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Azzollini J, Agnelli L, Conca E, Torelli T, Busico A, Capone I, Angelini M, Tamborini E, Perrone F, Vingiani A, Lorenzini D, Peissel B, Pruneri G, Manoukian S. Prevalence of BRCA homopolymeric indels in an ION Torrent-based tumour-to-germline testing workflow in high-grade ovarian carcinoma. Sci Rep 2023; 13:7781. [PMID: 37179432 PMCID: PMC10182972 DOI: 10.1038/s41598-023-33857-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 04/20/2023] [Indexed: 05/15/2023] Open
Abstract
Tumour DNA sequencing is essential for precision medicine since it guides therapeutic decisions but also fosters the identification of patients who may benefit from germline testing. Notwithstanding, the tumour-to-germline testing workflow presents a few caveats. The low sensitivity for indels at loci with sequences of identical bases (homopolymers) of ion semiconductor-based sequencing techniques represents a well-known limitation, but the prevalence of indels overlooked by these techniques in high-risk populations has not been investigated. In our study, we addressed this issue at the homopolymeric regions of BRCA1/2 in a retrospectively selected cohort of 157 patients affected with high-grade ovarian cancer and negative at tumour testing by ION Torrent sequencing. Variant allele frequency (VAF) of indels at each of the 29 investigated homopolymers was systematically revised with the IGV software. Thresholds to discriminate putative germline variants were defined by scaling the VAF to a normal distribution and calculating the outliers that exceeded the mean + 3 median-adjusted deviations of a control population. Sanger sequencing of the outliers confirmed the occurrence of only one of the five putative indels in both tumour and blood from a patient with a family history of breast cancer. Our results indicated that the prevalence of homopolymeric indels overlooked by ion semiconductor techniques is seemingly low. A careful evaluation of clinical and family history data would further help minimise this technique-bound limitation, highlighting cases in which a deeper look at these regions would be recommended.
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Affiliation(s)
- Jacopo Azzollini
- Unit of Medical Genetics, Department of Medical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale dei Tumori, via Venezian 1, 20133, Milan, Italy
| | - Luca Agnelli
- Department of Advanced Diagnostics, Fondazione IRCCS Istituto Nazionale dei Tumori, via Venezian 1, 20133, Milan, Italy
- Medical Oncology 1 Department, Fondazione IRCCS Istituto Nazionale dei Tumori, via Venezian 1, 20133, Milan, Italy
| | - Elena Conca
- Department of Advanced Diagnostics, Fondazione IRCCS Istituto Nazionale dei Tumori, via Venezian 1, 20133, Milan, Italy
| | - Tommaso Torelli
- Department of Advanced Diagnostics, Fondazione IRCCS Istituto Nazionale dei Tumori, via Venezian 1, 20133, Milan, Italy
- Medical Oncology 1 Department, Fondazione IRCCS Istituto Nazionale dei Tumori, via Venezian 1, 20133, Milan, Italy
| | - Adele Busico
- Department of Advanced Diagnostics, Fondazione IRCCS Istituto Nazionale dei Tumori, via Venezian 1, 20133, Milan, Italy
| | - Iolanda Capone
- Department of Advanced Diagnostics, Fondazione IRCCS Istituto Nazionale dei Tumori, via Venezian 1, 20133, Milan, Italy
| | - Marta Angelini
- Department of Advanced Diagnostics, Fondazione IRCCS Istituto Nazionale dei Tumori, via Venezian 1, 20133, Milan, Italy
| | - Elena Tamborini
- Department of Advanced Diagnostics, Fondazione IRCCS Istituto Nazionale dei Tumori, via Venezian 1, 20133, Milan, Italy
| | - Federica Perrone
- Department of Advanced Diagnostics, Fondazione IRCCS Istituto Nazionale dei Tumori, via Venezian 1, 20133, Milan, Italy
| | - Andrea Vingiani
- Department of Advanced Diagnostics, Fondazione IRCCS Istituto Nazionale dei Tumori, via Venezian 1, 20133, Milan, Italy
- Oncology and Hemato-Oncology Department, University of Milan, Milan, Italy
| | - Daniele Lorenzini
- Department of Advanced Diagnostics, Fondazione IRCCS Istituto Nazionale dei Tumori, via Venezian 1, 20133, Milan, Italy
| | - Bernard Peissel
- Unit of Medical Genetics, Department of Medical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale dei Tumori, via Venezian 1, 20133, Milan, Italy
| | - Giancarlo Pruneri
- Department of Advanced Diagnostics, Fondazione IRCCS Istituto Nazionale dei Tumori, via Venezian 1, 20133, Milan, Italy
- Oncology and Hemato-Oncology Department, University of Milan, Milan, Italy
| | - Siranoush Manoukian
- Unit of Medical Genetics, Department of Medical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale dei Tumori, via Venezian 1, 20133, Milan, Italy.
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2
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Collet A, Tarabeux J, Girard E, D’Enghien CD, Golmard L, Deshaies V, Lermine A, Laugé A, Moncoutier V, Lefol C, Copigny F, Dehainault C, Tenreiro H, Guy C, Abidallah K, Barbaroux C, Rouleau E, Servant N, Pauw AD, Stoppa-Lyonnet D, Houdayer C. Pros and cons of HaloPlex enrichment in cancer predisposition genetic diagnosis. AIMS GENETICS 2021. [DOI: 10.3934/genet.2015.4.263] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
AbstractPanel sequencing is a practical option in genetic diagnosis. Enrichment and library preparation steps are critical in the diagnostic setting. In order to test the value of HaloPlex technology in diagnosis, we designed a custom oncogenetic panel including 62 genes. The procedure was tested on a training set of 71 controls and then blindly validated on 48 consecutive hereditary breast/ovarian cancer (HBOC) patients tested negative for BRCA1/2 mutation. Libraries were sequenced on HiSeq2500 and data were analysed with our academic bioinformatics pipeline. Point mutations were detected using Varscan2, median size indels were detected using Pindel and large genomic rearrangements (LGR) were detected by DESeq. Proper coverage was obtained. However, highly variable read depth was observed within genes. Excluding pseudogene analysis, all point mutations were detected on the training set. All indels were also detected using Pindel. On the other hand, DESeq allowed LGR detection but with poor specificity, preventing its use in diagnostics. Mutations were detected in 8% of BRCA1/2-negative HBOC cases. HaloPlex technology appears to be an efficient and promising solution for gene panel diagnostics. Data analysis remains a major challenge and geneticists should enhance their bioinformatics knowledge in order to ensure good quality diagnostic results.
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Affiliation(s)
- Agnès Collet
- Institut Curie, Département de Biopathologie, Paris, France
| | | | - Elodie Girard
- Institut Curie, Paris, France
- Inserm U900, Paris, France
- Mines ParisTech, PSL-Research University, CBIO-Centre for Computational Biology, Fontainebleau, France
| | | | - Lisa Golmard
- Institut Curie, Département de Biopathologie, Paris, France
- Institut Curie, Inserm U830, Paris, France
| | - Vivien Deshaies
- Institut Curie, Paris, France
- Inserm U900, Paris, France
- Mines ParisTech, PSL-Research University, CBIO-Centre for Computational Biology, Fontainebleau, France
| | - Alban Lermine
- Institut Curie, Paris, France
- Inserm U900, Paris, France
- Mines ParisTech, PSL-Research University, CBIO-Centre for Computational Biology, Fontainebleau, France
| | - Anthony Laugé
- Institut Curie, Département de Biopathologie, Paris, France
| | | | - Cédrick Lefol
- Institut Curie, Département de Biopathologie, Paris, France
| | | | | | | | - Christophe Guy
- Institut Curie, Département de Biopathologie, Paris, France
| | | | | | | | - Nicolas Servant
- Institut Curie, Paris, France
- Inserm U900, Paris, France
- Mines ParisTech, PSL-Research University, CBIO-Centre for Computational Biology, Fontainebleau, France
| | | | - Dominique Stoppa-Lyonnet
- Institut Curie, Département de Biopathologie, Paris, France
- Institut Curie, Inserm U830, Paris, France
- Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Claude Houdayer
- Institut Curie, Département de Biopathologie, Paris, France
- Institut Curie, Inserm U830, Paris, France
- Faculté des Sciences pharmaceutiques et biologiques, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
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3
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Zamariolli M, Burssed B, Moysés-Oliveira M, Colovati M, Bellucco FTDS, Dos Santos LC, Alvarez Perez AB, Bragagnolo S, Melaragno MI. Novel MYT1 variants expose the complexity of oculo-auriculo-vertebral spectrum genetic mechanisms. Am J Med Genet A 2021; 185:2056-2064. [PMID: 33880880 DOI: 10.1002/ajmg.a.62217] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 02/10/2021] [Accepted: 03/22/2021] [Indexed: 12/17/2022]
Abstract
Oculo-auriculo-vertebral spectrum (OAVS) is a developmental disorder characterized by anomalies mainly involving the structures derived from the first and second pharyngeal arches. The spectrum presents with heterogeneous clinical features and complex etiology with genetic factors not yet completely understood. To date, MYT1 is the most important gene unambiguously associated with the spectrum and with functional data confirmation. In this work, we aimed to identify new single nucleotide variants (SNVs) affecting MYT1 in a cohort of 73 Brazilian patients diagnosed with OAVS. In addition, we investigated copy number variations (CNVs) encompassing this gene or its cis-regulatory elements and compared the frequency of these events in patients versus a cohort of 455 Brazilian control individuals. A new SNV, predicted as likely deleterious, was identified in five unrelated patients with OAVS. All five patients presented hearing impairment and orbital asymmetry suggesting an association with the variant. CNVs near MYT1, located in its neighboring topologically associating domain (TAD), were found to be enriched in patients when compared to controls, indicating a possible involvement of this region with OAVS pathogenicity. Our findings highlight the genetic complexity of the spectrum that seems to involve more than one variant type and inheritance patterns.
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Affiliation(s)
- Malú Zamariolli
- Division of Genetics, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Bruna Burssed
- Division of Genetics, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Mariana Moysés-Oliveira
- Division of Genetics, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Mileny Colovati
- Division of Genetics, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | | | - Leonardo Caires Dos Santos
- Division of Genetics, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Ana Beatriz Alvarez Perez
- Division of Genetics, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Silvia Bragagnolo
- Division of Genetics, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Maria Isabel Melaragno
- Division of Genetics, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
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4
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Abstract
Next generation DNA sequencing (NGS) has the potential to improve the diagnostic and prognostic utility of newborn screening programmes. This study assesses the feasibility of automating NGS on dried blood spot (DBS) DNA in a United Kingdom National Health Service (UK NHS) laboratory. An NGS panel targeting the entire coding sequence of five genes relevant to disorders currently screened for in newborns in the UK was validated on DBS DNA. An automated process for DNA extraction, NGS and bioinformatics analysis was developed. The process was tested on DBS to determine feasibility, turnaround time and cost. The analytical sensitivity of the assay was 100% and analytical specificity was 99.96%, with a mean 99.5% concordance of variant calls between DBS and venous blood samples in regions with ≥30× coverage (96.8% across all regions; all variant calls were single nucleotide variants (SNVs), with indel performance not assessed). The pipeline enabled processing of up to 1000 samples a week with a turnaround time of four days from receipt of sample to reporting. This study concluded that it is feasible to automate targeted NGS on routine DBS samples in a UK NHS laboratory setting, but it may not currently be cost effective as a first line test.
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5
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Dissection of major cancer gene variants in subsets of circulating tumor cells in advanced breast cancer. Sci Rep 2019; 9:17276. [PMID: 31754145 PMCID: PMC6872745 DOI: 10.1038/s41598-019-53660-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 11/04/2019] [Indexed: 02/07/2023] Open
Abstract
Enumeration of circulating tumor cells (CTCs) may reflect the metastatic potential of breast cancer (BC). By using the DEPArray, we investigated CTCs with respect to their epithelial-to-mesenchymal transition phenotype and compared their genomic heterogeneity with tissue biopsies. Seventeen stage IV BC patients were enrolled. Pre-enriched CTC suspensions were stained with fluorescent-labeled antibodies to epithelial (E) and mesenchymal (M) markers. CTC samples were processed by DEPArray system and clustered in relation to their markers. DNA from CTCs, as well as from primary tumor samples, was sequenced by next generation sequencing to assess the mutational state of 50 major cancer-related genes. We identified four different CTC subsets that harbored different gene variants. The most heterogenous CTC subsets included the M+/E− phenotype, which, however, expressed only 7 repeatedly mutated genes, while in the M−/E+ subset multiple mutations affected only 2 out of 50 genes. When matching all gene variants among CTC subsets, a small number of mutations was shared by only 4 genes, namely ATM, FGFR3, PIK3CA, and TP53 that, however, were absent in primary tumors. Our results postulate that the detected mutations in all CTC subsets may be considered as genomic markers of metastatic dissemination to be investigated during early stages of BC.
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6
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Nicolussi A, Belardinilli F, Silvestri V, Mahdavian Y, Valentini V, D'Inzeo S, Petroni M, Zani M, Ferraro S, Di Giulio S, Fabretti F, Fratini B, Gradilone A, Ottini L, Giannini G, Coppa A, Capalbo C. Identification of novel BRCA1 large genomic rearrangements by a computational algorithm of amplicon-based Next-Generation Sequencing data. PeerJ 2019; 7:e7972. [PMID: 31741787 PMCID: PMC6859874 DOI: 10.7717/peerj.7972] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 10/01/2019] [Indexed: 12/30/2022] Open
Abstract
Background Genetic testing for BRCA1/2 germline mutations in hereditary breast/ovarian cancer patients requires screening for single nucleotide variants, small insertions/deletions and large genomic rearrangements (LGRs). These studies have long been run by Sanger sequencing and multiplex ligation-dependent probe amplification (MLPA). The recent introduction of next-generation sequencing (NGS) platforms dramatically improved the speed and the efficiency of DNA testing for nucleotide variants, while the possibility to correctly detect LGRs by this mean is still debated. The purpose of this study was to establish whether and to which extent the development of an analytical algorithm could help us translating NGS sequencing via an Ion Torrent PGM platform into a tool suitable to identify LGRs in hereditary breast-ovarian cancer patients. Methods We first used NGS data of a group of three patients (training set), previously screened in our laboratory by conventional methods, to develop an algorithm for the calculation of the dosage quotient (DQ) to be compared with the Ion Reporter (IR) analysis. Then, we tested the optimized pipeline with a consecutive cohort of 85 uncharacterized probands (validation set) also subjected to MLPA analysis. Characterization of the breakpoints of three novel BRCA1 LGRs was obtained via long-range PCR and direct sequencing of the DNA products. Results In our cohort, the newly defined DQ-based algorithm detected 3/3 BRCA1 LGRs, demonstrating 100% sensitivity and 100% negative predictive value (NPV) (95% CI [87.6–99.9]) compared to 2/3 cases detected by IR (66.7% sensitivity and 98.2% NPV (95% CI [85.6–99.9])). Interestingly, DQ and IR shared 12 positive results, but exons deletion calls matched only in five cases, two of which confirmed by MLPA. The breakpoints of the 3 novel BRCA1 deletions, involving exons 16–17, 21–22 and 20, have been characterized. Conclusions Our study defined a DQ-based algorithm to identify BRCA1 LGRs using NGS data. Whether confirmed on larger data sets, this tool could guide the selection of samples to be subjected to MLPA analysis, leading to significant savings in time and money.
