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Fitch AK, Malhotra S, Conroy R. Differentiating monogenic and syndromic obesities from polygenic obesity: Assessment, diagnosis, and management. OBESITY PILLARS 2024; 11:100110. [PMID: 38766314 PMCID: PMC11101890 DOI: 10.1016/j.obpill.2024.100110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 04/18/2024] [Accepted: 04/18/2024] [Indexed: 05/22/2024]
Abstract
Background Obesity is a multifactorial neurohormonal disease that results from dysfunction within energy regulation pathways and is associated with increased morbidity, mortality, and reduced quality of life. The most common form is polygenic obesity, which results from interactions between multiple gene variants and environmental factors. Highly penetrant monogenic and syndromic obesities result from rare genetic variants with minimal environmental influence and can be differentiated from polygenic obesity depending on key symptoms, including hyperphagia; early-onset, severe obesity; and suboptimal responses to nontargeted therapies. Timely diagnosis of monogenic or syndromic obesity is critical to inform management strategies and reduce disease burden. We outline the physiology of weight regulation, role of genetics in obesity, and differentiating characteristics between polygenic and rare genetic obesity to facilitate diagnosis and transition toward targeted therapies. Methods In this narrative review, we focused on case reports, case studies, and natural history studies of patients with monogenic and syndromic obesities and clinical trials examining the efficacy, safety, and quality of life impact of nontargeted and targeted therapies in these populations. We also provide comprehensive algorithms for diagnosis of patients with suspected rare genetic causes of obesity. Results Patients with monogenic and syndromic obesities commonly present with hyperphagia (ie, pathologic, insatiable hunger) and early-onset, severe obesity, and the presence of hallmark characteristics can inform genetic testing and diagnostic approach. Following diagnosis, specialized care teams can address complex symptoms, and hyperphagia is managed behaviorally. Various pharmacotherapies show promise in these patient populations, including setmelanotide and glucagon-like peptide-1 receptor agonists. Conclusion Understanding the pathophysiology and differentiating characteristics of monogenic and syndromic obesities can facilitate diagnosis and management and has led to development of targeted pharmacotherapies with demonstrated efficacy for reducing body weight and hunger in the affected populations.
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Affiliation(s)
| | - Sonali Malhotra
- Harvard Medical School, Boston, MA, USA
- Rhythm Pharmaceuticals, Inc., Boston, MA, USA
- Massachussetts General Hospital, Boston, MA, USA
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Guha S, Reddi HV, Aarabi M, DiStefano M, Wakeling E, Dungan JS, Gregg AR. Laboratory testing for preconception/prenatal carrier screening: A technical standard of the American College of Medical Genetics and Genomics (ACMG). Genet Med 2024:101137. [PMID: 38814327 DOI: 10.1016/j.gim.2024.101137] [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: 03/29/2024] [Accepted: 04/01/2024] [Indexed: 05/31/2024] Open
Abstract
Carrier screening has historically assessed a relatively small number of autosomal recessive and X-linked conditions selected based on frequency in a specific subpopulation and association with severe morbidity or mortality. Advances in genomic technologies enable simultaneous screening of individuals for several conditions. The American College of Medical Genetics and Genomics recently published a clinical practice resource that presents a framework when offering screening for autosomal recessive and X-linked conditions during pregnancy and preconception and recommends a tier-based approach when considering the number of conditions to screen for and their frequency within the US population in general. This laboratory technical standard aims to complement the practice resource and to put forth considerations for clinical laboratories and clinicians who offer preconception/prenatal carrier screening.
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Affiliation(s)
| | - Honey V Reddi
- Department of Pathology and Laboratory Medicine, Medical College of Wisconsin, Milwaukee, WI
| | - Mahmoud Aarabi
- UPMC Medical Genetics and Genomics Laboratories, UPMC Magee-Womens Hospital, Pittsburgh, PA; Departments of Pathology and Obstetrics, Gynecology, and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | | | | | - Jeffrey S Dungan
- Department of Obstetrics and Gynecology, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Anthony R Gregg
- Department of Obstetrics and Gynecology, Prisma Health, Columbia, SC
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Yang Y, Wang P, Qaidi SE, Hardwidge PR, Huang J, Zhu G. Loss to gain: pseudogenes in microorganisms, focusing on eubacteria, and their biological significance. Appl Microbiol Biotechnol 2024; 108:328. [PMID: 38717672 PMCID: PMC11078800 DOI: 10.1007/s00253-023-12971-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 11/26/2023] [Accepted: 12/01/2023] [Indexed: 05/12/2024]
Abstract
Pseudogenes are defined as "non-functional" copies of corresponding parent genes. The cognition of pseudogenes continues to be refreshed through accumulating and updating research findings. Previous studies have predominantly focused on mammals, but pseudogenes have received relatively less attention in the field of microbiology. Given the increasing recognition on the importance of pseudogenes, in this review, we focus on several aspects of microorganism pseudogenes, including their classification and characteristics, their generation and fate, their identification, their abundance and distribution, their impact on virulence, their ability to recombine with functional genes, the extent to which some pseudogenes are transcribed and translated, and the relationship between pseudogenes and viruses. By summarizing and organizing the latest research progress, this review will provide a comprehensive perspective and improved understanding on pseudogenes in microorganisms. KEY POINTS: • Concept, classification and characteristics, identification and databases, content, and distribution of microbial pseudogenes are presented. • How pseudogenization contribute to pathogen virulence is highlighted. • Pseudogenes with potential functions in microorganisms are discussed.
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Affiliation(s)
- Yi Yang
- College of Veterinary Medicine, Yangzhou University, 12 East Wenhui Road, Yangzhou, 225009, Jiangsu, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China
- Joint Laboratory of International Cooperation On Prevention and Control Technology of Important Animal Diseases and Zoonoses of Jiangsu Higher Education Institutions, Yangzhou, 225009, China
| | - Pengzhi Wang
- College of Veterinary Medicine, Yangzhou University, 12 East Wenhui Road, Yangzhou, 225009, Jiangsu, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China
- Joint Laboratory of International Cooperation On Prevention and Control Technology of Important Animal Diseases and Zoonoses of Jiangsu Higher Education Institutions, Yangzhou, 225009, China
| | - Samir El Qaidi
- College of Veterinary Medicine, Kansas State University, Manhattan, KS, 66506, USA
| | - Philip R Hardwidge
- College of Veterinary Medicine, Kansas State University, Manhattan, KS, 66506, USA
| | - Jinlin Huang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China.
- Jiangsu Key Lab of Zoonosis, Yangzhou University, Yangzhou, 225009, Jiangsu, China.
- College of Bioscience and Biotechnology, Yangzhou University, 12 East Wenhui Road Yangzhou, Jiangsu, 225009, China.
| | - Guoqiang Zhu
- College of Veterinary Medicine, Yangzhou University, 12 East Wenhui Road, Yangzhou, 225009, Jiangsu, China.
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China.
- Joint Laboratory of International Cooperation On Prevention and Control Technology of Important Animal Diseases and Zoonoses of Jiangsu Higher Education Institutions, Yangzhou, 225009, China.
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SoRelle JA, Funke BH, Eno CC, Ji J, Santani A, Bayrak-Toydemir P, Wachsmann M, Wain KE, Mao R. Slice Testing-Considerations from Ordering to Reporting: A Joint Report of the Association for Molecular Pathology, College of American Pathologists, and National Society of Genetic Counselors. J Mol Diagn 2024; 26:159-167. [PMID: 38103592 DOI: 10.1016/j.jmoldx.2023.11.008] [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: 12/20/2022] [Revised: 10/09/2023] [Accepted: 11/29/2023] [Indexed: 12/19/2023] Open
Abstract
As the number of genes associated with various germline disorders continues to grow, it is becoming more difficult for clinical laboratories to maintain separate assays for interrogating disease-focused gene panels. One solution to this challenge is termed slice testing, where capture backbone is used to analyze data specific to a set of genes, and for this article, we will focus on exome. A key advantage to this strategy is greater flexibility by adding genes as they become associated with disease or the ability to accommodate specific provider requests. Here, we provide expert consensus recommendations and results from an Association for Molecular Pathology-sponsored survey of clinical laboratories performing exome sequencing to compare a slice testing approach with traditional static gene panels and comprehensive exome analysis. We explore specific considerations for slices, including gene selection, analytic performance, coverage, quality, and interpretation. Our goal is to provide comprehensive guidance for clinical laboratories interested in designing and using slice tests as a diagnostic.
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Affiliation(s)
- Jeffrey A SoRelle
- Whole Exome Sequencing Standards Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Birgit H Funke
- Whole Exome Sequencing Standards Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Sema4, Stamford, Connecticut; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Celeste C Eno
- Whole Exome Sequencing Standards Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Academic Pathology, Cedars-Sinai Medical Center, Los Angeles, California
| | - Jianling Ji
- Whole Exome Sequencing Standards Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California; Department of Pathology, University of Southern California, Los Angeles, California
| | - Avni Santani
- Whole Exome Sequencing Standards Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Pinar Bayrak-Toydemir
- Whole Exome Sequencing Standards Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, University of Utah, Salt Lake City, Utah; ARUP Laboratories, Salt Lake City, Utah
| | - Megan Wachsmann
- Whole Exome Sequencing Standards Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas; VA North Texas Health Care System, Dallas, Texas
| | - Karen E Wain
- Whole Exome Sequencing Standards Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; GeneDx, LLC, Gaithersburg, Maryland
| | - Rong Mao
- Whole Exome Sequencing Standards Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, University of Utah, Salt Lake City, Utah; ARUP Laboratories, Salt Lake City, Utah.
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Kingsmore SF, Nofsinger R, Ellsworth K. Rapid genomic sequencing for genetic disease diagnosis and therapy in intensive care units: a review. NPJ Genom Med 2024; 9:17. [PMID: 38413639 PMCID: PMC10899612 DOI: 10.1038/s41525-024-00404-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 02/15/2024] [Indexed: 02/29/2024] Open
Abstract
Single locus (Mendelian) diseases are a leading cause of childhood hospitalization, intensive care unit (ICU) admission, mortality, and healthcare cost. Rapid genome sequencing (RGS), ultra-rapid genome sequencing (URGS), and rapid exome sequencing (RES) are diagnostic tests for genetic diseases for ICU patients. In 44 studies of children in ICUs with diseases of unknown etiology, 37% received a genetic diagnosis, 26% had consequent changes in management, and net healthcare costs were reduced by $14,265 per child tested by URGS, RGS, or RES. URGS outperformed RGS and RES with faster time to diagnosis, and higher rate of diagnosis and clinical utility. Diagnostic and clinical outcomes will improve as methods evolve, costs decrease, and testing is implemented within precision medicine delivery systems attuned to ICU needs. URGS, RGS, and RES are currently performed in <5% of the ~200,000 children likely to benefit annually due to lack of payor coverage, inadequate reimbursement, hospital policies, hospitalist unfamiliarity, under-recognition of possible genetic diseases, and current formatting as tests rather than as a rapid precision medicine delivery system. The gap between actual and optimal outcomes in children in ICUs is currently increasing since expanded use of URGS, RGS, and RES lags growth in those likely to benefit through new therapies. There is sufficient evidence to conclude that URGS, RGS, or RES should be considered in all children with diseases of uncertain etiology at ICU admission. Minimally, diagnostic URGS, RGS, or RES should be ordered early during admissions of critically ill infants and children with suspected genetic diseases.
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Affiliation(s)
- Stephen F Kingsmore
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, CA, USA.
| | - Russell Nofsinger
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, CA, USA
| | - Kasia Ellsworth
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, CA, USA
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Kvapilova K, Misenko P, Radvanszky J, Brzon O, Budis J, Gazdarica J, Pos O, Korabecna M, Kasny M, Szemes T, Kvapil P, Paces J, Kozmik Z. Validated WGS and WES protocols proved saliva-derived gDNA as an equivalent to blood-derived gDNA for clinical and population genomic analyses. BMC Genomics 2024; 25:187. [PMID: 38365587 PMCID: PMC10873937 DOI: 10.1186/s12864-024-10080-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 02/02/2024] [Indexed: 02/18/2024] Open
Abstract
BACKGROUND Whole exome sequencing (WES) and whole genome sequencing (WGS) have become standard methods in human clinical diagnostics as well as in population genomics (POPGEN). Blood-derived genomic DNA (gDNA) is routinely used in the clinical environment. Conversely, many POPGEN studies and commercial tests benefit from easy saliva sampling. Here, we evaluated the quality of variant call sets and the level of genotype concordance of single nucleotide variants (SNVs) and small insertions and deletions (indels) for WES and WGS using paired blood- and saliva-derived gDNA isolates employing genomic reference-based validated protocols. METHODS The genomic reference standard Coriell NA12878 was repeatedly analyzed using optimized WES and WGS protocols, and data calls were compared with the truth dataset published by the Genome in a Bottle Consortium. gDNA was extracted from the paired blood and saliva samples of 10 participants and processed using the same protocols. A comparison of paired blood-saliva call sets was performed in the context of WGS and WES genomic reference-based technical validation results. RESULTS The quality pattern of called variants obtained from genomic-reference-based technical replicates correlates with data calls of paired blood-saliva-derived samples in all levels of tested examinations despite a higher rate of non-human contamination found in the saliva samples. The F1 score of 10 blood-to-saliva-derived comparisons ranged between 0.8030-0.9998 for SNVs and between 0.8883-0.9991 for small-indels in the case of the WGS protocol, and between 0.8643-0.999 for SNVs and between 0.7781-1.000 for small-indels in the case of the WES protocol. CONCLUSION Saliva may be considered an equivalent material to blood for genetic analysis for both WGS and WES under strict protocol conditions. The accuracy of sequencing metrics and variant-detection accuracy is not affected by choosing saliva as the gDNA source instead of blood but much more significantly by the genomic context, variant types, and the sequencing technology used.
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Affiliation(s)
- Katerina Kvapilova
- Faculty of Science, Charles University, Albertov 6, Prague, 128 00, Czech Republic.
