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Tenorio RB, Camargo CHF, Donis KC, Almeida CCB, Teive HAG. Diagnostic Yield of NGS Tests for Hereditary Ataxia: a Systematic Review. CEREBELLUM (LONDON, ENGLAND) 2024; 23:1552-1565. [PMID: 37950147 DOI: 10.1007/s12311-023-01629-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 10/30/2023] [Indexed: 11/12/2023]
Abstract
Next-generation sequencing (NGS), comprising targeted panels (TP), exome sequencing (ES), and genome sequencing (GS) became robust clinical tools for diagnosing hereditary ataxia (HA). Determining their diagnostic yield (DY) is crucial for optimal clinical decision-making. We conducted a comprehensive systematic literature review on the DY of NGS tests for HA. We searched PubMed and Embase databases for relevant studies between 2016 and 2022 and manually examined reference lists of relevant reviews. Eligible studies described the DY of NGS tests in patients with ataxia as a significant feature. Data from 33 eligible studies showed a median DY of 43% (IQR = 9.5-100%). The median DY for TP and ES was 46% and 41.9%, respectively. Higher DY was associated with specific phenotype selection, such as episodic ataxia at 68.35% and early and late onset of ataxia at 46.4% and 54.4%. Parental consanguinity had a DY of 52.4% (p = 0.009), and the presumed autosomal recessive (AR) inheritance pattern showed 62.5%. There was a difference between the median DY of studies that performed targeted sequencing (tandem repeat expansion, TRE) screening and those that did not (p = 0.047). A weak inverse correlation was found between DY and the extent of previous genetic investigation (rho = - 0.323; p = 0.065). The most common genes were CACNA1A and SACS. DY was higher for presumed AR inheritance pattern, positive family history, and parental consanguinity. ES appears more advantageous due to the inclusion of rare genes that might be excluded in TP.
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Affiliation(s)
- Renata Barreto Tenorio
- Postgraduate Program in Internal Medicine, Internal Medicine Department, Hospital de Clínicas, Federal University of Paraná, Curitiba, Paraná, Brazil.
| | - Carlos Henrique F Camargo
- Postgraduate Program in Internal Medicine, Internal Medicine Department, Hospital de Clínicas, Federal University of Paraná, Curitiba, Paraná, Brazil
- Movement Disorders Sector, Neurology Service, Internal Medicine Department, Hospital de Clínicas, Federal University of Paraná, Curitiba, Paraná, Brazil
| | - Karina Carvalho Donis
- Medical Genetics Service, Federal University of Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | | | - Hélio A G Teive
- Postgraduate Program in Internal Medicine, Internal Medicine Department, Hospital de Clínicas, Federal University of Paraná, Curitiba, Paraná, Brazil
- Movement Disorders Sector, Neurology Service, Internal Medicine Department, Hospital de Clínicas, Federal University of Paraná, Curitiba, Paraná, Brazil
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2
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van Dijk MJ, van Oirschot BA, Harrison AN, Recktenwald SM, Qiao M, Stommen A, Cloos AS, Vanderroost J, Terrasi R, Dey K, Bos J, Rab MAE, Bogdanova A, Minetti G, Muccioli GG, Tyteca D, Egée S, Kaestner L, Molday RS, van Beers EJ, van Wijk R. A novel missense variant in ATP11C is associated with reduced red blood cell phosphatidylserine flippase activity and mild hereditary hemolytic anemia. Am J Hematol 2023; 98:1877-1887. [PMID: 37671681 DOI: 10.1002/ajh.27088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 08/20/2023] [Accepted: 08/23/2023] [Indexed: 09/07/2023]
Abstract
Adenosine Triphosphatase (ATPase) Phospholipid Transporting 11C gene (ATP11C) encodes the major phosphatidylserine (PS) flippase in human red blood cells (RBCs). Flippases actively transport phospholipids (e.g., PS) from the outer to the inner leaflet to establish and maintain phospholipid asymmetry of the lipid bilayer of cell membranes. This asymmetry is crucial for survival since externalized PS triggers phagocytosis by splenic macrophages. Here we report on pathophysiological consequences of decreased flippase activity, prompted by a patient with hemolytic anemia and hemizygosity for a novel c.2365C > T p.(Leu789Phe) missense variant in ATP11C. ATP11C protein expression was strongly reduced by 58% in patient-derived RBC ghosts. Furthermore, functional characterization showed only 26% PS flippase activity. These results were confirmed by recombinant mutant ATP11C protein expression in HEK293T cells, which was decreased to 27% compared to wild type, whereas PS-stimulated ATPase activity was decreased by 57%. Patient RBCs showed a mild increase in PS surface exposure when compared to control RBCs, which further increased in the most dense RBCs after RBC storage stress. The increase in PS was not due to higher global membrane content of PS or other phospholipids. In contrast, membrane lipid lateral distribution showed increased abundance of cholesterol-enriched domains in RBC low curvature areas. Finally, more dense RBCs and subtle changes in RBC morphology under flow hint toward alterations in flow behavior of ATP11C-deficient RBCs. Altogether, ATP11C deficiency is the likely cause of hemolytic anemia in our patient, thereby underlining the physiological role and relevance of this flippase in human RBCs.
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Affiliation(s)
- Myrthe J van Dijk
- Central Diagnostic Laboratory-Research, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- Center for Benign Hematology, Thrombosis and Hemostasis-Van Creveldkliniek, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Brigitte A van Oirschot
- Central Diagnostic Laboratory-Research, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Alexander N Harrison
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, Canada
| | | | - Min Qiao
- Department of Experimental Physics, Saarland University, Saarbrücken, Germany
- Theoretical Medicine and Biosciences, Saarland University, Homburg, Germany
| | - Amaury Stommen
- CELL Unit and PICT Platform, de Duve Institute, UCLouvain, Brussels, Belgium
| | - Anne-Sophie Cloos
- CELL Unit and PICT Platform, de Duve Institute, UCLouvain, Brussels, Belgium
| | | | - Romano Terrasi
- Bioanalysis and Pharmacology of Bioactive Lipids Research Group, Louvain Drug Research Institute, UCLouvain, Brussels, Belgium
| | - Kuntal Dey
- Red Blood Cell Group, Institute of Veterinary Physiology, University of Zurich, Zurich, Switzerland
| | - Jennifer Bos
- Central Diagnostic Laboratory-Research, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Minke A E Rab
- Central Diagnostic Laboratory-Research, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- Department of Hematology, Erasmus Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Anna Bogdanova
- Red Blood Cell Group, Institute of Veterinary Physiology, University of Zurich, Zurich, Switzerland
| | - Giampaolo Minetti
- Department of Biology and Biotechnology "L. Spallanzani", Laboratories of Biochemistry, University of Pavia, Pavia, Italy
| | - Giulio G Muccioli
- Bioanalysis and Pharmacology of Bioactive Lipids Research Group, Louvain Drug Research Institute, UCLouvain, Brussels, Belgium
| | - Donatienne Tyteca
- CELL Unit and PICT Platform, de Duve Institute, UCLouvain, Brussels, Belgium
| | - Stéphane Egée
- UMR 8227 CNRS-Sorbonne Université, Station Biologique de Roscoff, Roscoff, France
| | - Lars Kaestner
- Department of Experimental Physics, Saarland University, Saarbrücken, Germany
- Theoretical Medicine and Biosciences, Saarland University, Homburg, Germany
| | - Robert S Molday
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, Canada
| | - Eduard J van Beers
- Center for Benign Hematology, Thrombosis and Hemostasis-Van Creveldkliniek, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Richard van Wijk
- Central Diagnostic Laboratory-Research, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
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Steinmetz EL, Noh S, Klöppel C, Fuhr MF, Bach N, Raffael ME, Hildebrandt K, Wittling F, Jann D, Walldorf U. Generation of Mutants from the 57B Region of Drosophila melanogaster. Genes (Basel) 2023; 14:2047. [PMID: 38002990 PMCID: PMC10671637 DOI: 10.3390/genes14112047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 11/01/2023] [Accepted: 11/03/2023] [Indexed: 11/26/2023] Open
Abstract
The 57B region of Drosophila melanogaster includes a cluster of the three homeobox genes orthopedia (otp), Drosophila Retinal homeobox (DRx), and homeobrain (hbn). In an attempt to isolate mutants for these genes, we performed an EMS mutagenesis and isolated lethal mutants from the 57B region, among them mutants for otp, DRx, and hbn. With the help of two newly generated deletions from the 57B region, we mapped additional mutants to specific chromosomal intervals and identified several of these mutants from the 57B region molecularly. In addition, we generated mutants for CG15651 and RIC-3 by gene targeting and mutants for the genes CG9344, CG15649, CG15650, and ND-B14.7 using the CRISPR/Cas9 system. We determined the lethality period during development for most isolated mutants. In total, we analysed alleles from nine different genes from the 57B region of Drosophila, which could now be used to further explore the functions of the corresponding genes in the future.
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Affiliation(s)
- Eva Louise Steinmetz
- Developmental Biology, ZHMB (Center of Human and Molecular Biology), Saarland University, Building 61, D-66421 Homburg, Germany
- Zoology & Physiology, ZHMB (Center of Human and Molecular Biology), Saarland University, Building B2.1, D-66123 Saarbrücken, Germany
| | - Sandra Noh
- Developmental Biology, ZHMB (Center of Human and Molecular Biology), Saarland University, Building 61, D-66421 Homburg, Germany
| | - Christine Klöppel
- Developmental Biology, ZHMB (Center of Human and Molecular Biology), Saarland University, Building 61, D-66421 Homburg, Germany
| | - Martin F. Fuhr
- Developmental Biology, ZHMB (Center of Human and Molecular Biology), Saarland University, Building 61, D-66421 Homburg, Germany
| | - Nicole Bach
- Developmental Biology, ZHMB (Center of Human and Molecular Biology), Saarland University, Building 61, D-66421 Homburg, Germany
| | - Mona Evelyn Raffael
- Developmental Biology, ZHMB (Center of Human and Molecular Biology), Saarland University, Building 61, D-66421 Homburg, Germany
| | - Kirsten Hildebrandt
- Developmental Biology, ZHMB (Center of Human and Molecular Biology), Saarland University, Building 61, D-66421 Homburg, Germany
| | - Fabienne Wittling
- Developmental Biology, ZHMB (Center of Human and Molecular Biology), Saarland University, Building 61, D-66421 Homburg, Germany
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarland University, Building E8.1, D-66123 Saarbrücken, Germany
| | - Doris Jann
- Developmental Biology, ZHMB (Center of Human and Molecular Biology), Saarland University, Building 61, D-66421 Homburg, Germany
- Medical Biochemistry & Molecular Biology, ZHMB (Center of Human and Molecular Biology), Saarland University, Building 45.2, D-66421 Homburg, Germany
| | - Uwe Walldorf
- Developmental Biology, ZHMB (Center of Human and Molecular Biology), Saarland University, Building 61, D-66421 Homburg, Germany
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Hartley T, Gillespie MK, Graham ID, Hayeems RZ, Li S, Sampson M, Boycott KM, Potter BK. Exome and genome sequencing for rare genetic disease diagnosis: A scoping review and critical appraisal of clinical guidance documents produced by genetics professional organizations. Genet Med 2023; 25:100948. [PMID: 37551668 DOI: 10.1016/j.gim.2023.100948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 07/27/2023] [Accepted: 07/28/2023] [Indexed: 08/09/2023] Open
Abstract
PURPOSE Exome and genome sequencing have rapidly transitioned from research methods to widely used clinical tests for diagnosing rare genetic diseases. We sought to synthesize the topics covered and appraise the development processes of clinical guidance documents generated by genetics professional organizations. METHODS We conducted a scoping review of guidance documents published since 2010, systematically identified in peer-reviewed and gray literature, using established methods and reporting guidelines. We coded verbatim recommendations by topic using content analysis and critically appraised documents using the Appraisal of Guidelines Research and Evaluation (AGREE) II tool. RESULTS We identified 30 guidance documents produced by 8 organizations (2012-2022), yielding 611 recommendations covering 21 topics. The most common topic related to findings beyond the primary testing indication. Mean AGREE II scores were low across all 6 quality domains; scores for items related to rigor of development were among the lowest. More recently published documents generally received higher scores. CONCLUSION Guidance documents included a broad range of recommendations but were of low quality, particularly in their rigor of development. Developers should consider using tools such as AGREE II and basing recommendations on living knowledge syntheses to improve guidance development in this evolving space.
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Affiliation(s)
- Taila Hartley
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada; University of Ottawa, Ottawa, Ontario, Canada.
| | - Meredith K Gillespie
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
| | - Ian D Graham
- University of Ottawa, Ottawa, Ontario, Canada; The Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
| | - Robin Z Hayeems
- Hospital for Sick Children, Toronto, Ontario, Canada; University of Toronto, Toronto, Ontario, Canada
| | - Sheena Li
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
| | - Margaret Sampson
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
| | - Kym M Boycott
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada; University of Ottawa, Ottawa, Ontario, Canada; Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
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Chen S, Jiang W, Du Y, Yang M, Pan Y, Li H, Cui M. Single-cell analysis technologies for cancer research: from tumor-specific single cell discovery to cancer therapy. Front Genet 2023; 14:1276959. [PMID: 37900181 PMCID: PMC10602688 DOI: 10.3389/fgene.2023.1276959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Accepted: 09/25/2023] [Indexed: 10/31/2023] Open
Abstract
Single-cell sequencing (SCS) technology is changing our understanding of cellular components, functions, and interactions across organisms, because of its inherent advantage of avoiding noise resulting from genotypic and phenotypic heterogeneity across numerous samples. By directly and individually measuring multiple molecular characteristics of thousands to millions of single cells, SCS technology can characterize multiple cell types and uncover the mechanisms of gene regulatory networks, the dynamics of transcription, and the functional state of proteomic profiling. In this context, we conducted systematic research on SCS techniques, including the fundamental concepts, procedural steps, and applications of scDNA, scRNA, scATAC, scCITE, and scSNARE methods, focusing on the unique clinical advantages of SCS, particularly in cancer therapy. We have explored challenging but critical areas such as circulating tumor cells (CTCs), lineage tracing, tumor heterogeneity, drug resistance, and tumor immunotherapy. Despite challenges in managing and analyzing the large amounts of data that result from SCS, this technique is expected to reveal new horizons in cancer research. This review aims to emphasize the key role of SCS in cancer research and promote the application of single-cell technologies to cancer therapy.