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Affiliation(s)
- Arianna Nicolussi
- Department of Experimental Medicine, University of Roma "La Sapienza", Roma, Italy
| | | | - Valentina Silvestri
- Department of Molecular Medicine, University of Roma "La Sapienza", Roma, Italy
| | - Yasaman Mahdavian
- Department of Molecular Medicine, University of Roma "La Sapienza", Roma, Italy
| | - Virginia Valentini
- Department of Molecular Medicine, University of Roma "La Sapienza", Roma, Italy
| | - Sonia D'Inzeo
- 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
| | - Stefano Di Giulio
- Department of Molecular Medicine, University of Roma "La Sapienza", Roma, Italy
| | - Francesca Fabretti
- Department of Molecular Medicine, University of Roma "La Sapienza", Roma, Italy
| | - Beatrice Fratini
- Department of Experimental Medicine, University of Roma "La Sapienza", Roma, Italy
| | - Angela Gradilone
- 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
| | - Anna Coppa
- Department of Experimental Medicine, University of Roma "La Sapienza", Roma, Italy
| | - Carlo Capalbo
- Department of Molecular Medicine, University of Roma "La Sapienza", Roma, Italy
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7
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Zamariolli M, Colovati M, Moysés-Oliveira M, Nunes N, Caires Dos Santos L, Alvarez Perez AB, Bragagnolo S, Melaragno MI. Rare single-nucleotide variants in oculo-auriculo-vertebral spectrum (OAVS). Mol Genet Genomic Med 2019; 7:e00959. [PMID: 31469246 PMCID: PMC6785430 DOI: 10.1002/mgg3.959] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 08/07/2019] [Indexed: 01/13/2023] Open
Abstract
Background Oculo‐auriculo‐vertebral spectrum (OAVS) is a craniofacial developmental disorder that affects structures derived from the first and second pharyngeal arches. The clinically heterogeneous phenotype involves mandibular, oral, and ear development anomalies. Etiology is complex and poorly understood. Genetic factors have been associated, evidenced by chromosomal abnormalities affecting different genomic regions and genes. However, known pathogenic single‐nucleotide variants (SNVs) have only been identified in MYT1 in a restricted number of patients. Therefore, investigations of SNVs on candidate genes may reveal other pathogenic mechanisms. Methods In a cohort of 73 patients, coding and untranslated regions (UTR) of 10 candidate genes (CRKL, YPEL1, MAPK1, NKX3‐2, HMX1, MYT1, OTX2, GSC, PUF60, HOXA2) were sequenced. Rare SNVs were selected and in silico predictions were performed to ascertain pathogenicity. Likely pathogenic variants were validated by Sanger sequencing and heritability was assessed when possible. Results Four likely pathogenic variants in heterozygous state were identified in different patients. Two SNVs were located in the 5’UTR of YPEL1; one in the 3’UTR of CRKL and one in the 3’UTR of OTX2. Conclusion Our work described variants in candidate genes for OAVS and supported the genetic heterogeneity of the spectrum.
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Affiliation(s)
- Malú Zamariolli
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Mileny Colovati
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Mariana Moysés-Oliveira
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Natália Nunes
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Leonardo Caires Dos Santos
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Ana B Alvarez Perez
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Silvia Bragagnolo
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Maria Isabel Melaragno
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
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8
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Vendrell JA, Vilquin P, Larrieux M, Van Goethem C, Solassol J. Benchmarking of Amplicon-Based Next-Generation Sequencing Panels Combined with Bioinformatics Solutions for Germline BRCA1 and BRCA2 Alteration Detection. J Mol Diagn 2018; 20:754-764. [PMID: 30055349 DOI: 10.1016/j.jmoldx.2018.06.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 04/27/2018] [Accepted: 06/05/2018] [Indexed: 11/16/2022] Open
Abstract
The recent deployment of next-generation sequencing approaches in routine laboratory analysis has considerably modified the landscape of BRCA1 and BRCA2 germline alteration detection in patients with a high risk of developing breast and/or ovarian cancer. Several commercial multiplex amplicon-based panels and bioinformatics solutions are currently available. In this study, we evaluated the combinations of several BRCA testing assays and bioinformatics solutions for the identification of single-nucleotide variants, insertion/deletion variants, and copy number variations (CNVs). Four assays (BRCA Tumor, BRCA HC, Ion AmpliSeq BRCA, and Access Array BRCA) and two commercial bioinformatics solutions (SeqNext software version 4.3.1 and Sophia DDM version 5.0.13) were tested on a set of 28 previously genotyped samples. All solutions exhibited accurate detection of single-nucleotide variants and insertion/deletion variants, except for Ion AmpliSeq BRCA, which exhibited a decrease in coverage. Of interest, for CNV analysis, the best accuracy was observed with the Sophia DDM platform regardless of the BRCA kit used. Finally, the performance of the most relevant combination (BRCA Tumor and Sophia DDM) was blindly validated on an independent set of 152 samples. Altogether, our results emphasize the need to accurately compare and control both molecular next-generation sequencing approaches and bioinformatics pipelines to limit the number of discrepant alterations and to provide a powerful tool for reliable detection of genetic alterations in BRCA1 and BRCA2, notably CNVs.
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Affiliation(s)
- Julie A Vendrell
- Solid Tumor Laboratory, Department of Pathology and Oncobiology, CHU Montpellier, University of Montpellier, Montpellier, France
| | - Paul Vilquin
- Solid Tumor Laboratory, Department of Pathology and Oncobiology, CHU Montpellier, University of Montpellier, Montpellier, France
| | - Marion Larrieux
- Solid Tumor Laboratory, Department of Pathology and Oncobiology, CHU Montpellier, University of Montpellier, Montpellier, France
| | - Charles Van Goethem
- Solid Tumor Laboratory, Department of Pathology and Oncobiology, CHU Montpellier, University of Montpellier, Montpellier, France
| | - Jérôme Solassol
- Solid Tumor Laboratory, Department of Pathology and Oncobiology, CHU Montpellier, University of Montpellier, Montpellier, France; The Institute of Cancer Research of Montpellier, INSERM U1194, University of Montpellier, Montpellier, France.
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9
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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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10
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Shin S, Kim Y, Chul Oh S, Yu N, Lee ST, Rak Choi J, Lee KA. Validation and optimization of the Ion Torrent S5 XL sequencer and Oncomine workflow for BRCA1 and BRCA2 genetic testing. Oncotarget 2018; 8:34858-34866. [PMID: 28422718 PMCID: PMC5471017 DOI: 10.18632/oncotarget.16799] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 03/24/2017] [Indexed: 01/09/2023] Open
Abstract
In this study, we validated the analytical performance of BRCA1/2 sequencing using Ion Torrent's new bench-top sequencer with amplicon panel with optimized bioinformatics pipelines. Using 43 samples that were previously validated by Illumina's MiSeq platform and/or by Sanger sequencing/multiplex ligation-dependent probe amplification, we amplified the target with the Oncomine™ BRCA Research Assay and sequenced on Ion Torrent S5 XL (Thermo Fisher Scientific, Waltham, MA, USA). We compared two bioinformatics pipelines for optimal processing of S5 XL sequence data: the Torrent Suite with a plug-in Torrent Variant Caller (Thermo Fisher Scientific), and commercial NextGENe software (Softgenetics, State College, PA, USA). All expected 681 single nucleotide variants, 15 small indels, and three copy number variants were correctly called, except one common variant adjacent to a rare variant on the primer-binding site. The sensitivity, specificity, false positive rate, and accuracy for detection of single nucleotide variant and small indels of S5 XL sequencing were 99.85%, 100%, 0%, and 99.99% for the Torrent Variant Caller and 99.85%, 99.99%, 0.14%, and 99.99% for NextGENe, respectively. The reproducibility of variant calling was 100%, and the precision of variant frequency also showed good performance with coefficients of variation between 0.32 and 5.29%. We obtained highly accurate data through uniform and sufficient coverage depth over all target regions and through optimization of the bioinformatics pipeline. We confirmed that our platform is accurate and practical for diagnostic BRCA1/2 testing in a clinical laboratory.
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Affiliation(s)
- Saeam Shin
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea.,Department of Laboratory Medicine, Hallym University College of Medicine, Kangnam Sacred Heart Hospital, Seoul, Republic of Korea
| | - Yoonjung Kim
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Seoung Chul Oh
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Nae Yu
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Seung-Tae Lee
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jong Rak Choi
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Kyung-A Lee
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
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11
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Mutational analysis of single circulating tumor cells by next generation sequencing in metastatic breast cancer. Oncotarget 2018; 7:26107-19. [PMID: 27034166 PMCID: PMC5041968 DOI: 10.18632/oncotarget.8431] [Citation(s) in RCA: 113] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 03/07/2016] [Indexed: 01/21/2023] Open
Abstract
Circulating Tumor Cells (CTCs) represent a “liquid biopsy” of the tumor potentially allowing real-time monitoring of cancer biology and therapies in individual patients. The purpose of the study was to explore the applicability of a protocol for the molecular characterization of single CTCs by Next Generation Sequencing (NGS) in order to investigate cell heterogeneity and provide a tool for a personalized medicine approach. CTCs were enriched and enumerated by CellSearch in blood from four metastatic breast cancer patients and singularly isolated by DEPArray. Upon whole genome amplification 3–5 single CTCs per patient were analyzed by NGS for 50 cancer-related genes. We found 51 sequence variants in 25 genes. We observed inter- and intra-patient heterogeneity in the mutational status of CTCs. The highest number of somatic deleterious mutations was found in the gene TP53, whose mutation is associated with adverse prognosis in breast cancer. The discordance between the mutational status of the primary tumor and CTCs observed in 3 patients suggests that, in advanced stages of cancer, CTC characteristics are more closely linked to the dynamic modifications of the disease status. In one patient the mutational profiles of CTCs before and during treatment shared only few sequence variants. This study supports the applicability of a non-invasive approach based on the liquid biopsy in metastatic breast cancer patients which, in perspective, should allow investigating the clonal evolution of the tumor for the development of new therapeutic strategies in precision medicine.
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12
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Concolino P, Rizza R, Mignone F, Costella A, Guarino D, Carboni I, Capoluongo E, Santonocito C, Urbani A, Minucci A. A comprehensive BRCA1/2 NGS pipeline for an immediate Copy Number Variation (CNV) detection in breast and ovarian cancer molecular diagnosis. Clin Chim Acta 2018; 480:173-179. [PMID: 29458049 DOI: 10.1016/j.cca.2018.02.012] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 02/10/2018] [Accepted: 02/13/2018] [Indexed: 02/07/2023]
Affiliation(s)
- Paola Concolino
- Laboratory of Molecular Biology, Institute of Biochemistry and Clinical Biochemistry, Catholic University of Sacred Heart, Largo A. Gemelli 8, 00168 Rome, Italy.
| | - Roberta Rizza
- Laboratory of Molecular Biology, Institute of Biochemistry and Clinical Biochemistry, Catholic University of Sacred Heart, Largo A. Gemelli 8, 00168 Rome, Italy
| | - Flavio Mignone
- Department of Science and Innovation Technology (DISIT), University of Piemonte Orientale, Alessandria, Italy
| | - Alessandra Costella
- Laboratory of Molecular Biology, Institute of Biochemistry and Clinical Biochemistry, Catholic University of Sacred Heart, Largo A. Gemelli 8, 00168 Rome, Italy
| | - Donatella Guarino
- Laboratory of Molecular Biology, Institute of Biochemistry and Clinical Biochemistry, Catholic University of Sacred Heart, Largo A. Gemelli 8, 00168 Rome, Italy
| | - Ilaria Carboni
- Institute of Legal Medicine, Catholic University of Sacred Heart, Largo A. Gemelli 8, 00168 Rome, Italy
| | - Ettore Capoluongo
- Laboratory of Molecular Biology, Institute of Biochemistry and Clinical Biochemistry, Catholic University of Sacred Heart, Largo A. Gemelli 8, 00168 Rome, Italy; Laboratory of Advanced Molecular Diagnostics (DIMA), Istituto Dermopatico dell'Immacolata, Fondazione Luigi Maria Monti, IRCCS, Rome, Italy
| | - Concetta Santonocito
- Laboratory of Molecular Biology, Institute of Biochemistry and Clinical Biochemistry, Catholic University of Sacred Heart, Largo A. Gemelli 8, 00168 Rome, Italy
| | - Andrea Urbani
- Laboratory of Molecular Biology, Institute of Biochemistry and Clinical Biochemistry, Catholic University of Sacred Heart, Largo A. Gemelli 8, 00168 Rome, Italy
| | - Angelo Minucci
- Laboratory of Molecular Biology, Institute of Biochemistry and Clinical Biochemistry, Catholic University of Sacred Heart, Largo A. Gemelli 8, 00168 Rome, Italy
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13
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Dos Santos ES, Caputo SM, Castera L, Gendrot M, Briaux A, Breault M, Krieger S, Rogan PK, Mucaki EJ, Burke LJ, Bièche I, Houdayer C, Vaur D, Stoppa-Lyonnet D, Brown MA, Lallemand F, Rouleau E. Assessment of the functional impact of germline BRCA1/2 variants located in non-coding regions in families with breast and/or ovarian cancer predisposition. Breast Cancer Res Treat 2017; 168:311-325. [PMID: 29236234 DOI: 10.1007/s10549-017-4602-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 11/28/2017] [Indexed: 12/19/2022]
Abstract
PURPOSE The molecular mechanism of breast and/or ovarian cancer susceptibility remains unclear in the majority of patients. While germline mutations in the regulatory non-coding regions of BRCA1 and BRCA2 genes have been described, screening has generally been limited to coding regions. The aim of this study was to evaluate the contribution of BRCA1/2 non-coding variants. METHODS Four BRCA1/2 non-coding regions were screened using high-resolution melting analysis/Sanger sequencing or next-generation sequencing on DNA extracted from index cases with breast and ovarian cancer predisposition (3926 for BRCA1 and 3910 for BRCA2). The impact of a set of variants on BRCA1/2 gene regulation was evaluated by site-directed mutagenesis, transfection, followed by Luciferase gene reporter assay. RESULTS We identified a total of 117 variants and tested twelve BRCA1 and 8 BRCA2 variants mapping to promoter and intronic regions. We highlighted two neighboring BRCA1 promoter variants (c.-130del; c.-125C > T) and one BRCA2 promoter variants (c.-296C > T) inhibiting significantly the promoter activity. In the functional assays, a regulating region within the intron 12 was found with the same enhancing impact as within the intron 2. Furthermore, the variants c.81-3980A > G and c.4186-2022C > T suppress the positive effect of the introns 2 and 12, respectively, on the BRCA1 promoter activity. We also found some variants inducing the promoter activities. CONCLUSION In this study, we highlighted some variants among many, modulating negatively the promoter activity of BRCA1 or 2 and thus having a potential impact on the risk of developing cancer. This selection makes it possible to conduct future validation studies on a limited number of variants.