- Institute of Applied Biotechnologies a.s, Služeb 4, Prague, 108 00, Czech Republic.
| | - Pavol Misenko
- Geneton s.r.o, Ilkovičova 8, Bratislava, 841 04, Slovakia
| | - Jan Radvanszky
- Geneton s.r.o, Ilkovičova 8, Bratislava, 841 04, Slovakia
- Institute of Clinical and Translational Research, Biomedical Research Center of the Slovak Academy of Sciences, Dúbravská Cesta 9, Bratislava, 845 05, Slovakia
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Ilkovičova 3278/6, Karlova Ves, Bratislava, 841 04, Slovakia
- Comenius University Science Park, Comenius University, Ilkovičova 8, Karlova Ves, Bratislava, 841 04, Slovakia
| | - Ondrej Brzon
- Institute of Applied Biotechnologies a.s, Služeb 4, Prague, 108 00, Czech Republic
| | - Jaroslav Budis
- Geneton s.r.o, Ilkovičova 8, Bratislava, 841 04, Slovakia
- Comenius University Science Park, Comenius University, Ilkovičova 8, Karlova Ves, Bratislava, 841 04, Slovakia
- Slovak Centre for Scientific and Technical Information, Staré Mesto, Lamačská Cesta 8A, Bratislava, 811 04, Slovakia
| | - Juraj Gazdarica
- Geneton s.r.o, Ilkovičova 8, Bratislava, 841 04, Slovakia
- Comenius University Science Park, Comenius University, Ilkovičova 8, Karlova Ves, Bratislava, 841 04, Slovakia
- Slovak Centre for Scientific and Technical Information, Staré Mesto, Lamačská Cesta 8A, Bratislava, 811 04, Slovakia
| | - Ondrej Pos
- Geneton s.r.o, Ilkovičova 8, Bratislava, 841 04, Slovakia
- Comenius University Science Park, Comenius University, Ilkovičova 8, Karlova Ves, Bratislava, 841 04, Slovakia
| | - Marie Korabecna
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Albertov 4, Prague, 128 00, Czech Republic
| | - Martin Kasny
- Institute of Applied Biotechnologies a.s, Služeb 4, Prague, 108 00, Czech Republic
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, Brno, 611 37, Czech Republic
| | - Tomas Szemes
- Geneton s.r.o, Ilkovičova 8, Bratislava, 841 04, Slovakia
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Ilkovičova 3278/6, Karlova Ves, Bratislava, 841 04, Slovakia
- Comenius University Science Park, Comenius University, Ilkovičova 8, Karlova Ves, Bratislava, 841 04, Slovakia
| | - Petr Kvapil
- Institute of Applied Biotechnologies a.s, Služeb 4, Prague, 108 00, Czech Republic
| | - Jan Paces
- Laboratory of Genomics and Bioinformatics, Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, Prague, 142 20, Czech Republic
| | - Zbynek Kozmik
- Laboratory of Transcriptional Regulation, Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, Prague, 142 20, Czech Republic
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Hijikata A, Suyama M, Kikugawa S, Matoba R, Naruto T, Enomoto Y, Kurosawa K, Harada N, Yanagi K, Kaname T, Miyako K, Takazawa M, Sasai H, Hosokawa J, Itoga S, Yamaguchi T, Kosho T, Matsubara K, Kuroki Y, Fukami M, Adachi K, Nanba E, Tsuchida N, Uchiyama Y, Matsumoto N, Nishimura K, Ohara O. Exome-wide benchmark of difficult-to-sequence regions using short-read next-generation DNA sequencing. Nucleic Acids Res 2024; 52:114-124. [PMID: 38015437 PMCID: PMC10783491 DOI: 10.1093/nar/gkad1140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 11/03/2023] [Accepted: 11/13/2023] [Indexed: 11/29/2023] Open
Abstract
Next-generation DNA sequencing (NGS) in short-read mode has recently been used for genetic testing in various clinical settings. NGS data accuracy is crucial in clinical settings, and several reports regarding quality control of NGS data, primarily focusing on establishing NGS sequence read accuracy, have been published thus far. Variant calling is another critical source of NGS errors that remains unexplored at the single-nucleotide level despite its established significance. In this study, we used a machine-learning-based method to establish an exome-wide benchmark of difficult-to-sequence regions at the nucleotide-residue resolution using 10 genome sequence features based on real-world NGS data accumulated in The Genome Aggregation Database (gnomAD) of the human reference genome sequence (GRCh38/hg38). The newly acquired metric, designated the 'UNMET score,' along with additional lines of structural information from the human genome, allowed us to assess the sequencing challenges within the exonic region of interest using conventional short-read NGS. Thus, the UNMET score could provide a basis for addressing potential sequential errors in protein-coding exons of the human reference genome sequence GRCh38/hg38 in clinical sequencing.
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Affiliation(s)
- Atsushi Hijikata
- Laboratory of Computational Genomics, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392, Japan
| | - Mikita Suyama
- Division of Bioinformatics, Medical Institute of Bioregulation, Kyushu University, Higashi-ku, Fukuoka 812-8582, Japan
| | | | - Ryo Matoba
- DNA Chip Research Inc., Minato-ku, Tokyo 105-0022, Japan
| | - Takuya Naruto
- Clinical Research Institute, Kanagawa Children's Medical Center, Minami-ku, Yokohama, Kanagawa 232-0066, Japan
| | - Yumi Enomoto
- Clinical Research Institute, Kanagawa Children's Medical Center, Minami-ku, Yokohama, Kanagawa 232-0066, Japan
| | - Kenji Kurosawa
- Clinical Research Institute, Kanagawa Children's Medical Center, Minami-ku, Yokohama, Kanagawa 232-0066, Japan
- Division of Medical Genetics, Kanagawa Children's Medical Center, Minami-ku, Yokohama, Kanagawa 232-0066, Japan
| | - Naoki Harada
- Department of Fundamental Cell Technology, Center for iPS Cell Research and Application (CiRA), Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan
| | - Kumiko Yanagi
- Department of Genome Medicine, National Center for Child Health and Development, Setagaya-ku, Tokyo 157-8535, Japan
| | - Tadashi Kaname
- Department of Genome Medicine, National Center for Child Health and Development, Setagaya-ku, Tokyo 157-8535, Japan
| | - Keisuke Miyako
- Department of Applied Genomics, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Masaki Takazawa
- Department of Applied Genomics, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Hideo Sasai
- Department of Applied Genomics, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
- Department of Pediatrics, Graduate School of Medicine, Gifu University, Gifu, Gifu 501-1194, Japan
| | - Junichi Hosokawa
- Department of Applied Genomics, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Sakae Itoga
- Department of Applied Genomics, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Tomomi Yamaguchi
- Department of Medical Genetics, Shinshu University School of Medicine, Matsumoto, Nagano 390-8621, Japan
- Center for Medical Genetics, Shinshu University Hospital, Matsumoto, Nagano 390-8621, Japan
- Division of Clinical Sequencing, Shinshu University School of Medicine, Matsumoto, Nagano 390-8621, Japan
| | - Tomoki Kosho
- Department of Medical Genetics, Shinshu University School of Medicine, Matsumoto, Nagano 390-8621, Japan
- Center for Medical Genetics, Shinshu University Hospital, Matsumoto, Nagano 390-8621, Japan
- Division of Clinical Sequencing, Shinshu University School of Medicine, Matsumoto, Nagano 390-8621, Japan
| | - Keiko Matsubara
- Division of Collaborative Research, National Research Institute for Child Health and Development, Setagaya-ku, Tokyo 157-8535, Japan
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Setagaya-ku, Tokyo 157-8535, Japan
| | - Yoko Kuroki
- Department of Genome Medicine, National Center for Child Health and Development, Setagaya-ku, Tokyo 157-8535, Japan
- Division of Collaborative Research, National Research Institute for Child Health and Development, Setagaya-ku, Tokyo 157-8535, Japan
| | - Maki Fukami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Setagaya-ku, Tokyo 157-8535, Japan
| | - Kaori Adachi
- Organization for Research Initiative and Promotion, Tottori University, Yonago, Tottori 680-8550, Japan
| | - Eiji Nanba
- Organization for Research Initiative and Promotion, Tottori University, Yonago, Tottori 680-8550, Japan
| | - Naomi Tsuchida
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Kanazawa-ku, Yokohama, Kanagawa 236-0027, Japan
- Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, Kanagawa 236-0027, Japan
| | - Yuri Uchiyama
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Kanazawa-ku, Yokohama, Kanagawa 236-0027, Japan
- Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, Kanagawa 236-0027, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Kanazawa-ku, Yokohama, Kanagawa 236-0027, Japan
| | | | - Osamu Ohara
- Department of Applied Genomics, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
- Division of Clinical Sequencing, Shinshu University School of Medicine, Matsumoto, Nagano 390-8621, Japan
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8
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Thomasová D, Zelinová M, Libik M, Geryk J, Votýpka P, Rajnochová Bloudíčková S, Krejčí K, Reiterová J, Jančová E, Machová J, Kollárová M, Rychík I, Havrda M, Horáčková M, Putzová M, Šafránek R, Kollár M, Macek M. The most common founder pathogenic variant c.868G > A (p.Val290Met) in the NPHS2 gene in a representative adult Czech cohort with focal segmental glomerulosclerosis is associated with a milder disease and its underdiagnosis in childhood. Front Med (Lausanne) 2023; 10:1320054. [PMID: 38170106 PMCID: PMC10759319 DOI: 10.3389/fmed.2023.1320054] [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: 10/11/2023] [Accepted: 11/24/2023] [Indexed: 01/05/2024] Open
Abstract
Background Genetic focal segmental glomerulosclerosis (FSGS) is caused by pathogenic variants in a broad spectrum of genes that have a variable representation based on subjects' ethnicity and/or age. The most frequently mutated autosomal recessive gene in FSGS is NPHS2. In this study, we analyzed the spectrum of NPHS2 variants and their associated phenotype in Czech adult FSGS patients. Methods A representative cohort of 234 adult patients with FSGS, derived from 225 families originating from all regions of Czechia, was analyzed by massively parallel sequencing. In this study, we focused on the comprehensive analysis of the NPHS2 gene. The histological classification of FSGS followed the Columbia classification. Results We detected seven (3%) cases bearing homozygous or compound heterozygous pathogenic NPHS2 variants. A single pathogenic variant c.868G > A (p.Val290Met) was found in the majority of NPHS2-positive cases (86%; 6 out of 7) in histologically confirmed instances of FSGS. Its allele frequency among unrelated NPHS2-associated FSGS patients was 50% (6/12), and Haplotype analysis predicted its origin to be a result of a founder effect. There is an identical V290M-related haplotype on all V290M alleles spanning a 0,7 Mb region flanking NPHS2 in Central European FSGS populations. The phenotype of the p.Val290Met NPHS2-associated FSGS demonstrated a later onset and a much milder course of the disease compared to other NPHS2 pathogenic variants associated with FSGS. The mean age of the FSGS diagnosis based on kidney biopsy evaluation was 31.2 ± 7.46 years. In 50% of all cases, the initial disease manifestation of proteinuria occurred only in adulthood, with 83% of these cases not presenting with edemas. One-third (33%) of the studied subjects progressed to ESRD (2 out of 6) at the mean age of 35.0 ± 2.82 years. Conclusions We identified the most prevalent pathogenic variant, p.Val290Met, in the NPHS2 gene among Czech adult FSGS patients, which has arisen due to a founder effect in Central Europe. The documented milder course of the disease associated with this variant leads to the underdiagnosis in childhood. We established the histopathological features of the NPHS2-associated adult FSGS cases based on the Columbia classification. This might improve patient stratification and optimize their treatment.
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Affiliation(s)
- Dana Thomasová
- Institute of Biology and Medical Genetics, University Hospital Motol and 2nd Faculty of Medicine, Charles University Prague, Prague, Czechia
| | - Michaela Zelinová
- Institute of Biology and Medical Genetics, University Hospital Motol and 2nd Faculty of Medicine, Charles University Prague, Prague, Czechia
| | - Malgorzata Libik
- Institute of Biology and Medical Genetics, University Hospital Motol and 2nd Faculty of Medicine, Charles University Prague, Prague, Czechia
| | - Jan Geryk
- Institute of Biology and Medical Genetics, University Hospital Motol and 2nd Faculty of Medicine, Charles University Prague, Prague, Czechia
| | - Pavel Votýpka
- Institute of Biology and Medical Genetics, University Hospital Motol and 2nd Faculty of Medicine, Charles University Prague, Prague, Czechia
| | | | - Karel Krejčí
- 3rd Department of Internal Medicine-Nephrology, Rheumatology and Endocrinology, University Hospital and Faculty of Medicine Palacký University Olomouc, Olomouc, Czechia
| | - Jana Reiterová
- Department of Nephrology, General University Hospital in Prague, First Faculty of Medicine, Charles University, Prague, Czechia
| | - Eva Jančová
- Department of Nephrology, General University Hospital in Prague, First Faculty of Medicine, Charles University, Prague, Czechia
| | - Jana Machová
- Department of Internal Medicine I, Faculty of Medicine in Pilsen, Charles University and Teaching Hospital, Pilsen, Czechia
- Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czechia
| | - Martina Kollárová
- Department of Internal Medicine, University Hospital Vinohrady and Third Faculty of Medicine, Charles University, Prague, Czechia
| | - Ivan Rychík
- Department of Internal Medicine, University Hospital Vinohrady and Third Faculty of Medicine, Charles University, Prague, Czechia
| | - Martin Havrda
- Department of Internal Medicine, University Hospital Vinohrady and Third Faculty of Medicine, Charles University, Prague, Czechia
| | - Miroslava Horáčková
- Department of Internal Medicine, University Hospital Motol and 2nd Faculty of Medicine, Charles University, Prague, Czechia
| | - Martina Putzová
- Biopticka Laboratory, Pilsen, Czechia
- Faculty of Medicine in Plzeň - Charles University, Pilsen, Czechia
| | - Roman Šafránek
- Department of Nephrology, University Hospital Hradec Králové, Faculty of Medicine in Hradec Králové, Charles University, Hradec Králové, Czechia
| | - Marek Kollár
- Department of Pathology, Institute for Clinical and Experimental Medicine, Prague, Czechia
| | - Milan Macek
- Institute of Biology and Medical Genetics, University Hospital Motol and 2nd Faculty of Medicine, Charles University Prague, Prague, Czechia
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9
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Gallagher JH, Vassy JL, Clayman ML. Navigating the uncertainty of precision cancer screening: The role of shared decision-making. PEC INNOVATION 2023; 2:100127. [PMID: 37214512 PMCID: PMC10194244 DOI: 10.1016/j.pecinn.2023.100127] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 01/20/2023] [Accepted: 01/23/2023] [Indexed: 05/24/2023]
Abstract
Objective Describe how applying a shared decision making (SDM) lens to the implementation of new technologies can improve patient-centeredness. Methods This paper argues that the emergence of polygenic risk scores (PRS) for cancer screening presents an illustrative opportunity to include SDM when novel technologies enter clinical care. Results PRS are novel tools that indicate an individual's genetic risk of a given disease relative to the population. PRS are anticipated to help identify individuals most and least likely to benefit from screening. However, PRS have several types of uncertainty, including validity across populations, disparate computational methods, and inclusion of different genomic data across laboratories. Conclusion Implementing SDM alongside new technologies could prove useful for their ethical and patient-centered utilization. SDM's importance as an approach to decision-making will not diminish, as evidence, uncertainty, and patient values will remain intrinsic to the art and science of clinical care. Innovation SDM can help providers and patients navigate the considerable uncertainty inherent in implementing new technologies, enabling decision-making based on existing evidence and patient values.
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Affiliation(s)
- Joseph H. Gallagher
- Virginia Commonwealth University School of Medicine, Richmond, VA, United States of America
| | - Jason L. Vassy
- Center for Healthcare Organization and Implementation Research (CHOIR), Veterans Health Administration, Bedford MA and Boston MA, United States
- Harvard Medical School, Boston, MA United States
- Brigham and Women’s Hospital, Boston, MA, United States
- Population Precision Health, Ariadne Labs, Boston, MA, United States
| | - Marla L. Clayman
- Center for Healthcare Organization and Implementation Research (CHOIR), Veterans Health Administration, Bedford MA and Boston MA, United States
- UMass Chan School of Medicine, Department of Population and Quantitative Health Sciences, Worcester, MA, United States
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10
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Zhang W, Yu B, Luo W, Sun B, Zhang X, Wang X, Mao J, Nie M, Wu X. In vitro functional study of fifteen SRD5A2 variants found in Chinese patients and the relation between the SRD5A2 genotypes and phenotypes. J Steroid Biochem Mol Biol 2023; 235:106421. [PMID: 37918676 DOI: 10.1016/j.jsbmb.2023.106421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 10/21/2023] [Accepted: 10/27/2023] [Indexed: 11/04/2023]
Abstract
The 5α-reductase type 2 (5α-RD2) deficiency is one of the most common etiology of 46, XY disorders of sex development and is caused by pathogenic variants in SRD5A2. Massively parallel sequencing contributes to identification of numerous novel SRD5A2 variants, in vitro functional study could help to determine their pathogenicity. In this study, we aim to present the functional study of fifteen SRD5A2 variants found in Chinese patients and explore the genotype-phenotype association. We collected the clinical manifestation and genotype of 38 patients with 5α-RD2 deficiency who visited our center between 2009 and 2021. The pathogenicity of seven missense SRD5A2 variants, were predicted by in-silico tools. Furthermore, fifteen SRD5A2 variants without reported functional assay were studied in vitro to analyze the role of these variants in enzymatic activity. Twenty-four SRD5A2 rare variants were identified in 38 patients with 5α-RD2 deficiency. Fifteen variants without reported functional assay decreased the conversation of testosterone (T) to dihydrotestosterone(DHT) and caused the almost complete loss of enzyme activity (<8 %) in our in-vitro functional study. Thirty-eight patients with three different external genital phenotypes (complete female, clitoromegaly and hypospadias) were found to have same variants. Patients with different testicular position (scrotum/clitoris and cryptorchidism) were found to have same variants. Our study showed 15 SRD5A2 variants caused complete loss of 5α-RD2 enzyme activity by functional study. Patients with different clinical phenotypes can have the same genotypes and no obvious genotype-phenotype association exist in our series patients.