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Affiliation(s)
- Siyuan Chen
- Department of Hepatobiliary and Pancreatic Surgery, The Second Hospital of Jilin University, Changchun, China
| | - Weibo Jiang
- Department of Orthopaedic, The Second Hospital of Jilin University, Changchun, China
| | - Yanhui Du
- Department of Orthopaedics, Jilin Province People’s Hospital, Changchun, China
| | - Manshi Yang
- Department of Hepatobiliary and Pancreatic Surgery, The Second Hospital of Jilin University, Changchun, China
| | - Yihan Pan
- Department of Hepatobiliary and Pancreatic Surgery, The Second Hospital of Jilin University, Changchun, China
| | - Huan Li
- Department of Hepatobiliary and Pancreatic Surgery, The Second Hospital of Jilin University, Changchun, China
| | - Mengying Cui
- Department of Hepatobiliary and Pancreatic Surgery, The Second Hospital of Jilin University, Changchun, China
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6
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Zhao Y, Li M, Liu J, Xue X, Zhong J, Lin J, Ye B, Chen J, Qiao Y. Dual guide RNA-mediated concurrent C&G-to-T&A and A&T-to-G&C conversions using CRISPR base editors. Comput Struct Biotechnol J 2023; 21:856-868. [PMID: 36698964 PMCID: PMC9842798 DOI: 10.1016/j.csbj.2022.12.055] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 12/30/2022] [Accepted: 12/30/2022] [Indexed: 01/04/2023] Open
Abstract
Base editing tools enable precise genome modifications, disease modeling, and promising gene therapy. However, many human genetic diseases are elicited by multi-nucleotide variants (MNVs) with heterogeneous substitutions at the same genomic locus. Based on the adenine and cytosine base editors, dual base editors that can catalyze concurrent C-to-T and A-to-G editing have been developed, while simultaneous C&G-to-T&A and A&T-to-G&C conversions on the same allele have not been achieved at the desirable site. Here we propose a strategy of combining base editors with dual guide RNAs (gRNAs) that target two overlapped neighboring loci on the opposite strands, which can induce simultaneous C&G-to-T&A and A&T-to-G&C conversions within their overlapping targeting windows. Moreover, one of the paired gRNAs is mutated to perfectly match another gRNA-edited sequence, efficiently facilitating concurrent base conversions on the same allele. To further expand the targeting scopes, PAMless SpRY Cas9-mediated base editors are combined with our optimized dual gRNAs system to induce expected concurrent base editing and to install neighboring pathogenic MNVs in TP53 in cancer cells. In addition, more complex mutation types can be achieved by integrating dual base editors and our dual gRNAs strategy. Thus, we establish a general strategy to efficiently induce MNVs in human genome, helping to dissect the functions of pathogenic MNVs with multifarious types.
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Affiliation(s)
- Yuting Zhao
- Precise Genome Engineering Center, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Min Li
- Precise Genome Engineering Center, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Jie Liu
- Guangzhou Medical University, Guangzhou 511495, China
| | - Xiaowen Xue
- Precise Genome Engineering Center, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Jingli Zhong
- Precise Genome Engineering Center, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Jianxiang Lin
- Precise Genome Engineering Center, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Bo Ye
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai 200030, China,Corresponding authors.
| | - Jun Chen
- Department of Endocrinology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan 250012, China,Corresponding authors.
| | - Yunbo Qiao
- Precise Genome Engineering Center, School of Life Sciences, Guangzhou University, Guangzhou 510006, China,Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200125, China,Shanghai Institute of Precision Medicine, Shanghai 200125, China,Corresponding author at: Precise Genome Engineering Center, School of Life Sciences, Guangzhou University, Guangzhou 510006, China.
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7
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Pervez MT, Hasnain MJU, Abbas SH, Moustafa MF, Aslam N, Shah SSM. A Comprehensive Review of Performance of Next-Generation Sequencing Platforms. BIOMED RESEARCH INTERNATIONAL 2022; 2022:3457806. [PMID: 36212714 PMCID: PMC9537002 DOI: 10.1155/2022/3457806] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 08/30/2022] [Indexed: 11/17/2022]
Abstract
Background Next-generation sequencing methods have been developed and proposed to investigate any query in genomics or clinical activity involving DNA. Technical advancement in these sequencing methods has enhanced sequencing volume to several billion nucleotides within a very short time and low cost. During the last few years, the usage of the latest DNA sequencing platforms in a large number of research projects helped to improve the sequencing methods and technologies, thus enabling a wide variety of research/review publications and applications of sequencing technologies. Objective The proposed study is aimed at highlighting the most fast and accurate NGS instruments developed by various companies by comparing output per hour, quality of the reads, maximum read length, reads per run, and their applications in various domains. This will help research institutions and biological/clinical laboratories to choose the sequencing instrument best suited to their environment. The end users will have a general overview about the history of the sequencing technologies, latest developments, and improvements made in the sequencing technologies till now. Results The proposed study, based on previous studies and manufacturers' descriptions, highlighted that in terms of output per hour, Nanopore PromethION outperformed all sequencers. BGI was on the second position, and Illumina was on the third position. Conclusion The proposed study investigated various sequencing instruments and highlighted that, overall, Nanopore PromethION is the fastest sequencing approach. BGI and Nanopore can beat Illumina, which is currently the most popular sequencing company. With respect to quality, Ion Torrent NGS instruments are on the top of the list, Illumina is on the second position, and BGI DNB is on the third position. Secondly, memory- and time-saving algorithms and databases need to be developed to analyze data produced by the 3rd- and 4th-generation sequencing methods. This study will help people to adopt the best suited sequencing platform for their research work, clinical or diagnostic activities.
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Affiliation(s)
- Muhammad Tariq Pervez
- Department of Bioinformatics and Computational Biology, Virtual University of Pakistan, Pakistan
| | - Mirza Jawad ul Hasnain
- Department of Bioinformatics and Computational Biology, Virtual University of Pakistan, Pakistan
| | - Syed Hassan Abbas
- Department of Bioinformatics and Computational Biology, Virtual University of Pakistan, Pakistan
| | - Mahmoud F. Moustafa
- Department of Biology, Faculty of Science, King Khalid University, Abha, Saudi Arabia
- Department of Botany and Microbiology, Faculty of Science, South Valley University, Qena, Egypt
| | - Naeem Aslam
- Department of Computer Science, NFCIET, Khanewal Road, Multan, Pakistan
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8
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Souche E, Beltran S, Brosens E, Belmont JW, Fossum M, Riess O, Gilissen C, Ardeshirdavani A, Houge G, van Gijn M, Clayton-Smith J, Synofzik M, de Leeuw N, Deans ZC, Dincer Y, Eck SH, van der Crabben S, Balasubramanian M, Graessner H, Sturm M, Firth H, Ferlini A, Nabbout R, De Baere E, Liehr T, Macek M, Matthijs G, Scheffer H, Bauer P, Yntema HG, Weiss MM. Recommendations for whole genome sequencing in diagnostics for rare diseases. Eur J Hum Genet 2022; 30:1017-1021. [PMID: 35577938 PMCID: PMC9437083 DOI: 10.1038/s41431-022-01113-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 04/21/2022] [Indexed: 12/23/2022] Open
Abstract
In 2016, guidelines for diagnostic Next Generation Sequencing (NGS) have been published by EuroGentest in order to assist laboratories in the implementation and accreditation of NGS in a diagnostic setting. These guidelines mainly focused on Whole Exome Sequencing (WES) and targeted (gene panels) sequencing detecting small germline variants (Single Nucleotide Variants (SNVs) and insertions/deletions (indels)). Since then, Whole Genome Sequencing (WGS) has been increasingly introduced in the diagnosis of rare diseases as WGS allows the simultaneous detection of SNVs, Structural Variants (SVs) and other types of variants such as repeat expansions. The use of WGS in diagnostics warrants the re-evaluation and update of previously published guidelines. This work was jointly initiated by EuroGentest and the Horizon2020 project Solve-RD. Statements from the 2016 guidelines have been reviewed in the context of WGS and updated where necessary. The aim of these recommendations is primarily to list the points to consider for clinical (laboratory) geneticists, bioinformaticians, and (non-)geneticists, to provide technical advice, aid clinical decision-making and the reporting of the results.
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Affiliation(s)
- Erika Souche
- Center for Human Genetics, KU Leuven, Gasthuisberg, Laboratory for Molecular Diagnosis, Leuven, Belgium
| | - Sergi Beltran
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona (UB), Barcelona, Spain
| | - Erwin Brosens
- Erasmus MC University Medical Center - Sophia Children's Hospital, Department of Clinical Genetics, Rotterdam, The Netherlands
| | - John W Belmont
- Illumina, Inc., Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Magdalena Fossum
- Dept of Pediatric Surgery, Rigshospitalet, Faculty of Health and Medical Sciences, Copenhagen University, Denmark, Dept. of Women's and Children's health, Karolinska Institute, Stockholm, Sweden
| | - Olaf Riess
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Christian Gilissen
- Department of Human Genetics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, 6525 GA, The Netherlands
| | | | - Gunnar Houge
- Department of Medical Genetics, Haukeland University Hospital, 5021, Bergen, Norway
| | - Marielle van Gijn
- Department of Genetics, University Medical Center Groningen, University Groningen, Groningen, The Netherlands
| | - Jill Clayton-Smith
- Manchester Centre For Genomic Medicine, University of Manchester, St Mary's Hospital, Manchester, M13 9WL, UK
- Division of Evolution and Genomic Sciences School of Biological Sciences University of Manchester, Manchester, UK
| | - Matthis Synofzik
- Hertie-Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Nicole de Leeuw
- Department of Human Genetics, and Donders Centre for Cognitive Neuroscience, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Zandra C Deans
- Genomics Quality Assessment, NHS Lothian, Edinburgh, Scotland
| | - Yasemin Dincer
- Lehrstuhl für Sozialpädiatrie, Technische Universität München, Munich, Germany
- Zentrum für Humangenetik und Laboratoriumsdiagnostik (MVZ), Martinsried, Germany
| | | | - Saskia van der Crabben
- Amsterdam University Medical Centers, location AMC, Department of Clinical Genetics, Amsterdam, The Netherlands
| | - Meena Balasubramanian
- Highly Specialised Osteogenesis Imperfecta Service and Sheffield Clinical Genetics Service, Sheffield Children's NHS Foundation Trust, Sheffield, UK
- Department of Oncology & Metabolism, University of Sheffield, Sheffield, UK
| | - Holm Graessner
- University Hospital Tübingen, Institute for Medical Genetics and Applied Genomics and Centre for Rare Diseases, Calwerstr. 7, 72076, Tübingen, Germany
| | - Marc Sturm
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Helen Firth
- Dept of Clinical Genetics, Box 134, Cambridge University Hospitals, Cambridge, UK
| | - Alessandra Ferlini
- Unit of Medical Genetics, University Hospital & Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Rima Nabbout
- Pediatric Neurology. reference centre for rare epilepsies. Hôpital Necker Enfants malades, APHP, Université de Paris, Institut Imagine (INSERM UMR 1163), Paris, France
| | - Elfride De Baere
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Thomas Liehr
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Jena, Germany
| | - Milan Macek
- Department of biology and medical genetics, 2nd Faculty of Medicine Charles University and University hospital Motol, Prague, Czechia
| | - Gert Matthijs
- Center for Human Genetics, KU Leuven, Gasthuisberg, Laboratory for Molecular Diagnosis, Leuven, Belgium
| | - Hans Scheffer
- Radboud university medical center, Department of Human Genetics, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Peter Bauer
- CENTOGENE GmbH, Am Strande 7, 18055, Rostock, Germany
| | - Helger G Yntema
- Radboud university medical center, Department of Human Genetics, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Marjan M Weiss
- Radboud university medical center, Department of Human Genetics, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands.
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9
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Kermode W, De Santis D, Truong L, Della Mina E, Salman S, Thompson G, Nolan D, Loh R, Mallon D, Mclean-Tooke A, John M, Tangye SG, O'Sullivan M, D'Orsogna LJ. A Novel Targeted Amplicon Next-Generation Sequencing Gene Panel for the Diagnosis of Common Variable Immunodeficiency Has a High Diagnostic Yield: Results from the Perth CVID Cohort Study. J Mol Diagn 2022; 24:586-599. [PMID: 35570134 DOI: 10.1016/j.jmoldx.2022.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 12/23/2021] [Accepted: 02/09/2022] [Indexed: 11/18/2022] Open
Abstract
With the advent of next-generation sequencing (NGS), monogenic forms of common variable immunodeficiency (CVID) have been increasingly described. Our study aimed to identify disease-causing variants in a Western Australian CVID cohort using a novel targeted NGS panel. Targeted amplicon NGS was performed on 22 unrelated subjects who met the formal European Society for Immunodeficiencies-Pan-American Group for Immunodeficiency diagnostic criteria for CVID and had at least one of the following additional criteria: disease onset at age <18 years, autoimmunity, low memory B lymphocytes, family history, and/or history of lymphoproliferation. Candidate variants were assessed by in silico predictions of deleteriousness, comparison to the literature, and classified according to the American College of Medical Genetics and Genomics-Association for Molecular Pathology criteria. All detected genetic variants were verified independently by an external laboratory, and additional functional studies were performed if required. Pathogenic or likely pathogenic variants were detected in 6 of 22 (27%) patients. Monoallelic variants of uncertain significance were also identified in a further 4 of 22 patients (18%). Pathogenic variants, likely pathogenic variants, or variants of uncertain significance were found in TNFRSF13B, TNFRSF13C, ICOS, AICDA, IL21R, NFKB2, and CD40LG, including novel variants and variants with unexpected inheritance pattern. Targeted amplicon NGS is an effective tool to identify monogenic disease-causing variants in CVID, and is comparable or superior to other NGS methods. Moreover, targeted amplicon NGS identified patients who may benefit from targeted therapeutic strategies and had important implications for family members.
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Affiliation(s)
- William Kermode
- School of Medicine, University of Western Australia, Perth, Western Australia, Australia
| | - Dianne De Santis
- School of Medicine, University of Western Australia, Perth, Western Australia, Australia; Department of Clinical Immunology and PathWest, Fiona Stanley Hospital, Perth, Western Australia, Australia
| | - Linh Truong
- Department of Clinical Immunology and PathWest, Fiona Stanley Hospital, Perth, Western Australia, Australia
| | - Erika Della Mina
- Immunology and Immunodeficiency Laboratory, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia; St Vincent's Clinical School, Faculty of Medicine, University of New South Wales Sydney, Kensington, New South Wales, Australia
| | - Sam Salman
- Department of Clinical Immunology and PathWest, Queen Elizabeth II Medical Centre, Perth, Western Australia, Australia
| | - Grace Thompson
- Department of Clinical Immunology and PathWest, Queen Elizabeth II Medical Centre, Perth, Western Australia, Australia
| | - David Nolan
- Department of Clinical Immunology, Royal Perth Hospital, Perth, Western Australia, Australia
| | - Richard Loh
- Department of Immunology, Perth Children's Hospital, Perth, Western Australia, Australia
| | - Dominic Mallon
- Department of Clinical Immunology and PathWest, Fiona Stanley Hospital, Perth, Western Australia, Australia
| | - Andrew Mclean-Tooke
- Department of Clinical Immunology and PathWest, Queen Elizabeth II Medical Centre, Perth, Western Australia, Australia
| | - Mina John
- Department of Clinical Immunology, Royal Perth Hospital, Perth, Western Australia, Australia; Institute for Immunology and Infectious Diseases, Murdoch University, Perth, Western Australia, Australia
| | - Stuart G Tangye
- Immunology and Immunodeficiency Laboratory, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia; St Vincent's Clinical School, Faculty of Medicine, University of New South Wales Sydney, Kensington, New South Wales, Australia
| | - Michael O'Sullivan
- Department of Clinical Immunology and PathWest, Fiona Stanley Hospital, Perth, Western Australia, Australia; Department of Immunology, Perth Children's Hospital, Perth, Western Australia, Australia
| | - Lloyd J D'Orsogna
- School of Medicine, University of Western Australia, Perth, Western Australia, Australia; Department of Clinical Immunology and PathWest, Fiona Stanley Hospital, Perth, Western Australia, Australia.
