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Hynst J, Navrkalova V, Pal K, Pospisilova S. Bioinformatic strategies for the analysis of genomic aberrations detected by targeted NGS panels with clinical application. PeerJ 2021; 9:e10897. [PMID: 33850640 PMCID: PMC8019320 DOI: 10.7717/peerj.10897] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 01/13/2021] [Indexed: 01/21/2023] Open
Abstract
Molecular profiling of tumor samples has acquired importance in cancer research, but currently also plays an important role in the clinical management of cancer patients. Rapid identification of genomic aberrations improves diagnosis, prognosis and effective therapy selection. This can be attributed mainly to the development of next-generation sequencing (NGS) methods, especially targeted DNA panels. Such panels enable a relatively inexpensive and rapid analysis of various aberrations with clinical impact specific to particular diagnoses. In this review, we discuss the experimental approaches and bioinformatic strategies available for the development of an NGS panel for a reliable analysis of selected biomarkers. Compliance with defined analytical steps is crucial to ensure accurate and reproducible results. In addition, a careful validation procedure has to be performed before the application of NGS targeted assays in routine clinical practice. With more focus on bioinformatics, we emphasize the need for thorough pipeline validation and management in relation to the particular experimental setting as an integral part of the NGS method establishment. A robust and reproducible bioinformatic analysis running on powerful machines is essential for proper detection of genomic variants in clinical settings since distinguishing between experimental noise and real biological variants is fundamental. This review summarizes state-of-the-art bioinformatic solutions for careful detection of the SNV/Indels and CNVs for targeted sequencing resulting in translation of sequencing data into clinically relevant information. Finally, we share our experience with the development of a custom targeted NGS panel for an integrated analysis of biomarkers in lymphoproliferative disorders.
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Affiliation(s)
- Jakub Hynst
- Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,Department of Internal Medicine-Hematology and Oncology, Faculty of Medicine and University Hospital Brno, Masaryk University, Brno, Czech Republic.,Department of Medical Genetics and Genomics, Faculty of Medicine and University Hospital Brno, Masaryk University, Brno, Czech Republic
| | - Veronika Navrkalova
- Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,Department of Internal Medicine-Hematology and Oncology, Faculty of Medicine and University Hospital Brno, Masaryk University, Brno, Czech Republic
| | - Karol Pal
- Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,Department of Hematology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Sarka Pospisilova
- Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,Department of Internal Medicine-Hematology and Oncology, Faculty of Medicine and University Hospital Brno, Masaryk University, Brno, Czech Republic.,Department of Medical Genetics and Genomics, Faculty of Medicine and University Hospital Brno, Masaryk University, Brno, Czech Republic
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Performance of In Silico Prediction Tools for the Detection of Germline Copy Number Variations in Cancer Predisposition Genes in 4208 Female Index Patients with Familial Breast and Ovarian Cancer. Cancers (Basel) 2021; 13:cancers13010118. [PMID: 33401422 PMCID: PMC7794674 DOI: 10.3390/cancers13010118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 12/17/2020] [Accepted: 12/22/2020] [Indexed: 12/12/2022] Open
Abstract
Simple Summary The identification of germline copy number variants (CNVs) by targeted nextgeneration sequencing frequently relies on in silico prediction tools with unknown sensitivities. We investigated the performances of four in silico CNV prediction tools in 17 cancer predisposition genes in a large series of 4208 female index patients with familial breast and/or ovarian cancer. We identified 77 CNVs in 76 out of 4208 patients; six CNVs were missed by at least one of the prediction tools. Experimental verification of in silico predicted CNVs is required due to high frequencies of false positive predictions. For female index patients with familial breast and/or ovarian cancer, CNV detection should not be restricted to BRCA1/2 due to the relevant proportion of CNVs in further cancer predisposition genes. Abstract The identification of germline copy number variants (CNVs) by targeted next-generation sequencing (NGS) frequently relies on in silico CNV prediction tools with unknown sensitivities. We investigated the performances of four in silico CNV prediction tools, including one commercial (Sophia Genetics DDM) and three non-commercial tools (ExomeDepth, GATK gCNV, panelcn.MOPS) in 17 cancer predisposition genes in 4208 female index patients with familial breast and/or ovarian cancer (BC/OC). CNV predictions were verified via multiplex ligation-dependent probe amplification. We identified 77 CNVs in 76 out of 4208 patients (1.81%); 33 CNVs were identified in genes other than BRCA1/2, mostly in ATM, CHEK2, and RAD51C and less frequently in BARD1, MLH1, MSH2, PALB2, PMS2, RAD51D, and TP53. The Sophia Genetics DDM software showed the highest sensitivity; six CNVs were missed by at least one of the non-commercial tools. The positive predictive values ranged from 5.9% (74/1249) for panelcn.MOPS to 79.1% (72/91) for ExomeDepth. Verification of in silico predicted CNVs is required due to high frequencies of false positive predictions, particularly affecting target regions at the extremes of the GC content or target length distributions. CNV detection should not be restricted to BRCA1/2 due to the relevant proportion of CNVs in further BC/OC predisposition genes.