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Affiliation(s)
- E Santana Dos Santos
- Department of Oncology, Center for Translational Oncology, Cancer Institute of the State of São Paulo - ICESP, São Paulo, Brazil
- Service de Génétique, Institut Curie, Paris, France
- A.C.Camargo Cancer Center, São Paulo, Brazil
| | - S M Caputo
- Service de Génétique, Institut Curie, Paris, France
| | - L Castera
- Laboratoire de Biologie et de Génétique du Cancer, CLCC François Baclesse, INSERM 1079 Centre Normand de Génomique et de MédecinePersonnalisée, Caen, France
| | - M Gendrot
- Service de Génétique, Institut Curie, Paris, France
| | - A Briaux
- Service de Génétique, Institut Curie, Paris, France
| | - M Breault
- Service de Génétique, Institut Curie, Paris, France
| | - S Krieger
- Laboratoire de Biologie et de Génétique du Cancer, CLCC François Baclesse, INSERM 1079 Centre Normand de Génomique et de MédecinePersonnalisée, Caen, France
| | - P K Rogan
- Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Canada
| | - E J Mucaki
- Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Canada
| | - L J Burke
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - I Bièche
- Service de Génétique, Institut Curie, Paris, France
- Université Paris Descartes, Paris, France
| | - C Houdayer
- Service de Génétique, Institut Curie, Paris, France
- Université Paris Descartes, Paris, France
| | - D Vaur
- Laboratoire de Biologie et de Génétique du Cancer, CLCC François Baclesse, INSERM 1079 Centre Normand de Génomique et de MédecinePersonnalisée, Caen, France
| | - D Stoppa-Lyonnet
- Service de Génétique, Institut Curie, Paris, France
- Université Paris Descartes, Paris, France
| | - M A Brown
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - F Lallemand
- Service de Génétique, Institut Curie, Paris, France.
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14
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Schmidt AY, Hansen TVO, Ahlborn LB, Jønson L, Yde CW, Nielsen FC. Next-Generation Sequencing-Based Detection of Germline Copy Number Variations in BRCA1/BRCA2: Validation of a One-Step Diagnostic Workflow. J Mol Diagn 2017; 19:809-816. [PMID: 28822785 DOI: 10.1016/j.jmoldx.2017.07.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 06/23/2017] [Accepted: 07/12/2017] [Indexed: 12/19/2022] Open
Abstract
Genetic testing of BRCA1/2 includes screening for single nucleotide variants and small insertions/deletions and for larger copy number variations (CNVs), primarily by Sanger sequencing and multiplex ligation-dependent probe amplification (MLPA). With the advent of next-generation sequencing (NGS), it has become feasible to provide CNV information and sequence data using a single platform. We report the use of NGS gene panel sequencing on the Illumina MiSeq platform and JSI SeqPilot SeqNext software to call germline CNVs in BRCA1 and BRCA2. For validation 18 different BRCA1/BRCA2 CNVs previously identified by MLPA in 48 Danish breast and/or ovarian cancer families were analyzed. Moreover, 120 patient samples previously determined as negative for BRCA1/BRCA2 CNVs by MLPA were included in the analysis. Comparison of the NGS data with the data from MLPA revealed that the sensitivity was 100%, whereas the specificity was 95%. Taken together, this study validates a one-step bioinformatics work-flow to call germline BRCA1/2 CNVs using data obtained by NGS of a breast cancer gene panel. The work-flow represents a robust and easy-to-use method for full BRCA1/2 screening, which can be easily implemented in routine diagnostic testing and adapted to genes other than BRCA1/2.
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Affiliation(s)
- Ane Y Schmidt
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Thomas V O Hansen
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Lise B Ahlborn
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Lars Jønson
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Christina W Yde
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Finn C Nielsen
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark.
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15
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Wallace AJ. New challenges for BRCA testing: a view from the diagnostic laboratory. Eur J Hum Genet 2017; 24 Suppl 1:S10-8. [PMID: 27514839 PMCID: PMC5141576 DOI: 10.1038/ejhg.2016.94] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
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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16
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Kringel D, Sisignano M, Zinn S, Lötsch J. Next-generation sequencing of the human TRPV1 gene and the regulating co-players LTB4R and LTB4R2 based on a custom AmpliSeq™ panel. PLoS One 2017; 12:e0180116. [PMID: 28658281 PMCID: PMC5489211 DOI: 10.1371/journal.pone.0180116] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2017] [Accepted: 06/11/2017] [Indexed: 01/08/2023] Open
Abstract
Background Transient receptor potential cation channel subfamily V member 1 (TRPV1) are sensitive to heat, capsaicin, pungent chemicals and other noxious stimuli. They play important roles in the pain pathway where in concert with proinflammatory factors such as leukotrienes they mediate sensitization and hyperalgesia. TRPV1 is the target of several novel analgesics drugs under development and therefore, TRPV1 genetic variants might represent promising candidates for pharmacogenetic modulators of drug effects. Methods A next-generation sequencing (NGS) panel was created for the human TRPV1 gene and in addition, for the leukotriene receptors BLT1 and BLT2 recently described to modulate TRPV1 mediated sensitisation processes rendering the coding genes LTB4R and LTB4R2 important co-players in pharmacogenetic approaches involving TRPV1. The NGS workflow was based on a custom AmpliSeq™ panel and designed for sequencing of human genes on an Ion PGM™ Sequencer. A cohort of 80 healthy subjects of Western European descent was screened to evaluate and validate the detection of exomic sequences of the coding genes with 25 base pair exon padding. Results The amplicons covered approximately 97% of the target sequence. A median of 2.81 x 106 reads per run was obtained. This identified approximately 140 chromosome loci where nucleotides deviated from the reference sequence GRCh37 hg19 comprising the three genes TRPV1, LTB4R and LTB4R2. Correspondence between NGS and Sanger derived nucleotide sequences was 100%. Conclusions Results suggested that the NGS approach based on AmpliSeq™ libraries and Ion Personal Genome Machine (PGM) sequencing is a highly efficient mutation detection method. It is suitable for large-scale sequencing of TRPV1 and functionally related genes. The method adds a large amount of genetic information as a basis for complete analysis of TRPV1 ion channel genetics and its functional consequences.
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Affiliation(s)
- Dario Kringel
- Institute of Clinical Pharmacology, Goethe - University, Frankfurt am Main, Germany
| | - Marco Sisignano
- Institute of Clinical Pharmacology, Goethe - University, Frankfurt am Main, Germany
| | - Sebastian Zinn
- Institute of Clinical Pharmacology, Goethe - University, Frankfurt am Main, Germany
| | - Jörn Lötsch
- Institute of Clinical Pharmacology, Goethe - University, Frankfurt am Main, Germany
- Fraunhofer Institute of Molecular Biology and Applied Ecology - Project Group Translational Medicine and Pharmacology (IME-TMP), Frankfurt am Main, Germany
- * E-mail:
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17
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Zhao Y, Feng Y, Ding X, Dong S, Zhang H, Ding J, Xia X. Identification of a novel hypertrophic cardiomyopathy-associated mutation using targeted next-generation sequencing. Int J Mol Med 2017; 40:121-129. [PMID: 28498465 PMCID: PMC5466385 DOI: 10.3892/ijmm.2017.2986] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2016] [Accepted: 05/04/2017] [Indexed: 01/21/2023] Open
Abstract
Hypertrophic cardiomyopathy (HCM), one of the most common forms of myocardial diseases, is the major cause of sudden cardiac death in young adults and competitive athletes. Analyses of gene mutations associated with HCM are valuable for its molecular diagnosis, genetic counseling, and management of familial HCM. To dissect the relationship between the clinical presentation and gene mutations of HCM, the genetic characterizations of 19 HCM-related genes in 18 patients (8 cases from 6 pedigrees with familial HCM and 10 cases without familial HCM) were detected using next-generation sequencing (NGS). As a result, 12 disease-related mutations were identified in the 18 subjects, including 6 single mutations and 3 double mutations [MYBPC3 (p.Gln998Glu) plus TNNI3 (p.Arg145Gly), PRKAG2 (p.Gly100Ser) plus MYBPC3 (p.Lys1209Serfs*28) and TNNI3 (p.Glu124Gln) plus GLA (p.Trp47*)]. The 3 heterozygous double mutations were discovered for the first time in the malignant familial HCM patients. Of the 6 single mutations, a novel mutation was found in tafazzin (TAZ, p.Ile208Val), and a mutation in β-myosin heavy chain gene (MYH7, p.Arg54Gln), which was reported as rare in the general population, was firstly found in one HCM patient. Identification of novel and rare mutations in HCM patients have added new data to the spectrum of gene mutations associated with this disease. These findings provide an essential basis for the molecular diagnosis and better management of family members at risk of familial HCM.
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Affiliation(s)
- Yue Zhao
- Faculty of Life Science and Technology, Research Center for Molecular Medicine in Yunnan Province, Kunming University of Science and Technology, Kunming, Yunnan 650500, P.R. China
| | - Yue Feng
- Faculty of Life Science and Technology, Research Center for Molecular Medicine in Yunnan Province, Kunming University of Science and Technology, Kunming, Yunnan 650500, P.R. China
| | - Xiaoxue Ding
- Department of Cardiology, The First People's Hospital of Yunnan Province, Kunming, Yunnan 650034, P.R. China
| | - Shuwei Dong
- Faculty of Life Science and Technology, Research Center for Molecular Medicine in Yunnan Province, Kunming University of Science and Technology, Kunming, Yunnan 650500, P.R. China
| | - Hong Zhang
- Department of Cardiology, The First People's Hospital of Yunnan Province, Kunming, Yunnan 650034, P.R. China
| | - Jiahuan Ding
- Faculty of Life Science and Technology, Research Center for Molecular Medicine in Yunnan Province, Kunming University of Science and Technology, Kunming, Yunnan 650500, P.R. China
| | - Xueshan Xia
- Faculty of Life Science and Technology, Research Center for Molecular Medicine in Yunnan Province, Kunming University of Science and Technology, Kunming, Yunnan 650500, P.R. China
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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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Elsensohn MH, Leblay N, Dimassi S, Campan-Fournier A, Labalme A, Roucher-Boulez F, Sanlaville D, Lesca G, Bardel C, Roy P. Statistical method to compare massive parallel sequencing pipelines. BMC Bioinformatics 2017; 18:139. [PMID: 28249565 PMCID: PMC5333416 DOI: 10.1186/s12859-017-1552-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2016] [Accepted: 02/16/2017] [Indexed: 02/01/2023] Open
Abstract
Background Today, sequencing is frequently carried out by Massive Parallel Sequencing (MPS) that cuts drastically sequencing time and expenses. Nevertheless, Sanger sequencing remains the main validation method to confirm the presence of variants. The analysis of MPS data involves the development of several bioinformatic tools, academic or commercial. We present here a statistical method to compare MPS pipelines and test it in a comparison between an academic (BWA-GATK) and a commercial pipeline (TMAP-NextGENe®), with and without reference to a gold standard (here, Sanger sequencing), on a panel of 41 genes in 43 epileptic patients. This method used the number of variants to fit log-linear models for pairwise agreements between pipelines. To assess the heterogeneity of the margins and the odds ratios of agreement, four log-linear models were used: a full model, a homogeneous-margin model, a model with single odds ratio for all patients, and a model with single intercept. Then a log-linear mixed model was fitted considering the biological variability as a random effect. Results Among the 390,339 base-pairs sequenced, TMAP-NextGENe® and BWA-GATK found, on average, 2253.49 and 1857.14 variants (single nucleotide variants and indels), respectively. Against the gold standard, the pipelines had similar sensitivities (63.47% vs. 63.42%) and close but significantly different specificities (99.57% vs. 99.65%; p < 0.001). Same-trend results were obtained when only single nucleotide variants were considered (99.98% specificity and 76.81% sensitivity for both pipelines). Conclusions The method allows thus pipeline comparison and selection. It is generalizable to all types of MPS data and all pipelines. Electronic supplementary material The online version of this article (doi:10.1186/s12859-017-1552-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- M H Elsensohn
- Service de Biostatistique-Bioinformatique, Hospices Civils de Lyon, 162 avenue Lacassagne, F-69003, Lyon, France. .,Université de Lyon, Lyon, France. .,Université Lyon 1, Villeurbanne, France. .,CNRS UMR5558, Laboratoire de Biométrie et Biologie Evolutive, Equipe Biostatistique Santé, Villeurbanne, France.
| | - N Leblay
- Service de Biostatistique-Bioinformatique, Hospices Civils de Lyon, 162 avenue Lacassagne, F-69003, Lyon, France.,Université de Lyon, Lyon, France.,Université Lyon 1, Villeurbanne, France.,CNRS UMR5558, Laboratoire de Biométrie et Biologie Evolutive, Equipe Biostatistique Santé, Villeurbanne, France
| | - S Dimassi
- Université de Lyon, Lyon, France.,Université Lyon 1, Villeurbanne, France.,Service de Génétique, Hospices Civils de Lyon, Lyon, France.,Centre de Recherche en Neurosciences de Lyon, CNRS UMR 5292, INSERM U1028, Lyon, France
| | - A Campan-Fournier
- Université de Lyon, Lyon, France.,Université Lyon 1, Villeurbanne, France.,Service de Génétique, Hospices Civils de Lyon, Lyon, France.,Centre de Recherche en Neurosciences de Lyon, CNRS UMR 5292, INSERM U1028, Lyon, France
| | - A Labalme
- Service de Génétique, Hospices Civils de Lyon, Lyon, France
| | - F Roucher-Boulez
- Université de Lyon, Lyon, France.,Université Lyon 1, Villeurbanne, France.,CNRS UMR5558, Laboratoire de Biométrie et Biologie Evolutive, Equipe Biostatistique Santé, Villeurbanne, France.,Service de Génétique, Hospices Civils de Lyon, Lyon, France
| | - D Sanlaville
- Université de Lyon, Lyon, France.,Université Lyon 1, Villeurbanne, France.,Service de Génétique, Hospices Civils de Lyon, Lyon, France.,Centre de Recherche en Neurosciences de Lyon, CNRS UMR 5292, INSERM U1028, Lyon, France
| | - G Lesca
- Université de Lyon, Lyon, France.,Université Lyon 1, Villeurbanne, France.,Service de Génétique, Hospices Civils de Lyon, Lyon, France.,Centre de Recherche en Neurosciences de Lyon, CNRS UMR 5292, INSERM U1028, Lyon, France
| | - C Bardel
- Service de Biostatistique-Bioinformatique, Hospices Civils de Lyon, 162 avenue Lacassagne, F-69003, Lyon, France.,Université de Lyon, Lyon, France.,Université Lyon 1, Villeurbanne, France.,CNRS UMR5558, Laboratoire de Biométrie et Biologie Evolutive, Equipe Biostatistique Santé, Villeurbanne, France
| | - P Roy
- Service de Biostatistique-Bioinformatique, Hospices Civils de Lyon, 162 avenue Lacassagne, F-69003, Lyon, France.,Université de Lyon, Lyon, France.,Université Lyon 1, Villeurbanne, France.,CNRS UMR5558, Laboratoire de Biométrie et Biologie Evolutive, Equipe Biostatistique Santé, Villeurbanne, France
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20
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Mosaicism and prenatal diagnosis options: insights from retinoblastoma. Eur J Hum Genet 2016; 25:381-383. [PMID: 28000698 DOI: 10.1038/ejhg.2016.174] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 09/23/2016] [Accepted: 11/01/2016] [Indexed: 01/17/2023] Open
Abstract
In sporadic cases, a post-zygotic mutational event signifies a somatic mosaicism in the affected child only, which implies that these mutations affect only a portion of the body. Therefore siblings do not need follow-up. On the other hand, a pre-zygotic mutation transmitted by an unaffected mosaic parent implies recurrent risks in offspring. To better estimate the contribution of pre- and post-zygotic events, we analysed 124 consecutive bilateral retinoblastoma probands, carrying a heterozygous RB1 pathogenic variant and their unaffected, non-carrier parents. In order to evaluate somatic mosaicism in blood, the deleterious RB1 pathogenic variant identified in the proband, was searched for in the unaffected parents, using targeted deep sequencing. Observed recurrences, which represent an estimation of germline and somatic mosaicisms, were recorded and computed in the sibships. Deep sequencing revealed one mosaic-unaffected parent out of 124 tested couples, which provides an estimation of the maximal risk of recurrence, due to parental mosaicism, at 0.4%. Follow-up in the sibships showed one recurrence, providing a maximal recurrence risk, due to parental mosaicism, at 0.8%. Two different statistical strategies led to close estimates (0.4 and 0.8% risks) which appeared 266-533-fold higher, as compared with the general population. These recurrence estimates could be considered when counselling couples with retinoblastoma or diseases with a high de novo mutation rate.