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10
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The patient with 41 reports: Analysis of laboratory exome sequencing reporting of a "virtual patient". Genet Med 2022; 24:1306-1315. [PMID: 35389343 DOI: 10.1016/j.gim.2022.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 02/27/2022] [Accepted: 03/03/2022] [Indexed: 11/20/2022] Open
Abstract
PURPOSE Few studies have systematically analyzed the structure and content of laboratory exome sequencing reports from the same patient. METHODS We merged 8 variants from patients into "normal" exomes to create virtual patient-parent trios. We provided laboratories worldwide with the data and patient phenotype information (developmental delay, dysmorphic features, and cardiac hypertrophy). Laboratories analyzed the data and issued a diagnostic exome report. Reports were scored using a coding matrix developed from existing guidelines. RESULTS In total, 41 laboratories representing 17 countries issued reports. Reporting of quality control statistics and technical information was poor (46.3%). Although 75.6% of the reports clearly stated the classification of all reported variants, few reports listed extensive evidence supporting variant classification. Only 53.1% of laboratories that reported unsolicited or secondary findings gave advice regarding health-related follow-up and 20.5% gave advice regarding cascade testing for relatives. Of the 147 variants reported, 105 (71.4%) were classified in agreement with classifications based on American College of Medical Genetics and Genomics/Association for Molecular Pathology and Association for Clinical Genomic Science guidelines. Concordance was higher for known pathogenic variants (86.3%) than for novel unpublished variants (56.8%). CONCLUSION The considerable variability identified in the components that laboratories included in their reports and their classification of variants suggests that existing guidelines are not being used consistently with significant implications for patient care.
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11
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Belien JAM, Kip AE, Swertz MA. Road to FAIR genomes: a gap analysis of NGS data generation and sharing in the Netherlands. BMJ OPEN SCIENCE 2022; 6:e100268. [PMID: 35505836 PMCID: PMC9014103 DOI: 10.1136/bmjos-2021-100268] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 03/16/2022] [Indexed: 12/17/2022] Open
Abstract
Objective This study investigates current standards and operational gaps in the management and sharing of next generation sequencing (NGS) data within the healthcare and research setting and according to Findable, Accessible, Interoperable and Reusable (FAIR) principles. Methods The analysis was performed as the basis from which to bridge identified gaps and develop widely accepted working standards that ensure optimal reusability of genomic data in healthcare and research settings in the Netherlands. This work is part of the ‘Rational Pharmacotherapy Program’ led by ZonMw, The Netherlands Organisation for Health Research and Development, which aims to promote the efficient implementation of NGS and personalised medicine within Dutch healthcare, with an initial focus on oncology and rare diseases. Results Based on this analysis and as part of this programme, a consortium was formed to develop an instruction manual for FAIR genomic data in clinical care and research based on an inventory of commonly used workflows and standards in the (inter)national field of genome analysis. Conclusions The gap analysis presented and discussed in this paper represents the starting point for this inventory and is a possible contribution from the Netherlands to the European 1+ Million Genomes Initiative. This paper addresses the topics of data generation, data quality, (meta)data standards, data storage and archiving and data integration and exchange.
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Affiliation(s)
- Jeroen A M Belien
- Pathology, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
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12
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Elsink K, Huibers MMH, Hollink IHIM, Simons A, Zonneveld-Huijssoon E, van der Veken LT, Leavis HL, Henriet SSV, van Deuren M, van de Veerdonk FL, Potjewijd J, Berghuis D, Dalm VASH, Vermont CL, van de Ven AAJM, Lambeck AJA, Abbott KM, van Hagen PM, de Bree GJ, Kuijpers TW, Frederix GWJ, van Gijn ME, van Montfrans JM. Implementation of Early Next-Generation Sequencing for Inborn Errors of Immunity: A Prospective Observational Cohort Study of Diagnostic Yield and Clinical Implications in Dutch Genome Diagnostic Centers. Front Immunol 2022; 12:780134. [PMID: 34992599 PMCID: PMC8724043 DOI: 10.3389/fimmu.2021.780134] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 12/01/2021] [Indexed: 01/07/2023] Open
Abstract
Objective Inborn errors of immunity (IEI) are a heterogeneous group of disorders, affecting different components of the immune system. Over 450 IEI related genes have been identified, with new genes continually being recognized. This makes the early application of next-generation sequencing (NGS) as a diagnostic method in the evaluation of IEI a promising development. We aimed to provide an overview of the diagnostic yield and time to diagnosis in a cohort of patients suspected of IEI and evaluated by an NGS based IEI panel early in the diagnostic trajectory in a multicenter setting in the Netherlands. Study Design We performed a prospective observational cohort study. We collected data of 165 patients with a clinical suspicion of IEI without prior NGS based panel evaluation that were referred for early NGS using a uniform IEI gene panel. The diagnostic yield was assessed in terms of definitive genetic diagnoses, inconclusive diagnoses and patients without abnormalities in the IEI gene panel. We also assessed time to diagnosis and clinical implications. Results For children, the median time from first consultation to diagnosis was 119 days versus 124 days for adult patients (U=2323; p=0.644). The median turn-around time (TAT) of genetic testing was 56 days in pediatric patients and 60 days in adult patients (U=1892; p=0.191). A definitive molecular diagnosis was made in 25/65 (24.6%) of pediatric patients and 9/100 (9%) of adults. Most diagnosed disorders were identified in the categories of immune dysregulation (n=10/25; 40%), antibody deficiencies (n=5/25; 20%), and phagocyte diseases (n=5/25; 20%). Inconclusive outcomes were found in 76/165 (46.1%) patients. Within the patient group with a genetic diagnosis, a change in disease management occurred in 76% of patients. Conclusion In this cohort, the highest yields of NGS based evaluation for IEI early in the diagnostic trajectory were found in pediatric patients, and in the disease categories immune dysregulation and phagocyte diseases. In cases where a definitive diagnosis was made, this led to important disease management implications in a large majority of patients. More research is needed to establish a uniform diagnostic pathway for cases with inconclusive diagnoses, including variants of unknown significance.
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Affiliation(s)
- Kim Elsink
- Department of Pediatric Immunology and Infectious Diseases, Wilhelmina's Children Hospital, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Manon M H Huibers
- Department of Genetics, Division Laboratories, Pharmacy and Biomedical Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Iris H I M Hollink
- Department of Clinical Genetics, Erasmus Medical Center, Erasmus University Rotterdam, Rotterdam, Netherlands
| | - Annet Simons
- Department of Human Genetics, Nijmegen Center for Molecular Life Sciences, Radboud University Medical Centre, Radboud University, Nijmegen, Netherlands.,Radboud Institute for Oncology, Radboud University Medical Center, Radboud University, Nijmegen, Netherlands
| | - Evelien Zonneveld-Huijssoon
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Lars T van der Veken
- Department of Genetics, Division Laboratories, Pharmacy and Biomedical Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Helen L Leavis
- Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Stefanie S V Henriet
- Department of Pediatric Infectious Diseases and Immunology, Amalia's Children Hospital, Radboud University Nijmegen Medical Centre, Radboud University, Nijmegen, Netherlands
| | - Marcel van Deuren
- Department of Internal Medicine, Radboud University Medical Center, Radboud Center for Infectious Diseases, Nijmegen, Netherlands
| | - Frank L van de Veerdonk
- Department of Internal Medicine, Radboud University Medical Center, Radboud Center for Infectious Diseases, Nijmegen, Netherlands
| | - Judith Potjewijd
- Department of Nephrology and Clinical Immunology, Maastricht University Medical Center, Maastricht University, Maastricht, Netherlands
| | - Dagmar Berghuis
- Willem-Alexander Children's Hospital, Department of Pediatrics, Leiden University Medical Center, Leiden University, Leiden, Netherlands
| | - Virgil A S H Dalm
- Department of Internal Medicine, Division of Allergy & Clinical Immunology; Department of Immunology, Erasmus University Medical Center Rotterdam, Erasmus University Rotterdam, Rotterdam, Netherlands
| | - Clementien L Vermont
- Department of Pediatric Infectious Diseases, Immunology and Rheumatology, Sophia Children's Hospital, Erasmus Medical Center, Erasmus University Rotterdam, Rotterdam, Netherlands
| | - Annick A J M van de Ven
- Department of Internal Medicine and Allergology, Rheumatology and Clinical Immunology, University Medical Center Groningen, Groningen, Netherlands
| | - Annechien J A Lambeck
- Department of Laboratory Medicine, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Kristin M Abbott
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - P Martin van Hagen
- Department of Internal Medicine, Division of Allergy & Clinical Immunology; Department of Immunology, Erasmus University Medical Center Rotterdam, Erasmus University Rotterdam, Rotterdam, Netherlands
| | - Godelieve J de Bree
- Department of Internal Medicine, Institute for Infection and Immunity, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Taco W Kuijpers
- Department of Pediatric Hematology, Immunology and Infectious Diseases, Emma Children's Hospital, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Geert W J Frederix
- Julius Center for Health Sciences and Primary Care, University Medical Centre Utrecht, Utrecht, Netherlands
| | - Mariëlle E van Gijn
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Joris M van Montfrans
- Department of Pediatric Immunology and Infectious Diseases, Wilhelmina's Children Hospital, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
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13
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Khalturina EO, Degtyareva ND, Bairashevskaia AV, Mulenkova AV, Degtyareva AV. Modern diagnostic capabilities of neonatal screening for primary immunodeficiencies in newborns. Clin Exp Pediatr 2021; 64:504-510. [PMID: 33781055 PMCID: PMC8498015 DOI: 10.3345/cep.2020.01270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 02/05/2021] [Indexed: 11/27/2022] Open
Abstract
Population screening of newborns is an extremely important and informative diagnostic approach that allows early identification of babies who are predisposed to the development of a number of serious diseases. Some of these diseases are known and have effective treatment methods. Neonatal screening enables the early diagnosis and subsequent timely initiation of therapy. This helps to prevent serious complications and reduce the percentage of disability and deaths among newborns and young children. Primary immunodeficiency diseases and primary immunodeficiency syndrome (PIDS) are a heterogeneous group of diseases and conditions based on impaired immune system function associated with developmental defects and characterized by various combinations of recurrent infections, development of autoimmune and lymphoproliferative syndromes (genetic defects in apoptosis, gene mutation Fas receptor or ligand), granulomatous process, and malignant neoplasms. Most of these diseases manifest in infancy and lead to serious illness, disability, and high mortality rates. Until recently, it was impossible to identify children with PIDS before the onset of the first clinical symptoms, which are usually accompanied by complications in the form of severe coinfections of a viral-bacterial-fungal etiology. Modern advances in medical laboratory technology have allowed the identification of children with severe PIDS, manifested by T- and/or B-cell lymphopenia and other disorders of the immune system. This review discusses the main existing strategies and directions used in PIDS screening programs for newborns, including approaches to screening based on excision of T-cell receptors and kappa-recombination excision circles, as well as the potential role and place of next-generation sequencing technology to increase the diagnostic accuracy of these diseases.
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Affiliation(s)
- Evgenia Olegovna Khalturina
- Federal State Autonomous Educational Institution of Higher Education, I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), Moscow, Russia.,National Medical Research Center for Obstetrics, Gynecology, and Perinatology named after Academician V.I. Kulakov of the Ministry of Health of the Russian Federation; Department of Pediatrics and Neonatology, Moscow, Russia
| | - Natalia Dmitrievna Degtyareva
- Federal State Autonomous Educational Institution of Higher Education, I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), Moscow, Russia
| | - Anastasiia Vasi'evna Bairashevskaia
- Federal State Autonomous Educational Institution of Higher Education, I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), Moscow, Russia
| | - Alena Valerievna Mulenkova
- Federal State Autonomous Educational Institution of Higher Education, I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), Moscow, Russia
| | - Anna Vladimirovna Degtyareva
- Federal State Autonomous Educational Institution of Higher Education, I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), Moscow, Russia.,National Medical Research Center for Obstetrics, Gynecology, and Perinatology named after Academician V.I. Kulakov of the Ministry of Health of the Russian Federation; Department of Pediatrics and Neonatology, Moscow, Russia
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14
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Sarkadi B, Liko I, Nyiro G, Igaz P, Butz H, Patocs A. Analytical Performance of NGS-Based Molecular Genetic Tests Used in the Diagnostic Workflow of Pheochromocytoma/Paraganglioma. Cancers (Basel) 2021; 13:4219. [PMID: 34439371 PMCID: PMC8392134 DOI: 10.3390/cancers13164219] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 08/16/2021] [Accepted: 08/18/2021] [Indexed: 12/30/2022] Open
Abstract
Next Generation Sequencing (NGS)-based methods are high-throughput and cost-effective molecular genetic diagnostic tools. Targeted gene panel and whole exome sequencing (WES) are applied in clinical practice for assessing mutations of pheochromocytoma/paraganglioma (PPGL) associated genes, but the best strategy is debated. Germline mutations of at the least 18 PPGL genes are present in approximately 20-40% of patients, thus molecular genetic testing is recommended in all cases. We aimed to evaluate the analytical and clinical performances of NGS methods for mutation detection of PPGL-associated genes. WES (three different library preparation and bioinformatics workflows) and an in-house, hybridization based gene panel (endocrine-onco-gene-panel- ENDOGENE) was evaluated on 37 (20 WES and 17 ENDOGENE) samples with known variants. After optimization of the bioinformatic workflow, 61 additional samples were tested prospectively. All clinically relevant variants were validated with Sanger sequencing. Target capture of PPGL genes differed markedly between WES platforms and genes tested. All known variants were correctly identified by all methods, but methods of library preparations, sequencing platforms and bioinformatical settings significantly affected the diagnostic accuracy. The ENDOGENE panel identified several pathogenic mutations and unusual genotype-phenotype associations suggesting that the whole panel should be used for identification of genetic susceptibility of PPGL.
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Affiliation(s)
- Balazs Sarkadi
- MTA-SE Hereditary Tumors Research Group, Eotvos Lorand Research Network, H-1089 Budapest, Hungary; (B.S.); (I.L.); (H.B.)
| | - Istvan Liko
- MTA-SE Hereditary Tumors Research Group, Eotvos Lorand Research Network, H-1089 Budapest, Hungary; (B.S.); (I.L.); (H.B.)
- Bionics Innovation Center, H-1089 Budapest, Hungary;
| | - Gabor Nyiro
- Bionics Innovation Center, H-1089 Budapest, Hungary;
- MTA-SE Molecular Medicine Research Group, Eotvos Lorand Research Network, H-1083 Budapest, Hungary;
| | - Peter Igaz
- MTA-SE Molecular Medicine Research Group, Eotvos Lorand Research Network, H-1083 Budapest, Hungary;
- Department of Endocrinology, Department of Internal Medicine and Oncology, Semmelweis University, H-1083 Budapest, Hungary
| | - Henriett Butz
- MTA-SE Hereditary Tumors Research Group, Eotvos Lorand Research Network, H-1089 Budapest, Hungary; (B.S.); (I.L.); (H.B.)