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Affiliation(s)
- Wei Zhang
- Department of Endocrinology, NHC Key laboratory of Endocrinology (Peking Union Medical College Hospital), Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Bingging Yu
- Department of Endocrinology, NHC Key laboratory of Endocrinology (Peking Union Medical College Hospital), Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China; Department of Ultrasonography, Peking University First Hospital, Beijing 100081, China
| | - Wei Luo
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Bang Sun
- Department of Endocrinology, NHC Key laboratory of Endocrinology (Peking Union Medical College Hospital), Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Xiaoxia Zhang
- Department of Endocrinology, NHC Key laboratory of Endocrinology (Peking Union Medical College Hospital), Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Xi Wang
- Department of Endocrinology, NHC Key laboratory of Endocrinology (Peking Union Medical College Hospital), Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Jiangfeng Mao
- Department of Endocrinology, NHC Key laboratory of Endocrinology (Peking Union Medical College Hospital), Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Min Nie
- Department of Endocrinology, NHC Key laboratory of Endocrinology (Peking Union Medical College Hospital), Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China.
| | - Xueyan Wu
- Department of Endocrinology, NHC Key laboratory of Endocrinology (Peking Union Medical College Hospital), Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China.
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11
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Wang D, Wang S, Zhang Y, Cheng X, Huang X, Han Y, Chen Z, Liu C, Li J, Zhang R. Validation and benchmarking of targeted panel sequencing for cancer genomic profiling. Am J Clin Pathol 2023; 160:507-523. [PMID: 37477357 DOI: 10.1093/ajcp/aqad078] [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: 03/28/2023] [Accepted: 06/22/2023] [Indexed: 07/22/2023] Open
Abstract
OBJECTIVES To validate a large next-generation sequencing (NGS) panel for comprehensive genomic profiling and improve patient access to more effective precision oncology treatment strategies. METHODS OncoPanScan was designed by targeting 825 cancer-related genes to detect a broad range of genomic alterations. A practical validation strategy was used to evaluate the assay's analytical performance, involving 97 tumor specimens with 25 paired blood specimens, 10 engineered cell lines, and 121 artificial reference DNA samples. RESULTS Overall, 1107 libraries were prepared and the sequencing failure rate was 0.18%. Across alteration classes, sensitivity ranged from 0.938 to more than 0.999, specificity ranged from 0.889 to more than 0.999, positive predictive value ranged from 0.867 to more than 0.999, repeatability ranged from 0.908 to more than 0.999, and reproducibility ranged from 0.832 to more than 0.999. The limit of detection for variants was established based on variant frequency, while for tumor mutation burden and microsatellite instability, it was based on tumor content, resulting in a minimum requirement of 20% tumor content. Benchmarking variant calls against validated NGS assays revealed that variations in the dry-bench processes were the primary cause of discordances. CONCLUSIONS This study presents a detailed validation framework and empirical recommendations for large panel validation and elucidates the sources of discordant alteration calls by comparing with "gold standard measures."
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Affiliation(s)
- Duo Wang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, China
- National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | | | - Yuanfeng Zhang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, China
- National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | | | - Xin Huang
- Genetron Health (Beijing), Beijing, China
| | - Yanxi Han
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, China
- National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | | | - Cong Liu
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, China
- National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | - Jinming Li
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, China
- National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | - Rui Zhang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, China
- National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
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12
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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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13
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Gaedigk A, Boone EC, Turner AJ, van Schaik RHN, Chernova D, Wang WY, Broeckel U, Granfield CA, Hodge JC, Ly RC, Lynnes TC, Mitchell MW, Moyer AM, Oliva J, Kalman LV. Characterization of Reference Materials for CYP3A4 and CYP3A5: A (GeT-RM) Collaborative Project. J Mol Diagn 2023; 25:655-664. [PMID: 37354993 DOI: 10.1016/j.jmoldx.2023.06.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 05/23/2023] [Accepted: 06/01/2023] [Indexed: 06/26/2023] Open
Abstract
Pharmacogenetic testing for CYP3A4 is increasingly provided by clinical and research laboratories; however, only a limited number of quality control and reference materials are currently available for many of the CYP3A4 variants included in clinical tests. To address this need, the Division of Laboratory Systems, CDC-based Genetic Testing Reference Material Coordination Program (GeT-RM), in collaboration with members of the pharmacogenetic testing and research communities and the Coriell Institute for Medical Research, has characterized 30 DNA samples derived from Coriell cell lines for CYP3A4. Samples were distributed to five volunteer laboratories for genotyping using a variety of commercially available and laboratory-developed tests. Sanger and next-generation sequencing were also utilized by some of the laboratories. Whole-genome sequencing data from the 1000 Genomes Projects were utilized to inform genotype. Twenty CYP3A4 alleles were identified in the 30 samples characterized for CYP3A4: CYP3A4∗4, ∗5, ∗6, ∗7, ∗8, ∗9, ∗10, ∗11, ∗12, ∗15, ∗16, ∗18, ∗19, ∗20, ∗21, ∗22, ∗23, ∗24, ∗35, and a novel allele, CYP3A4∗38. Nineteen additional samples with preexisting data for CYP3A4 or CYP3A5 were re-analyzed to generate comprehensive reference material panels for these genes. These publicly available and well-characterized materials can be used to support the quality assurance and quality control programs of clinical laboratories performing clinical pharmacogenetic testing.
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Affiliation(s)
- Andrea Gaedigk
- Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Children's Mercy Research Institute, Kansas City, Missouri; University of Missouri-Kansas City School of Medicine, Kansas City, Missouri
| | - Erin C Boone
- Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Children's Mercy Research Institute, Kansas City, Missouri
| | - Amy J Turner
- RPRD Diagnostics, Milwaukee, Wisconsin; Section on Genomic Pediatrics, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Ron H N van Schaik
- Department of Clinical Chemistry/International Federation of Clinical Chemistry and Laboratory Medicine Expert Center Pharmacogenetics, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Dilyara Chernova
- Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Children's Mercy Research Institute, Kansas City, Missouri
| | - Wendy Y Wang
- Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Children's Mercy Research Institute, Kansas City, Missouri
| | - Ulrich Broeckel
- RPRD Diagnostics, Milwaukee, Wisconsin; Section on Genomic Pediatrics, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Caitlin A Granfield
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana
| | - Jennelle C Hodge
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana
| | - Reynold C Ly
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana
| | - Ty C Lynnes
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana
| | | | - Ann M Moyer
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | | | - Lisa V Kalman
- Division of Laboratory Systems, Centers for Disease Control and Prevention, Atlanta, Georgia.
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14
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Chin CS, Behera S, Khalak A, Sedlazeck FJ, Sudmant PH, Wagner J, Zook JM. Multiscale analysis of pangenomes enables improved representation of genomic diversity for repetitive and clinically relevant genes. Nat Methods 2023; 20:1213-1221. [PMID: 37365340 PMCID: PMC10406601 DOI: 10.1038/s41592-023-01914-y] [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: 08/10/2022] [Accepted: 05/17/2023] [Indexed: 06/28/2023]
Abstract
Advancements in sequencing technologies and assembly methods enable the regular production of high-quality genome assemblies characterizing complex regions. However, challenges remain in efficiently interpreting variation at various scales, from smaller tandem repeats to megabase rearrangements, across many human genomes. We present a PanGenome Research Tool Kit (PGR-TK) enabling analyses of complex pangenome structural and haplotype variation at multiple scales. We apply the graph decomposition methods in PGR-TK to the class II major histocompatibility complex demonstrating the importance of the human pangenome for analyzing complicated regions. Moreover, we investigate the Y-chromosome genes, DAZ1/DAZ2/DAZ3/DAZ4, of which structural variants have been linked to male infertility, and X-chromosome genes OPN1LW and OPN1MW linked to eye disorders. We further showcase PGR-TK across 395 complex repetitive medically important genes. This highlights the power of PGR-TK to resolve complex variation in regions of the genome that were previously too complex to analyze.
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Affiliation(s)
- Chen-Shan Chin
- GeneDX, Stamford, CT, USA.
- Foundation of Biological Data Science, Belmont, CA, USA.
| | - Sairam Behera
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Asif Khalak
- Foundation of Biological Data Science, Belmont, CA, USA
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Peter H Sudmant
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA
| | - Justin Wagner
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Justin M Zook
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
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15
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Vimercati A, Tannorella P, Orlandini E, Calzari L, Moro M, Guzzetti S, Selicorni A, Crippa M, Larizza L, Bonati MT, Russo S. Case report: atypical Silver-Russell syndrome patient with hand dystonia: the valuable support of the consensus statement to the wide syndromic spectrum. Front Genet 2023; 14:1198821. [PMID: 37529781 PMCID: PMC10387531 DOI: 10.3389/fgene.2023.1198821] [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: 04/03/2023] [Accepted: 06/19/2023] [Indexed: 08/03/2023] Open
Abstract
The amount of Insulin Growth Factor 2 (IGF2) controls the rate of embryonal and postnatal growth. The IGF2 and adjacent H19 are the imprinted genes of the telomeric cluster in the 11p15 chromosomal region regulated by differentially methylated regions (DMRs) or imprinting centers (ICs): H19/IGF2:IG-DMR (IC1). Dysregulation due to IC1 Loss-of-Methylation (LoM) or Gain-of-Methyaltion (GoM) causes Silver-Russell syndrome (SRS) or Beckwith-Wiedemann syndrome (BWS) disorders associated with growth retardation or overgrowth, respectively. Specific features define each of the two syndromes, but isolated asymmetry is a common cardinal feature, which is considered sufficient for a diagnosis in the BWS spectrum. Here, we report the case of a girl with right body asymmetry, which suggested BWS spectrum. Later, BWS/SRS molecular analysis identified IC1_LoM revealing the discrepant diagnosis of SRS. A clinical re-evaluation identified a relative macrocephaly and previously unidentified growth rate at lower limits of normal at birth, feeding difficulties, and asymmetry. Interestingly, and never previously described in IC1_LoM SRS patients, since the age of 16, she has developed hand-writer's cramps, depression, and bipolar disorder. Trio-WES identified a VPS16 heterozygous variant [NM_022575.4:c.2185C>G:p.Leu729Val] inherited from her healthy mother. VPS16 is involved in the endolysosomal system, and its dysregulation is linked to autosomal dominant dystonia with incomplete penetrance and variable expressivity. IGF2 involvement in the lysosomal pathway led us to speculate that the neurological phenotype of the proband might be triggered by the concurrent IGF2 deficit and VPS16 alteration.
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Affiliation(s)
- Alessandro Vimercati
- Research Laboratory of Medical Cytogenetics and Molecular Genetics, IRCCS Istituto Auxologico Italiano, Milano, Italy
| | - Pierpaola Tannorella
- Research Laboratory of Medical Cytogenetics and Molecular Genetics, IRCCS Istituto Auxologico Italiano, Milano, Italy
| | - Eleonora Orlandini
- Specialty School of Pediatrics, Alma Mater University of Bologna, Bologna, Italy
| | - Luciano Calzari
- Bioinformatics and Statistical Genomics Unit, IRCCS Istituto Auxologico Italiano, Milano, Italy
| | - Mirella Moro
- Department of Endocrine and Metabolic Diseases and Lab of Endocrine and Metabolic Research, IRCCS Istituto Auxologico Italiano, Milano, Italy
| | - Sara Guzzetti
- Research Laboratory of Medical Cytogenetics and Molecular Genetics, IRCCS Istituto Auxologico Italiano, Milano, Italy
| | | | - Milena Crippa
- Research Laboratory of Medical Cytogenetics and Molecular Genetics, IRCCS Istituto Auxologico Italiano, Milano, Italy
| | - Lidia Larizza
- Research Laboratory of Medical Cytogenetics and Molecular Genetics, IRCCS Istituto Auxologico Italiano, Milano, Italy
| | - Maria Teresa Bonati
- Unit of Medical Genetics, Institute for Maternal and Child Health Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Burlo Garofalo, Trieste, Italy
| | - Silvia Russo
- Research Laboratory of Medical Cytogenetics and Molecular Genetics, IRCCS Istituto Auxologico Italiano, Milano, Italy
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16
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Gallanis AF, Davis JL. Unique challenges of risk-reducing surgery for hereditary diffuse gastric cancer syndrome: a narrative review. Eur J Cancer Prev 2023; 32:391-395. [PMID: 36977191 PMCID: PMC10249595 DOI: 10.1097/cej.0000000000000798] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 03/04/2023] [Indexed: 03/30/2023]
Abstract
The common use of genetic testing has reinvigorated discussions surrounding enhanced cancer surveillance, chemoprevention, and preventive surgery strategies due to increasing recognition of pathogenic germline genetic variants. Prophylactic surgery for hereditary cancer syndromes can significantly reduce the risk of developing cancer. Hereditary diffuse gastric cancer (HDGC), characterized by high penetrance and an autosomal dominant inheritance pattern, is causally linked to germline mutations in the CDH1 tumor suppressor gene. Risk-reducing total gastrectomy is currently recommended in patients with pathogenic and likely pathogenic CDH1 variants; however, the physical and psychosocial sequelae of complete stomach removal are substantial and need to be investigated further. In this review, we address the risks and benefits of prophylactic total gastrectomy for HDGC in the context of prophylactic surgery for other highly penetrant cancer syndromes.
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Affiliation(s)
- Amber F. Gallanis
- Surgical Oncology Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Jeremy L. Davis
- Surgical Oncology Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
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17
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Crooks KR, Farwell Hagman KD, Mandelker D, Santani A, Schmidt RJ, Temple-Smolkin RL, Lincoln SE. Recommendations for Next-Generation Sequencing Germline Variant Confirmation: A Joint Report of the Association for Molecular Pathology and National Society of Genetic Counselors. J Mol Diagn 2023; 25:411-427. [PMID: 37207865 DOI: 10.1016/j.jmoldx.2023.03.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 02/27/2023] [Accepted: 03/30/2023] [Indexed: 05/21/2023] Open
Abstract
Clinical laboratory implementation of next-generation sequencing (NGS)-based constitutional genetic testing has been rapid and widespread. In the absence of widely adopted comprehensive guidance, there remains substantial variability among laboratories in the practice of NGS. One issue of sustained discussion in the field is whether and to what extent orthogonal confirmation of genetic variants identified by NGS is necessary or helpful. The Association for Molecular Pathology Clinical Practice Committee convened the NGS Germline Variant Confirmation Working Group to assess current evidence regarding orthogonal confirmation and to establish recommendations for standardizing orthogonal confirmation practices to support quality patient care. On the basis of the results of a survey of the literature, a survey of laboratory practices, and subject expert matter consensus, eight recommendations are presented, providing a common framework for clinical laboratory professionals to develop or refine individualized laboratory policies and procedures regarding orthogonal confirmation of germline variants detected by NGS.
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Affiliation(s)
- Kristy R Crooks
- NGS Germline Variant Confirmation Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora, Colorado.
| | - Kelly D Farwell Hagman
- NGS Germline Variant Confirmation Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Clinical Diagnostics, Ambry Genetics, Aliso Viejo, California
| | - Diana Mandelker
- NGS Germline Variant Confirmation Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Avni Santani
- NGS Germline Variant Confirmation Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; LetsGetChecked, PrivaPath Diagnostics, Dublin, Ireland; Veritas Genetics, Danvers, Massachusetts
| | - Ryan J Schmidt
- NGS Germline Variant Confirmation Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California; Department of Pathology, Keck School of Medicine of the University of Southern California, Los Angeles, California
| | | | - Stephen E Lincoln
- NGS Germline Variant Confirmation Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; InVitae, Bethesda, Maryland
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18
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Powell CL, Saddoughi SA, Wigle DA. Progress in genome-inspired treatment decisions for multifocal lung adenocarcinoma. Expert Rev Respir Med 2023; 17:1009-1021. [PMID: 37982734 DOI: 10.1080/17476348.2023.2286277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 11/17/2023] [Indexed: 11/21/2023]
Abstract
INTRODUCTION Multifocal lung adenocarcinoma (MFLA) is becoming increasingly recognized as a distinct subset of lung cancer, with unique biology, disease course, and treatment outcomes. While definitions remain controversial, MFLA is characterized by the development and concurrent presence of multiple independent (non-metastatic) lesions on the lung adenocarcinoma spectrum. Disease progression typically follows an indolent course measured in years, with a lower propensity for nodal and distant metastases than other more common forms of non-small cell lung cancer. AREAS COVERED Traditional imaging and histopathological analyses of tumor biopsies are frequently unable to fully characterize the disease, prompting interest in molecular diagnosis. We highlight some of the key questions in the field, including accurate definitions to identify and stage MLFA, molecular tests to stratify patients and treatment decisions, and the lack of clinical trial data to delineate best management for this poorly understood subset of lung cancer patients. We review the existing literature and progress toward a genomic diagnosis for this unique disease entity. EXPERT OPINION Multifocal lung adenocarcinoma behaves differently than other forms of non-small cell lung cancer. Progress in molecular diagnosis may enhance potential for accurate definition, diagnosis, and optimizing treatment approach.