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21
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Serratì S, De Summa S, Pilato B, Petriella D, Lacalamita R, Tommasi S, Pinto R. Next-generation sequencing: advances and applications in cancer diagnosis. Onco Targets Ther 2016; 9:7355-7365. [PMID: 27980425 PMCID: PMC5144906 DOI: 10.2147/ott.s99807] [Citation(s) in RCA: 108] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Technological advances have led to the introduction of next-generation sequencing (NGS) platforms in cancer investigation. NGS allows massive parallel sequencing that affords maximal tumor genomic assessment. NGS approaches are different, and concern DNA and RNA analysis. DNA sequencing includes whole-genome, whole-exome, and targeted sequencing, which focuses on a selection of genes of interest for a specific disease. RNA sequencing facilitates the detection of alternative gene-spliced transcripts, posttranscriptional modifications, gene fusion, mutations/single-nucleotide polymorphisms, small and long noncoding RNAs, and changes in gene expression. Most applications are in the cancer research field, but lately NGS technology has been revolutionizing cancer molecular diagnostics, due to the many advantages it offers compared to traditional methods. There is greater knowledge on solid cancer diagnostics, and recent interest has been shown also in the field of hematologic cancer. In this review, we report the latest data on NGS diagnostic/predictive clinical applications in solid and hematologic cancers. Moreover, since the amount of NGS data produced is very large and their interpretation is very complex, we briefly discuss two bioinformatic aspects, variant-calling accuracy and copy-number variation detection, which are gaining a lot of importance in cancer-diagnostic assessment.
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Affiliation(s)
- Simona Serratì
- 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
| | - Brunella Pilato
- 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
| | - Stefania Tommasi
- Molecular Genetics Laboratory, IRCCS Istituto Tumori Giovanni Paolo II, Bari, Italy
| | - Rosamaria Pinto
- Molecular Genetics Laboratory, IRCCS Istituto Tumori Giovanni Paolo II, Bari, Italy
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Kringel D, Lötsch J. Next-generation sequencing of human opioid receptor genes based on a custom AmpliSeq™ library and ion torrent personal genome machine. Clin Chim Acta 2016; 463:32-38. [PMID: 27725223 PMCID: PMC5352731 DOI: 10.1016/j.cca.2016.10.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 09/12/2016] [Accepted: 10/07/2016] [Indexed: 12/21/2022]
Abstract
BACKGROUND The opioid system is involved in the control of pain, reward, addictive behaviors and vegetative effects. Opioids exert their pharmacological actions through the agonistic binding at opioid receptors and variation in the coding genes has been found to modulate opioid receptor expression or signaling. However, a limited selection of functional opioid receptor variants is perceived as insufficient in providing a genetic diagnosis of clinical phenotypes and therefore, unrestricted access to opioid receptor genetics is required. METHODS Next-generation sequencing (NGS) workflow was based on a custom AmpliSeq™ panel and designed for sequencing of human genes related to the opioid receptor group (OPRM1, OPRD1, OPRK1, SIGMA1, OPRL1) on an Ion PGM™ Sequencer. A cohort of 79 previously studied chronic pain patients was screened to evaluate and validate the detection of exomic sequences of the coding genes with 25 base pair exon padding. In-silico analysis was performed using SNP and Variation Suite® software. RESULTS The amplicons covered approximately 90% of the target sequence. A median of 2.54×106 reads per run was obtained generating a total of 35,447 nucleotide reads from each DNA sample. This identified approximately 100 chromosome loci where nucleotides deviated from the reference sequence GRCh37 hg19, including functional variants such as the OPRM1 rs1799971 SNP (118 A>G) as the most scientifically regarded variant or rs563649 SNP coding for μ-opioid receptor splice variants. Correspondence between NGS and Sanger derived nucleotide sequences was 100%. CONCLUSION Results suggested that the NGS approach based on AmpliSeq™ libraries and Ion PGM sequencing is a highly efficient mutation detection method. It is suitable for large-scale sequencing of opioid receptor genes. The method includes the variants studied so far for functional associations and adds a large amount of genetic information as a basis for complete analysis of human opioid receptor genetics and its functional consequences.
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Affiliation(s)
- Dario Kringel
- Institute of Clinical Pharmacology, Goethe - University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Jörn Lötsch
- Institute of Clinical Pharmacology, Goethe - University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany; Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Project Group Translational Medicine and Pharmacology TMP, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany.
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Wang NL, Lu YL, Zhang P, Zhang MH, Gong JY, Lu Y, Xie XB, Qiu YL, Yan YY, Wu BB, Wang JS. A Specially Designed Multi-Gene Panel Facilitates Genetic Diagnosis in Children with Intrahepatic Cholestasis: Simultaneous Test of Known Large Insertions/Deletions. PLoS One 2016; 11:e0164058. [PMID: 27706244 PMCID: PMC5051675 DOI: 10.1371/journal.pone.0164058] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 09/19/2016] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND AND AIMS Large indels are commonly identified in patients but are not detectable by routine Sanger sequencing and panel sequencing. We specially designed a multi-gene panel that could simultaneously test known large indels in addition to ordinary variants, and reported the diagnostic yield in patients with intrahepatic cholestasis. METHODS The panel contains 61 genes associated with cholestasis and 25 known recurrent large indels. The amplicon library was sequenced on Ion PGM system. Sequencing data were analyzed using a routine data analysis protocol and an internal program encoded for large indels test simultaneously. The validation phase was performed using 54 patients with known genetic diagnosis, including 5 with large insertions. At implement phase, 141 patients with intrahepatic cholestasis were evaluated. RESULTS At validation phase, 99.6% of the variations identified by Sanger sequencing could be detected by panel sequencing. Following the routine protocol, 99.8% of false positives could be filtered and 98.8% of retained variations were true positives. Large insertions in the 5 patients with known genetic diagnosis could be correctly detected using the internal program. At implementation phase, 96.9% of the retained variations, following the routine protocol, were confirmed to be true. Twenty-nine patients received a potential genetic diagnosis when panel sequencing data were analyzed using the routine protocol. Two additional patients, who were found to harbor large insertions in SLC25A13, obtained a potential genetic diagnosis when sequencing data were further analyzed using the internal program. A total of 31 (22.0%) patients obtained a potential genetic diagnosis. Nine different genetic disorders were diagnosed, and citrin deficiency was the commonest. CONCLUSION Specially designed multi-gene panel can correctly detect large indels simultaneously. By using it, we assigned a potential genetic diagnosis to 22.0% of patients with intrahepatic cholestasis.
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Affiliation(s)
- Neng-Li Wang
- Department of Pediatrics, Jinshan Hospital of Fudan University, Shanghai, China
| | - Yu-Lan Lu
- The Molecular Genetic Diagnosis Center, Shanghai Key Lab of Birth Defects, Pediatrics Research Institute, Children’s Hospital of Fudan University, Shanghai, China
| | - Ping Zhang
- The Molecular Genetic Diagnosis Center, Shanghai Key Lab of Birth Defects, Pediatrics Research Institute, Children’s Hospital of Fudan University, Shanghai, China
| | - Mei-Hong Zhang
- Department of Pediatrics, Jinshan Hospital of Fudan University, Shanghai, China
| | - Jing-Yu Gong
- Department of Pediatrics, Jinshan Hospital of Fudan University, Shanghai, China
| | - Yi Lu
- The Center for Pediatric Liver Diseases, Children’s Hospital of Fudan University, Shanghai, China
| | - Xin-Bao Xie
- The Center for Pediatric Liver Diseases, Children’s Hospital of Fudan University, Shanghai, China
| | - Yi-Ling Qiu
- The Center for Pediatric Liver Diseases, Children’s Hospital of Fudan University, Shanghai, China
| | - Yan-Yan Yan
- Department of Pediatrics, Jinshan Hospital of Fudan University, Shanghai, China
| | - Bing-bing Wu
- The Molecular Genetic Diagnosis Center, Shanghai Key Lab of Birth Defects, Pediatrics Research Institute, Children’s Hospital of Fudan University, Shanghai, China
- * E-mail: (JSW); (BBW)
| | - Jian-She Wang
- The Center for Pediatric Liver Diseases, Children’s Hospital of Fudan University, Shanghai, China
- * E-mail: (JSW); (BBW)
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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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Zhao Y, Cao H, Song Y, Feng Y, Ding X, Pang M, Zhang Y, Zhang H, Ding J, Xia X. Identification of novel mutations including a double mutation in patients with inherited cardiomyopathy by a targeted sequencing approach using the Ion Torrent PGM system. Int J Mol Med 2016; 37:1511-20. [PMID: 27082122 PMCID: PMC4867886 DOI: 10.3892/ijmm.2016.2565] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2015] [Accepted: 04/08/2016] [Indexed: 12/19/2022] Open
Abstract
Inherited cardiomyopathy is the major cause of sudden cardiac death (SCD) and heart failure (HF). The disease is associated with extensive genetic heterogeneity; pathogenic mutations in cardiac sarcomere protein genes, cytoskeletal protein genes and nuclear envelope protein genes have been linked to its etiology. Early diagnosis is conducive to clinical monitoring and allows for presymptomatic interventions as needed. In the present study, the entire coding sequences and flanking regions of 12 major disease (cardiomyopathy)-related genes [namely myosin, heavy chain 7, cardiac muscle, β (MYH7); myosin binding protein C, cardiac (MYBPC3); lamin A/C (LMNA); troponin I type 3 (cardiac) (TNNI3); troponin T type 2 (cardiac) (TNNT2); actin, α, cardiac muscle 1 (ACTC1); tropomyosin 1 (α) (TPM1); sodium channel, voltage gated, type V alpha subunit (SCN5A); myosin, light chain 2, regulatory, cardiac, slow (MYL2); myosin, heavy chain 6, cardiac muscle, α (MYH6); myosin, light chain 3, alkali, ventricular, skeletal, slow (MYL3); and protein kinase, AMP-activated, gamma 2 non-catalytic subunit (PRKAG2)] in 8 patients with dilated cardiomyopathy (DCM) and in 8 patients with hypertrophic cardiomyopathy (HCM) were amplified and then sequenced using the Ion Torrent Personal Genome Machine (PGM) system. As a result, a novel heterozygous mutation (MYH7, p.Asn885Thr) and a variant of uncertain significance (TNNT2, p.Arg296His) were identified in 2 patients with HCM. These 2 missense mutations, which were absent in the samples obtained from the 200 healthy control subjects, altered the amino acid that was evolutionarily conserved among a number of vertebrate species; this illustrates that these 2 non-synonymous mutations play a role in the pathogenesis of HCM. Moreover, a double heterozygous mutation (PRKAG2, p.Gly100Ser plus MYH7, p.Arg719Trp) was identified in a patient with severe familial HCM, for the first time to the best of our knowledge. This patient provided us with more information regarding the genotype-phenotype correlation between mutations of MYH7 and PRKAG2. Taken together, these findings provide insight into the molecular mechanisms underlying inherited cardiomyopathy. The mutations identified in this study may be further investigated in the future in order to improve the diagnosis and treatment of patients with inherited cardiomyopathy. Furthermore, our findings indicated that sequencing using the Ion Torrent PGM system is a useful approach for the identification of pathogenic mutations associated with inherited cardiomyopathy, and it may be used for the risk evaluation of individuals with a possible susceptibility to inherited cardiomyopathy.
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Affiliation(s)
- Yue Zhao
- Faculty of Life Science and Technology, Research Center for Molecular Medicine in Yunnan Province, Kunming University of Science and Technology, Kunming, Yunnan 650500, P.R. China
| | - Hong Cao
- Department of Cardiology, The First Hospital of Yunnan Province, Kunming, Yunnan 650034, P.R. China
| | - Yindi Song
- Department of Cardiology, The First Hospital of Yunnan Province, Kunming, Yunnan 650034, P.R. China
| | - Yue Feng
- Faculty of Life Science and Technology, Research Center for Molecular Medicine in Yunnan Province, Kunming University of Science and Technology, Kunming, Yunnan 650500, P.R. China
| | - Xiaoxue Ding
- Department of Cardiology, The First Hospital of Yunnan Province, Kunming, Yunnan 650034, P.R. China
| | - Mingjie Pang
- Department of Cardiology, The First Hospital of Yunnan Province, Kunming, Yunnan 650034, P.R. China
| | - Yunmei Zhang
- Department of Cardiology, The First Hospital of Yunnan Province, Kunming, Yunnan 650034, P.R. China
| | - Hong Zhang
- Department of Cardiology, The First Hospital of Yunnan Province, Kunming, Yunnan 650034, P.R. China
| | - Jiahuan Ding
- Faculty of Life Science and Technology, Research Center for Molecular Medicine in Yunnan Province, Kunming University of Science and Technology, Kunming, Yunnan 650500, P.R. China
| | - Xueshan Xia
- Faculty of Life Science and Technology, Research Center for Molecular Medicine in Yunnan Province, Kunming University of Science and Technology, Kunming, Yunnan 650500, P.R. China
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Calmels N, Greff G, Obringer C, Kempf N, Gasnier C, Tarabeux J, Miguet M, Baujat G, Bessis D, Bretones P, Cavau A, Digeon B, Doco-Fenzy M, Doray B, Feillet F, Gardeazabal J, Gener B, Julia S, Llano-Rivas I, Mazur A, Michot C, Renaldo-Robin F, Rossi M, Sabouraud P, Keren B, Depienne C, Muller J, Mandel JL, Laugel V. Uncommon nucleotide excision repair phenotypes revealed by targeted high-throughput sequencing. Orphanet J Rare Dis 2016; 11:26. [PMID: 27004399 PMCID: PMC4804614 DOI: 10.1186/s13023-016-0408-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2015] [Accepted: 03/16/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Deficient nucleotide excision repair (NER) activity causes a variety of autosomal recessive diseases including xeroderma pigmentosum (XP) a disorder which pre-disposes to skin cancer, and the severe multisystem condition known as Cockayne syndrome (CS). In view of the clinical overlap between NER-related disorders, as well as the existence of multiple phenotypes and the numerous genes involved, we developed a new diagnostic approach based on the enrichment of 16 NER-related genes by multiplex amplification coupled with next-generation sequencing (NGS). METHODS Our test cohort consisted of 11 DNA samples, all with known mutations and/or non pathogenic SNPs in two of the tested genes. We then used the same technique to analyse samples from a prospective cohort of 40 patients. Multiplex amplification and sequencing were performed using AmpliSeq protocol on the Ion Torrent PGM (Life Technologies). RESULTS We identified causative mutations in 17 out of the 40 patients (43%). Four patients showed biallelic mutations in the ERCC6(CSB) gene, five in the ERCC8(CSA) gene: most of them had classical CS features but some had very mild and incomplete phenotypes. A small cohort of 4 unrelated classic XP patients from the Basque country (Northern Spain) revealed a common splicing mutation in POLH (XP-variant), demonstrating a new founder effect in this population. Interestingly, our results also found ERCC2(XPD), ERCC3(XPB) or ERCC5(XPG) mutations in two cases of UV-sensitive syndrome and in two cases with mixed XP/CS phenotypes. CONCLUSIONS Our study confirms that NGS is an efficient technique for the analysis of NER-related disorders on a molecular level. It is particularly useful for phenotypes with combined features or unusually mild symptoms. Targeted NGS used in conjunction with DNA repair functional tests and precise clinical evaluation permits rapid and cost-effective diagnosis in patients with NER-defects.