- Department of Laboratory Medicine, Semmelweis University, H-1089 Budapest, Hungary
- Department of Molecular Genetics, National Institute of Oncology, H-1122 Budapest, Hungary
| | - Attila Patocs
- MTA-SE Hereditary Tumors Research Group, Eotvos Lorand Research Network, H-1089 Budapest, Hungary; (B.S.); (I.L.); (H.B.)
- Bionics Innovation Center, H-1089 Budapest, Hungary;
- Department of Laboratory Medicine, Semmelweis University, H-1089 Budapest, Hungary
- Department of Molecular Genetics, National Institute of Oncology, H-1122 Budapest, Hungary
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15
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Ahmad-Nejad P, Ashavaid T, Vacaflores Salinas A, Huggett J, Harris K, Linder MW, Baluchova K, Steimer W, Payne DA. Current and future challenges in quality assurance in molecular diagnostics. Clin Chim Acta 2021; 519:239-246. [PMID: 33971158 DOI: 10.1016/j.cca.2021.05.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 05/04/2021] [Accepted: 05/05/2021] [Indexed: 02/08/2023]
Abstract
The development and performance of molecular genetic assays has required increasingly complex quality assurance in recent years and continues to pose new challenges. Quality management officers, as well as academic and technical personnel are confronted with new molecular genetic parameters, methods, changing regulatory environments, questions regarding appropriate validation, and quality control for these innovative assays that are increasingly applying quantification and/or multiplex formats. Yet, quality assurance and quality control guidelines are still not widely available or in some circumstances have become outdated. For these reasons, the need for solutions to provide test confidence continues to grow. In order to integrate new test procedures into existing quality assurance measures, the ISO 15189 guideline can serve as an orientation. The ISO 15189 guideline describes requirements for medical laboratories and thus includes those performing molecular diagnostics. This article gives an overview of the possibilities and challenges in quality assurance of molecular parameters and shows possible solutions.
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Affiliation(s)
- Parviz Ahmad-Nejad
- Institute for Medicine Laboratory Diagnostics, Centre for Clinical and Translational Research (CCTR), HELIOS University Hospital, Wuppertal, Witten/Herdecke University, Germany.
| | - Tester Ashavaid
- Department of Laboratory Medicine, P.D. Hinduja National Hospital and Medical Research Center, Mumbai, India
| | | | - Jim Huggett
- National Measurement Laboratory (NML) at LGC, Queens Rd, Teddington, TW11 0LY, United Kingdom; School of Biosciences & Medicine, Faculty of Health & Medical Science, University of Surrey, Guildford GU2 7XH, United Kingdom
| | - Kathryn Harris
- Microbiology Department, Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - Mark W Linder
- Department of Pathology and Laboratory Medicine, University of Louisville School of Medicine, Louisville, KY, USA
| | - Katarina Baluchova
- OncoLab Diagnostics GmbH Technologie- und Forschungszentrum, Viktor-Kaplan-Straße 2, 2700 Wiener Neustadt, Austria
| | - Werner Steimer
- Institute for Clinical Chemistry and Pathobiochemistry, Munich University of Technology, Klinikum rechts der Isar, D-81675 Munich, Germany
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16
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Veldman BCF, Kuper WFE, Lilien M, Schuurs-Hoeijmakers JHM, Marcelis C, Phan M, Hettinga Y, Talsma HE, van Hasselt PM, Haijes HA. Beyond nephronophthisis: Retinal dystrophy in the absence of kidney dysfunction in childhood expands the clinical spectrum of CEP83 deficiency. Am J Med Genet A 2021; 185:2204-2210. [PMID: 33938610 PMCID: PMC8252653 DOI: 10.1002/ajmg.a.62225] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 03/31/2021] [Accepted: 04/01/2021] [Indexed: 12/12/2022]
Abstract
The CEP83 protein is an essential part in the first steps of ciliogenesis, causing a ciliopathy if deficient. As a core component of the distal appendages of the centriole, CEP83 is located in almost all cell types and is involved in the primary cilium assembly. Previously reported CEP83 deficient patients all presented with nephronophthisis and kidney dysfunction. Despite retinal degeneration being a common feature in ciliopathies, only one patient also had retinitis. Here, we present two unrelated patients, who both presented with retinitis pigmentosa, without nephronophthisis or any form of kidney dysfunction. Both patients harbor bi‐allelic variants in CEP83. This report expands the current clinical spectrum of CEP83 deficiency. For timely diagnosis of CEP83 deficiency, we advocate that CEP83 should be included in gene panels for inherited retinal diseases.
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Affiliation(s)
- Bram C F Veldman
- Department of Metabolic Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Willemijn F E Kuper
- Department of Metabolic Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Marc Lilien
- Department of Pediatric Nephrology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Carlo Marcelis
- Department of Clinical Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Milan Phan
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ymkje Hettinga
- Bartiméus Diagnostic Center for Complex Visual Disorders, Zeist, The Netherlands
| | - Herman E Talsma
- Bartiméus Diagnostic Center for Complex Visual Disorders, Zeist, The Netherlands
| | - Peter M van Hasselt
- Department of Metabolic Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Hanneke A Haijes
- Department of Metabolic Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
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17
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Vrijenhoek T, Tonisson N, Kääriäinen H, Leitsalu L, Rigter T. Clinical genetics in transition-a comparison of genetic services in Estonia, Finland, and the Netherlands. J Community Genet 2021; 12:277-290. [PMID: 33704686 PMCID: PMC7948164 DOI: 10.1007/s12687-021-00514-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 02/18/2021] [Indexed: 11/25/2022] Open
Abstract
Genetics has traditionally enabled the reliable diagnosis of patients with rare genetic disorders, thus empowering the key role of today's clinical geneticists in providing healthcare. With the many novel technologies that have expanded the genetic toolkit, genetics is increasingly evolving beyond rare disease diagnostics. When placed in a transition context-like we do here-clinical genetics is likely to become a fully integral part of future healthcare and clinical genetic expertise will be required increasingly outside traditional clinical genetic settings. We explore transition effects on the thinking (culture), organizing (structure), and performing (practice) in clinical genetics, taking genetic healthcare in Estonia, Finland, and the Netherlands as examples. Despite clearly distinct healthcare histories, all three countries have initially implemented genetic healthcare in a rather similar fashion: as a diagnostic tool for predominantly rare congenital diseases, with clinical geneticists as the main providers. Dynamics at different levels, such as emerging technologies, biobanks and data infrastructure, and legislative frameworks, may require development of a new system attuned with the demands and (historic) context of specific countries. Here, we provide an overview of genetic service provisions in Estonia, Finland, and the Netherlands to consider the impact of historic and recent events on prospective developments in genetic healthcare.
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Affiliation(s)
- T Vrijenhoek
- Department of Genetics, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - N Tonisson
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
- Dept. of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia
| | - H Kääriäinen
- Finnish Institute for Health and Welfare, Helsinki, Finland
| | - L Leitsalu
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - T Rigter
- Department of Clinical Genetics, Section Community Genetics & Amsterdam Public Health Research Institute, Amsterdam University Medical Centre, Location VUmc, Amsterdam, The Netherlands.
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18
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François-Heude MC, Walther-Louvier U, Espil-Taris C, Beze-Beyrie P, Rivier F, Baudou E, Uro-Coste E, Rigau V, Martin Negrier ML, Rendu J, Morales RJ, Pégeot H, Thèze C, Lacourt D, Coville AC, Cossée M, Cances C. Evaluating next-generation sequencing in neuromuscular diseases with neonatal respiratory distress. Eur J Paediatr Neurol 2021; 31:78-87. [PMID: 33667896 DOI: 10.1016/j.ejpn.2021.01.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 12/18/2020] [Accepted: 01/19/2021] [Indexed: 02/09/2023]
Abstract
With the exception of infantile spinal muscular atrophy (SMA) and congenital myotonic dystrophy 1 (DM1), congenital myopathies and muscular dystrophies with neonatal respiratory distress pose diagnostic challenges. Next-generation sequencing (NGS) provides hope for the diagnosis of these rare diseases. We evaluated the efficiency of next-generation sequencing (NGS) in ventilated newborns with peripheral hypotonia. We compared the results of our previous study in a cohort of 19 patients analysed by Sanger sequencing from 2007 to 2012, with a diagnostic yield of 26% (5/19), and those of a new retrospective study in 28 patients from 2007 to 2018 diagnosed using MyoPanel, a neuromuscular disease panel, with a diagnostic yield of 43% (12/28 patients). Pathogenic variants were found in five genes: ACTA1 (n = 4 patients), RYR1 (n = 2), CACNA1S (n = 1), NEB (n = 3), and MTM1 (n = 2). Myopanel increased the diagnosis of congenital neuromuscular diseases, but more than half the patients remained undiagnosed. Whole exome sequencing did not seem to fully respond to this diagnostic limitation. Therefore, explorations with whole genome sequencing will be the next step.
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Affiliation(s)
- Marie-Céline François-Heude
- AOC (Atlantique-Occitanie-Caraïbe) Reference Centre for Neuromuscular Disorders, Neuropaediatric Department, Toulouse University Hospital, Toulouse, France
| | - Ulrike Walther-Louvier
- AOC (Atlantique-Occitanie-Caraïbe) Reference Centre for Neuromuscular Disorders, Neuropaediatric Department, Montpellier University Hospital, Montpellier, France
| | - Caroline Espil-Taris
- AOC (Atlantique-Occitanie-Caraïbe) Reference Centre for Neuromuscular Disorders, Neuropaediatric Department, Bordeaux University Hospital, Aquitaine, France
| | | | - François Rivier
- AOC (Atlantique-Occitanie-Caraïbe) Reference Centre for Neuromuscular Disorders, Neuropaediatric Department, Montpellier University Hospital, Montpellier, France
| | - Eloise Baudou
- AOC (Atlantique-Occitanie-Caraïbe) Reference Centre for Neuromuscular Disorders, Neuropaediatric Department, Toulouse University Hospital, Toulouse, France
| | - Emmanuelle Uro-Coste
- Department of Pathology, Toulouse University Hospital, Toulouse, France; INSERM U1037, Cancer Research Centre of Toulouse (CRCT), Toulouse, France
| | - Valérie Rigau
- AOC (Atlantique-Occitanie-Caraïbe) Reference Centre for Neuromuscular Disorders, Aquitaine, France; Department of Pathology, Centre Hospitalier Universitaire Montpellier, Montpellier, France
| | | | - John Rendu
- INSERM U1216, Grenoble Alpes University Hospital, University of Grenoble Alpes, Grenoble, France
| | - Raul Juntas Morales
- Laboratory of Rare Genetic Diseases (LGMR), University of Montpellier, Montpellier, France
| | - Henri Pégeot
- Molecular Genetics Laboratory, Montpellier University Hospital Centre, Montpellier, France
| | - Corinne Thèze
- Molecular Genetics Laboratory, Montpellier University Hospital Centre, Montpellier, France
| | - Delphine Lacourt
- Molecular Genetics Laboratory, Montpellier University Hospital Centre, Montpellier, France
| | - Anne Cécile Coville
- AOC (Atlantique-Occitanie-Caraïbe) Reference Centre for Neuromuscular Disorders, Neuropaediatric Department, Toulouse University Hospital, Toulouse, France
| | - Mireille Cossée
- Laboratory of Rare Genetic Diseases (LGMR), University of Montpellier, Montpellier, France; Molecular Genetics Laboratory, Montpellier University Hospital Centre, Montpellier, France
| | - Claude Cances
- AOC (Atlantique-Occitanie-Caraïbe) Reference Centre for Neuromuscular Disorders, Neuropaediatric Department, Toulouse University Hospital, Toulouse, France.
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19
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Westland R, Renkema KY, Knoers NV. Clinical Integration of Genome Diagnostics for Congenital Anomalies of the Kidney and Urinary Tract. Clin J Am Soc Nephrol 2021; 16:128-137. [PMID: 32312792 PMCID: PMC7792653 DOI: 10.2215/cjn.14661119] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Revolutions in genetics, epigenetics, and bioinformatics are currently changing the outline of diagnostics and clinical medicine. From a nephrologist's perspective, individuals with congenital anomalies of the kidney and urinary tract (CAKUT) are an important patient category: not only is CAKUT the predominant cause of kidney failure in children and young adults, but the strong phenotypic and genotypic heterogeneity of kidney and urinary tract malformations has hampered standardization of clinical decision making until now. However, patients with CAKUT may benefit from precision medicine, including an integrated diagnostics trajectory, genetic counseling, and personalized management to improve clinical outcomes of developmental kidney and urinary tract defects. In this review, we discuss the present understanding of the molecular etiology of CAKUT and the currently available genome diagnostic modalities in the clinical care of patients with CAKUT. Finally, we discuss how clinical integration of findings from large-scale genetic, epigenetic, and gene-environment interaction studies may improve the prognosis of all individuals with CAKUT.
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Affiliation(s)
- Rik Westland
- Department of Pediatric Nephrology, Amsterdam UMC, Amsterdam, The Netherlands
| | - Kirsten Y. Renkema
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Nine V.A.M. Knoers
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands,Department of Genetics, University Medical Centre Groningen, Groningen, The Netherlands
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20
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Elsink K, Huibers MMH, Hollink IHIM, van der Veken LT, Ernst RF, Simons A, Zonneveld-Huijssoon E, van der Hout AH, Abbott KM, Hoischen A, Pieterse M, Kuijpers TW, van Montfrans JM, van Gijn ME. National external quality assessment for next-generation sequencing-based diagnostics of primary immunodeficiencies. Eur J Hum Genet 2021; 29:20-28. [PMID: 32733070 PMCID: PMC7852558 DOI: 10.1038/s41431-020-0702-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 06/10/2020] [Accepted: 07/21/2020] [Indexed: 11/09/2022] Open
Abstract
Dutch genome diagnostic centers (GDC) use next-generation sequencing (NGS)-based diagnostic applications for the diagnosis of primary immunodeficiencies (PIDs). The interpretation of genetic variants in many PIDs is complicated because of the phenotypic and genetic heterogeneity. To analyze uniformity of variant filtering, interpretation, and reporting in NGS-based diagnostics for PID, an external quality assessment was performed. Four main Dutch GDCs participated in the quality assessment. Unannotated variant call format (VCF) files of two PID patient analyses per laboratory were distributed among the four GDCs, analyzed, and interpreted (eight analyses in total). Variants that would be reported to the clinician and/or advised for further investigation were compared between the centers. A survey measuring the experiences of clinical laboratory geneticists was part of the study. Analysis of samples with confirmed diagnoses showed that all centers reported at least the variants classified as likely pathogenic (LP) or pathogenic (P) variants in all samples, except for variants in two genes (PSTPIP1 and BTK). The absence of clinical information complicated correct classification of variants. In this external quality assessment, the final interpretation and conclusions of the genetic analyses were uniform among the four participating genetic centers. Clinical and immunological data provided by a medical specialist are required to be able to draw proper conclusions from genetic data.