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Affiliation(s)
- Chelsea L Powell
- Division of Thoracic Surgery, Department of Surgery, Mayo Clinic, Rochester, MN, USA
| | - Sahar A Saddoughi
- Division of Thoracic Surgery, Department of Surgery, Mayo Clinic, Rochester, MN, USA
| | - Dennis A Wigle
- Division of Thoracic Surgery, Department of Surgery, Mayo Clinic, Rochester, MN, USA
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19
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Zhang K, Lin G, Han Y, Peng R, Li J. Analysis of Clinical Laboratory Detecting Challenging Variants from Exome Sequencing Using Simulated Patient-Parent Trio Sample: Pilot Study for Neurodevelopmental Disorder de Novo Variants. J Mol Diagn 2023; 25:378-387. [PMID: 37208049 DOI: 10.1016/j.jmoldx.2023.02.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 02/19/2023] [Accepted: 02/24/2023] [Indexed: 05/21/2023] Open
Abstract
To date, there has been no systematic analysis for the clinical laboratory in detecting technically challenging variants using the trio-based exome sequencing (ES) approach. Here, we present an interlaboratory pilot proficiency testing study that used synthetic patient-parent specimens to assess the detection of challenging variants with de novo dominant inheritance modes for neurodevelopmental disorders using various trio-based ES. In total, 27 clinical laboratories that performed diagnostic exome analyses participated in the survey. One of the 26 challenging variants was identified by all laboratories, whereas all 26 variants were identified by only nine laboratories. The lack of identification of mosaic variants was often due to the bioinformatics analysis that excluded the variant. For missing intended heterozygous variants, probable root causes were related to the technical bioinformatics pipeline and variant interpretation and reporting. For each missing variant, there may be more than one probable reason from the different laboratories. There was considerable variation in interlaboratory performance for detecting challenging variants using trio-based ES. This finding may have important implications for the design and validation of tests for different variant types in clinical laboratories, especially for technically challenging variants, and necessary workflow modification can potentially improve trio-based ES performance.
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Affiliation(s)
- Kuo Zhang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, China
| | - Guigao Lin
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, China
| | - Yanxi Han
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, China
| | - Rongxue Peng
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, China
| | - Jinming Li
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, China.
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20
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Liu Q, Yang S, Tan Y, Cui L. High-throughput sequencing technology facilitates the discovery of novel biomarkers for antiphospholipid syndrome. Front Immunol 2023; 14:1128245. [PMID: 37275905 PMCID: PMC10235516 DOI: 10.3389/fimmu.2023.1128245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 05/09/2023] [Indexed: 06/07/2023] Open
Abstract
Antiphospholipid syndrome (APS) is characterized by arterial and venous thrombosis and/or morbid pregnancy, accompanied by persistent antiphospholipid antibody (aPL) positivity. However, due to the complex pathogenesis of APS and the large individual differences in the expression of aPL profiles of patients, the problem of APS diagnosis, prognosis judgment, and risk assessment may not be solved only from the antibody level. It is necessary to use new technologies and multiple dimensions to explore novel APS biomarkers. The application of next-generation sequencing (NGS) technology in diseases with a high incidence of somatic mutations, such as genetic diseases and tumors, has been very mature. Thus, we try to know the research and application progress of APS by NGS technology from genome, transcriptome, epigenome and other aspects. This review will describe the related research of NGS technology in APS and provide more reference for the deep understanding of APS-related screening markers and disease pathogenesis.
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Affiliation(s)
- Qi Liu
- Department of Clinical Laboratory, Peking University Third Hospital, Beijing, China
- Core Unit of National Clinical Research Center for Laboratory Medicine, Peking University Third Hospital, Beijing, China
- Institute of Medical Technology, Peking University Health Science Center, Beijing, China
| | - Shuo Yang
- Department of Clinical Laboratory, Peking University Third Hospital, Beijing, China
- Core Unit of National Clinical Research Center for Laboratory Medicine, Peking University Third Hospital, Beijing, China
| | - Yuan Tan
- Department of Clinical Laboratory, Peking University Third Hospital, Beijing, China
- Core Unit of National Clinical Research Center for Laboratory Medicine, Peking University Third Hospital, Beijing, China
- Institute of Medical Technology, Peking University Health Science Center, Beijing, China
| | - Liyan Cui
- Department of Clinical Laboratory, Peking University Third Hospital, Beijing, China
- Core Unit of National Clinical Research Center for Laboratory Medicine, Peking University Third Hospital, Beijing, China
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21
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Chovanec J, Tunc I, Hughes J, Halstead J, Mateja A, Liu Y, O’Connell MP, Kim J, Park YH, Wang Q, Le Q, Pirooznia M, Trivedi NN, Bai Y, Yin Y, Hsu AP, McElwee J, Lassiter S, Nelson C, Bandoh J, DiMaggio T, Šelb J, Rijavec M, Carter MC, Komarow HD, Sabato V, Steinberg J, Hafer KM, Feuille E, Hourigan CS, Lack J, Khoury P, Maric I, Zanotti R, Bonadonna P, Schwartz LB, Milner JD, Glover SC, Ebo DG, Korošec P, Caughey GH, Brittain EH, Busby B, Metcalfe DD, Lyons JJ. Genetically defined individual reference ranges for tryptase limit unnecessary procedures and unmask myeloid neoplasms. Blood Adv 2023; 7:1796-1810. [PMID: 36170795 PMCID: PMC10164828 DOI: 10.1182/bloodadvances.2022007936] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 08/09/2022] [Accepted: 08/26/2022] [Indexed: 11/20/2022] Open
Abstract
Serum tryptase is a biomarker used to aid in the identification of certain myeloid neoplasms, most notably systemic mastocytosis, where basal serum tryptase (BST) levels >20 ng/mL are a minor criterion for diagnosis. Although clonal myeloid neoplasms are rare, the common cause for elevated BST levels is the genetic trait hereditary α-tryptasemia (HαT) caused by increased germline TPSAB1 copy number. To date, the precise structural variation and mechanism(s) underlying elevated BST in HαT and the general clinical utility of tryptase genotyping, remain undefined. Through cloning, long-read sequencing, and assembling of the human tryptase locus from an individual with HαT, and validating our findings in vitro and in silico, we demonstrate that BST elevations arise from overexpression of replicated TPSAB1 loci encoding canonical α-tryptase protein owing to coinheritance of a linked overactive promoter element. Modeling BST levels based on TPSAB1 replication number, we generate new individualized clinical reference values for the upper limit of normal. Using this personalized laboratory medicine approach, we demonstrate the clinical utility of tryptase genotyping, finding that in the absence of HαT, BST levels >11.4 ng/mL frequently identify indolent clonal mast cell disease. Moreover, substantial BST elevations (eg, >100 ng/mL), which would ordinarily prompt bone marrow biopsy, can result from TPSAB1 replications alone and thus be within normal limits for certain individuals with HαT.
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Affiliation(s)
- Jack Chovanec
- Translational Allergic Immunopathology Unit, Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD
| | - Ilker Tunc
- Bioinformatics and Computational Biology Core, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD
| | | | - Joseph Halstead
- Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham, United Kingdom
| | - Allyson Mateja
- Clinical Monitoring Research Program Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Yihui Liu
- Translational Allergic Immunopathology Unit, Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD
| | - Michael P. O’Connell
- Translational Allergic Immunopathology Unit, Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD
| | - Jiwon Kim
- Translational Allergic Immunopathology Unit, Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD
| | - Young Hwan Park
- Translational Allergic Immunopathology Unit, Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD
| | - Qinlu Wang
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, NIAID, NIH, Bethesda, MD
| | - Quang Le
- Department of Internal Medicine, Virginia Commonwealth University, Richmond, VA
| | - Mehdi Pirooznia
- Bioinformatics and Computational Biology Core, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD
| | - Neil N. Trivedi
- Cardiovascular Research Institute and Department of Medicine, University of California San Francisco, San Francisco, CA
- Veterans Affairs Medical Center, San Francisco, CA
| | - Yun Bai
- Mast Cell Biology Section, Laboratory of Allergic Diseases, NIAID, NIH, Bethesda, MD
| | - Yuzhi Yin
- Mast Cell Biology Section, Laboratory of Allergic Diseases, NIAID, NIH, Bethesda, MD
| | - Amy P. Hsu
- Immunopathogenesis Section, Laboratory of Clinical Immunology and Microbiology, NIAID, NIH, Bethesda, MD
| | | | - Sheryce Lassiter
- Clinical Research Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Celeste Nelson
- Translational Allergic Immunopathology Unit, Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD
| | - Judy Bandoh
- Translational Allergic Immunopathology Unit, Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD
| | - Thomas DiMaggio
- Fungal Pathogenesis Section, Laboratory of Clinical Immunology and Microbiology, NIAID, NIH, Bethesda, MD
| | - Julij Šelb
- University Clinic of Respiratory and Allergic Diseases Golnik, Golnik, Slovenia
| | - Matija Rijavec
- University Clinic of Respiratory and Allergic Diseases Golnik, Golnik, Slovenia
| | - Melody C. Carter
- Mast Cell Biology Section, Laboratory of Allergic Diseases, NIAID, NIH, Bethesda, MD
| | - Hirsh D. Komarow
- Mast Cell Biology Section, Laboratory of Allergic Diseases, NIAID, NIH, Bethesda, MD
| | - Vito Sabato
- Department of Immunology, Allergology, and Rheumatology, Infla-Med Centre of Excellence, Antwerp University Hospital, University of Antwerp, Antwerp, Belgium
| | - Joshua Steinberg
- Division of Allergy and Clinical Immunology, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI
| | - Kurt M. Hafer
- Department of Medicine, Stanford University, Stanford, CA
| | - Elizabeth Feuille
- Division of Allergy and Clinical Immunology, Department of Pediatrics, Weill Cornell Medical College, Cornell University, New York, NY
| | | | - Justin Lack
- NIAID Collaborative Bioinformatics Resource, NIAID, NIH, Bethesda, MD
| | - Paneez Khoury
- Human Eosinophil Section, Laboratory of Parasitic Diseases, NIAID, NIH, Bethesda, MD
| | - Irina Maric
- Hematology Service, Department of Laboratory Medicine, Clinical Center, NIH, Bethesda, MD
| | - Roberta Zanotti
- Department of Medicine, Section of Hematology, Verona University Hospital, Verona, Italy
| | | | | | - Joshua D. Milner
- Division of Allergy, Immunology and Rheumatology, Columbia University, New York, NY
| | - Sarah C. Glover
- Division of Digestive Diseases, Department of Medicine, University of Mississippi Medical Center, Jackson, MS
| | - Didier G. Ebo
- Department of Immunology, Allergology, and Rheumatology, Infla-Med Centre of Excellence, Antwerp University Hospital, University of Antwerp, Antwerp, Belgium
| | - Peter Korošec
- University Clinic of Respiratory and Allergic Diseases Golnik, Golnik, Slovenia
| | - George H. Caughey
- Cardiovascular Research Institute and Department of Medicine, University of California San Francisco, San Francisco, CA
- Veterans Affairs Medical Center, San Francisco, CA
| | | | - Ben Busby
- National Library of Medicine, National Center for Biotechnology Information, NIH, Bethesda, MD
| | - Dean D. Metcalfe
- Mast Cell Biology Section, Laboratory of Allergic Diseases, NIAID, NIH, Bethesda, MD
| | - Jonathan J. Lyons
- Translational Allergic Immunopathology Unit, Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD
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22
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Deignan JL, De Castro M, Horner VL, Johnston T, Macaya D, Maleszewski JJ, Reddi HV, Tayeh MK. Points to consider in the practice of postmortem genetic testing: A statement of the American College of Medical Genetics and Genomics (ACMG). Genet Med 2023; 25:100017. [PMID: 36799919 DOI: 10.1016/j.gim.2023.100017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 01/11/2023] [Indexed: 02/18/2023] Open
Affiliation(s)
- Joshua L Deignan
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA Health, Los Angeles, CA
| | - Mauricio De Castro
- DHA Genetics Reference Laboratory, Air Force Medical Genetics Center, Keesler Air Force Base, Biloxi, MS; Division of Medical Genetics, Department of Pediatrics, University of Mississippi Medical Center, Jackson, MS
| | - Vanessa L Horner
- Department of Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin, Madison, WI; Wisconsin State Laboratory of Hygiene, University of Wisconsin, Madison, WI
| | | | | | | | - Honey V Reddi
- Department of Pathology & Laboratory Medicine, Medical College of Wisconsin, Milwaukee, WI
| | - Marwan K Tayeh
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN
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23
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Aloi C, Salina A, Caroli F, Bocciardi R, Tappino B, Bassi M, Minuto N, d'Annunzio G, Maghnie M. Next Generation Sequencing (NGS) Target Approach for Undiagnosed Dysglycaemia. Life (Basel) 2023; 13:life13051080. [PMID: 37240725 DOI: 10.3390/life13051080] [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: 03/30/2023] [Revised: 04/18/2023] [Accepted: 04/21/2023] [Indexed: 05/28/2023] Open
Abstract
Next-generation sequencing (NGS) has revolutionized the field of genomics and created new opportunities for basic research. We described the strategy for the NGS validation of the "dysglycaemia panel" composed by 44 genes related to glucose metabolism disorders (MODY, Wolfram syndrome) and familial renal glycosuria using Ion AmpliSeq technology combined with Ion-PGM. Anonymized DNA of 32 previously genotyped cases with 33 different variants were used to optimize the methodology. Standard protocol was used to generate the primer design, library, template preparation, and sequencing. Ion Reporter tool was used for data analysis. In all the runs, the mean coverage was over 200×. Twenty-nine out of thirty three variants (96.5%) were detected; four frameshift variants were missed. All point mutations were detected with high sensitivity. We identified three further variants of unknown significance in addition to pathogenic mutations previously identified by Sanger sequencing. The NGS panel allowed us to identify pathogenic variants in multiple genes in a short time. This could help to identify several defects in children and young adults that have to receive the genetic diagnosis necessary for optimal treatment. In order not to lose any pathogenic variants, Sanger sequencing is included in our analytical protocol to avoid missing frameshift variants.
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Affiliation(s)
- Concetta Aloi
- LABSIEM (Laboratory for the Study of Inborn Errors of Metabolism), IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy
| | - Alessandro Salina
- LABSIEM (Laboratory for the Study of Inborn Errors of Metabolism), IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy
| | - Francesco Caroli
- UOC Genetica Medica, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy
| | - Renata Bocciardi
- UOC Genetica Medica, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy
- Department of Neuroscience, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DINOGMI), University of Genoa, 16100 Genoa, Italy
| | - Barbara Tappino
- LABSIEM (Laboratory for the Study of Inborn Errors of Metabolism), IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy
| | - Marta Bassi
- Department of Neuroscience, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DINOGMI), University of Genoa, 16100 Genoa, Italy
- Department of Pediatrics, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy
| | - Nicola Minuto
- Department of Pediatrics, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy
| | - Giuseppe d'Annunzio
- Department of Pediatrics, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy
| | - Mohamad Maghnie
- Department of Neuroscience, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DINOGMI), University of Genoa, 16100 Genoa, Italy
- Department of Pediatrics, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy
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24
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Perrier S, Guerrero K, Tran LT, Michell-Robinson MA, Legault G, Brais B, Sylvain M, Dorman J, Demos M, Köhler W, Pastinen T, Thiffault I, Bernard G. Solving inherited white matter disorder etiologies in the neurology clinic: Challenges and lessons learned using next-generation sequencing. Front Neurol 2023; 14:1148377. [PMID: 37077564 PMCID: PMC10108901 DOI: 10.3389/fneur.2023.1148377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 02/23/2023] [Indexed: 04/05/2023] Open
Abstract
IntroductionRare neurodevelopmental disorders, including inherited white matter disorders or leukodystrophies, often present a diagnostic challenge on a genetic level given the large number of causal genes associated with a range of disease subtypes. This study aims to demonstrate the challenges and lessons learned in the genetic investigations of leukodystrophies through presentation of a series of cases solved using exome or genome sequencing.MethodsEach of the six patients had a leukodystrophy associated with hypomyelination or delayed myelination on MRI, and inconclusive clinical diagnostic genetic testing results. We performed next generation sequencing (case-based exome or genome sequencing) to further investigate the genetic cause of disease.ResultsFollowing different lines of investigation, molecular diagnoses were obtained for each case, with patients harboring pathogenic variants in a range of genes including TMEM106B, GJA1, AGA, POLR3A, and TUBB4A. We describe the lessons learned in reaching the genetic diagnosis, including the importance of (a) utilizing proper multi-gene panels in clinical testing, (b) assessing the reliability of biochemical assays in supporting diagnoses, and (c) understanding the limitations of exome sequencing methods in regard to CNV detection and region coverage in GC-rich areas.DiscussionThis study illustrates the importance of applying a collaborative diagnostic approach by combining detailed phenotyping data and metabolic results from the clinical environment with advanced next generation sequencing analysis techniques from the research environment to increase the diagnostic yield in patients with genetically unresolved leukodystrophies.
