980-8579 Japan
- />United Centers for Advanced Research and Translational Medicine, Tohoku University Graduate School of Medicine, 1 Seiryo-machi, Aoba-ku, Sendai, 980-8575 Japan
| | - Kaoru Tsuda
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Junji Yokozawa
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Kazuhiko Igarashi
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
- />Department of Biochemistry, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Aoba-ku, Sendai, 980-8575 Japan
| | - Naoko Minegishi
- />Department of Biobank, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Osamu Tanabe
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Nobuo Fuse
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Masao Nagasaki
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Kengo Kinoshita
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
- />Department of Applied Information Sciences, Graduate School of Information Sciences, Tohoku University, 6-6-05 Aramaki Aza Aoba, Aoba-ku, Sendai, Miyagi, 980-8579 Japan
- />Institute of Development, Aging, and Cancer, Tohoku University, 4-1 Seiryo-machi, Aoba-ku Sendai, Sendai, 980-8575 Japan
| | - Jun Yasuda
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Masayuki Yamamoto
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
- />Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Aoba-ku, Sendai, 980-8575 Japan
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Yeo ZX, Wong JCL, Rozen SG, Lee ASG. Evaluation and optimisation of indel detection workflows for ion torrent sequencing of the BRCA1 and BRCA2 genes. BMC Genomics 2014; 15:516. [PMID: 24962530 PMCID: PMC4079958 DOI: 10.1186/1471-2164-15-516] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Accepted: 06/19/2014] [Indexed: 12/30/2022] Open
Abstract
Background The Ion Torrent PGM is a popular benchtop sequencer that shows promise in replacing conventional Sanger sequencing as the gold standard for mutation detection. Despite the PGM’s reported high accuracy in calling single nucleotide variations, it tends to generate many false positive calls in detecting insertions and deletions (indels), which may hinder its utility for clinical genetic testing. Results Recently, the proprietary analytical workflow for the Ion Torrent sequencer, Torrent Suite (TS), underwent a series of upgrades. We evaluated three major upgrades of TS by calling indels in the BRCA1 and BRCA2 genes. Our analysis revealed that false negative indels could be generated by TS under both default calling parameters and parameters adjusted for maximum sensitivity. However, indel calling with the same data using the open source variant callers, GATK and SAMtools showed that false negatives could be minimised with the use of appropriate bioinformatics analysis. Furthermore, we identified two variant calling measures, Quality-by-Depth (QD) and VARiation of the Width of gaps and inserts (VARW), which substantially reduced false positive indels, including non-homopolymer associated errors without compromising sensitivity. In our best case scenario that involved the TMAP aligner and SAMtools, we achieved 100% sensitivity, 99.99% specificity and 29% False Discovery Rate (FDR) in indel calling from all 23 samples, which is a good performance for mutation screening using PGM. Conclusions New versions of TS, BWA and GATK have shown improvements in indel calling sensitivity and specificity over their older counterpart. However, the variant caller of TS exhibits a lower sensitivity than GATK and SAMtools. Our findings demonstrate that although indel calling from PGM sequences may appear to be noisy at first glance, proper computational indel calling analysis is able to maximize both the sensitivity and specificity at the single base level, paving the way for the usage of this technology for future clinical genetic testing. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-516) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | - Steven G Rozen
- Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Singapore.
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Justino A, Dias P, João Pina M, Sousa S, Cirnes L, Berta Sousa A, Carlos Machado J, Costa JL. Comprehensive massive parallel DNA sequencing strategy for the genetic diagnosis of the neuro-cardio-facio-cutaneous syndromes. Eur J Hum Genet 2014; 23:347-53. [PMID: 24896146 DOI: 10.1038/ejhg.2014.97] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 04/03/2014] [Accepted: 04/08/2014] [Indexed: 11/09/2022] Open
Abstract
Variants in 11 genes of the RAS/MAPK signaling pathway have been causally linked to the neuro-cardio-facio-cutaneous syndromes group (NCFCS). Recently, A2ML1 and RIT1 were also associated with these syndromes. Because of the genetic and clinical heterogeneity of NCFCS, it is challenging to define strategies for their molecular diagnosis. The aim of this study was to develop and validate a massive parallel sequencing (MPS)-based strategy for the molecular diagnosis of NCFCS. A multiplex PCR-based strategy for the enrichment of the 13 genes and a variant prioritization pipeline was established. Two sets of genomic DNA samples were studied using the Ion PGM System: (1) training set (n =15) to optimize the strategy and (2) validation set (n = 20) to validate and evaluate the power of the new methodology. Sanger sequencing was performed to confirm all variants and low covered regions. All variants identified by Sanger sequencing were detected with our MPS approach. The methodology resulted in an experimental approach with a specificity of 99.0% and a maximum analytical sensitivity of ≥ 98.2% with a confidence of 99%. Importantly, two patients (out of 20) harbored described disease-causing variants in genes that are not routinely tested (RIT1 and SHOC2). The addition of less frequently altered genes increased in ≈ 10% the diagnostic yield of the strategy currently used. The presented workflow provides a comprehensive genetic screening strategy for patients with NCFCS in a fast and cost-efficient manner. This approach demonstrates the potential of a combined MPS-Sanger sequencing-based strategy as an effective diagnostic tool for heterogeneous diseases.
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Affiliation(s)
- Ana Justino
- 1] Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal [2] Abel Salazar Institute for the Biomedical Sciences of the University of Porto, Porto, Portugal
| | - Patrícia Dias
- Department of Genetics, Hospital de Santa Maria, Lisboa, Portugal
| | - Maria João Pina
- Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
| | - Sónia Sousa
- Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
| | - Luís Cirnes
- Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
| | - Ana Berta Sousa
- Department of Genetics, Hospital de Santa Maria, Lisboa, Portugal
| | - José Carlos Machado
- 1] Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal [2] Faculty of Medicine, University of Porto, Porto, Portugal
| | - José Luis Costa
- 1] Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal [2] Faculty of Medicine, University of Porto, Porto, Portugal
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Kunz M. New developments in dermatological oncogenetics. J Dtsch Dermatol Ges 2014; 11:831-6. [PMID: 23957481 DOI: 10.1111/ddg.12157] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Accepted: 03/16/2013] [Indexed: 12/20/2022]
Abstract
Activated intracellular signaling pathways based on mutations in oncogenes and tumor suppressor genes play an important role in a variety of malignant tumors. In dermatology, such mutations have been identified in melanoma, basal cell carcinoma and squamous cell carcinoma. These have partly led to the establishment of new, targeted therapies. Treatment successes have been particularly impressive for melanoma with small molecule inhibitors directed against the mutated BRAF oncogene and in basal cell carcinoma with inhibitors directed against the hedgehog signaling pathway. New sequencing technologies, in particular next generation sequencing, have led to a better and more comprehensive understanding of malignant tumors. This approach confirmed the pathogenic role of BRAF, NRAS and MAP kinase pathways for melanoma. At the same time, a series of further interesting target molecules with oncogenic mutations such as ERBB4, GRIN2A, GRM3, PREX2, RAC1 and TP53 were identified. New aspects have recently been shown for squamous cell carcinoma by detection of mutations in the NOTCH signaling pathway. A better understanding of the pathogenesis of these and other tumors should lead to improved and maybe even individualized treatment. The current developments in dermatological oncogenetics based on the new sequencing technologies are reviewed.
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Affiliation(s)
- Manfred Kunz
- Department of Dermatology, Venereology and Allergology, University of Leipzig, Germany
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