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Affiliation(s)
- Kim Elsink
- Department of Pediatric Immunology and Infectious Diseases, University Medical Center Utrecht, Utrecht, University, Utrecht, The Netherlands
| | - Manon M H Huibers
- Department of Genetics, Division Laboratories, Pharmacy and Biomedical Genetics, University Medical Center Utrecht, Utrecht, University, Utrecht, The Netherlands
| | - Iris H I M Hollink
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Lars T van der Veken
- Department of Genetics, Division Laboratories, Pharmacy and Biomedical Genetics, University Medical Center Utrecht, Utrecht, University, Utrecht, The Netherlands
| | - Robert F Ernst
- Department of Genetics, Division Laboratories, Pharmacy and Biomedical Genetics, University Medical Center Utrecht, Utrecht, University, Utrecht, The Netherlands
| | - Annet Simons
- Department of Human Genetics, Nijmegen Center for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
- Radboud Institute for Oncology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Evelien Zonneveld-Huijssoon
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Annemieke H van der Hout
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Kristin M Abbott
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Alexander Hoischen
- Department of Human Genetics, Nijmegen Center for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
- Radboud Expertise Center for Immunodeficiency and Autoinflammation, Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Human Genetics and Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Marc Pieterse
- Department of Human Genetics, Nijmegen Center for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Taco W Kuijpers
- Department of Pediatric Hematology, Immunology and Infectious Diseases, Emma Children's Hospital, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Joris M van Montfrans
- Department of Pediatric Immunology and Infectious Diseases, University Medical Center Utrecht, Utrecht, University, Utrecht, The Netherlands
| | - Mariëlle E van Gijn
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.
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21
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Schubert SA, Morreau H, de Miranda NFCC, van Wezel T. The missing heritability of familial colorectal cancer. Mutagenesis 2020; 35:221-231. [PMID: 31605533 PMCID: PMC7352099 DOI: 10.1093/mutage/gez027] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 09/05/2019] [Indexed: 02/06/2023] Open
Abstract
Pinpointing heritability factors is fundamental for the prevention and early detection of cancer. Up to one-quarter of colorectal cancers (CRCs) occur in the context of familial aggregation of this disease, suggesting a strong genetic component. Currently, only less than half of the heritability of CRC can be attributed to hereditary syndromes or common risk loci. Part of the missing heritability of this disease may be explained by the inheritance of elusive high-risk variants, polygenic inheritance, somatic mosaicism, as well as shared environmental factors, among others. A great deal of the missing heritability in CRC is expected to be addressed in the coming years with the increased application of cutting-edge next-generation sequencing technologies, routine multigene panel testing and tumour-focussed germline predisposition screening approaches. On the other hand, it will be important to define the contribution of environmental factors to familial aggregation of CRC incidence. This review provides an overview of the known genetic causes of familial CRC and aims at providing clues that explain the missing heritability of this disease.
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Affiliation(s)
- Stephanie A Schubert
- Department of Pathology, Leiden University Medical Center, Leiden University, Leiden, The Netherlands
| | - Hans Morreau
- Department of Pathology, Leiden University Medical Center, Leiden University, Leiden, The Netherlands
| | - Noel F C C de Miranda
- Department of Pathology, Leiden University Medical Center, Leiden University, Leiden, The Netherlands
| | - Tom van Wezel
- Department of Pathology, Leiden University Medical Center, Leiden University, Leiden, The Netherlands
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22
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Winter EM, Ireland A, Butterfield NC, Haffner-Luntzer M, Horcajada MN, Veldhuis-Vlug AG, Oei L, Colaianni G, Bonnet N. Pregnancy and lactation, a challenge for the skeleton. Endocr Connect 2020; 9:R143-R157. [PMID: 32438342 PMCID: PMC7354730 DOI: 10.1530/ec-20-0055] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 05/12/2020] [Indexed: 12/19/2022]
Abstract
In this review we discuss skeletal adaptations to the demanding situation of pregnancy and lactation. Calcium demands are increased during pregnancy and lactation, and this is effectuated by a complex series of hormonal changes. The changes in bone structure at the tissue and whole bone level observed during pregnancy and lactation appear to largely recover over time. The magnitude of the changes observed during lactation may relate to the volume and duration of breastfeeding and return to regular menses. Studies examining long-term consequences of pregnancy and lactation suggest that there are small, site-specific benefits to bone density and that bone geometry may also be affected. Pregnancy- and lactation-induced osteoporosis (PLO) is a rare disease for which the pathophysiological mechanism is as yet incompletely known; here, we discuss and speculate on the possible roles of genetics, oxytocin, sympathetic tone and bone marrow fat. Finally, we discuss fracture healing during pregnancy and lactation and the effects of estrogen on this process.
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Affiliation(s)
- E M Winter
- Leiden University Medical Center, Department of Internal Medicine, Division of Endocrinology, Center for Bone Quality, Leiden, the Netherlands
- Correspondence should be addressed to E M Winter:
| | - A Ireland
- Musculoskeletal Science and Sports Medicine Research Centre, Department of Life Sciences, Manchester Metropolitan University, Manchester, United Kingdom
| | - N C Butterfield
- Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College London, Commonwealth Building, DuCane Road, London, United Kingdom
| | - M Haffner-Luntzer
- Institute of Orthopaedic Research and Biomechanics, University Medical Center Ulm, Ulm, Germany
| | - M-N Horcajada
- Nestlé Research, Department of Musculoskeletal Health, Innovation EPFL Park, Lausanne, Switzerland.
| | - A G Veldhuis-Vlug
- Leiden University Medical Center, Department of Internal Medicine, Division of Endocrinology, Center for Bone Quality, Leiden, the Netherlands
- Jan van Goyen Medical Center, Department of Internal Medicine, Amsterdam, the Netherlands
| | - L Oei
- Department of Internal Medicine, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - G Colaianni
- Department of Emergency and Organ Transplantation, University of Bari, Bari, Italy
| | - N Bonnet
- Nestlé Research, Department of Musculoskeletal Health, Innovation EPFL Park, Lausanne, Switzerland.
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23
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Diagnostic yield of next-generation sequencing applied to neurological disorders. J Clin Neurosci 2019; 67:14-18. [DOI: 10.1016/j.jocn.2019.06.041] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Revised: 04/20/2019] [Accepted: 06/21/2019] [Indexed: 10/26/2022]
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24
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Vears DF, Sénécal K, Borry P. Exploration of genetic health professional - laboratory specialist interactions in diagnostic genomic sequencing. Eur J Med Genet 2019; 63:103749. [PMID: 31472303 DOI: 10.1016/j.ejmg.2019.103749] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 08/14/2019] [Accepted: 08/24/2019] [Indexed: 10/26/2022]
Abstract
Like any new technology, rapid integration of genomic sequencing (GS) into the clinical setting can pose challenges for genetic health professionals (GHPs) using it to diagnose patients. We conducted semi-structured interviews with 31 clinical geneticists and genetic counsellors across Europe, Australia and Canada to gain a better understanding of the issues they were experiencing when requesting GS and receiving reports from laboratories. There was a spectrum of interactions between genetic health professionals and laboratories. This ranged from those that almost exclusively request sequencing from the laboratory that is affiliated with their genetic service, to those who do not have access to exome sequencing 'in-house' and instead send patient samples to a selection of different external laboratories. In general, a closer interaction between the clinicians and the laboratory scientists increased the involvement of the clinicians in the analysis/interpretation process. This appeared to lead to fewer, but more clinically relevant variants being reported, and greater GHP satisfaction in what is reported. Our findings suggest that GHPs consider integration of clinical expertise into the analysis/interpretation process is critical to ensure that the variants reported are of high clinical significance to patients. They also highlight the importance of providing GHPs with training in report interpretation.
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Affiliation(s)
- Danya F Vears
- Melbourne Law School, University of Melbourne, Carlton, Australia; Murdoch Children's Research Institute, The Royal Children's Hospital, Parkville, Australia; Center for Biomedical Ethics and Law, Department of Public Health and Primary Care, KU Leuven, Belgium; Leuven Institute for Human Genetics and Society, Leuven, Belgium.
| | - Karine Sénécal
- Centre of Genomics and Policy, McGill University, Montreal, Canada
| | - Pascal Borry
- Center for Biomedical Ethics and Law, Department of Public Health and Primary Care, KU Leuven, Belgium; Leuven Institute for Human Genetics and Society, Leuven, Belgium
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25
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Hippman C, Nislow C. Pharmacogenomic Testing: Clinical Evidence and Implementation Challenges. J Pers Med 2019; 9:jpm9030040. [PMID: 31394823 PMCID: PMC6789586 DOI: 10.3390/jpm9030040] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 07/23/2019] [Accepted: 08/02/2019] [Indexed: 12/25/2022] Open
Abstract
Pharmacogenomics can enhance patient care by enabling treatments tailored to genetic make-up and lowering risk of serious adverse events. As of June 2019, there are 132 pharmacogenomic dosing guidelines for 99 drugs and pharmacogenomic information is included in 309 medication labels. Recently, the technology for identifying individual-specific genetic variants (genotyping) has become more accessible. Next generation sequencing (NGS) is a cost-effective option for genotyping patients at many pharmacogenomic loci simultaneously, and guidelines for implementation of these data are available from organizations such as the Clinical Pharmacogenetics Implementation Consortium (CPIC) and the Dutch Pharmacogenetics Working Group (DPWG). NGS and related technologies are increasing knowledge in the research sphere, yet rates of genomic literacy remain low, resulting in a widening gap in knowledge translation to the patient. Multidisciplinary teams—including physicians, nurses, genetic counsellors, and pharmacists—will need to combine their expertise to deliver optimal pharmacogenomically-informed care.
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Affiliation(s)
- Catriona Hippman
- Department of Psychiatry, Faculty of Medicine, University of British Columbia, Vancouver, BC, V6T 2A1, Canada.
- BC Mental Health and Addictions Research Institute, 3rd Floor - 938 West 28th Avenue, Vancouver, BC, V5Z 4H4, Canada.
| | - Corey Nislow
- Faculty of Pharmaceutical Sciences, University of British Columbia, 6619-2405 Wesbrook Mall, Vancouver, BC, V6T 1Z3, Canada.
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26
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Phylogenomic Pipeline Validation for Foodborne Pathogen Disease Surveillance. J Clin Microbiol 2019; 57:JCM.01816-18. [PMID: 30728194 DOI: 10.1128/jcm.01816-18] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Foodborne pathogen surveillance in the United States is transitioning from strain identification using restriction digest technology (pulsed-field gel electrophoresis [PFGE]) to shotgun sequencing of the entire genome (whole-genome sequencing [WGS]). WGS requires a new suite of analysis tools, some of which have long histories in academia but are new to the field of public health and regulatory decision making. Although the general workflow is fairly standard for collecting and analyzing WGS data for disease surveillance, there are a number of differences in how the data are collected and analyzed across public health agencies, both nationally and internationally. This impedes collaborative public health efforts, so national and international efforts are underway to enable direct comparison of these different analysis methods. Ultimately, the harmonization efforts will allow the (mutually trusted and understood) production and analysis of WGS data by labs and agencies worldwide, thus improving outbreak response capabilities globally. This review provides a historical perspective on the use of WGS for pathogen tracking and summarizes the efforts underway to ensure the major steps in phylogenomic pipelines used for pathogen disease surveillance can be readily validated. The tools for doing this will ensure that the results produced are sound, reproducible, and comparable across different analytic approaches.
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27
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Daoud H, Ghani M, Nfonsam L, Potter R, Ordorica S, Haslett V, Santos N, Derksen H, Lahey D, McGill M, Trudel V, Antoniuk B, Vasli N, Chisholm C, Mettler G, Sinclair-Bourque E, McGowan-Jordan J, Smith A, Roberts R, Jarinova O. Genetic Diagnostic Testing for Inherited Cardiomyopathies: Considerations for Offering Multi-Gene Tests in a Health Care Setting. J Mol Diagn 2019; 21:437-448. [PMID: 30731207 DOI: 10.1016/j.jmoldx.2019.01.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 11/16/2018] [Accepted: 01/03/2019] [Indexed: 02/07/2023] Open
Abstract
Inherited cardiomyopathies (ICs) are a major cause of heart disease. Given their marked clinical and genetic heterogeneity, the content and clinical utility of IC multi-gene panels has been the topic of continuous debate. Our genetics diagnostic laboratory has been providing clinical diagnostic testing for ICs since 2012. We began by testing nine genes and expanded our panel by fivefold in 2015. Here, we describe the implementation of a cost-effective next-generation sequencing (NGS)-based assay for testing of IC genes, including a protocol that minimizes the amount of Sanger sequencing required to confirm variants identified by NGS, which reduces the cost and time of testing. The NGS assay was developed for the simultaneous analysis of 45 IC genes and was assessed for the impact of panel expansion on variant detection, turnaround time, and cost of testing in a cohort of 993 patients. The assay led to a considerable reduction in test cost and turnaround time. However, only a marginal increase was observed in the diagnostic yield, whereas the rate of inconclusive findings increased considerably. These findings suggest that the ongoing evaluation of gene content and monitoring of clinical utility for multi-gene tests are essential to achieve maximum clinical utility of multi-gene tests in a publicly funded health care setting.
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Affiliation(s)
- Hussein Daoud
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada.
| | - Mahdi Ghani
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Landry Nfonsam
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Ryan Potter
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Shelley Ordorica
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Virginia Haslett
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Nathaniel Santos
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Heather Derksen
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Donelda Lahey
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Martha McGill
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Vanessa Trudel
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Brittany Antoniuk
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Nasim Vasli
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Caitlin Chisholm
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Gabrielle Mettler
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | | | - Jean McGowan-Jordan
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada; Department of Pathology and Laboratory Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Amanda Smith
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada; Department of Pathology and Laboratory Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Robert Roberts
- University of Arizona College of Medicine, Tucson, Arizona
| | - Olga Jarinova
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada; Department of Pathology and Laboratory Medicine, University of Ottawa, Ottawa, Ontario, Canada.
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28
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Silva M, de Leeuw N, Mann K, Schuring-Blom H, Morgan S, Giardino D, Rack K, Hastings R. European guidelines for constitutional cytogenomic analysis. Eur J Hum Genet 2019; 27:1-16. [PMID: 30275486 PMCID: PMC6303289 DOI: 10.1038/s41431-018-0244-x] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 06/26/2018] [Accepted: 07/17/2018] [Indexed: 11/28/2022] Open
Abstract
With advancing technology and the consequent shift towards an increasing application of molecular genetic techniques (e.g., microarrays, next-generation sequencing) with the potential for higher resolution in specific contexts, as well as the application of combined testing strategies for the diagnosis of chromosomal disorders, it is crucial that cytogenetic/cytogenomic services keep up to date with technology and have documents that provide guidance in this constantly evolving scenario. These new guidelines therefore aim to provide an updated, practical and easily available document that will enable genetic laboratories to operate within acceptable standards and to maintain a quality service.