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Affiliation(s)
- Stefanie Perrier
- Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada
- Child Health and Human Development Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Kether Guerrero
- Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada
- Child Health and Human Development Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Luan T. Tran
- Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada
- Child Health and Human Development Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Mackenzie A. Michell-Robinson
- Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada
- Child Health and Human Development Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Geneviève Legault
- Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada
- Child Health and Human Development Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
- Department of Pediatrics, McGill University, Montreal, QC, Canada
| | - Bernard Brais
- Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada
- Montreal Neurological Institute, McGill University, Montreal, QC, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Michel Sylvain
- Division of Pediatric Neurology, Centre Mère-Enfant Soleil du CHU de Québec - Université Laval, Québec City, QC, Canada
| | - James Dorman
- John H. Stroger Jr. Hospital of Cook County, Chicago, IL, United States
- Department of Neurological Sciences, Rush Medical College, Chicago, IL, United States
| | - Michelle Demos
- Division of Neurology, Department of Pediatrics, University of British Columbia, BC Children's Hospital, Vancouver, BC, Canada
| | - Wolfgang Köhler
- Leukodystrophy Center, University of Leipzig Medical Center, Leipzig, Germany
| | - Tomi Pastinen
- Genomic Medicine Center, Children's Mercy Hospital, Kansas City, MO, United States
- University of Missouri Kansas City School of Medicine, Kansas City, MO, United States
| | - Isabelle Thiffault
- Genomic Medicine Center, Children's Mercy Hospital, Kansas City, MO, United States
- University of Missouri Kansas City School of Medicine, Kansas City, MO, United States
- Department of Pathology and Laboratory Medicine, Children's Mercy Hospital, Kansas City, MO, United States
- Isabelle Thiffault
| | - Geneviève Bernard
- Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada
- Child Health and Human Development Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
- Department of Pediatrics, McGill University, Montreal, QC, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Department of Specialized Medicine, Division of Medical Genetics, McGill University Health Center, Montreal, QC, Canada
- *Correspondence: Geneviève Bernard
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25
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Tayeh MK, Chen M, Fullerton SM, Gonzales PR, Huang SJ, Massingham LJ, O'Daniel JM, Stewart DR, Stiles AR, Evans BJ. The designated record set for clinical genetic and genomic testing: A points to consider statement of the American College of Medical Genetics and Genomics (ACMG). Genet Med 2023; 25:100342. [PMID: 36547466 DOI: 10.1016/j.gim.2022.11.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 11/15/2022] [Indexed: 12/24/2022] Open
Affiliation(s)
| | - Margaret Chen
- Western Michigan University Homer Stryker M.D. School of Medicine, Kalamazoo, MI; GeneDx, Gaithersburg, MD
| | - Stephanie M Fullerton
- Division of Medical Genetics, Department of Medicine, University of Washington School of Medicine, Seattle, WA; Department of Bioethics & Humanities, University of Washington School of Medicine, Seattle, WA
| | - Patrick R Gonzales
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Lenexa, KS
| | - Samuel J Huang
- Division of Medical Genetics, Marshfield Clinic, Marshfield, WI
| | - Lauren J Massingham
- Division of Medical Genetics, Department of Pediatrics, Hasbro Children's Hospital, Providence, RI; The Warren Alpert School of Medicine at Brown University, Providence, RI
| | - Julianne M O'Daniel
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Douglas R Stewart
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD
| | - Ashlee R Stiles
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC
| | - Barbara J Evans
- Levin College of Law, University of Florida, Gainesville, FL; Herbert Wertheim College of Engineering, University of Florida, Gainesville, FL
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- American College of Medical Genetics and Genomics, Bethesda, MD
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26
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Bencurova E, Akash A, Dobson RC, Dandekar T. DNA storage-from natural biology to synthetic biology. Comput Struct Biotechnol J 2023; 21:1227-1235. [PMID: 36817961 PMCID: PMC9932295 DOI: 10.1016/j.csbj.2023.01.045] [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: 11/19/2022] [Revised: 01/30/2023] [Accepted: 01/31/2023] [Indexed: 02/04/2023] Open
Abstract
Natural DNA storage allows cellular differentiation, evolution, the growth of our children and controls all our ecosystems. Here, we discuss the fundamental aspects of DNA storage and recent advances in this field, with special emphasis on natural processes and solutions that can be exploited. We point out new ways of efficient DNA and nucleotide storage that are inspired by nature. Within a few years DNA-based information storage may become an attractive and natural complementation to current electronic data storage systems. We discuss rapid and directed access (e.g. DNA elements such as promotors, enhancers), regulatory signals and modulation (e.g. lncRNA) as well as integrated high-density storage and processing modules (e.g. chromosomal territories). There is pragmatic DNA storage for use in biotechnology and human genetics. We examine DNA storage as an approach for synthetic biology (e.g. light-controlled nucleotide processing enzymes). The natural polymers of DNA and RNA offer much for direct storage operations (read-in, read-out, access control). The inbuilt parallelism (many molecules at many places working at the same time) is important for fast processing of information. Using biology concepts from chromosomal storage, nucleic acid processing as well as polymer material sciences such as electronical effects in enzymes, graphene, nanocellulose up to DNA macramé , DNA wires and DNA-based aptamer field effect transistors will open up new applications gradually replacing classical information storage methods in ever more areas over time (decades).
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Affiliation(s)
- Elena Bencurova
- Department of Bioinformatics, University of Würzburg, Würzburg, Germany
| | - Aman Akash
- Department of Bioinformatics, University of Würzburg, Würzburg, Germany
| | - Renwick C.J. Dobson
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand,Department of Biochemistry and Pharmacology, University of Melbourne, Melbourne, Australia
| | - Thomas Dandekar
- Department of Bioinformatics, University of Würzburg, Würzburg, Germany,Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany,Corresponding author at: Department of Bioinformatics, University of Würzburg, Würzburg, Germany.
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Points to consider in the detection of germline structural variants using next-generation sequencing: A statement of the American College of Medical Genetics and Genomics (ACMG). Genet Med 2023; 25:100316. [PMID: 36507974 DOI: 10.1016/j.gim.2022.09.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 09/29/2022] [Accepted: 09/30/2022] [Indexed: 12/14/2022] Open
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Vora NL, Norton ME. Prenatal exome and genome sequencing for fetal structural abnormalities. Am J Obstet Gynecol 2023; 228:140-149. [PMID: 36027950 PMCID: PMC9877148 DOI: 10.1016/j.ajog.2022.08.040] [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: 05/03/2022] [Revised: 08/07/2022] [Accepted: 08/17/2022] [Indexed: 01/28/2023]
Abstract
As prenatal exome sequencing becomes integrated into clinical care, it is critical that providers caring for women with fetal anomalies recognize not only the benefits, but also the challenges and considerations related to this technology. This overview of prenatal sequencing includes information about indications for sequencing, methods, diagnostic yield, clinical utility, variant interpretation, ethical considerations and dilemmas, practical considerations (ie, turnaround time and cost), pre- and posttest counseling points, and psychological impact of testing on families.
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Affiliation(s)
- Neeta L Vora
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, University of North Carolina at Chapel Hill, Chapel Hill, NC.
| | - Mary E Norton
- Division of Maternal-Fetal Medicine, Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Francisco, San Francisco, CA
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Alonso-Gonzalez A, Tosco-Herrera E, Molina-Molina M, Flores C. Idiopathic pulmonary fibrosis and the role of genetics in the era of precision medicine. Front Med (Lausanne) 2023; 10:1152211. [PMID: 37181377 PMCID: PMC10172674 DOI: 10.3389/fmed.2023.1152211] [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: 01/27/2023] [Accepted: 04/03/2023] [Indexed: 05/16/2023] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a chronic, rare progressive lung disease, characterized by lung scarring and the irreversible loss of lung function. Two anti-fibrotic drugs, nintedanib and pirfenidone, have been demonstrated to slow down disease progression, although IPF mortality remains a challenge and the patients die after a few years from diagnosis. Rare pathogenic variants in genes that are involved in the surfactant metabolism and telomere maintenance, among others, have a high penetrance and tend to co-segregate with the disease in families. Common recurrent variants in the population with modest effect sizes have been also associated with the disease risk and progression. Genome-wide association studies (GWAS) support at least 23 genetic risk loci, linking the disease pathogenesis with unexpected molecular pathways including cellular adhesion and signaling, wound healing, barrier function, airway clearance, and innate immunity and host defense, besides the surfactant metabolism and telomere biology. As the cost of high-throughput genomic technologies continuously decreases and new technologies and approaches arise, their widespread use by clinicians and researchers is efficiently contributing to a better understanding of the pathogenesis of progressive pulmonary fibrosis. Here we provide an overview of the genetic factors known to be involved in IPF pathogenesis and discuss how they will continue to further advance in this field. We also discuss how genomic technologies could help to further improve IPF diagnosis and prognosis as well as for assessing genetic risk in unaffected relatives. The development and validation of evidence-based guidelines for genetic-based screening of IPF will allow redefining and classifying this disease relying on molecular characteristics and contribute to the implementation of precision medicine approaches.
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Affiliation(s)
- Aitana Alonso-Gonzalez
- Unidad de Investigación, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain
- Universidad de Santiago de Compostela, Santiago de Compostela, Spain
| | - Eva Tosco-Herrera
- Unidad de Investigación, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain
| | - Maria Molina-Molina
- Servei de Pneumologia, Laboratori de Pneumologia Experimental, IDIBELL, Barcelona, Spain
- Campus de Bellvitge, Universitat de Barcelona, Barcelona, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Carlos Flores
- Unidad de Investigación, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
- Facultad de Ciencias de la Salud, Universidad Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain
- *Correspondence: Carlos Flores,
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The Diagnostic Yield of Next Generation Sequencing in Inherited Retinal Diseases: A Systematic Review and Meta-analysis. Am J Ophthalmol 2022; 249:57-73. [PMID: 36592879 DOI: 10.1016/j.ajo.2022.12.027] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 11/16/2022] [Accepted: 12/23/2022] [Indexed: 01/01/2023]
Abstract
PURPOSE Accurate genotyping of individuals with inherited retinal diseases (IRD) is essential for patient management and identifying suitable candidates for gene therapies. This study evaluated the diagnostic yield of next generation sequencing (NGS) in IRDs. DESIGN Systematic review and meta-analysis. METHODS This systematic review was prospectively registered (CRD42021293619). Ovid MEDLINE and Ovid Embase were searched on 6 June 2022. Clinical studies evaluating the diagnostic yield of NGS in individuals with IRDs were eligible for inclusion. Risk of bias assessment was performed. Studies were pooled using a random...effects inverse variance model. Sources of heterogeneity were explored using stratified analysis, meta-regression, and sensitivity analysis. RESULTS This study included 105 publications from 28 countries. Most studies (90 studies) used targeted gene panels. The diagnostic yield of NGS was 61.3% (95% confidence interval: 57.8-64.7%; 51 studies) in mixed IRD phenotypes, 58.2% (51.6-64.6%; 41 studies) in rod-cone dystrophies, 57.7% (46.8-68.3%; eight studies) in macular and cone/cone-rod dystrophies, and 47.6% (95% CI: 41.0-54.3%; four studies) in familial exudative vitreoretinopathy. For mixed IRD phenotypes, a higher diagnostic yield was achieved pooling studies published between 2018-2022 (64.2% [59.5-68.7%]), studies using exome sequencing (73.5% [58.9-86.1%]), and studies using the American College of Medical Genetics variant interpretation standards (65.6% [60.8-70.4%]). CONCLUSION The current diagnostic yield of NGS in IRDs is between 52-74%. The certainty of the evidence was judged as low or very low. A key limitation of the current evidence is the significant heterogeneity between studies. Adoption of standardized reporting guidelines could improve confidence in future meta-analyses.
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Wen XL, Wang YZ, Zhang XL, Tu JQ, Zhang ZJ, Liu XX, Lu HY, Hao GP, Wang XH, Yang LH, Zhang RJ. Compound heterozygous p.L483P and p.S310G mutations in GBA1 cause type 1 adult Gaucher disease: A case report. World J Clin Cases 2022; 10:13426-13434. [PMID: 36683633 PMCID: PMC9851016 DOI: 10.12998/wjcc.v10.i36.13426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 10/20/2022] [Accepted: 11/30/2022] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Gaucher disease (GD) is caused by a GBA1 gene mutation that leads to decreased acid β-glucosidase activity [glucocerebrosidase (GCase)]. This study aimed to identify and characterise compound heterozygous mutations in GBA1 in a patient with type 1 GD.
CASE SUMMARY Here, we report a rare adult-onset type 1 GD in a 46-year-old female patient with clinical manifestations of giant spleen, thrombocytopenia, and bone pain, diagnosed by enzymatic and genetic testing. Enzymology and whole exome sequencing revealed heterozygous missense mutations in exon 10 c.1448T>C (p.L483P) and exon 7 c.928A>G (p.S310G) of GBA1. The latter was first reported in patients with GD. Structural modelling showed that p.S310G and p.L483P were distant from the GCase active site. The p.S310G mutation in domain 1 may decrease stability between the α2 and α3 helices of GBA1. The p.L483P mutation in domain 2 reduced the van der Waals force of the side chain and disrupted the C-terminal β-sheet. The patient was treated with imiglucerase replacement therapy, and her condition was stable.
CONCLUSION The p.L483P/p.S310G novel compound heterozygous mutation underlies type 1 GD and likely affects GCase protein function. This is the first description of p.S310G being associated with mild type 1 GD in the context of a coinherited p.L483P mutation.