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Chinn IK, Chan AY, Chen K, Chou J, Dorsey MJ, Hajjar J, Jongco AM, Keller MD, Kobrynski LJ, Kumanovics A, Lawrence MG, Leiding JW, Lugar PL, Orange JS, Patel K, Platt CD, Puck JM, Raje N, Romberg N, Slack MA, Sullivan KE, Tarrant TK, Torgerson TR, Walter JE. Diagnostic interpretation of genetic studies in patients with primary immunodeficiency diseases: A working group report of the Primary Immunodeficiency Diseases Committee of the American Academy of Allergy, Asthma & Immunology. J Allergy Clin Immunol 2019; 145:46-69. [PMID: 31568798 DOI: 10.1016/j.jaci.2019.09.009] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 09/02/2019] [Accepted: 09/20/2019] [Indexed: 12/19/2022]
Abstract
Genetic testing has become an integral component of the diagnostic evaluation of patients with suspected primary immunodeficiency diseases. Results of genetic testing can have a profound effect on clinical management decisions. Therefore clinical providers must demonstrate proficiency in interpreting genetic data. Because of the need for increased knowledge regarding this practice, the American Academy of Allergy, Asthma & Immunology Primary Immunodeficiency Diseases Committee established a work group that reviewed and summarized information concerning appropriate methods, tools, and resources for evaluating variants identified by genetic testing. Strengths and limitations of tests frequently ordered by clinicians were examined. Summary statements and tables were then developed to guide the interpretation process. Finally, the need for research and collaboration was emphasized. Greater understanding of these important concepts will improve the diagnosis and management of patients with suspected primary immunodeficiency diseases.
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Affiliation(s)
- Ivan K Chinn
- Department of Pediatrics, Baylor College of Medicine, Houston, Tex; Section of Immunology, Allergy, and Rheumatology, Texas Children's Hospital, Houston, Tex.
| | - Alice Y Chan
- Department of Pediatrics, Division of Allergy, Immunology, and Bone Marrow Transplantation, University of California at San Francisco, San Francisco, Calif
| | - Karin Chen
- Division of Allergy and Immunology, Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, Utah
| | - Janet Chou
- Department of Pediatrics, Harvard Medical School, Boston, Mass; Division of Allergy and Immunology, Boston Children's Hospital, Boston, Mass
| | - Morna J Dorsey
- Department of Pediatrics, Division of Allergy, Immunology, and Bone Marrow Transplantation, University of California at San Francisco, San Francisco, Calif
| | - Joud Hajjar
- Department of Pediatrics, Baylor College of Medicine, Houston, Tex; Section of Immunology, Allergy, and Rheumatology, Texas Children's Hospital, Houston, Tex
| | - Artemio M Jongco
- Departments of Medicine and Pediatrics, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Great Neck, NY; Center for Health Innovations and Outcomes Research, Feinstein Institute for Medical Research, Great Neck, NY; Division of Allergy & Immunology, Cohen Children's Medical Center of New York, Great Neck, NY
| | - Michael D Keller
- Department of Allergy and Immunology, Children's National Hospital, Washington, DC
| | - Lisa J Kobrynski
- Department of Pediatrics, Division of Allergy and Immunology, Emory University School of Medicine, Atlanta, Ga
| | - Attila Kumanovics
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minn
| | - Monica G Lawrence
- Department of Medicine, Division of Asthma, Allergy and Immunology, University of Virginia Health System, Charlottesville, Va
| | - Jennifer W Leiding
- Departments of Pediatrics and Medicine, University of South Florida, St Petersburg, Fla; Division of Pediatric Allergy/Immunology, Johns Hopkins-All Children's Hospital, St Petersburg, Fla; Cancer and Blood Disorders Institute, Johns Hopkins-All Children's Hospital, St Petersburg, Fla
| | - Patricia L Lugar
- Department of Medicine, Division of Pulmonary, Allergy, and Critical Care Medicine, Duke University Medical Center, Durham, NC
| | - Jordan S Orange
- Department of Pediatrics, Columbia University College of Physicians and Surgeons, New York, NY; New York Presbyterian Morgan Stanley Children's Hospital, New York, NY
| | - Kiran Patel
- Department of Pediatrics, Division of Allergy and Immunology, Emory University School of Medicine, Atlanta, Ga
| | - Craig D Platt
- Department of Pediatrics, Harvard Medical School, Boston, Mass; Division of Allergy and Immunology, Boston Children's Hospital, Boston, Mass