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Affiliation(s)
- Marisa Silva
- Departamento de Genética Humana, Instituto Nacional de Saúde Dr. Ricardo Jorge, Lisboa, Portugal
| | - Nicole de Leeuw
- Department of Human Genetics, Nijmegen Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Kathy Mann
- Genetics Department, Viapath Analytics, Guy's Hospital, London, SE1 9RT, UK
| | - Heleen Schuring-Blom
- Department of Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Sian Morgan
- All Wales Genetics Laboratory, Institute of Medical Genetics, University Hospital of Wales, Cardiff, Wales, UK
| | - Daniela Giardino
- Lab. Citogenetica Medica, Istituto Auxologico Italiano, Milano, Italy
| | - Katrina Rack
- CEQAS/GenQA, John Radcliffe Hospital, Oxford University Hospitals NHS Trust, Oxford, OX3 9DU, UK
| | - Ros Hastings
- CEQAS/GenQA, John Radcliffe Hospital, Oxford University Hospitals NHS Trust, Oxford, OX3 9DU, UK.
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29
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Medendorp NM, Hillen MA, Murugesu L, Aalfs CM, Stiggelbout AM, Smets EMA. Uncertainty related to multigene panel testing for cancer: a qualitative study on counsellors' and counselees' views. J Community Genet 2018; 10:303-312. [PMID: 30430454 PMCID: PMC6435776 DOI: 10.1007/s12687-018-0393-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 10/19/2018] [Indexed: 11/18/2022] Open
Abstract
Multigene panel testing is mainly used to improve identification of genetic causes in families with characteristics fitting multiple possible cancer syndromes. This technique may yield uncertainty, for example when variants of unknown significance are identified. This study explores counsellors’ and counselees’ experiences with uncertainty, and how they discuss uncertainties and decide about multigene panel testing. Six focus groups were conducted including 38 counsellors. Twelve counselees who had received genetic counselling about a multigene panel test were interviewed. The focus group sessions and interviews were audio-recorded and transcribed verbatim. Transcripts were analysed inductively by two independent coders and data were examined to obtain a comprehensive list of themes. Counsellors identified several uncertainties, e.g. finding a variant of unknown significance, or detecting an unsolicited finding. Most difficulty was experienced in deciding what uncertain information to communicate to counselees and how to do so. The extent and manner of providing uncertain information differed between centres and between counsellors. Counsellors attached more value to counselees’ preferences in decision making compared to less extended tests. Counselees experienced difficulty in recalling which uncertainties had been discussed during genetic counselling. They primarily reported to have experienced uncertainty about their own and their relatives’ risk of developing cancer. Counselees felt they had had a say in the decision. This study showed that counsellors need more guidance on whether and how to convey uncertainty. Undesirable practice variation in the communication of uncertainty may be prevented by determining what information should minimally be discussed to enable informed decision making.
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Affiliation(s)
- Niki M Medendorp
- Department of Medical Psychology - Amsterdam UMC, University of Amsterdam, P.O. Box 22700, 1100 DE, Amsterdam, The Netherlands. .,Amsterdam Public Health research institute, Amsterdam, The Netherlands. .,Cancer Center Amsterdam, Amsterdam, The Netherlands.
| | - Marij A Hillen
- Department of Medical Psychology - Amsterdam UMC, University of Amsterdam, P.O. Box 22700, 1100 DE, Amsterdam, The Netherlands.,Amsterdam Public Health research institute, Amsterdam, The Netherlands.,Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Laxsini Murugesu
- Department of Medical Psychology - Amsterdam UMC, University of Amsterdam, P.O. Box 22700, 1100 DE, Amsterdam, The Netherlands
| | - Cora M Aalfs
- Department of Clinical Genetics - Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands.,Department of Clinical Genetics - Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Anne M Stiggelbout
- Medical Decision Making, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
| | - Ellen M A Smets
- Department of Medical Psychology - Amsterdam UMC, University of Amsterdam, P.O. Box 22700, 1100 DE, Amsterdam, The Netherlands.,Amsterdam Public Health research institute, Amsterdam, The Netherlands.,Cancer Center Amsterdam, Amsterdam, The Netherlands
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30
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Challenges of Identifying Clinically Actionable Genetic Variants for Precision Medicine. JOURNAL OF HEALTHCARE ENGINEERING 2018; 2016:3617572. [PMID: 27195526 PMCID: PMC4955563 DOI: 10.1155/2016/3617572] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 03/17/2016] [Indexed: 12/30/2022]
Abstract
Advances in genomic medicine have the potential to change the way we treat human disease, but translating these advances into reality for improving healthcare outcomes depends essentially on our ability to discover disease- and/or drug-associated clinically actionable genetic mutations. Integration and manipulation of diverse genomic data and comprehensive electronic health records (EHRs) on a big data infrastructure can provide an efficient and effective way to identify clinically actionable genetic variants for personalized treatments and reduce healthcare costs. We review bioinformatics processing of next-generation sequencing (NGS) data, bioinformatics infrastructures for implementing precision medicine, and bioinformatics approaches for identifying clinically actionable genetic variants using high-throughput NGS data and EHRs.
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31
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Tack V, Spans L, Schuuring E, Keppens C, Zwaenepoel K, Pauwels P, Van Houdt J, Dequeker EMC. Describing the Reportable Range Is Important for Reliable Treatment Decisions: A Multiple Laboratory Study for Molecular Tumor Profiling Using Next-Generation Sequencing. J Mol Diagn 2018; 20:743-753. [PMID: 30055348 DOI: 10.1016/j.jmoldx.2018.06.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 05/14/2018] [Accepted: 06/05/2018] [Indexed: 01/04/2023] Open
Abstract
Because interpretation of next-generation sequencing (NGS) data remains challenging, optimization of the NGS process is needed to obtain correct sequencing results. Therefore, extensive validation and continuous monitoring of the quality is essential. NGS performance was compared with traditional detection methods and technical quality of nine NGS technologies was assessed. First, nine formalin-fixed, paraffin-embedded patient samples were analyzed by 114 laboratories by using different detection methods. No significant differences in performance were observed between analyses with NGS and traditional techniques. Second, two DNA control samples were analyzed for a selected number of variants by 26 participants with the use of nine different NGS technologies. Quality control metrics were analyzed from raw data files and a survey about routine procedures. Results showed large differences in coverages, but observed variant allele frequencies in raw data files were in line with predefined variant allele frequencies. Many false negative results were found because of low-quality regions, which were not reported as such. It is recommended to disclose the reportable range, the fraction of targeted genomic regions for which calls of acceptable quality can be generated, to avoid any errors in therapy decisions. NGS can be a reliable technique, only if essential quality control during analysis is applied and reported.
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Affiliation(s)
- Véronique Tack
- Biomedical Quality Assurance Research Unit, Department of Public Health and Primary Care, University of Leuven, Leuven, Belgium
| | - Lien Spans
- Center for Human Genetics, University of Leuven, Leuven, Belgium
| | - Ed Schuuring
- Department of Pathology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Cleo Keppens
- Biomedical Quality Assurance Research Unit, Department of Public Health and Primary Care, University of Leuven, Leuven, Belgium
| | - Karen Zwaenepoel
- Department of Pathology, University Hospital Antwerp, Edegem, Belgium
| | - Patrick Pauwels
- Center for Oncologic Research (CORE), University of Antwerp, Antwerp, Belgium
| | | | - Elisabeth M C Dequeker
- Biomedical Quality Assurance Research Unit, Department of Public Health and Primary Care, University of Leuven, Leuven, Belgium; Department of Medical Diagnostics, University Hospital Leuven, Leuven, Belgium.
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32
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Soto JL, Blanco I, Díez O, García Planells J, Lorda I, Matthijs G, Robledo M, Souche E, Lázaro C. Documento de consenso sobre la implementación de la secuenciación masiva de nueva generación en el diagnóstico genético de la predisposición hereditaria al cáncer. Med Clin (Barc) 2018; 151:80.e1-80.e10. [DOI: 10.1016/j.medcli.2017.12.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 12/13/2017] [Accepted: 12/14/2017] [Indexed: 01/20/2023]
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33
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Zenagui R, Lacourt D, Pegeot H, Yauy K, Juntas Morales R, Theze C, Rivier F, Cances C, Sole G, Renard D, Walther-Louvier U, Ferrer-Monasterio X, Espil C, Arné-Bes MC, Cintas P, Uro-Coste E, Martin Negrier ML, Rigau V, Bieth E, Goizet C, Claustres M, Koenig M, Cossée M. A Reliable Targeted Next-Generation Sequencing Strategy for Diagnosis of Myopathies and Muscular Dystrophies, Especially for the Giant Titin and Nebulin Genes. J Mol Diagn 2018; 20:533-549. [DOI: 10.1016/j.jmoldx.2018.04.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 03/30/2018] [Accepted: 04/05/2018] [Indexed: 01/05/2023] Open
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34
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Stallmeyer B, Dittmann S, Schulze-Bahr E. Genetische Diagnostik zur Vermeidung des plötzlichen Herztods. Internist (Berl) 2018; 59:776-789. [DOI: 10.1007/s00108-018-0462-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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35
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Loules G, Zamanakou M, Parsopoulou F, Vatsiou S, Psarros F, Csuka D, Porebski G, Obtulowicz K, Valerieva A, Staevska M, López-Lera A, López-Trascasa M, Moldovan D, Magerl M, Maurer M, Speletas M, Farkas H, Germenis AE. Targeted next-generation sequencing for the molecular diagnosis of hereditary angioedema due to C1-inhibitor deficiency. Gene 2018; 667:76-82. [PMID: 29753808 DOI: 10.1016/j.gene.2018.05.029] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 05/03/2018] [Accepted: 05/09/2018] [Indexed: 11/29/2022]
Abstract
SERPING1 genotyping of subjects suspicious for hereditary angioedema due to C1-INH deficiency (C1-INH-HAE) is important for clinical practice as well as for research reasons. Conventional approaches towards the detection of C1-INH-HAE-associated SERPING1 variants are cumbersome and time-demanding with many pitfalls. To take advantage of the benefits of next-generation sequencing (NGS) technology, we developed and validated a custom NGS platform that, by targeting the entire SERPING1 gene, facilitates genetic testing of C1-INH-HAE patients in clinical practice. In total, 135 different C1-INH-HAE-associated SERPING1 variants, out of the approximately 450 reported, along with 115 negative controls and 95 randomly selected DNA samples from affected family members of C1-INH-HAE index patients, were included in the forward and reverse validation processes of this platform. Our platform's performance, i.e. analytical sensitivity of 98.96%, a false negative rate of 1.05%, analytical specificity 100%, a false positive rate equal to zero, accuracy of 99.35%, and repeatability of 100% recommends its implementation as a first line approach for the genetic testing of C1-INH-HAE patients or as a confirmatory method. A noteworthy advantage of our platform is the concomitant detection of single nucleotide variants and copy number variations throughout the whole length of the SERPING1 gene, moreover providing information about the size and the localization of the latter. During our study, 15 novel C1-INH-HAE-related SERPING1 variants were detected.
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Affiliation(s)
- Gedeon Loules
- CeMIA SA, 31 Makrigianni street, GR-41334 Larissa, Greece.
| | | | - Faidra Parsopoulou
- CeMIA SA, 31 Makrigianni street, GR-41334 Larissa, Greece; Department of Immunology & Histocompatibility, University of Thessaly, School of Health Sciences, Faculty of Medicine, 3 Panepistimiou street, Biopolis, GR-41500 Larissa, Greece.
| | - Sofia Vatsiou
- CeMIA SA, 31 Makrigianni street, GR-41334 Larissa, Greece; Department of Immunology & Histocompatibility, University of Thessaly, School of Health Sciences, Faculty of Medicine, 3 Panepistimiou street, Biopolis, GR-41500 Larissa, Greece.
| | - Fotis Psarros
- Department of Allergology, Navy Hospital, 70 Dinoktatous street, GR-11521 Athens, Greece.
| | - Dorottya Csuka
- Hungarian Angioedema Center, 3rd Department of Internal Medicine, Semmelweis University, Kutvolgyi ut 4, H-1125 Budapest, Hungary.
| | - Grzegorz Porebski
- Department of Clinical and Environmental Allergology, Jagiellonian University Medical College, ul. Śniadeckich 10, 31-531 Krakow, Poland.
| | - Krystyna Obtulowicz
- Department of Clinical and Environmental Allergology, Jagiellonian University Medical College, ul. Śniadeckich 10, 31-531 Krakow, Poland.
| | - Anna Valerieva
- Clinic of Allergy and Asthma, Medical University of Sofia, 1 Georgi Sofiyski St, 1431 Sofia, Bulgaria
| | - Maria Staevska
- Clinic of Allergy and Asthma, Medical University of Sofia, 1 Georgi Sofiyski St, 1431 Sofia, Bulgaria
| | - Alberto López-Lera
- Hospital La Paz Health Research Institute-IdiPAZ-Research and Center for Biomedical Network Research on Rare Diseases (CIBERER U754), Paseo de la Castellana 261, 28046 Madrid, Spain
| | - Margarita López-Trascasa
- Hospital La Paz Health Research Institute-IdiPAZ-Research and Center for Biomedical Network Research on Rare Diseases (CIBERER U754), Paseo de la Castellana 261, 28046 Madrid, Spain.
| | - Dumitru Moldovan
- University of Medicine and Pharmacy, Tirgu Mures 540103, Romania
| | - Markus Magerl
- Department of Dermatology and Allergy, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany.
| | - Marcus Maurer
- Department of Dermatology and Allergy, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany.
| | - Matthaios Speletas
- Department of Immunology & Histocompatibility, University of Thessaly, School of Health Sciences, Faculty of Medicine, 3 Panepistimiou street, Biopolis, GR-41500 Larissa, Greece.
| | - Henriette Farkas
- Hungarian Angioedema Center, 3rd Department of Internal Medicine, Semmelweis University, Kutvolgyi ut 4, H-1125 Budapest, Hungary.
| | - Anastasios E Germenis
- CeMIA SA, 31 Makrigianni street, GR-41334 Larissa, Greece; Department of Immunology & Histocompatibility, University of Thessaly, School of Health Sciences, Faculty of Medicine, 3 Panepistimiou street, Biopolis, GR-41500 Larissa, Greece.
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36
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Assessment of concordance between fresh-frozen and formalin-fixed paraffin embedded tumor DNA methylation using a targeted sequencing approach. Oncotarget 2018; 8:48126-48137. [PMID: 28611295 PMCID: PMC5564631 DOI: 10.18632/oncotarget.18296] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 04/03/2017] [Indexed: 12/28/2022] Open
Abstract
DNA methylation is altered in many types of disease, including metastatic colorectal cancer. However, the methylome has not yet been fully described in archival formalin-fixed paraffin embedded (FFPE) samples in the context of matched fresh-frozen (FF) tumor material at base-pair resolution using a targeted approach. Using next-generation sequencing, we investigated three pairs of matched FFPE and FF samples to determine the extent of their similarity. We identified a ‘bowing’ pattern specific to FFPE samples categorized by a lower CG proportion at the start of sequence reads. We have found no evidence that this affected methylation calling, nor concordance of results. We also found no significant increase in deamination, measured by C>T transitions, previously considered a result of crosslinking DNA by formalin fixation and a barrier to the use of FFPE in methylation studies. The methods used in this study have shown sensitivity of between 60-70% based on positions also methylated in colorectal cancer cell lines. We demonstrate that FFPE material is a useful source of tumor material for methylation studies using targeted sequencing.