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Affiliation(s)
- Xiao-Ling Wen
- Department of Hematology, The First People’s Hospital of Yibin, Yibin 644000, Sichuan Province, China
- Department of Hematology, The Second Hospital of Shanxi Medical University, Taiyuan 030001, Shanxi Province, China
| | - Yao-Zi Wang
- Department of Hematology, The Second Hospital of Shanxi Medical University, Taiyuan 030001, Shanxi Province, China
| | - Xia-Lin Zhang
- Department of Hematology, The Third Hospital of Shanxi Medical University, The Shanxi Bethune Hospital, The Shanxi Academy of Medical Sciences, The Tongji Shanxi Hospital, The Shanxi Medical University, Taiyuan 030032, Shanxi Province, China
| | - Jia-Qiang Tu
- Department of Hematology, The First People’s Hospital of Yibin, Yibin 644000, Sichuan Province, China
| | - Zhi-Juan Zhang
- Department of Hematology, The Second Hospital of Shanxi Medical University, Taiyuan 030001, Shanxi Province, China
| | - Xia-Xia Liu
- Department of Hematology, The Second Hospital of Shanxi Medical University, Taiyuan 030001, Shanxi Province, China
| | - Hai-Yan Lu
- Department of Hematology, The Children’s Hospital of Shanxi, Taiyuan 030006, Shanxi Province, China
| | - Guo-Ping Hao
- Department of Hematology, The Children’s Hospital of Shanxi, Taiyuan 030006, Shanxi Province, China
| | - Xiao-Huan Wang
- Department of Hematology, The Children’s Hospital of Shanxi, Taiyuan 030006, Shanxi Province, China
| | - Lin-Hua Yang
- Department of Hematology, The Second Hospital of Shanxi Medical University, Taiyuan 030001, Shanxi Province, China
| | - Rui-Juan Zhang
- Department of Hematology, The Third Hospital of Shanxi Medical University, The Shanxi Bethune Hospital, The Shanxi Academy of Medical Sciences, The Tongji Shanxi Hospital, The Shanxi Medical University, Taiyuan 030032, Shanxi Province, China
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Wu D, Zhang L, Qiang Y, Wang K. Improved detection of SBDS gene mutation by a new method of next-generation sequencing analysis based on the Chinese mutation spectrum. PLoS One 2022; 17:e0269029. [PMID: 36512530 PMCID: PMC9747038 DOI: 10.1371/journal.pone.0269029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 05/13/2022] [Indexed: 12/15/2022] Open
Abstract
Next-generation sequencing (NGS) is a useful molecular diagnostic tool for genetic diseases. However, due to the presence of highly homologous pseudogenes, it is challenging to use short-read NGS for analyzing mutations of the Shwachman-Bodian-Diamond syndrome (SBDS) gene. The SBDS mutation spectrum was analyzed in the Chinese population, which revealed that SBDS variants were primarily from sequence exchange between SBDS and its pseudogene at the base-pair level, predominantly in the coding region and splice junction of exon two. The c.258+2T>C and c.185_184TA>GT variants were the two most common pathogenic SBDS variants in the Chinese population, resulting in a total carrier frequency of 1.19%. When analyzing pathogenic variants in the SBDS gene from the NGS data, the misalignment was identified as a common issue, and there were different probabilities of misalignment for different pathogenic variants. Here, we present a novel mathematical method for identifying pathogenic variants in the SBDS gene from the NGS data, which utilizes read-depth of the paralogous sequence variant (PSV) loci of SBDS and its pseudogene. Combined with PCR and STR orthogonal experiments, SBDS gene mutation analysis results were improved in 40% of clinical samples, and various types of mutations such as homozygous, compound heterozygous, and uniparental diploid were explored. The findings effectively reduce the impact of misalignment in NGS-based SBDS mutation analysis and are helpful for the clinical diagnosis of SBDS-related diseases, the research into population variation, and the carrier screening.
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Affiliation(s)
- Dong Wu
- Department of Obstetrics and Gynecology, 900 Hospital of the Joint Logistics Team or Dongfang Hospital, Fuzhou, Fujian, People’s Republic of China
| | - Li Zhang
- Fulgent (Fujian) Technologies, Fuzhou, Fujian, People’s Republic of China
| | - Yuzhen Qiang
- Fulgent (Fujian) Technologies, Fuzhou, Fujian, People’s Republic of China
| | - Kaiyu Wang
- Fulgent (Fujian) Technologies, Fuzhou, Fujian, People’s Republic of China
- * E-mail:
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Senaratne TN, Saitta SC. Evaluating Genetic Disorders in the Neonate: The Role of Exome Sequencing in the NICU. Neoreviews 2022; 23:e829-e840. [PMID: 36450644 DOI: 10.1542/neo.23-12-e829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
With recent advances in the technologies used for genetic diagnosis as well as our understanding of the genetic basis of disease, a growing list of options is available for providers when caring for a newborn with features suggesting an underlying genetic etiology. The choice of the most appropriate genetic test for a specific situation includes clinical considerations such as the phenotypic features and type of genetic abnormality suspected, as well as practical considerations such as cost and turnaround time. In this review, we discuss clinical exome sequencing in the context of genetic evaluation of newborns, including technical considerations, variant interpretation, and incidental/secondary findings. Strengths and limitations of exome sequencing are discussed and compared with those of other commonly known tests such as karyotype analysis, fluorescence in situ hybridization, chromosomal microarray, and sequencing panels, along with integration of results from prenatal testing if available. We also review future directions including genome sequencing and other emerging technologies that are starting to be used in clinical settings.
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Affiliation(s)
- T Niroshi Senaratne
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA
| | - Sulagna C Saitta
- Division of Clinical Genetics, Department of Pediatrics, Division of Reproductive Genetics, Department of Obstetrics and Gynecology, David Geffen School of Medicine at UCLA, Los Angeles, CA
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Lei H, Zhang M, Zhang L, Hemminki K, Wang XJ, Chen T. Overview on population screening for carriers with germline BRCA mutation in China. Front Oncol 2022; 12:1002360. [PMID: 36439508 PMCID: PMC9682265 DOI: 10.3389/fonc.2022.1002360] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 10/24/2022] [Indexed: 12/01/2023] Open
Abstract
Carriers with BRCA1/2 germline pathogenic variants are associated with a high risk of breast and ovarian cancers (also pancreatic and prostate cancers). While the spectrum on germline BRCA mutations among the Chinese population shows ethnic specificity, the identification of carriers with germline BRCA mutation before cancer onset is the most effective approach to protect them. This review focused on the current status of BRCA1/2 screening, the surveillance and prevention measures, and discussed the issues and potential impact of BRCA1/2 population screening in China. We conducted literature research on databases PubMed and Google Scholar, as well as Chinese databases CNKI and Wangfang Med Online database (up to 31 March 2022). Latest publications on germline BRCA1/2 prevalence, spectrum, genetic screening as well as carrier counseling, surveillance and prevention were captured where available. While overall 15,256 records were retrieved, 72 publications using germline BRCA1/2 testing were finally retained for further analyses. Germline BRCA1/2 mutations are common in Chinese patients with hereditary breast, ovarian, prostate and pancreatic cancers. Within previous studies, a unique BRCA mutation spectrum in China was revealed. Next-generation sequencing panel was considered as the most common method for BRCA1/2 screening. Regular surveillance and preventive surgeries were tailored to carriers with mutated-BRCA1/2. We recommend that all Chinese diagnosed with breast, ovarian, pancreatic or prostate cancers and also healthy family members, shall undergo BRCA1/2 gene test to provide risk assessment. Subsequently, timely preventive measures for mutation carriers are recommended after authentic genetic counseling.
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Affiliation(s)
- Huijun Lei
- Department of Cancer Prevention/Zhejiang Cancer Institute, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, China
- Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, China
| | - Min Zhang
- School of Public Health, Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Luyao Zhang
- Department of Cancer Epidemiology and Prevention, Henan Engineering Research Center of Cancer Prevention and Control, Henan International Joint Laboratory of Cancer Prevention, The Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
| | - Kari Hemminki
- Biomedical Center, Faculty of Medicine, Charles University in Pilsen, Pilsen, Czechia
- Division of Cancer Epidemiology, German Cancer Research Center Deutsches Krebsforschungszentrum (DKFZ), Im Neuenheimer Feld, Heidelberg, Germany
| | - Xiao-jia Wang
- Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, China
- Department of Breast Medical Oncology, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, China
| | - Tianhui Chen
- Department of Cancer Prevention/Zhejiang Cancer Institute, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, China
- Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, China
- Department of Preventive Medicine, School of Medicine, Ningbo University, Ningbo, China
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Zhang K, Yu L, Lin G, Li J. A multi-laboratory assessment of clinical exome sequencing for detection of hereditary disease variants: 4441 ClinVar variants for clinical genomic test development and validation. Clin Chim Acta 2022; 535:99-107. [PMID: 35985503 DOI: 10.1016/j.cca.2022.08.008] [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: 03/14/2022] [Revised: 08/01/2022] [Accepted: 08/05/2022] [Indexed: 11/30/2022]
Abstract
BACKGROUND AND AIMS Whole-exome sequencing (WES) technology has become an essential tool in the clinical diagnostic for rare genetic disorders, however, the issues that reduce testing precision, sensitivity, and concordance are not clear under routine testing conditions. The study is to systematically evaluate the comparability of clinical WES testing results in laboratories under routine conditions. METHODS We designed a multi-laboratory study across 24 participating laboratories in China. We assessed sequencing quality across capture methods and sequencing platforms, benchmarked the impact of coverage and callable regions on detecting single nucleotide variants (SNVs), small insertions and deletions (Indels) under the same computational approaches, and compared the sensitivity, precision and reproducibility on detecting mutations across laboratories. RESULTS High inter-laboratory variability on variants detection were found across participating laboratories. Sample DNA concentration and sequencing evenness are two major variables that lead to the coverage variation. The difference in bioinformatics tools and computational settings affect the sensitivity and precision of the final output. Besides, copy-number variants (CNVs) identification is less reproducible than SNVs and Indels in the WES testing. We also compiled a list of 4441 low coverage ClinVar variants of 1176 genes from this study, which can be used as a source for creating in silico and synthetic DNA reference materials for clinical genetic disorder detection. CONCLUSIONS The considerable inter-laboratory variability seen in both sequencing coverage evenness and variants detection highlights the urgent need to improve the precision, sensitivity and comparability of the results generated across different laboratories. The list of low coverage variants can have important implications for the development and validation of clinical genetic disorder tests by laboratories. This study also serves to best practice inform guidelines for detecting clinical genetic disorders by exome sequencing.
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Affiliation(s)
- Kuo Zhang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, PR China
| | - Lijia Yu
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, PR China; National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, PR China
| | - Guigao Lin
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, PR China
| | - Jinming Li
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, PR China; National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, PR China.
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Swanson K, Norton ME, Lianoglou BR, Jelin AC, Hodoglugil U, Van Ziffle J, Devine P, Sparks TN. The utility of pathologic examination and comprehensive phenotyping for accurate diagnosis with perinatal exome sequencing. Prenat Diagn 2022; 42:1288-1294. [PMID: 35723972 PMCID: PMC9531346 DOI: 10.1002/pd.6197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 05/29/2022] [Accepted: 06/13/2022] [Indexed: 11/09/2022]
Abstract
OBJECTIVE Exome sequencing (ES) offers the ability to assess for variants in thousands of genes and is particularly useful in the setting of fetal anomalies. However, the ES pipeline relies on a thorough understanding of an individual patient's phenotype, which may be limited in the prenatal setting. Additional pathology evaluations in the pre- and postnatal settings can add phenotypic details important for clearly establishing and characterizing a diagnosis. METHODS This is a case series of prenatal ES performed at our institution in which pathology evaluations, including autopsy, dysmorphology examination, histology, and peripheral blood smear, augmented the understanding of the fetal phenotype. ES was performed at our institution and a multidisciplinary panel reviewed and classified the variants for each case. RESULTS We present four cases wherein pathology evaluations were beneficial for supporting a perinatal diagnosis identified with ES. In each of these cases, pathology findings provided additional data to support a more complete understanding of the relationship between the perinatal phenotype and variants identified with ES. CONCLUSION These cases highlight challenges of perinatal ES related to incomplete prenatal phenotyping, demonstrate the utility of pathology evaluations to support diagnoses identified with ES, and further characterize the disease manifestations of specific genetic variants.
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Affiliation(s)
- Kate Swanson
- Department of Obstetrics, Gynecology and Reproductive Sciences, Division of Maternal-Fetal Medicine, University of California, San Francisco, California, USA
- Department of Pediatrics, Division of Medical Genetics, University of California, San Francisco, California, USA
| | - Mary E. Norton
- Department of Obstetrics, Gynecology and Reproductive Sciences, Division of Maternal-Fetal Medicine, University of California, San Francisco, California, USA
- Department of Pediatrics, Division of Medical Genetics, University of California, San Francisco, California, USA
- Fetal Treatment Center, University of California, San Francisco, California, USA
- Institute for Human Genetics, University of California, San Francisco, California, USA
| | - Billie R. Lianoglou
- Fetal Treatment Center, University of California, San Francisco, California, USA
| | - Angie C. Jelin
- Department of Gynecology and Obstetrics, Johns Hopkins Hospital, Baltimore, Maryland, USA
| | - Ugur Hodoglugil
- Genomic Medicine Laboratory, University of California, San Francisco, California, USA
| | - Jessica Van Ziffle
- Genomic Medicine Laboratory, University of California, San Francisco, California, USA
| | - Patrick Devine
- Genomic Medicine Laboratory, University of California, San Francisco, California, USA
| | - Teresa N. Sparks
- Department of Obstetrics, Gynecology and Reproductive Sciences, Division of Maternal-Fetal Medicine, University of California, San Francisco, California, USA
- Fetal Treatment Center, University of California, San Francisco, California, USA
- Institute for Human Genetics, University of California, San Francisco, California, USA
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Ceyhan-Birsoy O. Germline Testing for the Evaluation of Hereditary Cancer Predisposition. Clin Lab Med 2022; 42:497-506. [DOI: 10.1016/j.cll.2022.04.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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38
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Owen MJ, Lefebvre S, Hansen C, Kunard CM, Dimmock DP, Smith LD, Scharer G, Mardach R, Willis MJ, Feigenbaum A, Niemi AK, Ding Y, Van Der Kraan L, Ellsworth K, Guidugli L, Lajoie BR, McPhail TK, Mehtalia SS, Chau KK, Kwon YH, Zhu Z, Batalov S, Chowdhury S, Rego S, Perry J, Speziale M, Nespeca M, Wright MS, Reese MG, De La Vega FM, Azure J, Frise E, Rigby CS, White S, Hobbs CA, Gilmer S, Knight G, Oriol A, Lenberg J, Nahas SA, Perofsky K, Kim K, Carroll J, Coufal NG, Sanford E, Wigby K, Weir J, Thomson VS, Fraser L, Lazare SS, Shin YH, Grunenwald H, Lee R, Jones D, Tran D, Gross A, Daigle P, Case A, Lue M, Richardson JA, Reynders J, Defay T, Hall KP, Veeraraghavan N, Kingsmore SF. An automated 13.5 hour system for scalable diagnosis and acute management guidance for genetic diseases. Nat Commun 2022; 13:4057. [PMID: 35882841 PMCID: PMC9325884 DOI: 10.1038/s41467-022-31446-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 06/08/2022] [Indexed: 12/31/2022] Open
Abstract
While many genetic diseases have effective treatments, they frequently progress rapidly to severe morbidity or mortality if those treatments are not implemented immediately. Since front-line physicians frequently lack familiarity with these diseases, timely molecular diagnosis may not improve outcomes. Herein we describe Genome-to-Treatment, an automated, virtual system for genetic disease diagnosis and acute management guidance. Diagnosis is achieved in 13.5 h by expedited whole genome sequencing, with superior analytic performance for structural and copy number variants. An expert panel adjudicated the indications, contraindications, efficacy, and evidence-of-efficacy of 9911 drug, device, dietary, and surgical interventions for 563 severe, childhood, genetic diseases. The 421 (75%) diseases and 1527 (15%) effective interventions retained are integrated with 13 genetic disease information resources and appended to diagnostic reports ( https://gtrx.radygenomiclab.com ). This system provided correct diagnoses in four retrospectively and two prospectively tested infants. The Genome-to-Treatment system facilitates optimal outcomes in children with rapidly progressive genetic diseases.