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Affiliation(s)
- Nadège Calmels
- Laboratoire de Diagnostic Génétique, Institut de Génétique Médicale d'Alsace (IGMA), Hôpitaux Universitaires de Strasbourg, 1 place de l'hôpital, Strasbourg, France.
| | - Géraldine Greff
- Laboratoire de Diagnostic Génétique, Institut de Génétique Médicale d'Alsace (IGMA), Hôpitaux Universitaires de Strasbourg, 1 place de l'hôpital, Strasbourg, France
| | - Cathy Obringer
- Laboratoire de Génétique Médicale - INSERM U1112, Institut de Génétique Médicale d'Alsace (IGMA), Faculté de médecine de Strasbourg, 11 rue Humann, Strasbourg, France
| | - Nadine Kempf
- Laboratoire de Diagnostic Génétique, Institut de Génétique Médicale d'Alsace (IGMA), Hôpitaux Universitaires de Strasbourg, 1 place de l'hôpital, Strasbourg, France
| | - Claire Gasnier
- Laboratoire de Diagnostic Génétique, Institut de Génétique Médicale d'Alsace (IGMA), Hôpitaux Universitaires de Strasbourg, 1 place de l'hôpital, Strasbourg, France
| | - Julien Tarabeux
- Laboratoire de Diagnostic Génétique, Institut de Génétique Médicale d'Alsace (IGMA), Hôpitaux Universitaires de Strasbourg, 1 place de l'hôpital, Strasbourg, France
| | - Marguerite Miguet
- Laboratoire de Diagnostic Génétique, Institut de Génétique Médicale d'Alsace (IGMA), Hôpitaux Universitaires de Strasbourg, 1 place de l'hôpital, Strasbourg, France
| | - Geneviève Baujat
- Centre de Référence Maladies Osseuses Constitutionnelles, Département de Génétique, Hôpital Necker-Enfants malades, Paris, France
| | - Didier Bessis
- Département de Dermatologie, Hôpital Saint-Éloi, 80 avenue Augustin-Fliche, 34295, Montpellier, France
| | - Patricia Bretones
- Service d'Endocrinologie Pédiatrique, diabète et maladies héréditaires du métabolisme, Hôpital Femme Mère enfant, GH Est, 59 boulevard Pinel, Bron, France
| | - Anne Cavau
- Service de Pédiatrie Générale, Hôpital Necker-Enfants malades, Paris, France
| | - Béatrice Digeon
- Service de Pédiatrie, CHU de Reims, Hôpital Maison Blanche, 45 rue Cognacq-Jay, Reims, France
| | - Martine Doco-Fenzy
- Service de Génétique et Biologie de la Reproduction CHU de Reims, Hôpital Maison Blanche, 45 rue Cognacq-Jay, Reims, France
| | - Bérénice Doray
- Service de Génétique, CHU La Réunion, Hôpital Félix Guyon, Allée des Topazes, Saint-Denis, France
| | - François Feillet
- Centre de Référence des Maladies Héréditaires du Métabolisme, Service de Médecine Infantile, INSERM NGERE 954, CHU Brabois Enfants, Allée du Morvan, Vandœuvre les Nancy, France
| | - Jesus Gardeazabal
- Servicio de Dermatología, Cruces University Hospital, BioCruces Health Research Institute, Baracaldo Vizcaya, Spain
| | - Blanca Gener
- Servicio de Genética, Cruces University Hospital, BioCruces Health Research Institute, Baracaldo Vizcaya, Spain
| | - Sophie Julia
- Service de Génétique Médicale, CHU de Toulouse - Hôpital Purpan, Place du Docteur Baylac, Toulouse, France
| | - Isabel Llano-Rivas
- Servicio de Genética, Cruces University Hospital, BioCruces Health Research Institute, Baracaldo Vizcaya, Spain
| | - Artur Mazur
- Department of Pediatrics, Pediatric Endocrinology and Diabetes, Faculty of Medicine, University of Rzeszów, Rzeszów, Poland
| | - Caroline Michot
- Service de Génétique Médicale, Hôpital Necker Enfants-Malades, 24 Bd du Montparnasse, Paris, France
| | | | - Massimiliano Rossi
- Centre de Référence des Anomalies du Développement, Service de Génétique, Hospices Civils de Lyon, Lyon, France.,INSERM U1028; CNRS UMR5292; CNRL TIGER Team, Lyon, France
| | - Pascal Sabouraud
- Service de Pédiatrie A - Neurologie pédiatrique, CHU de Reims - American Memorial Hospital, 47 rue Cognacq Jay, Reims, France
| | - Boris Keren
- AP-HP, Hôpital de la Pitié-Salpêtrière, Département de Génétique, F-75013, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, Inserm, CNRS, UM 75, U 1127, UMR 7225, ICM, F-75013, Paris, France
| | - Christel Depienne
- AP-HP, Hôpital de la Pitié-Salpêtrière, Département de Génétique, F-75013, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, Inserm, CNRS, UM 75, U 1127, UMR 7225, ICM, F-75013, Paris, France
| | - Jean Muller
- Laboratoire de Diagnostic Génétique, Institut de Génétique Médicale d'Alsace (IGMA), Hôpitaux Universitaires de Strasbourg, 1 place de l'hôpital, Strasbourg, France.,Laboratoire de Génétique Médicale - INSERM U1112, Institut de Génétique Médicale d'Alsace (IGMA), Faculté de médecine de Strasbourg, 11 rue Humann, Strasbourg, France
| | - Jean-Louis Mandel
- Laboratoire de Diagnostic Génétique, Institut de Génétique Médicale d'Alsace (IGMA), Hôpitaux Universitaires de Strasbourg, 1 place de l'hôpital, Strasbourg, France
| | - Vincent Laugel
- Laboratoire de Génétique Médicale - INSERM U1112, Institut de Génétique Médicale d'Alsace (IGMA), Faculté de médecine de Strasbourg, 11 rue Humann, Strasbourg, France.,Service de Pédiatrie, Hôpitaux Universitaires de Strasbourg, 1 avenue Molière, Strasbourg, France
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Zhou S, Ling H, Ma Y, Zhou Y, Du W, Cui M, Xia Y, Yan L, Yao H, Qi Z. Label-Free and Sensitive Detection of BRCA1 and TB4 DNA Sequences with Water-Soluble Cationic Polythiophenes. Aust J Chem 2016. [DOI: 10.1071/ch15395] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
A sensitive method for BRCA1 and TB4 DNA sequences detection using water-soluble cationic polythiophenes, poly(3-(1′-ethoxy-2′-N-methyl imidazole)thiophene) (PT) is presented. The fluorescence of PT could be dramatically quenched by the addition of single-stranded DNA (ssDNA; TB4 and BRCA1 sequences). The KSV (Stern–Volmer constant) for TB4 and BRCA1 DNA sequences are 1.46 × 108 and 3.28 × 108 M–1 respectively, and the limits of detection of these two sequences are 1.26 × 10–10 and 0.483 × 10–10 M respectively. The fluorescence of PT would recover to its initial intensity after the addition of complementary ssDNA, whereas sequences with one to three mismatched bases would not. The influences of buffer pH and concentration of NaCl were also investigated systemically in order to further improve the sensitivity. This assay can be completed in a short period of time without any further procedure. Hence, this sensitive, cost-effective, and rapid detection method for BRCA1 and TB4 DNA sequences may contribute to the clinical diagnosis of breast cancer gene mutations in the future.
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Chanavat V, Janin A, Millat G. A fast and cost-effective molecular diagnostic tool for genetic diseases involved in sudden cardiac death. Clin Chim Acta 2015; 453:80-5. [PMID: 26688388 DOI: 10.1016/j.cca.2015.12.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 12/08/2015] [Accepted: 12/09/2015] [Indexed: 12/11/2022]
Abstract
BACKGROUND Cardiomyopathies and arrhythmia syndromes are common genetic cardiac diseases that account for a significant number of sudden cardiac death (SCD) cases. METHODS NGS workflow based on a panel of 95 genes was developed on Illumina NextSeq500™ sequencer for sequencing prevalent SCD-causing genes. A cohort of 90 patients (56 genotype-positive, 27 genotype-negative and 7 new cases) was screened to evaluate this strategy in terms of sensitivity, specificity, practicability and cost. In silico analysis were performed using a pipeline based on NextGENe® software and a personalized Sophia Genetics pipeline. RESULTS Using our panel custom, 100% of targeted sequences were efficiently covered and all previously identified genetic variants were readily detected. Applied to 27 genotype-negative patients, this molecular strategy allowed the identification of pathogenic or likely pathogenic variants into 12 cases. It confirmed the involvement of HCN4 mutations in the combined bradycardia–myocardial non-compaction phenotype, and also suggested, for the first time, the involvement of PKP2, usually associated with arrhythmogenic right ventricular dysplasia, in ventricular non-compaction. CONCLUSION This NGS approach is a fast, cheap, sensitive and high-throughput mutation detection method that is ready to be deployed in clinical laboratories and would provide new insights on physiopathology of SCD, more particularly of cardiomyopathies and arrhythmia syndromes.
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Affiliation(s)
- Valérie Chanavat
- Laboratoire de Cardiogénétique Moléculaire, Centre de Biologie et Pathologie Est, Hospices Civils de Lyon, Lyon, France; NGS Sequencing Platform for Molecular Diagnosis, Hospices Civils de Lyon, Lyon, France
| | - Alexandre Janin
- Laboratoire de Cardiogénétique Moléculaire, Centre de Biologie et Pathologie Est, Hospices Civils de Lyon, Lyon, France; Université de Lyon, Lyon F-69003, France; Université Lyon 1, Lyon, France
| | - Gilles Millat
- Laboratoire de Cardiogénétique Moléculaire, Centre de Biologie et Pathologie Est, Hospices Civils de Lyon, Lyon, France; NGS Sequencing Platform for Molecular Diagnosis, Hospices Civils de Lyon, Lyon, France; Université de Lyon, Lyon F-69003, France; Université Lyon 1, Lyon, France.
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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: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [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. Electronic supplementary material The online version of this article (doi:10.1186/s13742-015-0088-z) contains supplementary material, which is available to authorized users.