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37
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Exome sequencing has higher diagnostic yield compared to simulated disease-specific panels in children with suspected monogenic disorders. Eur J Hum Genet 2018; 26:644-651. [PMID: 29453417 DOI: 10.1038/s41431-018-0099-1] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 12/11/2017] [Accepted: 01/11/2018] [Indexed: 01/13/2023] Open
Abstract
As test costs decline, whole-exome sequencing (WES) has become increasingly used for clinical diagnosis, and now represents the primary alternative to gene panel testing for patients with a suspected genetic disorder. We sought to compare the diagnostic yield of singleton-WES with simulated application of commercial gene panels in children suspected of having a genetically heterogeneous condition. Recruitment, singleton-WES and phenotype-driven variant analysis was completed for 145 paediatric patients. At recruitment, clinicians were required to propose commercial gene panel tests as an alternative to WES and nominate a phenotype-driven candidate gene list. In WES-diagnosed children, three commercial options for each proposed panel were identified and evaluated for hypothetical diagnostic yield assuming 100% analytical sensitivity and specificity. We compared the price of WES with the least costly panel in WES-diagnosed children. In WES-undiagnosed children, we evaluated the exonic coverage of their phenotype-driven gene list using aggregate data. WES diagnoses were made in genes not included in at least one-of-three commercial panels in 42% of cases. Had a panel been selected instead, 23% of WES-diagnosed children would not have been diagnosed. In 26% of cases, the least costly panel option would have been more expensive than WES. Evaluation of WES coverage found that at the most stringent level of 20× coverage, the likelihood of missing a clinically relevant variant in a candidate gene list was maximally 8%. The broader coverage of WES makes it a superior alternative to gene panel testing at similar financial cost for children with suspected complex monogenic phenotypes.
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38
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Abstract
The majority of rare diseases affect children, most of whom have an underlying genetic cause for their condition. However, making a molecular diagnosis with current technologies and knowledge is often still a challenge. Paediatric genomics is an immature but rapidly evolving field that tackles this issue by incorporating next-generation sequencing technologies, especially whole-exome sequencing and whole-genome sequencing, into research and clinical workflows. This complex multidisciplinary approach, coupled with the increasing availability of population genetic variation data, has already resulted in an increased discovery rate of causative genes and in improved diagnosis of rare paediatric disease. Importantly, for affected families, a better understanding of the genetic basis of rare disease translates to more accurate prognosis, management, surveillance and genetic advice; stimulates research into new therapies; and enables provision of better support.
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39
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Apessos A, Agiannitopoulos K, Pepe G, Tsaousis GN, Papadopoulou E, Metaxa-Mariatou V, Tsirigoti A, Efstathiadou C, Markopoulos C, Xepapadakis G, Venizelos V, Tsiftsoglou A, Natsiopoulos I, Nasioulas G. Comprehensive BRCA mutation analysis in the Greek population. Experience from a single clinical diagnostic center. Cancer Genet 2018; 220:1-12. [DOI: 10.1016/j.cancergen.2017.10.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 10/09/2017] [Accepted: 10/12/2017] [Indexed: 12/28/2022]
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40
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Vears DF, Sénécal K, Clarke AJ, Jackson L, Laberge AM, Lovrecic L, Piton A, Van Gassen KLI, Yntema HG, Knoppers BM, Borry P. Points to consider for laboratories reporting results from diagnostic genomic sequencing. Eur J Hum Genet 2018; 26:36-43. [PMID: 29184171 PMCID: PMC5839050 DOI: 10.1038/s41431-017-0043-9] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 10/31/2017] [Indexed: 11/09/2022] Open
Abstract
Although NGS technologies are well-embedded in the clinical setting for identification of genetic causes of disease, guidelines issued by professional bodies are inconsistent regarding some aspects of reporting results. Most recommendations do not give detailed guidance about whether variants of uncertain significance (VUS) should be reported by laboratory personnel to clinicians, and give conflicting messages regarding whether unsolicited findings (UF) should be reported. There are also differences both in their recommendations regarding whether actively searching for secondary findings (SF) is appropriate, and in the extent to which they address the duty (or lack thereof) to reanalyse variants when new information arises. An interdisciplinary working group considered the current guidelines, their own experiences, and data from a recent qualitative study to develop a set of points to consider for laboratories reporting results from diagnostic NGS. These points to consider fall under six categories: (i) Testing approaches and technologies used, (ii) Approaches for VUS; (iii) Approaches for reporting UF, (iv) Approaches regarding SF; (v) Reanalysis of data & re-contact; and vi) Minors. While it is unclear whether uniformity in reporting across all laboratories is desirable, we hope these points to consider will be useful to diagnostic laboratories as they develop their processes for making decisions about reporting VUS and UF from NGS in the diagnostic context.
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Affiliation(s)
- D F Vears
- Center for Biomedical Ethics and Law, Department of Public Health and Primary Care, KU Leuven, Leuven, Belgium.
- Leuven Institute for Human Genetics and Society, Leuven, Belgium.
| | - K Sénécal
- Centre of Genomics and Policy, McGill University, Montreal, Canada
| | - A J Clarke
- Division of Cancer & Genetics, School of Medicine, Cardiff University, Cardiff, Wales, United Kingdom
| | - L Jackson
- University of Exeter Medical School, University of Exeter, Exeter, United Kingdom
| | - A M Laberge
- Department of Pediatrics, Université de Montréal, Medical Genetics, CHU Sainte-Justine; CHU Sainte-Justine Research Center, Montreal, Quebec, Canada
| | - L Lovrecic
- Clinical Institute of Medical Genetics, University Medical Center Ljubljana, Ljubljana, Slovenia
| | - A Piton
- Molecular diagnostic laboratory, Strasbourg University Hospitals, Strasbourg, France
| | - K L I Van Gassen
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - H G Yntema
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - B M Knoppers
- Centre of Genomics and Policy, McGill University, Montreal, Canada
| | - P Borry
- Center for Biomedical Ethics and Law, Department of Public Health and Primary Care, KU Leuven, Leuven, Belgium
- Leuven Institute for Human Genetics and Society, Leuven, Belgium
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41
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Characterizing reduced coverage regions through comparison of exome and genome sequencing data across 10 centers. Genet Med 2017; 20:855-866. [PMID: 29144510 PMCID: PMC6456263 DOI: 10.1038/gim.2017.192] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 09/05/2017] [Indexed: 01/21/2023] Open
Abstract
PURPOSE: As massively parallel sequencing is increasingly being used for
clinical decision-making, it has become critical to understand parameters
that affect sequencing quality and to establish methods for measuring and
reporting clinical sequencing standards. In this report, we propose a
definition for reduced coverage regions and have
established a set of standards for variant calling in clinical sequencing
applications. METHODS: To enable sequencing centers to assess the regions of poor sequencing
quality in their own data, we optimized and used a tool
(ExCid) to identify reduced coverage loci within genes
or regions of particular interest. We used this framework to examine
sequencing data from 500 patients generated in ten projects from sequencing
centers in the NHGRI/NCI Clinical Sequencing Exploratory Research (CSER)
Consortium. RESULTS: This approach identified reduced coverage regions in clinically
relevant genes, including known clinically relevant loci that were uniquely
missed at individual centers, in multiple centers, and in all centers. CONCLUSIONS: This report provides a process roadmap for clinical sequencing
centers looking to perform similar analyses on their data.
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42
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Ilyas M. Next-Generation Sequencing in Diagnostic Pathology. Pathobiology 2017; 84:292-305. [PMID: 29131018 DOI: 10.1159/000480089] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 08/06/2017] [Indexed: 12/26/2022] Open
Abstract
Interrogation of tissue informs on patient management through delivery of a diagnosis together with associated clinically relevant data. The diagnostic pathologist will usually evaluate the morphological appearances of a tissue sample and, occasionally, the pattern of expression of a limited number of biomarkers. Recent developments in sequencing technology mean that DNA and RNA from tissue samples can now be interrogated in great detail. These new technologies, collectively known as next-generation sequencing (NGS), generate huge amounts of data which can be used to support patient management. In order to maximize the utility of tissue interrogation, the molecular data need to be interpreted and integrated with the morphological data. However, in order to interpret the molecular data, the pathologist must understand the utility and the limitations of NGS data. In this review, the principles behind NGS technologies are described. In addition, the caveats in the interpretation of the data are discussed, and a scheme is presented to "classify" the types of data which are generated. Finally, a glossary of new terminology is included to help pathologists become familiar with the lexicon of NGS-derived molecular data.
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43
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Sekse C, Holst-Jensen A, Dobrindt U, Johannessen GS, Li W, Spilsberg B, Shi J. High Throughput Sequencing for Detection of Foodborne Pathogens. Front Microbiol 2017; 8:2029. [PMID: 29104564 PMCID: PMC5655695 DOI: 10.3389/fmicb.2017.02029] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 10/04/2017] [Indexed: 12/23/2022] Open
Abstract
High-throughput sequencing (HTS) is becoming the state-of-the-art technology for typing of microbial isolates, especially in clinical samples. Yet, its application is still in its infancy for monitoring and outbreak investigations of foods. Here we review the published literature, covering not only bacterial but also viral and Eukaryote food pathogens, to assess the status and potential of HTS implementation to inform stakeholders, improve food safety and reduce outbreak impacts. The developments in sequencing technology and bioinformatics have outpaced the capacity to analyze and interpret the sequence data. The influence of sample processing, nucleic acid extraction and purification, harmonized protocols for generation and interpretation of data, and properly annotated and curated reference databases including non-pathogenic "natural" strains are other major obstacles to the realization of the full potential of HTS in analytical food surveillance, epidemiological and outbreak investigations, and in complementing preventive approaches for the control and management of foodborne pathogens. Despite significant obstacles, the achieved progress in capacity and broadening of the application range over the last decade is impressive and unprecedented, as illustrated with the chosen examples from the literature. Large consortia, often with broad international participation, are making coordinated efforts to cope with many of the mentioned obstacles. Further rapid progress can therefore be prospected for the next decade.
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Affiliation(s)
- Camilla Sekse
- Department of Animal Health and Food Safety, Norwegian Veterinary Institute, Oslo, Norway
| | - Arne Holst-Jensen
- Department of Animal Health and Food Safety, Norwegian Veterinary Institute, Oslo, Norway
| | - Ulrich Dobrindt
- Institute of Hygiene, University of Münster, Münster, Germany
| | - Gro S. Johannessen
- Department of Animal Health and Food Safety, Norwegian Veterinary Institute, Oslo, Norway
| | - Weihua Li
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University–University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Bjørn Spilsberg
- Department of Analysis and Diagnostics, Norwegian Veterinary Institute, Oslo, Norway
| | - Jianxin Shi
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University–University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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44
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White SJ, Laros JF, Bakker E, Cambon‐Thomsen A, Eden M, Leonard S, Lochmüller H, Matthijs G, Mattocks C, Patton S, Payne K, Scheffer H, Souche E, Thomassen E, Thompson R, Traeger‐Synodinos J, Vooren S, Janssen B, den Dunnen JT. Critical points for an accurate human genome analysis. Hum Mutat 2017; 38:912-921. [DOI: 10.1002/humu.23238] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 04/13/2017] [Accepted: 04/23/2017] [Indexed: 12/16/2022]
Affiliation(s)
- Stefan J. White
- Department of Human Genetics, Leiden University Medical Center The Netherlands
| | - Jeroen F.J. Laros
- Department of Human Genetics, Leiden University Medical Center The Netherlands
- Clinical GeneticsLeiden University Medical Center The Netherlands
- GenomeScan Leiden The Netherlands
| | - Egbert Bakker
- Clinical GeneticsLeiden University Medical Center The Netherlands
| | - Anne Cambon‐Thomsen
- Epidemiology and Public Health Analyses, Inserm and Université Toulouse III Paul Sabatier Toulouse UMR 1027 France
| | - Martin Eden
- Manchester Centre for Health Economics, University of Manchester Manchester UK
| | - Samantha Leonard
- Epidemiology and Public Health Analyses, Inserm and Université Toulouse III Paul Sabatier Toulouse UMR 1027 France
| | - Hanns Lochmüller
- Institute of Genetic Medicine, Newcastle University Newcastle upon Tyne UK
| | | | | | - Simon Patton
- Central Manchester University Hospitals Foundation Trust, EMQN Manchester UK
| | - Katherine Payne
- Manchester Centre for Health Economics, University of Manchester Manchester UK
| | | | | | - Ellen Thomassen
- Department of Human Genetics, Leiden University Medical Center The Netherlands
| | - Rachel Thompson
- Institute of Genetic Medicine, Newcastle University Newcastle upon Tyne UK
| | | | | | | | - Johan T. den Dunnen
- Department of Human Genetics, Leiden University Medical Center The Netherlands
- Clinical GeneticsLeiden University Medical Center The Netherlands
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45
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Abstract
Most genetic disorders are clinically and genetically heterogeneous. Next-generation sequencing (NGS) has revolutionized the field and is providing rapidly growing insights into the pathomechanism of hereditary nephropathies. Current best-practice guidelines for most hereditary nephropathies include genetic diagnostics. The increasing number of genes that have to be considered in patients with hereditary nephropathies is often challenging when addressed by conventional techniques and largely benefits from NGS-based approaches that allow the parallel analysis of all disease genes in a single test at relatively low cost, e.g., by the use of multi-gene panels. Knowledge of the underlying genotype is of advantage in discussions with regard to transplantation and therapeutic options. Further, genetics may aid the early detection and treatment of renal and extrarenal complications and the reduction of invasive procedures. An accurate genetic diagnosis is crucial for genetic counselling, provides information about the recurrence risk and may help to improve the clinical management of patients and their families. The bottleneck in genetics is no longer the primary wet lab process but the interpretation of the obtained genetic data, which is by far the most challenging and work-intensive part of the analysis. This can only be managed in a multidisciplinary setting that brings together expert knowledge in genetics and the respective medical field. In the future, bench and bedside benefits can be expected from this kind of digitized medicine.
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46
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Abstract
Genetic aortic syndromes (GAS) include Marfan, Loeys-Dietz, vascular Ehlers-Danlos, and Turner syndrome as well as congenital bicuspid aortic valve. The clinical management of these diseases has certain similarities and differences. We employed medical strategy analysis to test the utility of genetic diagnostics in the management of GAS. We chose the standpoint of the cardiologist for our analysis. In the first step, the medical goals in the management of GAS are specified. In the second step, the accuracy of genetic diagnostics for GAS is examined. Finally, conclusions can be drawn about the utility of genetic diagnostics in managing GAS. We found that genetic diagnostics is necessary to exclude GAS, to diagnose GAS, and to specify disease types. Second, combining phenotype with genotype information maximizes the predictability of the course of disease. Third, with genetic diagnostics it is possible to predict the birth of children with causative mutations for GAS and to initiate drug therapy to prevent the onset of aortic dilatation or to slow down its progression to aortic aneurysm. Finally, genetic diagnostics improves prognostic predictions and thereby contributes to a better timing of elective surgery and to a better choice of procedures. The findings of our medical strategy analysis indicate the high utility of genetic diagnostics for managing GAS.