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Affiliation(s)
- Mallory J. Owen
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Sebastien Lefebvre
- grid.422288.60000 0004 0408 0730Alexion Pharmaceuticals, Inc., Boston, MA 02210 USA
| | - Christian Hansen
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Chris M. Kunard
- grid.185669.50000 0004 0507 3954Illumina, Inc., San Diego, CA 92122 USA
| | - David P. Dimmock
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA ,grid.419735.d0000 0004 0615 8415Keck Graduate Institute, Claremont, CA 91711 USA
| | - Laurie D. Smith
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA
| | - Gunter Scharer
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA
| | - Rebecca Mardach
- grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA ,grid.266100.30000 0001 2107 4242Department of Pediatrics, University of California San Diego, San Diego, CA 92093 USA
| | - Mary J. Willis
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA
| | - Annette Feigenbaum
- grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA ,grid.266100.30000 0001 2107 4242Department of Pediatrics, University of California San Diego, San Diego, CA 92093 USA
| | - Anna-Kaisa Niemi
- grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA ,grid.266100.30000 0001 2107 4242Department of Pediatrics, University of California San Diego, San Diego, CA 92093 USA
| | - Yan Ding
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Luca Van Der Kraan
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Katarzyna Ellsworth
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Lucia Guidugli
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Bryan R. Lajoie
- grid.185669.50000 0004 0507 3954Illumina, Inc., San Diego, CA 92122 USA
| | | | | | - Kevin K. Chau
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Yong H. Kwon
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Zhanyang Zhu
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Sergey Batalov
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Shimul Chowdhury
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA ,grid.419735.d0000 0004 0615 8415Keck Graduate Institute, Claremont, CA 91711 USA
| | - Seema Rego
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA
| | - James Perry
- grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA ,grid.266100.30000 0001 2107 4242Department of Pediatrics, University of California San Diego, San Diego, CA 92093 USA
| | - Mark Speziale
- grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA ,grid.266100.30000 0001 2107 4242Department of Pediatrics, University of California San Diego, San Diego, CA 92093 USA
| | - Mark Nespeca
- grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA ,grid.266100.30000 0001 2107 4242Department of Pediatrics, University of California San Diego, San Diego, CA 92093 USA ,grid.266100.30000 0001 2107 4242Department of Neuroscience, University of California San Diego, San Diego, CA 92093 USA
| | - Meredith S. Wright
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA ,grid.419735.d0000 0004 0615 8415Keck Graduate Institute, Claremont, CA 91711 USA
| | | | | | - Joe Azure
- Fabric Genomics, Inc., Oakland, CA 94612 USA
| | - Erwin Frise
- Fabric Genomics, Inc., Oakland, CA 94612 USA
| | | | - Sandy White
- Fabric Genomics, Inc., Oakland, CA 94612 USA
| | - Charlotte A. Hobbs
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA ,grid.266100.30000 0001 2107 4242Department of Pediatrics, University of California San Diego, San Diego, CA 92093 USA
| | - Sheldon Gilmer
- grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Gail Knight
- grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA ,grid.266100.30000 0001 2107 4242Department of Pediatrics, University of California San Diego, San Diego, CA 92093 USA
| | - Albert Oriol
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Jerica Lenberg
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA ,grid.419735.d0000 0004 0615 8415Keck Graduate Institute, Claremont, CA 91711 USA
| | - Shareef A. Nahas
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Kate Perofsky
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA ,grid.266100.30000 0001 2107 4242Department of Pediatrics, University of California San Diego, San Diego, CA 92093 USA
| | - Kyu Kim
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA ,grid.266100.30000 0001 2107 4242Department of Pediatrics, University of California San Diego, San Diego, CA 92093 USA
| | - Jeanne Carroll
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA ,grid.266100.30000 0001 2107 4242Department of Pediatrics, University of California San Diego, San Diego, CA 92093 USA
| | - Nicole G. Coufal
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA ,grid.266100.30000 0001 2107 4242Department of Pediatrics, University of California San Diego, San Diego, CA 92093 USA
| | - Erica Sanford
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA
| | - Kristen Wigby
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA ,grid.266100.30000 0001 2107 4242Department of Pediatrics, University of California San Diego, San Diego, CA 92093 USA
| | - Jacqueline Weir
- grid.185669.50000 0004 0507 3954Illumina, Inc., San Diego, CA 92122 USA
| | - Vicki S. Thomson
- grid.185669.50000 0004 0507 3954Illumina, Inc., San Diego, CA 92122 USA
| | - Louise Fraser
- grid.185669.50000 0004 0507 3954Illumina, Inc., San Diego, CA 92122 USA
| | - Seka S. Lazare
- grid.185669.50000 0004 0507 3954Illumina, Inc., San Diego, CA 92122 USA
| | - Yoon H. Shin
- grid.185669.50000 0004 0507 3954Illumina, Inc., San Diego, CA 92122 USA
| | | | - Richard Lee
- grid.185669.50000 0004 0507 3954Illumina, Inc., San Diego, CA 92122 USA
| | - David Jones
- grid.185669.50000 0004 0507 3954Illumina, Inc., San Diego, CA 92122 USA
| | - Duke Tran
- grid.185669.50000 0004 0507 3954Illumina, Inc., San Diego, CA 92122 USA
| | - Andrew Gross
- grid.185669.50000 0004 0507 3954Illumina, Inc., San Diego, CA 92122 USA
| | - Patrick Daigle
- grid.185669.50000 0004 0507 3954Illumina, Inc., San Diego, CA 92122 USA
| | - Anne Case
- grid.185669.50000 0004 0507 3954Illumina, Inc., San Diego, CA 92122 USA
| | - Marisa Lue
- grid.185669.50000 0004 0507 3954Illumina, Inc., San Diego, CA 92122 USA
| | | | - John Reynders
- grid.422288.60000 0004 0408 0730Alexion Pharmaceuticals, Inc., Boston, MA 02210 USA
| | - Thomas Defay
- grid.422288.60000 0004 0408 0730Alexion Pharmaceuticals, Inc., Boston, MA 02210 USA
| | - Kevin P. Hall
- grid.185669.50000 0004 0507 3954Illumina, Inc., San Diego, CA 92122 USA
| | - Narayanan Veeraraghavan
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Stephen F. Kingsmore
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA ,grid.419735.d0000 0004 0615 8415Keck Graduate Institute, Claremont, CA 91711 USA
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39
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Choi IH, Seo GH, Park J, Kim YM, Cheon CK, Kim YM, Oh A, Byeon JH, Kang E, Shin YL, Lee JE, Kim SJ, Yu HJ, Kim WJ, Choi BY, Kim BJ, Kim YH, Im GJ, Lee HJ, Kim HJ, Han SH, Lee BH, Eun BL. Evaluation of users' level of satisfaction for an artificial intelligence-based diagnostic program in pediatric rare genetic diseases. Medicine (Baltimore) 2022; 101:e29424. [PMID: 35838999 PMCID: PMC11132333 DOI: 10.1097/md.0000000000029424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
The artificial intelligence (AI)-based genetic diagnostic program has been applied to genome sequencing to facilitate the diagnostic process. The objective of the current study was to evaluate the experience and level of satisfaction of participants using an AI-based diagnostic program for rare pediatric genetic diseases. The patients with neurodevelopmental disorders or hearing impairments, their guardians, and their physicians from 16 tertiary general hospitals were enrolled. The study period was from April 2020 to March 2021. A survey was designed to assess their experience and level of satisfaction. A total of 30 physicians and 243 patients and guardians (199 neurodevelopmental disorders and 44 hearing impairments) completed the survey. DNA samples of the subjects were collected through buccal swabs or blood collection: 211 subjects (86.8%) through buccal swab and 29 subjects (11.9%) through blood collection. Average turnaround time for result receipt was 57.54 ± 32.42 days. For the sampling method, 193 patients and guardians (81.1%) and 28 physicians (93.3%) preferred buccal swab. The level of satisfaction of the 2 groups participating in the AI-based diagnostic program was 8.31 ± 1.71 out of 10 in the patient and guardian group and 8.42 ± 1.23 in the physician group. Clinicians, patients, and guardians are satisfied with the AI-based diagnostic program in general. With an increase in AI-based precision medicine solutions, the evaluation of the user's satisfaction with appropriate provision will help improve personal health care.
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Affiliation(s)
- In Hee Choi
- Department of Genetic Counseling, University of Ulsan College of Medicine, Seoul, South Korea
| | | | - JeongYun Park
- Department of Clinical Nursing, University of Ulsan, Seoul, South Korea
| | - Yoon-Myung Kim
- Department of Pediatrics, Gangneung Asan Hospital, College of Medicine, University of Ulsan, Gangneung, South Korea
| | - Chong Kun Cheon
- Division of Medical Genetics and Metabolism, Department of Pediatrics, Pusan National University School of Medicine, Pusan National University Children's Hospital, South Korea
| | - Yoo-Mi Kim
- Department of Pediatrics, Pediatric Center, Chungnam National University Sejong Hospital, College of Medicine, Chungnam National University, Sejong, South Korea
| | - Arum Oh
- Department of Pediatrics, Chungbuk National University Hospital, Chungbuk National University College of Medicine, Cheongju, South Korea
| | - Jung Hye Byeon
- Department of Pediatrics, Korea University College of Medicine, Seoul, South Korea
| | - Eungu Kang
- Department of Pediatrics, Korea University College of Medicine, Seoul, South Korea
| | - Young-Lim Shin
- Department of Pediatrics, Soonchunhyang University Bucheon Hospital, Soonchunhyang University College of Medicine, Bucheon, South Korea
| | - Ji Eun Lee
- Department of Pediatrics, Inha University Hospital, Inha University College of Medicine, Incheon, South Korea
| | - Su Jin Kim
- Department of Pediatrics, Inha University Hospital, Inha University College of Medicine, Incheon, South Korea
| | - Hee Joon Yu
- Department of Pediatrics, Hallym University Sacred Heart Hospital, Gyeonggi-do, South Korea
| | - Woo Jin Kim
- EONE Laboratories, Harmony-ro, Yeonsu-gu, Incheon, South Korea
| | - Byung Yoon Choi
- Department of Otorhinolaryngology, Seoul National University Bundang Hospital, Seongnam, South Korea
| | - Bong Jik Kim
- Department of Otolaryngology-Head and Neck Surgery, Chungnam National University College of Medicine, Chungnam National University Sejong Hospital, Sejong, South Korea
| | - Young Ho Kim
- Department of Otorhinolaryngology, Seoul National University Boramae Medical Center, Seoul National University College of Medicine, Seoul, South Korea
| | - Gi Jung Im
- Department of Otorhinolaryngology, Korea University College of Medicine, Seoul, South Korea
| | - Hyo-Jeong Lee
- Department of Otorhinolaryngology-Head and Neck Surgery, Hallym University College of Medicine, Chuncheon, South Korea
| | - Hyun Ji Kim
- Department of Otorhinolaryngology-Head and Neck Surgery, Inha University College of Medicine, Incheon, South Korea
| | - Se-Hee Han
- Korea University Guro Hospital, Seoul, South Korea
| | - Beom Hee Lee
- Medical Genetics Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | - Baik-Lin Eun
- Department of Pediatrics, Korea University College of Medicine, Seoul, South Korea
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40
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Amico G, Hemphill WO, Severino M, Moratti C, Pascarella R, Bertamino M, Napoli F, Volpi S, Rosamilia F, Signa S, Perrino F, Zedde M, Ceccherini I. Genotype-Phenotype Correlation and Functional Insights for Two Monoallelic TREX1 Missense Variants Affecting the Catalytic Core. Genes (Basel) 2022; 13:genes13071179. [PMID: 35885962 PMCID: PMC9323106 DOI: 10.3390/genes13071179] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 06/24/2022] [Accepted: 06/28/2022] [Indexed: 02/01/2023] Open
Abstract
The TREX1 exonuclease degrades DNA to prevent aberrant nucleic-acid sensing through the cGAS-STING pathway, and dominant Aicardi–Goutières Syndrome type 1 (AGS1) represents one of numerous TREX1-related autoimmune diseases. Monoallelic TREX1 mutations were identified in patients showing early-onset cerebrovascular disease, ascribable to small vessel disease, and CADASIL-like neuroimaging. We report the clinical-neuroradiological features of two patients with AGS-like (Patient A) and CADASIL-like (Patient B) phenotypes carrying the heterozygous p.A136V and p.R174G TREX1 variants, respectively. Genetic findings, obtained by a customized panel including 183 genes associated with monogenic stroke, were combined with interferon signature testing and biochemical assays to determine the mutations’ effects in vitro. Our results for the p.A136V variant are inconsistent with prior biochemistry-pathology correlates for dominant AGS-causing TREX1 mutants. The p.R174G variant modestly altered exonuclease activity in a manner consistent with perturbation of substrate interaction rather than catalysis, which represents the first robust enzymological data for a TREX1 variant identified in a CADASIL-like patient. In conclusion, functional analysis allowed us to interpret the impact of TREX1 variants on patients’ phenotypes. While the p.A136V variant is unlikely to be causative for AGS in Patient A, Patient B’s phenotype is potentially related to the p.R174G variant. Therefore, further functional investigations of TREX1 variants found in CADASIL-like patients are warranted to determine any causal link and interrogate the molecular disease mechanism(s).
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Affiliation(s)
- Giulia Amico
- Department of Neuroscience, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DINOGMI), University of Genoa, 16132 Genoa, Italy;
- Laboratory of Genetics and Genomics of Rare Diseases, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy;
| | - Wayne O. Hemphill
- Center for Structural Biology, Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC 27101, USA
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80303, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Correspondence: (W.O.H.); (F.P.)
| | | | - Claudio Moratti
- Neuroradiology Unit, Azienda Unità Sanitaria Locale—IRCCS di Reggio Emilia, 42122 Reggio Emilia, Italy; (C.M.); (R.P.)
| | - Rosario Pascarella
- Neuroradiology Unit, Azienda Unità Sanitaria Locale—IRCCS di Reggio Emilia, 42122 Reggio Emilia, Italy; (C.M.); (R.P.)
| | - Marta Bertamino
- Physical Medicine and Rehabilitation Unit, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy;
| | - Flavia Napoli
- Departments of Pediatrics, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy;
| | - Stefano Volpi
- Autoinflammatory Diseases and Immunodeficiencies Center, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy; (S.V.); (S.S.)
| | - Francesca Rosamilia
- Biostatistic Unit, Health Science Department (DISSAL), University of Genoa, 16132 Genoa, Italy;
| | - Sara Signa
- Autoinflammatory Diseases and Immunodeficiencies Center, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy; (S.V.); (S.S.)
| | - Fred Perrino
- Center for Structural Biology, Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC 27101, USA
- Correspondence: (W.O.H.); (F.P.)
| | - Marialuisa Zedde
- Neurology Unit, Stroke Unit, Azienda Unità Sanitaria Locale—IRCCS di Reggio Emilia, 42122 Reggio Emilia, Italy;
| | - Isabella Ceccherini
- Laboratory of Genetics and Genomics of Rare Diseases, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy;
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41
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Analytical Validation of a Computational Method for Pharmacogenetic Genotyping from Clinical Whole Exome Sequencing. J Mol Diagn 2022; 24:576-585. [PMID: 35452844 DOI: 10.1016/j.jmoldx.2022.03.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/31/2022] [Accepted: 03/04/2022] [Indexed: 12/24/2022] Open
Abstract
Germline whole exome sequencing from molecular tumor boards has the potential to be repurposed to support clinical pharmacogenomics. However, accurately calling pharmacogenomics-relevant genotypes from exome sequencing data remains challenging. Accordingly, this study assessed the analytical validity of the computational tool, Aldy, in calling pharmacogenomics-relevant genotypes from exome sequencing data for 13 major pharmacogenes. Germline DNA from whole blood was obtained for 164 subjects seen at an institutional molecular solid tumor board. All subjects had whole exome sequencing from Ashion Analytics and panel-based genotyping from an institutional pharmacogenomics laboratory. Aldy version 3.3 was operationalized on the LifeOmic Precision Health Cloud with copy number fixed to two copies per gene. Aldy results were compared with those from genotyping for 56 star allele-defining variants within CYP2B6, CYP2C8, CYP2C9, CYP2C19, CYP2D6, CYP3A4, CYP3A5, CYP4F2, DPYD, G6PD, NUDT15, SLCO1B1, and TPMT. Read depth was >100× for all variants except CYP3A4∗22. For 75 subjects in the validation cohort, all 3393 Aldy variant calls were concordant with genotyping. Aldy calls for 736 diplotypes containing alleles assessed by both platforms were also concordant. Aldy identified additional star alleles not covered by targeted genotyping for 139 diplotypes. Aldy accurately called variants and diplotypes for 13 major pharmacogenes, except for CYP2D6 variants involving copy number variations, thus allowing repurposing of whole exome sequencing to support clinical pharmacogenomics.