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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
| | - Jose A Figueroa
- 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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Dimassi S, Simonet T, Labalme A, Boutry-Kryza N, Campan-Fournier A, Lamy R, Bardel C, Elsensohn MH, Roucher-Boulez F, Chatron N, Putoux A, de Bellescize J, Ville D, Schaeffer L, Roy P, Mougou-Zerelli S, Saad A, Calender A, Sanlaville D, Lesca G. Comparison of two next-generation sequencing kits for diagnosis of epileptic disorders with a user-friendly tool for displaying gene coverage, DeCovA. Appl Transl Genom 2015; 7:19-25. [PMID: 27054081 PMCID: PMC4803767 DOI: 10.1016/j.atg.2015.10.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Revised: 09/25/2015] [Accepted: 10/06/2015] [Indexed: 11/30/2022]
Affiliation(s)
- Sarra Dimassi
- Department of Medical Genetics, Lyon University Hospital, Lyon, France
- CNRL, CNRS UMR 5292, INSERM U1028, Lyon, France
- Claude Bernard Lyon I University, Lyon, France
| | - Thomas Simonet
- Department of Cell Biotechnology, Lyon, France
- Ecole Normale Supérieure de Lyon, Lyon, France
| | - Audrey Labalme
- Department of Medical Genetics, Lyon University Hospital, Lyon, France
| | | | | | - Raphaelle Lamy
- Department of Medical Genetics, Lyon University Hospital, Lyon, France
| | - Claire Bardel
- Claude Bernard Lyon I University, Lyon, France
- Service de Biostatistique, Hospices Civils de Lyon, Lyon, France
- CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, Equipe Biostatistique-Santé, Villeurbanne, France
| | - Mad-Hélénie Elsensohn
- Claude Bernard Lyon I University, Lyon, France
- Service de Biostatistique, Hospices Civils de Lyon, Lyon, France
- CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, Equipe Biostatistique-Santé, Villeurbanne, France
| | - Florence Roucher-Boulez
- Claude Bernard Lyon I University, Lyon, France
- CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, Equipe Biostatistique-Santé, Villeurbanne, France
- Cytogenetics and Reproductive Biology Department, Farhat Hached University Teaching Hospital, Sousse, Tunisia
| | - Nicolas Chatron
- Department of Medical Genetics, Lyon University Hospital, Lyon, France
| | - Audrey Putoux
- Department of Medical Genetics, Lyon University Hospital, Lyon, France
- CNRL, CNRS UMR 5292, INSERM U1028, Lyon, France
- Claude Bernard Lyon I University, Lyon, France
| | - Julitta de Bellescize
- Common Service Units for Research in Genetics, Faculty of Medicine of Sousse, University of Sousse, Sousse, Tunisia
| | - Dorothée Ville
- Department of Neuropediatrics, Reference Center for Tuberous Sclerosis and Rare Epileptic Syndromes, Lyon University Hospital, Lyon, France
| | - Laurent Schaeffer
- Claude Bernard Lyon I University, Lyon, France
- Department of Cell Biotechnology, Lyon, France
- Ecole Normale Supérieure de Lyon, Lyon, France
| | - Pascal Roy
- Claude Bernard Lyon I University, Lyon, France
- Service de Biostatistique, Hospices Civils de Lyon, Lyon, France
- CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, Equipe Biostatistique-Santé, Villeurbanne, France
| | - Soumaya Mougou-Zerelli
- Cytogenetics and Reproductive Biology Department, Farhat Hached University Teaching Hospital, Sousse, Tunisia
- Common Service Units for Research in Genetics, Faculty of Medicine of Sousse, University of Sousse, Sousse, Tunisia
| | - Ali Saad
- Cytogenetics and Reproductive Biology Department, Farhat Hached University Teaching Hospital, Sousse, Tunisia
- Common Service Units for Research in Genetics, Faculty of Medicine of Sousse, University of Sousse, Sousse, Tunisia
| | - Alain Calender
- Department of Medical Genetics, Lyon University Hospital, Lyon, France
- Claude Bernard Lyon I University, Lyon, France
| | - Damien Sanlaville
- Department of Medical Genetics, Lyon University Hospital, Lyon, France
- CNRL, CNRS UMR 5292, INSERM U1028, Lyon, France
- Claude Bernard Lyon I University, Lyon, France
- Corresponding author at: Service de Génétique, Groupement Hospitalier Est, 59 Boulevard Pinel, 69677 Bron, France.Service de GénétiqueGroupement Hospitalier Est59 Boulevard PinelBron69677France
| | - Gaetan Lesca
- Department of Medical Genetics, Lyon University Hospital, Lyon, France
- CNRL, CNRS UMR 5292, INSERM U1028, Lyon, France
- Claude Bernard Lyon I University, Lyon, France
- Corresponding author at: Service de Génétique, Groupement Hospitalier Est, 59 Boulevard Pinel, 69677 Bron, France.Service de GénétiqueGroupement Hospitalier Est59 Boulevard PinelBron69677France
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Manié E, Popova T, Battistella A, Tarabeux J, Caux-Moncoutier V, Golmard L, Smith NK, Mueller CR, Mariani O, Sigal-Zafrani B, Dubois T, Vincent-Salomon A, Houdayer C, Stoppa-Lyonnet D, Stern MH. Genomic hallmarks of homologous recombination deficiency in invasive breast carcinomas. Int J Cancer 2015; 138:891-900. [DOI: 10.1002/ijc.29829] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Revised: 06/25/2015] [Accepted: 07/30/2015] [Indexed: 01/09/2023]
Affiliation(s)
- Elodie Manié
- Centre De Recherche; Institut Curie; Paris F-75248 France
- INSERM U830; Paris F-75248 France
| | - Tatiana Popova
- Centre De Recherche; Institut Curie; Paris F-75248 France
- INSERM U830; Paris F-75248 France
| | - Aude Battistella
- Centre De Recherche; Institut Curie; Paris F-75248 France
- INSERM U830; Paris F-75248 France
| | - Julien Tarabeux
- Centre De Recherche; Institut Curie; Paris F-75248 France
- INSERM U830; Paris F-75248 France
| | | | - Lisa Golmard
- Centre De Recherche; Institut Curie; Paris F-75248 France
- INSERM U830; Paris F-75248 France
- Département De Biologie Des Tumeurs; Institut Curie; Paris F-75248 France
| | - Nicholas K. Smith
- Centre De Recherche; Institut Curie; Paris F-75248 France
- INSERM U830; Paris F-75248 France
| | - Christopher R. Mueller
- Centre De Recherche; Institut Curie; Paris F-75248 France
- INSERM U830; Paris F-75248 France
- Queen's Cancer Research Institute, Queen's University, Kingston; Ontario K7L 3N6 Canada
| | - Odette Mariani
- Département De Biologie Des Tumeurs; Institut Curie; Paris F-75248 France
- Centre De Ressources Biologiques; Institut Curie; Paris F-75248 France
| | | | - Thierry Dubois
- Centre De Recherche; Institut Curie; Paris F-75248 France
- Département De Recherche Translationnelle; Institut Curie; Paris F-75248 France
| | | | - Claude Houdayer
- Centre De Recherche; Institut Curie; Paris F-75248 France
- INSERM U830; Paris F-75248 France
- Département De Biologie Des Tumeurs; Institut Curie; Paris F-75248 France
| | - Dominique Stoppa-Lyonnet
- Centre De Recherche; Institut Curie; Paris F-75248 France
- INSERM U830; Paris F-75248 France
- Département De Biologie Des Tumeurs; Institut Curie; Paris F-75248 France
- Sorbonne Paris Cité; University Paris-Descartes; Paris F-75270 France
| | - Marc-Henri Stern
- Centre De Recherche; Institut Curie; Paris F-75248 France
- INSERM U830; Paris F-75248 France
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Butler KS, Young MYL, Li Z, Elespuru RK, Wood SC. Performance characteristics of the AmpliSeq Cancer Hotspot panel v2 in combination with the Ion Torrent Next Generation Sequencing Personal Genome Machine. Regul Toxicol Pharmacol 2015; 74:178-86. [PMID: 26387931 DOI: 10.1016/j.yrtph.2015.09.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 09/07/2015] [Indexed: 12/20/2022]
Abstract
Next-Generation Sequencing is a rapidly advancing technology that has research and clinical applications. For many cancers, it is important to know the precise mutation(s) present, as specific mutations could indicate or contra-indicate certain treatments as well as be indicative of prognosis. Using the Ion Torrent Personal Genome Machine and the AmpliSeq Cancer Hotspot panel v2, we sequenced two pancreatic cancer cell lines, BxPC-3 and HPAF-II, alone or in mixtures, to determine the error rate, sensitivity, and reproducibility of this system. The system resulted in coverage averaging 2000× across the various amplicons and was able to reliably and reproducibly identify mutations present at a rate of 5%. Identification of mutations present at a lower rate was possible by altering the parameters by which calls were made, but with an increase in erroneous, low-level calls. The panel was able to identify known mutations in these cell lines that are present in the COSMIC database. In addition, other, novel mutations were also identified that may prove clinically useful. The system was assessed for systematic errors such as homopolymer effects, end of amplicon effects and patterns in NO CALL sequence. Overall, the system is adequate at identifying the known, targeted mutations in the panel.
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Affiliation(s)
- Kimberly S Butler
- U.S. Food and Drug Administration, Office of Medical Products and Tobacco, Center for Devices and Radiological Health, Office of Science and Engineering Laboratories, Division of Biology, Chemistry and Materials Science, 10903 New Hampshire Ave, Silver Spring, MD 20993, United States
| | - Megan Y L Young
- U.S. Food and Drug Administration, Office of Medical Products and Tobacco, Center for Devices and Radiological Health, Office of Science and Engineering Laboratories, Division of Biology, Chemistry and Materials Science, 10903 New Hampshire Ave, Silver Spring, MD 20993, United States
| | - Zhihua Li
- U.S. Food and Drug Administration, Office of Medical Products and Tobacco, Center for Drug Evaluation and Research, Office of Translational Sciences, Office of Clinical Pharmacology, Division of Applied Regulatory Science, 10903 New Hampshire Ave, Silver Spring, MD 20993, United States
| | - Rosalie K Elespuru
- U.S. Food and Drug Administration, Office of Medical Products and Tobacco, Center for Devices and Radiological Health, Office of Science and Engineering Laboratories, Division of Biology, Chemistry and Materials Science, 10903 New Hampshire Ave, Silver Spring, MD 20993, United States
| | - Steven C Wood
- U.S. Food and Drug Administration, Office of Medical Products and Tobacco, Center for Devices and Radiological Health, Office of Science and Engineering Laboratories, Division of Biology, Chemistry and Materials Science, 10903 New Hampshire Ave, Silver Spring, MD 20993, United States.
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Rusmini M, Federici S, Caroli F, Grossi A, Baldi M, Obici L, Insalaco A, Tommasini A, Caorsi R, Gallo E, Olivieri AN, Marzano A, Coviello D, Ravazzolo R, Martini A, Gattorno M, Ceccherini I. Next-generation sequencing and its initial applications for molecular diagnosis of systemic auto-inflammatory diseases. Ann Rheum Dis 2015; 75:1550-7. [PMID: 26386126 DOI: 10.1136/annrheumdis-2015-207701] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 08/28/2015] [Indexed: 01/05/2023]
Abstract
OBJECTIVES Systemic auto-inflammatory disorders (SAIDs) are a heterogeneous group of monogenic diseases sharing a primary dysfunction of the innate immune system. More than 50% of patients with SAID does not show any mutation at gene(s) tested because of lack of precise clinical classification criteria and/or incomplete gene screening. To improve the molecular diagnosis and genotype interpretation of SAIDs, we undertook the development of a next-generation sequencing (NGS)-based protocol designed to simultaneous screening of 10 genes. METHODS Fifty patients with SAID, already genotyped for the respective causative gene(s), were massively sequenced for the coding portions of MEFV, MVK, TNFRSF1A, NLRP3, NLRP12, NOD2, PSTPIP1, IL1RN, LPIN2 and PSMB8. Three different bioinformatic pipelines (Ion Reporter, CLC Bio Genomics Workbench, GATK-based in-house workflow) were compared. RESULTS Once resulting variants were compared with the expected mutation list, no workflow turned out to be able to detect all the 79 variants known in the 50 DNAs. Additional variants were also detected, validated by Sanger sequencing and compared to assess true and false positive detection rates of the three workflows. Finally, the overall clinical picture of 34 patients was re-evaluated in the light of the new mutations found. CONCLUSIONS The present gene panel has resulted suitable for molecular diagnosis of SAIDs. Moreover, genotype-phenotype correlation has confirmed that the interpretation of NGS data in patients with an undefined inflammatory phenotype is remarkably difficult, thus supporting the need of evidence-based and validated clinical criteria to be used concurrently with the genetic analysis for the final diagnosis and classification of patients with SAIDs.
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Affiliation(s)
- Marta Rusmini
- UOC Medical Genetics, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Silvia Federici
- UOC Pediatric Rheumatology, Lab Immunology Rheumatic Diseases, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Francesco Caroli
- UOC Medical Genetics, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Alice Grossi
- UOC Medical Genetics, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Maurizia Baldi
- Laboratory of Human Genetics, Ospedali Galliera, Genoa, Italy
| | - Laura Obici
- Amyloidosis Research and Treatment Centre, Biotechnology Research Laboratories, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Antonella Insalaco
- Division of Rheumatology, Department of Pediatric Medicine, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Alberto Tommasini
- Department of Pediatrics, Institute for Maternal and Child Health, IRCCS Burlo Garofolo, Trieste, Italy
| | - Roberta Caorsi
- UOC Pediatric Rheumatology, Lab Immunology Rheumatic Diseases, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Eleonora Gallo
- Dipartimento di Salute Pubblica e Pediatria, Universita' di Torino, Torino, Italy
| | - Alma Nunzia Olivieri
- Dipartimento della Donna, del Bambino e di Chirurgia Generale e Specialistica, Seconda Universita' degli Studi di Napoli, Napoli, Italia
| | - AngeloValerio Marzano
- UO Dermatologia, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico-Dipartimento di Fisiopatologia Medico-Chirurgica e dei Trapianti, Università degli Studi di Milano, Milan, Italy
| | | | - Roberto Ravazzolo
- UOC Medical Genetics, IRCCS Istituto Giannina Gaslini, Genoa, Italy Dipartimento Neuroscienze, Riabilitazione, Oftalmologia, Genetica e Scienze Materno-Infantili (DiNOGMI), Università degli Studi di Genova, Genova, Italy
| | - Alberto Martini
- UOC Pediatric Rheumatology, Lab Immunology Rheumatic Diseases, IRCCS Istituto Giannina Gaslini, Genoa, Italy Dipartimento Neuroscienze, Riabilitazione, Oftalmologia, Genetica e Scienze Materno-Infantili (DiNOGMI), Università degli Studi di Genova, Genova, Italy
| | - Marco Gattorno
- UOC Pediatric Rheumatology, Lab Immunology Rheumatic Diseases, IRCCS Istituto Giannina Gaslini, Genoa, Italy
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Børsting C, Morling N. Next generation sequencing and its applications in forensic genetics. Forensic Sci Int Genet 2015; 18:78-89. [DOI: 10.1016/j.fsigen.2015.02.002] [Citation(s) in RCA: 268] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Revised: 01/12/2015] [Accepted: 02/11/2015] [Indexed: 12/13/2022]
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Hasheminasab SM, Tzvetkov MV, Schumann C, Rüdiger S, Boeck S, Heinemann V, Kächele V, Steffens M, Scholl C, Hichert V, Seufferlein T, Brockmöller J, Stingl JC. High-throughput screening identified inherited genetic variations in the EGFR pathway contributing to skin toxicity of EGFR inhibitors. Pharmacogenomics 2015; 16:1605-19. [DOI: 10.2217/pgs.15.97] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Aim: To identify genomic variants in the EGFR pathway and in cytokines predisposing to skin toxicity from EGFR inhibitors. Patients & methods: In 126 patients with cancer and EGFR inhibitor therapy skin toxicity was quantified and EGFR and inflammatory pathway genes were analyzed by deep sequencing. Results: We found 1437 SNPs in the 382-kb target region. Three SNPs in EGFR intron 1 were found exclusively in patients without skin rash. Another EGFR intron 23 SNP was associated with skin rash, overall survival and IL8 plasma concentrations. Moreover, carriers of the PIK3R1 326I variant were predisposed to skin rash and better survival. Conclusion: Comprehensive pathway-based resequencing revealed some new but only moderately strong genomic predictors of skin toxicity.