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Povysil G, Tzika A, Vogt J, Haunschmid V, Messiaen L, Zschocke J, Klambauer G, Hochreiter S, Wimmer K. panelcn.MOPS: Copy-number detection in targeted NGS panel data for clinical diagnostics. Hum Mutat 2017; 38:889-897. [PMID: 28449315 PMCID: PMC5518446 DOI: 10.1002/humu.23237] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 04/21/2017] [Accepted: 04/22/2017] [Indexed: 11/10/2022]
Abstract
Targeted next‐generation‐sequencing (NGS) panels have largely replaced Sanger sequencing in clinical diagnostics. They allow for the detection of copy‐number variations (CNVs) in addition to single‐nucleotide variants and small insertions/deletions. However, existing computational CNV detection methods have shortcomings regarding accuracy, quality control (QC), incidental findings, and user‐friendliness. We developed panelcn.MOPS, a novel pipeline for detecting CNVs in targeted NGS panel data. Using data from 180 samples, we compared panelcn.MOPS with five state‐of‐the‐art methods. With panelcn.MOPS leading the field, most methods achieved comparably high accuracy. panelcn.MOPS reliably detected CNVs ranging in size from part of a region of interest (ROI), to whole genes, which may comprise all ROIs investigated in a given sample. The latter is enabled by analyzing reads from all ROIs of the panel, but presenting results exclusively for user‐selected genes, thus avoiding incidental findings. Additionally, panelcn.MOPS offers QC criteria not only for samples, but also for individual ROIs within a sample, which increases the confidence in called CNVs. panelcn.MOPS is freely available both as R package and standalone software with graphical user interface that is easy to use for clinical geneticists without any programming experience. panelcn.MOPS combines high sensitivity and specificity with user‐friendliness rendering it highly suitable for routine clinical diagnostics.
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Affiliation(s)
- Gundula Povysil
- Institute of Bioinformatics, Johannes Kepler University Linz, Linz, Austria
| | - Antigoni Tzika
- Division of Human Genetics, Medical University Innsbruck, Innsbruck, Austria
| | - Julia Vogt
- Division of Human Genetics, Medical University Innsbruck, Innsbruck, Austria
| | - Verena Haunschmid
- Institute of Bioinformatics, Johannes Kepler University Linz, Linz, Austria
| | - Ludwine Messiaen
- Medical Genomics Laboratory, Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama
| | - Johannes Zschocke
- Division of Human Genetics, Medical University Innsbruck, Innsbruck, Austria
| | - Günter Klambauer
- Institute of Bioinformatics, Johannes Kepler University Linz, Linz, Austria
| | - Sepp Hochreiter
- Institute of Bioinformatics, Johannes Kepler University Linz, Linz, Austria
| | - Katharina Wimmer
- Division of Human Genetics, Medical University Innsbruck, Innsbruck, Austria
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48
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van Egmond ME, Lugtenberg CHA, Brouwer OF, Contarino MF, Fung VSC, Heiner-Fokkema MR, van Hilten JJ, van der Hout AH, Peall KJ, Sinke RJ, Roze E, Verschuuren-Bemelmans CC, Willemsen MA, Wolf NI, Tijssen MA, de Koning TJ. A post hoc study on gene panel analysis for the diagnosis of dystonia. Mov Disord 2017; 32:569-575. [PMID: 28186668 DOI: 10.1002/mds.26937] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2016] [Revised: 12/21/2016] [Accepted: 01/08/2017] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Genetic disorders causing dystonia show great heterogeneity. Recent studies have suggested that next-generation sequencing techniques such as gene panel analysis can be effective in diagnosing heterogeneous conditions. The objective of this study was to investigate whether dystonia patients with a suspected genetic cause could benefit from the use of gene panel analysis. METHODS In this post hoc study, we describe gene panel analysis results of 61 dystonia patients (mean age, 31 years; 72% young onset) in our tertiary referral center. The panel covered 94 dystonia-associated genes. As comparison with a historic cohort was not possible because of the rapidly growing list of dystonia genes, we compared the diagnostic workup with and without gene panel analysis in the same patients. The workup without gene panel analysis (control group) included theoretical diagnostic strategies formulated by independent experts in the field, based on detailed case descriptions. The primary outcome measure was diagnostic yield; secondary measures were cost and duration of diagnostic workup. RESULTS Workup with gene panel analysis led to a confirmed molecular diagnosis in 14.8%, versus 7.4% in the control group (P = 0.096). In the control group, on average 3 genes/case were requested. The mean costs were lower in the gene panel analysis group (€1822/case) than in the controls (€2660/case). The duration of the workup was considerably shorter with gene panel analysis (28 vs 102 days). CONCLUSIONS Gene panel analysis facilitates molecular diagnosis in complex cases of dystonia, with a good diagnostic yield (14.8%), a quicker diagnostic workup, and lower costs, representing a major improvement for patients and their families. © 2016 International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Martje E van Egmond
- University of Groningen, University Medical Centre Groningen, Department of Neurology, Groningen, the Netherlands.,Ommelander Ziekenhuis Groningen, Department of Neurology, Delfzijl and Winschoten, the Netherlands
| | - Coen H A Lugtenberg
- University of Groningen, University Medical Centre Groningen, Department of Neurology, Groningen, the Netherlands
| | - Oebele F Brouwer
- University of Groningen, University Medical Centre Groningen, Department of Neurology, Groningen, the Netherlands
| | - Maria Fiorella Contarino
- Department of Neurology, Leiden University Medical Centre, Leiden, the Netherlands.,Department of Neurology, Haga Teaching Hospital, The Hague, the Netherlands
| | - Victor S C Fung
- Movement Disorders Unit, Department of Neurology, Westmead Hospital & Sydney Medical School, University of Sydney, Sydney, Australia
| | - M Rebecca Heiner-Fokkema
- University of Groningen, University Medical Centre Groningen, Department of Laboratory Medicine, Groningen, the Netherlands
| | - Jacobus J van Hilten
- Department of Neurology, Leiden University Medical Centre, Leiden, the Netherlands
| | - Annemarie H van der Hout
- University of Groningen, University Medical Centre Groningen, Department of Genetics, Groningen, the Netherlands
| | - Kathryn J Peall
- MRC Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, United Kingdom
| | - Richard J Sinke
- University of Groningen, University Medical Centre Groningen, Department of Genetics, Groningen, the Netherlands
| | - Emmanuel Roze
- Département de Neurologie, AP-HP, Hôpital Pitié-Salpêtrière and Sorbonne Universités, Université Pierre and Marie Curie, Institut du Cerveau et de la Moelle épinière, Paris, France
| | | | - Michel A Willemsen
- Radboud University Medical Centre, Department of Paediatric Neurology, Nijmegen, the Netherlands
| | - Nicole I Wolf
- VU University Medical Centre, Department of Child Neurology and Neuroscience Campus Amsterdam, Amsterdam, the Netherlands
| | - Marina A Tijssen
- University of Groningen, University Medical Centre Groningen, Department of Neurology, Groningen, the Netherlands
| | - Tom J de Koning
- University of Groningen, University Medical Centre Groningen, Department of Neurology, Groningen, the Netherlands.,University of Groningen, University Medical Centre Groningen, Department of Genetics, Groningen, the Netherlands.,University of Groningen, University Medical Centre Groningen, Department of Paediatrics, Groningen, the Netherlands
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49
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Feliubadaló L, Tonda R, Gausachs M, Trotta JR, Castellanos E, López-Doriga A, Teulé À, Tornero E, Del Valle J, Gel B, Gut M, Pineda M, González S, Menéndez M, Navarro M, Capellá G, Gut I, Serra E, Brunet J, Beltran S, Lázaro C. Benchmarking of Whole Exome Sequencing and Ad Hoc Designed Panels for Genetic Testing of Hereditary Cancer. Sci Rep 2017; 7:37984. [PMID: 28050010 PMCID: PMC5209723 DOI: 10.1038/srep37984] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 11/02/2016] [Indexed: 12/14/2022] Open
Abstract
Next generation sequencing panels have been developed for hereditary cancer, although there is some debate about their cost-effectiveness compared to exome sequencing. The performance of two panels is compared to exome sequencing. Twenty-four patients were selected: ten with identified mutations (control set) and fourteen suspicious of hereditary cancer but with no mutation (discovery set). TruSight Cancer (94 genes) and a custom panel (122 genes) were assessed alongside exome sequencing. Eighty-three genes were targeted by the two panels and exome sequencing. More than 99% of bases had a read depth of over 30x in the panels, whereas exome sequencing covered 94%. Variant calling with standard settings identified the 10 mutations in the control set, with the exception of MSH6 c.255dupC using TruSight Cancer. In the discovery set, 240 unique non-silent coding and canonic splice-site variants were identified in the panel genes, 7 of them putatively pathogenic (in ATM, BARD1, CHEK2, ERCC3, FANCL, FANCM, MSH2). The three approaches identified a similar number of variants in the shared genes. Exomes were more expensive than panels but provided additional data. In terms of cost and depth, panels are a suitable option for genetic diagnostics, although exomes also identify variants in non-targeted genes.
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Affiliation(s)
- Lídia Feliubadaló
- Hereditary Cancer Program, Joint Program on Hereditary Cancer, Catalan Institute of Oncology, IDIBELL campus in Hospitalet de Llobregat, Catalonia, Spain
| | - Raúl Tonda
- Centro Nacional de Análisis Genómico (CNAG-CRG), Center for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Barcelona, Catalonia, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Catalonia, Spain
| | - Mireia Gausachs
- Hereditary Cancer Program, Joint Program on Hereditary Cancer, Catalan Institute of Oncology, IDIBELL campus in Hospitalet de Llobregat, Catalonia, Spain
| | - Jean-Rémi Trotta
- Centro Nacional de Análisis Genómico (CNAG-CRG), Center for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Barcelona, Catalonia, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Catalonia, Spain
| | - Elisabeth Castellanos
- Genetic Variation in Cancer Group, Joint Program on Hereditary Cancer, Institut de Medicina Predictiva i Personalitzada del Càncer, Badalona, Catalonia, Spain
| | - Adriana López-Doriga
- Hereditary Cancer Program, Joint Program on Hereditary Cancer, Catalan Institute of Oncology, IDIBELL campus in Hospitalet de Llobregat, Catalonia, Spain
| | - Àlex Teulé
- Hereditary Cancer Program, Joint Program on Hereditary Cancer, Catalan Institute of Oncology, IDIBELL campus in Hospitalet de Llobregat, Catalonia, Spain
| | - Eva Tornero
- Hereditary Cancer Program, Joint Program on Hereditary Cancer, Catalan Institute of Oncology, IDIBELL campus in Hospitalet de Llobregat, Catalonia, Spain
| | - Jesús Del Valle
- Hereditary Cancer Program, Joint Program on Hereditary Cancer, Catalan Institute of Oncology, IDIBELL campus in Hospitalet de Llobregat, Catalonia, Spain
| | - Bernat Gel
- Genetic Variation in Cancer Group, Joint Program on Hereditary Cancer, Institut de Medicina Predictiva i Personalitzada del Càncer, Badalona, Catalonia, Spain
| | - Marta Gut
- Centro Nacional de Análisis Genómico (CNAG-CRG), Center for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Barcelona, Catalonia, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Catalonia, Spain
| | - Marta Pineda
- Hereditary Cancer Program, Joint Program on Hereditary Cancer, Catalan Institute of Oncology, IDIBELL campus in Hospitalet de Llobregat, Catalonia, Spain
| | - Sara González
- Hereditary Cancer Program, Joint Program on Hereditary Cancer, Catalan Institute of Oncology, IDIBELL campus in Hospitalet de Llobregat, Catalonia, Spain
| | - Mireia Menéndez
- Hereditary Cancer Program, Joint Program on Hereditary Cancer, Catalan Institute of Oncology, IDIBELL campus in Hospitalet de Llobregat, Catalonia, Spain
| | - Matilde Navarro
- Hereditary Cancer Program, Joint Program on Hereditary Cancer, Catalan Institute of Oncology, IDIBELL campus in Hospitalet de Llobregat, Catalonia, Spain
| | - Gabriel Capellá
- Hereditary Cancer Program, Joint Program on Hereditary Cancer, Catalan Institute of Oncology, IDIBELL campus in Hospitalet de Llobregat, Catalonia, Spain
| | - Ivo Gut
- Centro Nacional de Análisis Genómico (CNAG-CRG), Center for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Barcelona, Catalonia, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Catalonia, Spain
| | - Eduard Serra
- Genetic Variation in Cancer Group, Joint Program on Hereditary Cancer, Institut de Medicina Predictiva i Personalitzada del Càncer, Badalona, Catalonia, Spain
| | - Joan Brunet
- Hereditary Cancer Program, Joint Program on Hereditary Cancer, Catalan Institute of Oncology, IdibGi in Girona, Catalonia, Spain
| | - Sergi Beltran
- Centro Nacional de Análisis Genómico (CNAG-CRG), Center for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Barcelona, Catalonia, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Catalonia, Spain
| | - Conxi Lázaro
- Hereditary Cancer Program, Joint Program on Hereditary Cancer, Catalan Institute of Oncology, IDIBELL campus in Hospitalet de Llobregat, Catalonia, Spain
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50
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A comprehensive custom panel design for routine hereditary cancer testing: preserving control, improving diagnostics and revealing a complex variation landscape. Sci Rep 2017; 7:39348. [PMID: 28051113 PMCID: PMC5209725 DOI: 10.1038/srep39348] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 11/22/2016] [Indexed: 01/02/2023] Open
Abstract
We wanted to implement an NGS strategy to globally analyze hereditary cancer with diagnostic quality while retaining the same degree of understanding and control we had in pre-NGS strategies. To do this, we developed the I2HCP panel, a custom bait library covering 122 hereditary cancer genes. We improved bait design, tested different NGS platforms and created a clinically driven custom data analysis pipeline. The I2HCP panel was developed using a training set of hereditary colorectal cancer, hereditary breast and ovarian cancer and neurofibromatosis patients and reached an accuracy, analytical sensitivity and specificity greater than 99%, which was maintained in a validation set. I2HCP changed our diagnostic approach, involving clinicians and a genetic diagnostics team from panel design to reporting. The new strategy improved diagnostic sensitivity, solved uncertain clinical diagnoses and identified mutations in new genes. We assessed the genetic variation in the complete set of hereditary cancer genes, revealing a complex variation landscape that coexists with the disease-causing mutation. We developed, validated and implemented a custom NGS-based strategy for hereditary cancer diagnostics that improved our previous workflows. Additionally, the existence of a rich genetic variation in hereditary cancer genes favors the use of this panel to investigate their role in cancer risk.
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