| | - Jennifer M Puck
- Department of Pediatrics, Division of Allergy, Immunology, and Bone Marrow Transplantation, University of California at San Francisco, San Francisco, Calif
| | - Nikita Raje
- Department of Pediatrics, University of Missouri-Kansas City, Kansas City, Mo; Division of Allergy/Asthma/Immunology, Children's Mercy Hospital, Kansas City, Mo
| | - Neil Romberg
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pa; Division of Allergy/Immunology, Children's Hospital of Philadelphia, Philadelphia, Pa
| | - Maria A Slack
- Department of Medicine, Division of Allergy, Immunology, and Rheumatology, University of Rochester Medical Center, Rochester, NY; Department of Pediatrics, Division of Pediatric Allergy and Immunology, University of Rochester Medical Center, Rochester, NY
| | - Kathleen E Sullivan
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pa; Division of Allergy/Immunology, Children's Hospital of Philadelphia, Philadelphia, Pa
| | - Teresa K Tarrant
- Department of Medicine, Division of Rheumatology and Immunology, Duke University Medical Center, Durham, NC
| | - Troy R Torgerson
- Department of Pediatrics, University of Washington School of Medicine, Seattle, Wash; Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, Wash
| | - Jolan E Walter
- Departments of Pediatrics and Medicine, University of South Florida, St Petersburg, Fla; Division of Pediatric Allergy/Immunology, Johns Hopkins-All Children's Hospital, St Petersburg, Fla; Division of Pediatric Allergy Immunology, Massachusetts General Hospital, Boston, Mass
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Ho CC, Tai SM, Lee ECN, Mak TSH, Liu TKT, Tang VWL, Poon WT. Rapid Identification of Pathogenic Variants in Two Cases of Charcot-Marie-Tooth Disease by Gene-Panel Sequencing. Int J Mol Sci 2017; 18:ijms18040770. [PMID: 28379183 PMCID: PMC5412354 DOI: 10.3390/ijms18040770] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 03/28/2017] [Accepted: 03/31/2017] [Indexed: 12/14/2022] Open
Abstract
Charcot-Marie-Tooth disease (CMT) is a common inherited peripheral neuropathy affecting up to 1 in 1214 of the general population with more than 60 nuclear genes implicated in its pathogenesis. Traditional molecular diagnostic pathways based on relative prevalence and clinical phenotyping are limited by long turnaround time, population-specific prevalence of causative variants and inability to assess multiple co-existing variants. In this study, a CMT gene panel comprising 27 genes was used to uncover the pathogenic mutations in two index patients. The first patient is a 15-year-old boy, born of consanguineous parents, who has had frequent trips and falls since infancy, and was later found to have inverted champagne bottle appearance of bilateral legs and foot drop. His elder sister is similarly affected. The second patient is a 37-year-old woman referred for pre-pregnancy genetic diagnosis. During early adulthood, she developed progressive lower limb weakness, difficulties in tip-toe walking and thinning of calf muscles. Both patients are clinically compatible with CMT, have undergone multiple genetic testings and have not previously received a definitive genetic diagnosis. Patients 1 and 2 were found to have pathogenic homozygous HSPB1:NM_001540:c.250G>A (p.G84R) variant and heterozygous GDAP1:NM_018972:c.358C>T (p.R120W) variant, respectively. Advantages and limitations of the current approach are discussed.
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Affiliation(s)
- Chi-Chun Ho
- Department of Clinical Pathology, Pamela Youde Nethersole Eastern Hospital, Chai Wan, Hong Kong, China.
| | - Shuk-Mui Tai
- Department of Paediatrics & Adolescent Medicine, Pamela Youde Nethersole Eastern Hospital, Chai Wan, Hong Kong, China.
| | - Edmond Chi-Nam Lee
- Department of Medicine, Pamela Youde Nethersole Eastern Hospital, Chai Wan, Hong Kong, China.
| | - Timothy Shin-Heng Mak
- Centre for Genomic Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong, China.
| | - Timothy Kam-Tim Liu
- Department of Paediatrics & Adolescent Medicine, Pamela Youde Nethersole Eastern Hospital, Chai Wan, Hong Kong, China.
| | - Victor Wai-Lun Tang
- Department of Clinical Pathology, Pamela Youde Nethersole Eastern Hospital, Chai Wan, Hong Kong, China.
| | - Wing-Tat Poon
- Department of Clinical Pathology, Pamela Youde Nethersole Eastern Hospital, Chai Wan, Hong Kong, China.
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