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Affiliation(s)
- Sayed-Mohammad Hasheminasab
- Institute for Clinical Pharmacology, University Medical Center Göttingen, Georg-August University, Robert-Koch-Str. 40, 37075, Göttingen, Germany
| | - Mladen V Tzvetkov
- Institute for Clinical Pharmacology, University Medical Center Göttingen, Georg-August University, Robert-Koch-Str. 40, 37075, Göttingen, Germany
| | | | - Stefan Rüdiger
- Department of Internal Medicine II, University of Ulm, Ulm, Germany
| | - Stefan Boeck
- Department of Internal Medicine III & Comprehensive Cancer Center, Ludwig-Maximilian's University of Munich, Munich, Germany
| | - Volker Heinemann
- Department of Internal Medicine III & Comprehensive Cancer Center, Ludwig-Maximilian's University of Munich, Munich, Germany
| | - Volker Kächele
- Private Practice for Hematology & Oncology, Ulm, Germany
| | - Michael Steffens
- Research Division, Federal Institute of Drugs & Medical Devices (BfArM), Bonn, Germany
| | - Catharina Scholl
- Research Division, Federal Institute of Drugs & Medical Devices (BfArM), Bonn, Germany
| | - Vivien Hichert
- Research Division, Federal Institute of Drugs & Medical Devices (BfArM), Bonn, Germany
| | | | - Jürgen Brockmöller
- Institute for Clinical Pharmacology, University Medical Center Göttingen, Georg-August University, Robert-Koch-Str. 40, 37075, Göttingen, Germany
| | - Julia C Stingl
- Research Division, Federal Institute of Drugs & Medical Devices (BfArM), Bonn, Germany
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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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Millat G, Chanavat V, Rousson R. Evaluation of a new high-throughput next-generation sequencing method based on a custom AmpliSeq™ library and ion torrent PGM™ sequencing for the rapid detection of genetic variations in long QT syndrome. Mol Diagn Ther 2015; 18:533-9. [PMID: 24687331 DOI: 10.1007/s40291-014-0099-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
BACKGROUND AND OBJECTIVE Inherited long QT syndrome (LQTS) is a cardiac channelopathy associated with a high risk of sudden death. The prevalence has been estimated at close to 1:2,000. Due to large cohorts to investigate and high rate of private mutations, mutational screening must be performed using an extremely sensitive and specific detection method. Mutational screening is crucial as this may have implications for therapy and management of LQTS patients. METHODS Next-generation sequencing (NGS) workflow based on a custom AmpliSeq™ panel was designed for sequencing the five most prevalent cardiomyopathy-causing genes (KCNQ1, KCNH2, SCN5A, KCNE1, KCNE2) on Ion PGM™ Sequencer. A cohort of 30 previously studied patients was screened to evaluate this strategy in terms of sensitivity, specificity, practicability, and cost. In silico analysis was performed using NextGENe(®) software. RESULTS Our AmpliSeq™ custom panel allowed us to explore 86 % of targeted sequences efficiently. Using adjusted alignment settings, all genetic variants (40 substitutions, 17 indels) present in covered regions and previously detected by high-resolution melt (HRM)/sequencing were readily identified. Uncovered targeted regions, which were mainly located in KCNH2, were further analyzed by HRM/sequencing strategy. Complete molecular investigation was performed faster and cheaper than with previously used mutation detection methods. CONCLUSION Finally, these results suggested that our new NGS approach based on AmpliSeq™ libraries and Ion PGM™ sequencing is a highly efficient, fast, and cheap high-throughput mutation detection method that is ready to be deployed in clinical laboratories. This method will allow fast identification of LQTS mutations that will have further implications for therapeutics.
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Affiliation(s)
- Gilles Millat
- Laboratoire de Cardiogénétique Moléculaire, Centre de Biologie et Pathologie Est, Hospices Civils de Lyon, Lyon, 69677, Bron Cedex, France,
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Breast and ovarian cancer predisposition due to de novo BRCA1 and BRCA2 mutations. Oncogene 2015; 35:1324-7. [PMID: 26028024 DOI: 10.1038/onc.2015.181] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Revised: 04/02/2015] [Accepted: 04/07/2015] [Indexed: 02/02/2023]
Abstract
BRCA1 and BRCA2 are the two major genes predisposing to breast and ovarian cancer. Whereas high de novo mutation rates have been demonstrated for several genes, only 11 cases of de novo BRCA1/2 mutations have been reported to date and the BRCA1/2 de novo mutation rate remains unknown. The present study was designed to fill this gap based on a series of 12 805 consecutive unrelated patients diagnosed with breast and/or ovarian cancer who met the inclusion criteria for BRCA1/2 gene analysis according to French guidelines. BRCA1/2 mutations were detected in 1527 (12%) patients, and three BRCA1 mutations and one BRCA2 mutation were de novo. The BRCA1/2 de novo mutation rate was estimated to be 0.3% (0.1%; 0.7%). Although rare, it may be useful to take the possibility of de novo BRCA1/2 mutation into account in genetic counseling of relatives and to improve the understanding of complex family histories of breast and ovarian cancers.
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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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Lai S, Brookes C, Prosser DO, Lan CC, Doherty E, Love DR. Diagnostic Screening Workflow for Mutations in the BRCA1 and BRCA2 Genes. Sultan Qaboos Univ Med J 2015; 15:e58-e70. [PMID: 25685387 PMCID: PMC4318608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2014] [Revised: 09/04/2014] [Accepted: 10/02/2014] [Indexed: 06/04/2023] Open
Abstract
OBJECTIVES Screening for mutations in large genes is challenging in a molecular diagnostic environment. Sanger-based DNA sequencing methods are largely used; however, massively parallel sequencing (MPS) can accommodate increasing test demands and financial constraints. This study aimed to establish a simple workflow to amplify and screen all coding regions of the BRCA1 and BRCA2 (BRCA1/2) genes by Sanger-based sequencing as well as to assess a MPS approach encompassing multiplex polymerase chain reaction (PCR) and pyrosequencing. METHODS This study was conducted between July 2011 and April 2013. A total of 20 patients were included in the study who had been referred to Genetic Health Services New Zealand (Northern Hub) for BRCA1/2 mutation screening. Patients were randomly divided into a MPS evaluation and validation cohort (n = 10 patients each). Primers were designed to amplify all coding exons of BRCA1/2 (28 and 42 primer pairs, respectively). Primers overlying known variants were avoided to circumvent allelic drop-out. The MPS approach necessitated utilisation of a complementary fragment analysis assay to eliminate apparent false-positives at homopolymeric regions. Variants were filtered on the basis of their frequency and sequence depth. RESULTS Sanger-based sequencing of PCR-amplified coding regions was successfully achieved. Sensitivity and specificity of the combined MPS/homopolymer protocol was determined to be 100% and 99.5%, respectively. CONCLUSION In comparison to traditional Sanger-based sequencing, the MPS workflow led to a reduction in both cost and analysis time for BRCA1/2 screening. MPS analysis achieved high analytical sensitivity and specificity, but required complementary fragment analysis combined with Sanger-based sequencing confirmation in some instances.
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Lebofsky R, Decraene C, Bernard V, Kamal M, Blin A, Leroy Q, Rio Frio T, Pierron G, Callens C, Bieche I, Saliou A, Madic J, Rouleau E, Bidard FC, Lantz O, Stern MH, Le Tourneau C, Pierga JY. Circulating tumor DNA as a non-invasive substitute to metastasis biopsy for tumor genotyping and personalized medicine in a prospective trial across all tumor types. Mol Oncol 2015. [PMID: 25579085 DOI: 10.1016/j.molonc.2014.12.003] [] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Cell-free tumor DNA (ctDNA) has the potential to enable non-invasive diagnostic tests for personalized medicine in providing similar molecular information as that derived from invasive tumor biopsies. The histology-independent phase II SHIVA trial matches patients with targeted therapeutics based on previous screening of multiple somatic mutations using metastatic biopsies. To evaluate the utility of ctDNA in this trial, as an ancillary study we performed de novo detection of somatic mutations using plasma DNA compared to metastasis biopsies in 34 patients covering 18 different tumor types, scanning 46 genes and more than 6800 COSMIC mutations with a multiplexed next-generation sequencing panel. In 27 patients, 28 of 29 mutations identified in metastasis biopsies (97%) were detected in matched ctDNA. Among these 27 patients, one additional mutation was found in ctDNA only. In the seven other patients, mutation detection from metastasis biopsy failed due to inadequate biopsy material, but was successful in all plasma DNA samples providing three more potential actionable mutations. These results suggest that ctDNA analysis is a potential alternative and/or replacement to analyses using costly, harmful and lengthy tissue biopsies of metastasis, irrespective of cancer type and metastatic site, for multiplexed mutation detection in selecting personalized therapies based on the patient's tumor genetic content.
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Affiliation(s)
- Ronald Lebofsky
- Circulating Cancer Biomarkers Lab, SiRIC, Translational Research Department, Institut Curie, Paris, France
| | - Charles Decraene
- Circulating Cancer Biomarkers Lab, SiRIC, Translational Research Department, Institut Curie, Paris, France; CNRS UMR144, Institut Curie, Paris, France
| | | | - Maud Kamal
- Department of Medical Oncology, Institut Curie, Paris and Saint-Cloud, France
| | - Anthony Blin
- ICGex NGS Platform, Institut Curie, Paris, France
| | | | | | | | | | - Ivan Bieche
- Oncogenetic Laboratory, Institut Curie, Paris, France
| | - Adrien Saliou
- Circulating Cancer Biomarkers Lab, SiRIC, Translational Research Department, Institut Curie, Paris, France
| | - Jordan Madic
- Circulating Cancer Biomarkers Lab, SiRIC, Translational Research Department, Institut Curie, Paris, France
| | | | - François-Clément Bidard
- Circulating Cancer Biomarkers Lab, SiRIC, Translational Research Department, Institut Curie, Paris, France; Department of Medical Oncology, Institut Curie, Paris and Saint-Cloud, France
| | - Olivier Lantz
- INSERM U932, Institut Curie, Paris, France; CIC-BT-507, Institut Curie, Paris, France
| | | | - Christophe Le Tourneau
- Department of Medical Oncology, Institut Curie, Paris and Saint-Cloud, France; INSERM U900, Institut Curie, Paris, France
| | - Jean-Yves Pierga
- Circulating Cancer Biomarkers Lab, SiRIC, Translational Research Department, Institut Curie, Paris, France; Department of Medical Oncology, Institut Curie, Paris and Saint-Cloud, France; University Paris Descartes, Paris, France.
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43
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Lebofsky R, Decraene C, Bernard V, Kamal M, Blin A, Leroy Q, Rio Frio T, Pierron G, Callens C, Bieche I, Saliou A, Madic J, Rouleau E, Bidard FC, Lantz O, Stern MH, Le Tourneau C, Pierga JY. Circulating tumor DNA as a non-invasive substitute to metastasis biopsy for tumor genotyping and personalized medicine in a prospective trial across all tumor types. Mol Oncol 2014; 9:783-90. [PMID: 25579085 DOI: 10.1016/j.molonc.2014.12.003] [Citation(s) in RCA: 209] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Revised: 11/26/2014] [Accepted: 12/10/2014] [Indexed: 12/18/2022] Open
Abstract
Cell-free tumor DNA (ctDNA) has the potential to enable non-invasive diagnostic tests for personalized medicine in providing similar molecular information as that derived from invasive tumor biopsies. The histology-independent phase II SHIVA trial matches patients with targeted therapeutics based on previous screening of multiple somatic mutations using metastatic biopsies. To evaluate the utility of ctDNA in this trial, as an ancillary study we performed de novo detection of somatic mutations using plasma DNA compared to metastasis biopsies in 34 patients covering 18 different tumor types, scanning 46 genes and more than 6800 COSMIC mutations with a multiplexed next-generation sequencing panel. In 27 patients, 28 of 29 mutations identified in metastasis biopsies (97%) were detected in matched ctDNA. Among these 27 patients, one additional mutation was found in ctDNA only. In the seven other patients, mutation detection from metastasis biopsy failed due to inadequate biopsy material, but was successful in all plasma DNA samples providing three more potential actionable mutations. These results suggest that ctDNA analysis is a potential alternative and/or replacement to analyses using costly, harmful and lengthy tissue biopsies of metastasis, irrespective of cancer type and metastatic site, for multiplexed mutation detection in selecting personalized therapies based on the patient's tumor genetic content.
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Affiliation(s)
- Ronald Lebofsky
- Circulating Cancer Biomarkers Lab, SiRIC, Translational Research Department, Institut Curie, Paris, France
| | - Charles Decraene
- Circulating Cancer Biomarkers Lab, SiRIC, Translational Research Department, Institut Curie, Paris, France; CNRS UMR144, Institut Curie, Paris, France
| | | | - Maud Kamal
- Department of Medical Oncology, Institut Curie, Paris and Saint-Cloud, France
| | - Anthony Blin
- ICGex NGS Platform, Institut Curie, Paris, France
| | | | | | | | | | - Ivan Bieche
- Oncogenetic Laboratory, Institut Curie, Paris, France
| | - Adrien Saliou
- Circulating Cancer Biomarkers Lab, SiRIC, Translational Research Department, Institut Curie, Paris, France
| | - Jordan Madic
- Circulating Cancer Biomarkers Lab, SiRIC, Translational Research Department, Institut Curie, Paris, France
| | | | - François-Clément Bidard
- Circulating Cancer Biomarkers Lab, SiRIC, Translational Research Department, Institut Curie, Paris, France; Department of Medical Oncology, Institut Curie, Paris and Saint-Cloud, France
| | - Olivier Lantz
- INSERM U932, Institut Curie, Paris, France; CIC-BT-507, Institut Curie, Paris, France
| | | | - Christophe Le Tourneau
- Department of Medical Oncology, Institut Curie, Paris and Saint-Cloud, France; INSERM U900, Institut Curie, Paris, France
| | - Jean-Yves Pierga
- Circulating Cancer Biomarkers Lab, SiRIC, Translational Research Department, Institut Curie, Paris, France; Department of Medical Oncology, Institut Curie, Paris and Saint-Cloud, France; University Paris Descartes, Paris, France.
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Bennett NC, Farah CS. Next-generation sequencing in clinical oncology: next steps towards clinical validation. Cancers (Basel) 2014; 6:2296-312. [PMID: 25412366 PMCID: PMC4276967 DOI: 10.3390/cancers6042296] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2014] [Revised: 11/07/2014] [Accepted: 11/10/2014] [Indexed: 02/05/2023] Open
Abstract
Compelling evidence supports the transition of next generation sequencing (NGS) technology from a research environment into clinical practice. Before NGS technologies are fully adopted in the clinic, they should be thoroughly scrutinised for their potential as powerful diagnostic and prognostic tools. The importance placed on generating accurate NGS data, and consequently appropriate clinical interpretation, has stimulated much international discussion regarding the creation and implementation of strict guidelines and regulations for NGS clinical use. In the context of clinical oncology, NGS technologies are currently transitioning from a clinical research background into a setting where they will contribute significantly to individual patient cancer management. This paper explores the steps that have been taken, and those still required, for the transition of NGS into the clinical area, with particular emphasis placed on validation in the setting of clinical oncology.
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Affiliation(s)
- Nigel C Bennett
- The University of Queensland, UQ Centre for Clinical Research, Herston Qld 4029, Australia.
| | - Camile S Farah
- The University of Queensland, UQ Centre for Clinical Research, Herston Qld 4029, Australia.
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45
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Sapari NS, Elahi E, Wu M, Loh M, Ng HK, Han X, Yap HL, Klemm TP, Pang B, Benoukraf T, Teo YY, Iacopetta B, Lee SC, Soong R. Feasibility of low-throughput next generation sequencing for germline DNA screening. Clin Chem 2014; 60:1549-57. [PMID: 25338684 DOI: 10.1373/clinchem.2014.227728] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND Next generation sequencing (NGS) promises many benefits for clinical diagnostics. However, current barriers to its adoption include suboptimal amenability for low clinical throughputs and uncertainty over data accuracy and analytical procedures. We assessed the feasibility and performance of low-throughput NGS for detecting germline mutations for Lynch syndrome (LS). METHODS Sequencing depth, time, and cost of 6 formats on the MiSeq and Personal Genome Machine platforms at 1-12 samples/run were calculated. Analytical performance was assessed from 3 runs of 3 DNA samples annotated for 7500 nucleotides by BeadChip arrays. The clinical performance of low-throughput NGS and 9 analytical processes were assessed through blinded analysis of DNA samples from 12 LS cases confirmed by Sanger sequencing, and 3 control cases. RESULTS The feasibility analysis revealed different formats were optimal at different throughputs. Detection was reproducible for 2619/2635 (99.39%) replicate variants, and sensitivity and specificity to array annotation were 99.42% and 99.99% respectively. Eleven of 16 inconsistently detected variants could be specifically identified by having allele frequencies ≤ 0.15, strand biases >-35, or genotype quality scores ≤ 80. Positive selection for variants in the Human Genome Mutation Database (colorectal cancer, nonpolyposis) and variants with ≤ 5% frequency in the Asian population gave the best clinical performance (92% sensitivity, 67% specificity). CONCLUSIONS Low-throughput NGS can be a cost-efficient and reliable approach for screening germline variants; however, its clinical utility is subject to the quality of annotation of clinically relevant variants.