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42
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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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43
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Baker TG, Glen WB, Wilson RC, Batalis NI, Wolff DJ, Welsh CT. Postmortem Diagnosis of the Proteus Syndrome by Next Generation Sequencing of Affected Brain Tissue. Acad Forensic Pathol 2022; 12:52-57. [PMID: 35799996 PMCID: PMC9254014 DOI: 10.1177/19253621221097294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 04/08/2022] [Indexed: 11/15/2022]
Abstract
We report a case of a somatic overgrowth syndrome diagnosed at forensic autopsy with the aid of next generation sequencing as Proteus syndrome. Somatic overgrowth syndromes result from spontaneous somatic mutations that arise early in development and display a mosaic pattern of expression in patient tissues. Due to the temporal and anatomic heterogeneity of these syndromes, phenotypes vary widely, resulting in clinical overlap. Furthermore, the variable ratio of mutated to nonmutated cells in patient tissue can result in low-level mutations that could be missed using Sanger sequencing. Due to these factors, recent literature points to next generation sequencing (NGS) as an adjunct to diagnosis of these rare entities. A male in his fourth decade of life presented to our forensic autopsy service with physical features suggestive of a somatic overgrowth syndrome. Due to the paucity of clinical information accompanying the individual, a definitive diagnosis based on physical characteristics, alone, was not possible. Next generation sequencing of affected formalin-fixed and paraffin-embedded brain tissue confirmed the presence of the variant in AKT1 (c.49G>A, p.Glu17Lys, in 14.13% of reads) found in Proteus syndrome. To our knowledge, this is the first report of the mosaic variant of AKT1 detected in brain tissue and the first reported case of a postmortem diagnosis of Proteus syndrome with the aid of NGS. We conclude that NGS can be used as an adjunctive method to support a specific diagnosis among the somatic overgrowth syndromes postmortem in the absence of sufficient clinical history.
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Affiliation(s)
- Tiffany G. Baker
- Tiffany G. Baker, MD, PhD,
Department of Pathology and Laboratory Medicine, Medical University of
South Carolina, Charleston, SC;
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44
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Horak P, Griffith M, Danos AM, Pitel BA, Madhavan S, Liu X, Chow C, Williams H, Carmody L, Barrow-Laing L, Rieke D, Kreutzfeldt S, Stenzinger A, Tamborero D, Benary M, Rajagopal PS, Ida CM, Lesmana H, Satgunaseelan L, Merker JD, Tolstorukov MY, Campregher PV, Warner JL, Rao S, Natesan M, Shen H, Venstrom J, Roy S, Tao K, Kanagal-Shamanna R, Xu X, Ritter DI, Pagel K, Krysiak K, Dubuc A, Akkari YM, Li XS, Lee J, King I, Raca G, Wagner AH, Li MM, Plon SE, Kulkarni S, Griffith OL, Chakravarty D, Sonkin D. Standards for the classification of pathogenicity of somatic variants in cancer (oncogenicity): Joint recommendations of Clinical Genome Resource (ClinGen), Cancer Genomics Consortium (CGC), and Variant Interpretation for Cancer Consortium (VICC). Genet Med 2022; 24:986-998. [PMID: 35101336 PMCID: PMC9081216 DOI: 10.1016/j.gim.2022.01.001] [Citation(s) in RCA: 56] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 12/22/2021] [Accepted: 01/03/2022] [Indexed: 01/21/2023] Open
Abstract
PURPOSE Several professional societies have published guidelines for the clinical interpretation of somatic variants, which specifically address diagnostic, prognostic, and therapeutic implications. Although these guidelines for the clinical interpretation of variants include data types that may be used to determine the oncogenicity of a variant (eg, population frequency, functional, and in silico data or somatic frequency), they do not provide a direct, systematic, and comprehensive set of standards and rules to classify the oncogenicity of a somatic variant. This insufficient guidance leads to inconsistent classification of rare somatic variants in cancer, generates variability in their clinical interpretation, and, importantly, affects patient care. Therefore, it is essential to address this unmet need. METHODS Clinical Genome Resource (ClinGen) Somatic Cancer Clinical Domain Working Group and ClinGen Germline/Somatic Variant Subcommittee, the Cancer Genomics Consortium, and the Variant Interpretation for Cancer Consortium used a consensus approach to develop a standard operating procedure (SOP) for the classification of oncogenicity of somatic variants. RESULTS This comprehensive SOP has been developed to improve consistency in somatic variant classification and has been validated on 94 somatic variants in 10 common cancer-related genes. CONCLUSION The comprehensive SOP is now available for classification of oncogenicity of somatic variants.
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Affiliation(s)
- Peter Horak
- National Center for Tumor Diseases (NCT), German Cancer Research Center (DKFZ), Heidelberg, Germany.
| | - Malachi Griffith
- Washington University School of Medicine in St. Louis, St. Louis, MO
| | - Arpad M Danos
- Washington University School of Medicine in St. Louis, St. Louis, MO
| | | | | | - Xuelu Liu
- Dana-Farber Cancer Institute, Boston, MA
| | - Cynthia Chow
- BC Cancer Agency, Vancouver, British Columbia, Canada
| | | | - Leigh Carmody
- The Jackson Laboratory for Genomic Medicine, Farmington, CT
| | | | - Damian Rieke
- Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Simon Kreutzfeldt
- National Center for Tumor Diseases (NCT), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | | | | | - Padma Sheila Rajagopal
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | | | - Harry Lesmana
- Genomic Medicine Institute, Cleveland Clinic Lerner Research Institute, Cleveland, OH
| | | | - Jason D Merker
- UNC School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC
| | | | | | | | - Shruti Rao
- Georgetown University Medical Center, Washington, DC
| | - Maya Natesan
- Washington University School of Medicine in St. Louis, St. Louis, MO
| | - Haolin Shen
- Washington University School of Medicine in St. Louis, St. Louis, MO
| | | | - Somak Roy
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Kayoko Tao
- National Cancer Center Hospital, Tokyo, Japan
| | | | | | | | - Kym Pagel
- Johns Hopkins University, Baltimore, MD
| | - Kilannin Krysiak
- Washington University School of Medicine in St. Louis, St. Louis, MO
| | - Adrian Dubuc
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | | | | | - Jennifer Lee
- Frederick National Laboratory for Cancer Research, National Cancer Institute, Rockville, MD
| | - Ian King
- University Health Network, Toronto, Ontario, Canada
| | - Gordana Raca
- University of Southern California, Los Angeles, CA
| | - Alex H Wagner
- Nationwide Children's Hospital, Columbus, OH; The Ohio State University College of Medicine, Columbus, OH
| | - Marylin M Li
- Children's Hospital of Philadelphia, Philadelphia, PA
| | | | | | - Obi L Griffith
- Washington University School of Medicine in St. Louis, St. Louis, MO
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Austin-Tse CA, Jobanputra V, Perry DL, Bick D, Taft RJ, Venner E, Gibbs RA, Young T, Barnett S, Belmont JW, Boczek N, Chowdhury S, Ellsworth KA, Guha S, Kulkarni S, Marcou C, Meng L, Murdock DR, Rehman AU, Spiteri E, Thomas-Wilson A, Kearney HM, Rehm HL. Best practices for the interpretation and reporting of clinical whole genome sequencing. NPJ Genom Med 2022; 7:27. [PMID: 35395838 PMCID: PMC8993917 DOI: 10.1038/s41525-022-00295-z] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 02/17/2022] [Indexed: 01/19/2023] Open
Abstract
Whole genome sequencing (WGS) shows promise as a first-tier diagnostic test for patients with rare genetic disorders. However, standards addressing the definition and deployment practice of a best-in-class test are lacking. To address these gaps, the Medical Genome Initiative, a consortium of leading health care and research organizations in the US and Canada, was formed to expand access to high quality clinical WGS by convening experts and publishing best practices. Here, we present best practice recommendations for the interpretation and reporting of clinical diagnostic WGS, including discussion of challenges and emerging approaches that will be critical to harness the full potential of this comprehensive test.
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Affiliation(s)
- Christina A Austin-Tse
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA. .,Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, MA, USA. .,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Vaidehi Jobanputra
- Molecular Diagnostics Laboratory, New York Genome Center, New York, NY, USA.,Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | | | - David Bick
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | | | - Eric Venner
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Ted Young
- Genome Diagnostics, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, ON, Canada
| | - Sarah Barnett
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | | | - Nicole Boczek
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA.,Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Shimul Chowdhury
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | | | - Saurav Guha
- Molecular Diagnostics Laboratory, New York Genome Center, New York, NY, USA
| | - Shashikant Kulkarni
- Baylor Genetics and Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Cherisse Marcou
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Linyan Meng
- Baylor Genetics and Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - David R Murdock
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Atteeq U Rehman
- Molecular Diagnostics Laboratory, New York Genome Center, New York, NY, USA
| | - Elizabeth Spiteri
- Department of Pathology, Stanford Medicine, Stanford University, Stanford, CA, USA
| | | | - Hutton M Kearney
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Heidi L Rehm
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
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46
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Tong F, Wang J, Xiao R, Wu BB, Zou CC, Wu DW, Wang H, Zou H, Han LS, Yang L, Zou L, Hei MY, Yang RL, Yuan TM, Wen W, Huang XW, Gu XF, Yang YL, Huang YL, Zhang YJ, Yu YG, Xu ZF, Zhou WH, Zhao ZY. Application of next generation sequencing in the screening of monogenic diseases in China, 2021: a consensus among Chinese newborn screening experts. World J Pediatr 2022; 18:235-242. [PMID: 35292922 DOI: 10.1007/s12519-022-00522-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 01/23/2022] [Indexed: 11/24/2022]
Affiliation(s)
- Fan Tong
- Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, 3333 Binsheng Road, Binjiang District, Hangzhou, 310052, China
| | - Jian Wang
- Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Rui Xiao
- National Engineering Laboratory for Key Technology of Birth Defect Control and Prevention, Screening and Diagnostic R and D Center, Hangzhou, China
| | - Bing-Bing Wu
- Center for Molecular Medicine, Children's Hospital of Fudan University, 399 Wan Yuan Road, Min Xing District, Shanghai, 200000, China
| | - Chao-Chun Zou
- Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, 3333 Binsheng Road, Binjiang District, Hangzhou, 310052, China
| | - Ding-Wen Wu
- Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, 3333 Binsheng Road, Binjiang District, Hangzhou, 310052, China
| | - Hua Wang
- National Health Commission Key Laboratory for Birth Defect Research and Prevention, Maternal and Child Health Hospital of Hunan Province, Changsha, China
| | - Hui Zou
- Jinan Maternity and Child Care Hospital Affiliated To Shandong First Medical University, Jinan, China
| | - Lian-Shu Han
- Xinhua Hospital, Shanghai Institute for Pediatric Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lin Yang
- Clinical Genetic Center, Children's Hospital of Fudan University, Shanghai, China
| | - Lin Zou
- Children's Hospital, Shanghai Jiaotong University, Shanghai, China
| | - Ming-Yan Hei
- Neonatal Center, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Ru-Lai Yang
- Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, 3333 Binsheng Road, Binjiang District, Hangzhou, 310052, China
| | - Tian-Ming Yuan
- Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, 3333 Binsheng Road, Binjiang District, Hangzhou, 310052, China
| | - Wei Wen
- Affiliated Shenzhen Maternity and Child Healthcare Hospital, Southern Medical University, Shenzhen, China
| | - Xin-Wen Huang
- Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, 3333 Binsheng Road, Binjiang District, Hangzhou, 310052, China
| | - Xue-Fan Gu
- Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | | | - Yong-Lan Huang
- Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Yong-Jun Zhang
- Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Yong-Guo Yu
- Xinhua Hospital, Shanghai Institute for Pediatric Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zheng-Feng Xu
- Center of Genetic Medicine, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Wen-Hao Zhou
- Center for Molecular Medicine, Children's Hospital of Fudan University, 399 Wan Yuan Road, Min Xing District, Shanghai, 200000, China.
| | - Zheng-Yan Zhao
- Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, 3333 Binsheng Road, Binjiang District, Hangzhou, 310052, China.
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47
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48
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Malgorzata M, Maria S, Michał W. Genetic testing-whether to allow complete freedom? Direct to consumer tests versus genetic tests for medical purposes. J Appl Genet 2022; 63:119-126. [PMID: 34826052 PMCID: PMC8755658 DOI: 10.1007/s13353-021-00670-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 10/04/2021] [Accepted: 11/12/2021] [Indexed: 10/26/2022]
Abstract
Direct-to-consumer tests opened the opportunity of genetic testing without medical supervision, e.g., without medical referral and medical interpretation of the results. Thus, these approaches allow for free access to information concerning individual genetic profile increasing the area of personal freedom, but also posing the risk of false (positive and negative) or misinterpreted results along with health and psychological negative consequences. The paper discusses medical and non-medical applications of DTC, exploring also the legal framework implemented by European states and organizations. These legal acts strive to control the developing DTC market through such basic principles as patient protection, informed consent, medical information confidentiality, and the rights to know and to refuse knowledge about one's genetic predispositions.
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Affiliation(s)
- Madej Malgorzata
- Institute of Political Science, University of Wroclaw, Wrocław, Poland
| | - Sąsiadek Maria
- Department of Genetics, Medical University of Wroclaw, Wrocław, Poland.
| | - Witt Michał
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
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49
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Ghoorah AW, Chaplain T, Rindra R, Goorah S, Chinien G, Jaufeerally-Fakim Y. Population Structure of the South West Indian Ocean Islands: Implications for Precision Medicine. Front Genet 2021; 12:758563. [PMID: 34899843 PMCID: PMC8653818 DOI: 10.3389/fgene.2021.758563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Accepted: 10/28/2021] [Indexed: 11/21/2022] Open
Abstract
Precision medicine has brought new hopes for patients around the world with the applications of novel technologies for understanding genetics of complex diseases and their translation into clinical services. Such applications however require a foundation of skills, knowledge and infrastructure to translate genetics for health care. The crucial element is no doubt the availability of genomics data for the target populations, which is seriously lacking for most parts of Africa. We discuss here why it is vital to prioritize genomics data for the South West Indian Ocean region where a mosaic of ethnicities co-exist. The islands of the SWIO, which comprise Madagascar, La Reunion, Mauritius, Seychelles and Comoros, have been the scene for major explorations and trade since the 17th century being on the route to Asia. This part of the world has lived through active passage of slaves from East Africa to Arabia and further. Today’s demography of the islands is a diverse mix of ancestries including European, African and Asian. The extent of admixtures has yet to be resolved. Except for a few studies in Madagascar, there is very little published data on human genetics for these countries. Isolation and small population sizes have likely resulted in reduced genetic variation and possible founder effects. There is a significant prevalence of diabetes, particularly in individuals of Indian descent, while breast and prostate cancers are on the rise. The island of La Reunion is a French overseas territory with a high standard of health care and close ties to Mauritius. Its demography is comparable to that of Mauritius but with a predominantly mixed population and a smaller proportion of people of Indian descent. On the other hand, Madagascar’s African descendants inhabit mostly the lower coastal zones of the West and South regions, while the upper highlands are occupied by peoples of mixed African-Indonesian ancestries. Historical records confirm the Austronesian contribution to the Madagascar genomes. With the rapid progress in genomic medicine, there is a growing demand for sequencing services in the clinical settings to explore the incidence of variants in candidate disease genes and other markers. Genome sequence data has become a priority in order to understand the population sub-structures and to identify specific pathogenic variants among the different groups of inhabitants on the islands. Genomic data is increasingly being used to advise families at risk and propose diagnostic screening measures to enhance the success of therapies. This paper discusses the complexity of the islands’ populations and argues for the needs for genotyping and understanding the genetic factors associated with disease risks. The benefits to patients and improvement in health services through a concerted regional effort are depicted. Some private patients are having recourse to external facilities for molecular profiling with no return of data for research. Evidence of disease variants through sequencing represents a valuable source of medical data that can guide policy decisions at the national level. There are presently no such records for future implementation of strategies for genomic medicine.
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Affiliation(s)
| | - Toto Chaplain
- University of Toamasina, Barikadimy, Toamasina, Madagascar
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50
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Lehmann U, Stenzinger A. [The molecular pathology breviary: read depth and coverage in NGS analysis]. DER PATHOLOGE 2021; 43:65-66. [PMID: 34643752 DOI: 10.1007/s00292-021-01009-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 08/02/2021] [Indexed: 11/24/2022]
Affiliation(s)
- Ulrich Lehmann
- Molekularpathologie, Institut für Pathologie, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, OE5110, 30625, Hannover, Deutschland.
| | - Albrecht Stenzinger
- Molekularpathologisches Zentrum, Pathologisches Institut, Universität Heidelberg, Im Neuenheimer Feld 224, 69120, Heidelberg, Deutschland
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