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Affiliation(s)
- Nur Sabrina Sapari
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Eiram Elahi
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Mengchu Wu
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Marie Loh
- Department of Epidemiology and Biostatistics, Imperial College London, London, United Kingdom
| | - Hong Kiat Ng
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Xiao Han
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Hui Ling Yap
- Department of Haematology Oncology, National University Cancer Institute, National University Health System, Singapore
| | | | - Brendan Pang
- Department of Pathology, National University Health System, Singapore
| | - Touati Benoukraf
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Yik Ying Teo
- School of Public Health, National University Health System, Singapore
| | - Barry Iacopetta
- School of Surgery, The University of Western Australia, Perth, Australia
| | - Soo Chin Lee
- Department of Haematology Oncology, National University Cancer Institute, National University Health System, Singapore
| | - Richie Soong
- Cancer Science Institute of Singapore, National University of Singapore, Singapore; Department of Pathology, National University Health System, Singapore;
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Rauch F, Lalic L, Glorieux FH, Moffatt P, Roughley P. Targeted sequencing of a pediatric metabolic bone gene panel using a desktop semiconductor next-generation sequencer. Calcif Tissue Int 2014; 95:323-31. [PMID: 25086671 DOI: 10.1007/s00223-014-9897-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Accepted: 07/16/2014] [Indexed: 12/17/2022]
Abstract
Metabolic bone disorders in children frequently are heritable, but the expanding number of genes associated with these conditions makes it difficult to perform molecular diagnosis. In the present study, we therefore evaluated a semiconductor (SC)-based sequencing system for this purpose. A total of 65 DNA samples were analyzed comprising 24 samples from patients with 27 known pathogenic mutations, 6 samples from patients with prior negative Sanger sequencing, and 35 consecutive samples from patients with suspected heritable metabolic bone disorders who had not had prior molecular diagnosis. In the samples with known pathogenic mutations, 26 of 27 mutations were identified by SC sequencing. All single nucleotide variants were correctly identified, but a 7-nucleotide duplication in CYP27B1 was not detected. SC sequencing revealed two pathogenic mutations in the six samples where prior Sanger sequencing had failed to identify a mutation. Finally, pathogenic mutations were found in 27 samples of patients with unknown mutation status (15 in COL1A1, 9 in COL1A2, 1 in LEPRE1, 1 in LRP5, 1 in PHEX). Subsequent Sanger sequencing confirmed the mutations in all 27 samples. In conclusion, we found that SC sequencing is suitable for the diagnosis of heritable metabolic bone disorders in children.
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Affiliation(s)
- Frank Rauch
- Shriners Hospital for Children and McGill University, 1529 Cedar Avenue, Montreal, QC, H3G 1A6, Canada,
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Auber B, Heinecke K, Morlot S, Schlegelberger B, Steinemann D. Massive parallele Sequenzierung in der Diagnostik hereditärer BRCA1-/-2-Mutationen. MED GENET-BERLIN 2014. [DOI: 10.1007/s11825-014-0443-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Zusammenfassung
Die massive parallele Sequenzierung (MPS) findet in der molekulargenetischen Diagnostik erblicher Krebserkrankungen zunehmend Einsatz, hier insbesondere bei Verdacht auf erblichen Brust- und Eierstockkrebs. Die potenziellen Vorteile von MPS im Vergleich zu bisher verwendeten (z. B. Sanger-sequenzbasierten) Methoden sind ein höherer Probendurchsatz, kürzere Bearbeitungszeiten und verminderte Kosten. Der Einsatz in der Routinediagnostik wird durch die Verfügbarkeit von zertifizierten Kits für die Probenvorbereitung vereinfacht. Hier wird die Validierung von 2 verschiedenen MPS-Geräten für die BRCA1-/-2-Diagnostik beschrieben. Bei Verwendung der Technik müssen die jeweiligen Vor- und Nachteile der einzelnen Geräte bedacht werden. Die Ergebnisse der MPS-Sequenzierung entsprechen denen, die mit Sanger-Sequenzierung ermittelt wurden.
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Affiliation(s)
- B. Auber
- Aff1 grid.10423.34 0000000095299877 Institut für Zell- und Molekularpathologie Medizinische Hochschule Hannover Hannover Deutschland
| | - K. Heinecke
- Aff1 grid.10423.34 0000000095299877 Institut für Zell- und Molekularpathologie Medizinische Hochschule Hannover Hannover Deutschland
| | - S. Morlot
- Aff1 grid.10423.34 0000000095299877 Institut für Zell- und Molekularpathologie Medizinische Hochschule Hannover Hannover Deutschland
| | - B. Schlegelberger
- Aff1 grid.10423.34 0000000095299877 Institut für Zell- und Molekularpathologie Medizinische Hochschule Hannover Hannover Deutschland
| | - D. Steinemann
- Aff1 grid.10423.34 0000000095299877 Institut für Zell- und Molekularpathologie Medizinische Hochschule Hannover Hannover Deutschland
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Servant N, Roméjon J, Gestraud P, La Rosa P, Lucotte G, Lair S, Bernard V, Zeitouni B, Coffin F, Jules-Clément G, Yvon F, Lermine A, Poullet P, Liva S, Pook S, Popova T, Barette C, Prud'homme F, Dick JG, Kamal M, Le Tourneau C, Barillot E, Hupé P. Bioinformatics for precision medicine in oncology: principles and application to the SHIVA clinical trial. Front Genet 2014; 5:152. [PMID: 24910641 PMCID: PMC4039073 DOI: 10.3389/fgene.2014.00152] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Accepted: 05/08/2014] [Indexed: 11/13/2022] Open
Abstract
Precision medicine (PM) requires the delivery of individually adapted medical care based on the genetic characteristics of each patient and his/her tumor. The last decade witnessed the development of high-throughput technologies such as microarrays and next-generation sequencing which paved the way to PM in the field of oncology. While the cost of these technologies decreases, we are facing an exponential increase in the amount of data produced. Our ability to use this information in daily practice relies strongly on the availability of an efficient bioinformatics system that assists in the translation of knowledge from the bench towards molecular targeting and diagnosis. Clinical trials and routine diagnoses constitute different approaches, both requiring a strong bioinformatics environment capable of (i) warranting the integration and the traceability of data, (ii) ensuring the correct processing and analyses of genomic data, and (iii) applying well-defined and reproducible procedures for workflow management and decision-making. To address the issues, a seamless information system was developed at Institut Curie which facilitates the data integration and tracks in real-time the processing of individual samples. Moreover, computational pipelines were developed to identify reliably genomic alterations and mutations from the molecular profiles of each patient. After a rigorous quality control, a meaningful report is delivered to the clinicians and biologists for the therapeutic decision. The complete bioinformatics environment and the key points of its implementation are presented in the context of the SHIVA clinical trial, a multicentric randomized phase II trial comparing targeted therapy based on tumor molecular profiling versus conventional therapy in patients with refractory cancer. The numerous challenges faced in practice during the setting up and the conduct of this trial are discussed as an illustration of PM application.
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Affiliation(s)
- Nicolas Servant
- Institut Curie, Paris France ; INSERM U900, Paris France ; Mines ParisTech, Fontainebleau France
| | - Julien Roméjon
- Institut Curie, Paris France ; INSERM U900, Paris France ; Mines ParisTech, Fontainebleau France
| | - Pierre Gestraud
- Institut Curie, Paris France ; INSERM U900, Paris France ; Mines ParisTech, Fontainebleau France
| | - Philippe La Rosa
- Institut Curie, Paris France ; INSERM U900, Paris France ; Mines ParisTech, Fontainebleau France
| | - Georges Lucotte
- Institut Curie, Paris France ; INSERM U900, Paris France ; Mines ParisTech, Fontainebleau France
| | - Séverine Lair
- Institut Curie, Paris France ; INSERM U900, Paris France ; Mines ParisTech, Fontainebleau France
| | | | - Bruno Zeitouni
- Institut Curie, Paris France ; INSERM U900, Paris France ; Mines ParisTech, Fontainebleau France
| | - Fanny Coffin
- Institut Curie, Paris France ; INSERM U900, Paris France ; Mines ParisTech, Fontainebleau France
| | - Gérôme Jules-Clément
- Institut Curie, Paris France ; INSERM U900, Paris France ; Mines ParisTech, Fontainebleau France ; INSERM U932, Paris France
| | - Florent Yvon
- Institut Curie, Paris France ; INSERM U900, Paris France ; Mines ParisTech, Fontainebleau France
| | - Alban Lermine
- Institut Curie, Paris France ; INSERM U900, Paris France ; Mines ParisTech, Fontainebleau France
| | - Patrick Poullet
- Institut Curie, Paris France ; INSERM U900, Paris France ; Mines ParisTech, Fontainebleau France
| | - Stéphane Liva
- Institut Curie, Paris France ; INSERM U900, Paris France ; Mines ParisTech, Fontainebleau France
| | - Stuart Pook
- Institut Curie, Paris France ; INSERM U900, Paris France ; Mines ParisTech, Fontainebleau France
| | - Tatiana Popova
- Institut Curie, Paris France ; INSERM U830, Paris France
| | - Camille Barette
- Institut Curie, Paris France ; INSERM U900, Paris France ; Mines ParisTech, Fontainebleau France ; Institut Curie, Informatic Department, Paris France
| | - François Prud'homme
- Institut Curie, Paris France ; INSERM U900, Paris France ; Mines ParisTech, Fontainebleau France ; Institut Curie, Informatic Department, Paris France ; Institut Curie, Sequencing Facility ICGex, Paris France
| | | | - Maud Kamal
- Institut Curie, Translational Research Department, Paris France
| | - Christophe Le Tourneau
- INSERM U900, Paris France ; Mines ParisTech, Fontainebleau France ; Department of Medical Oncology, Institut Curie, Paris France
| | - Emmanuel Barillot
- Institut Curie, Paris France ; INSERM U900, Paris France ; Mines ParisTech, Fontainebleau France
| | - Philippe Hupé
- Institut Curie, Paris France ; INSERM U900, Paris France ; Mines ParisTech, Fontainebleau France ; CNRS UMR144, Paris France
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Millat G, Chanavat V, Rousson R. Evaluation of a new NGS method based on a custom AmpliSeq library and Ion Torrent PGM sequencing for the fast detection of genetic variations in cardiomyopathies. Clin Chim Acta 2014; 433:266-71. [PMID: 24721642 DOI: 10.1016/j.cca.2014.03.032] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2013] [Revised: 03/25/2014] [Accepted: 03/26/2014] [Indexed: 11/28/2022]
Abstract
BACKGROUND Hypertrophic and dilated cardiomyopathies are common genetic cardiac diseases. Due to large cohorts to investigate, large number of causative genes and high rate of private mutations, mutational screening must be performed using an extremely sensitive and specific detection method. METHODS NGS workflow based on a custom AmpliSeq panel was designed for sequencing most prevalent cardiomyopathy-causing genes on the Ion PGM™ Sequencer. A cohort of 75 previously studied patients was screened to evaluate this strategy in terms of sensibility, specificity, practicability and cost. In silico analysis was performed using the NextGENe® software. RESULTS Our AmpliSeq custom panel allowed us to efficiently explore 96% of targeted sequences. Using adjusted alignment settings, all genetic variants (57 substitutions, 34 indels) present in covered regions and previously detected by HRM/sequencing were readily identified except a 73-bp MYBPC3 deletion (analytical sensitivity: 98.9%). Uncovered targeted regions were further analysed by a HRM/sequencing strategy. Complete molecular investigation was performed faster and cheaper than with previously used mutation detection methods. CONCLUSION Finally, these results suggested that our new NGS approach based on Ampliseq libraries and Ion PGM sequencing is a highly efficient, fast and cheap high-throughput mutation detection method that is ready to be deployed in clinical laboratories.
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Affiliation(s)
- Gilles Millat
- Laboratoire de Cardiogénétique Moléculaire, Centre de Biologie et Pathologie Est, Hospices Civils de Lyon, Lyon, France; NGS sequencing platform for molecular diagnosis, Hospices Civils de Lyon, Lyon, France; Université Lyon 1, Lyon, France.
| | - Valérie Chanavat
- Laboratoire de Cardiogénétique Moléculaire, Centre de Biologie et Pathologie Est, Hospices Civils de Lyon, Lyon, France; NGS sequencing platform for molecular diagnosis, Hospices Civils de Lyon, Lyon, France
| | - Robert Rousson
- Laboratoire de Cardiogénétique Moléculaire, Centre de Biologie et Pathologie Est, Hospices Civils de Lyon, Lyon, France; NGS sequencing platform for molecular diagnosis, Hospices Civils de Lyon, Lyon, France; Université Lyon 1, Lyon, France
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Next-generation sequencing for the diagnosis of hereditary breast and ovarian cancer using genomic capture targeting multiple candidate genes. Eur J Hum Genet 2014; 22:1305-13. [PMID: 24549055 DOI: 10.1038/ejhg.2014.16] [Citation(s) in RCA: 184] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Revised: 01/15/2014] [Accepted: 01/16/2014] [Indexed: 02/08/2023] Open
Abstract
To optimize the molecular diagnosis of hereditary breast and ovarian cancer (HBOC), we developed a next-generation sequencing (NGS)-based screening based on the capture of a panel of genes involved, or suspected to be involved in HBOC, on pooling of indexed DNA and on paired-end sequencing in an Illumina GAIIx platform, followed by confirmation by Sanger sequencing or MLPA/QMPSF. The bioinformatic pipeline included CASAVA, NextGENe, CNVseq and Alamut-HT. We validated this procedure by the analysis of 59 patients' DNAs harbouring SNVs, indels or large genomic rearrangements of BRCA1 or BRCA2. We also conducted a blind study in 168 patients comparing NGS versus Sanger sequencing or MLPA analyses of BRCA1 and BRCA2. All mutations detected by conventional procedures were detected by NGS. We then screened, using three different versions of the capture set, a large series of 708 consecutive patients. We detected in these patients 69 germline deleterious alterations within BRCA1 and BRCA2, and 4 TP53 mutations in 468 patients also tested for this gene. We also found 36 variations inducing either a premature codon stop or a splicing defect among other genes: 5/708 in CHEK2, 3/708 in RAD51C, 1/708 in RAD50, 7/708 in PALB2, 3/708 in MRE11A, 5/708 in ATM, 3/708 in NBS1, 1/708 in CDH1, 3/468 in MSH2, 2/468 in PMS2, 1/708 in BARD1, 1/468 in PMS1 and 1/468 in MLH3. These results demonstrate the efficiency of NGS in performing molecular diagnosis of HBOC. Detection of mutations within other genes than BRCA1 and BRCA2 highlights the genetic heterogeneity of HBOC.
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