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Mistry NA, Roellinger SE, Manninen MC, Gandham M, Koganti T, Balan J, Basu S, Blake EJ, Tandale PP, Holdren MA, Hoenig MF, Urban RM, Veith RL, Kendzior MC, Wang C, Gupta S, Shen W. Variant Detection in 3' Exons of PMS2 Using Exome Sequencing Data. J Mol Diagn 2024; 26:843-850. [PMID: 38925456 DOI: 10.1016/j.jmoldx.2024.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 05/11/2024] [Accepted: 06/11/2024] [Indexed: 06/28/2024] Open
Abstract
PMS2 is one of the DNA-mismatch repair genes included in routine genetic testing for Lynch syndrome and colorectal, ovarian, and endometrial cancers. PMS2 is also included in the American College of Medical Genetics and Genomics' List of Secondary Findings Genes in the context of clinical exome and genome sequencing. However, sequencing of PMS2 by short-read-based next-generation sequencing technologies is complicated by the presence of the pseudogene PMS2CL, and is often supplemented by long-range-based approaches, such as long-range PCR or long-read-based next-generation sequencing, which increases the complexity and cost. This article describes a bioinformatics homology triage workflow that can eliminate the need for long-read-based testing for PMS2 in the vast majority of patients undergoing exome sequencing, thus simplifying PMS2 testing and reducing the associated cost.
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Affiliation(s)
- Nipun A Mistry
- Division of Computational Biology, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
| | - Samantha E Roellinger
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Matthew C Manninen
- Division of Computational Biology, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
| | - Mallika Gandham
- Division of Computational Biology, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
| | - Tejaswi Koganti
- Division of Computational Biology, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
| | - Jagadheshwar Balan
- Division of Computational Biology, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
| | - Shubham Basu
- Division of Computational Biology, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
| | - Emily J Blake
- Division of Computational Biology, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
| | - Pratyush P Tandale
- Division of Computational Biology, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
| | - Megan A Holdren
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Megan F Hoenig
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Rhianna M Urban
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Rebecca L Veith
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | | | - Chen Wang
- Division of Computational Biology, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
| | - Sounak Gupta
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Wei Shen
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota.
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Das A, MacFarland SP, Meade J, Hansford JR, Schneider KW, Kuiper RP, Jongmans MCJ, Lesmana H, Schultz KAP, Nichols KE, Durno C, Zelley K, Porter CC, States LJ, Ben-Shachar S, Savage SA, Kalish JM, Walsh MF, Scott HS, Plon SE, Tabori U. Clinical Updates and Surveillance Recommendations for DNA Replication Repair Deficiency Syndromes in Children and Young Adults. Clin Cancer Res 2024; 30:3378-3387. [PMID: 38860976 DOI: 10.1158/1078-0432.ccr-23-3994] [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: 12/21/2023] [Revised: 02/29/2024] [Accepted: 05/02/2024] [Indexed: 06/12/2024]
Abstract
Replication repair deficiency (RRD) is a pan-cancer mechanism characterized by abnormalities in the DNA mismatch repair (MMR) system due to pathogenic variants in the PMS2, MSH6, MSH2, or MLH1 genes, and/or in the polymerase-proofreading genes POLE and POLD1. RRD predisposition syndromes (constitutional MMR deficiency, Lynch, and polymerase proofreading-associated polyposis) share overlapping phenotypic and biological characteristics. Moreover, cancers stemming from germline defects of one mechanism can acquire somatic defects in another, leading to complete RRD. Here we describe the recent advances in the diagnostics, surveillance, and clinical management for children with RRD syndromes. For patients with constitutional MMR deficiency, new data combining clinical insights and cancer genomics have revealed genotype-phenotype associations and helped in the development of novel functional assays, diagnostic guidelines, and surveillance recommendations. Recognition of non-gastrointestinal/genitourinary malignancies, particularly aggressive brain tumors, in select children with Lynch and polymerase proofreading-associated polyposis syndromes harboring an RRD biology have led to new management considerations. Additionally, universal hypermutation and microsatellite instability have allowed immunotherapy to be a paradigm shift in the treatment of RRD cancers independent of their germline etiology. These advances have also stimulated a need for expert recommendations about genetic counseling for these patients and their families. Future collaborative work will focus on newer technologies such as quantitative measurement of circulating tumor DNA and functional genomics to tailor surveillance and clinical care, improving immune surveillance; develop prevention strategies; and deliver these novel discoveries to resource-limited settings to maximize benefits for patients globally.
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Affiliation(s)
- Anirban Das
- Division of Haematology Oncology, The Hospital for Sick Children, Toronto, Ontario, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Paediatrics, University of Toronto, Toronto, Ontario, Canada
| | - Suzanne P MacFarland
- Division of Oncology, Cancer Predisposition Program, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Julia Meade
- University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Jordan R Hansford
- Michael Rice Centre for Hematology and Oncology, Adelaide, South Australia, Australia
- South Australia Health and Medical Research Institute, Adelaide, South Australia, Australia
- South Australia ImmunoGENomics Cancer Institute, University of Adelaide, Adelaide, South Australia, Australia
| | - Kami W Schneider
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Roland P Kuiper
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Department of Genetics, Utrecht University Medical Center, Utrecht, the Netherlands
| | - Marjolijn C J Jongmans
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Department of Genetics, Utrecht University Medical Center, Utrecht, the Netherlands
| | - Harry Lesmana
- Department of Pediatric Hematology/Oncology and BMT, Cleveland Clinic, Cleveland, Ohio
| | - Kris Ann P Schultz
- Cancer and Blood Disorders, Children's Minnesota, Minneapolis, Minnesota
| | - Kim E Nichols
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Carol Durno
- Division of Gastroenterology and Hepatology, The Hospital for Sick Children, Toronto, Ontario, Canada
- The Zane Cohen Center, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Kristin Zelley
- Hereditary Cancer Predisposition Program, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | | | - Lisa J States
- Department of Radiology, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Shay Ben-Shachar
- Clalit Research Institute, Ramat-Gan, Tel Aviv University, Tel-Aviv, Israel
| | - Sharon A Savage
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Jennifer M Kalish
- Division of Human Genetics and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
- Departments of Pediatrics and Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Michael F Walsh
- Divisions of Solid Tumor and Clinical Genetics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Hamish S Scott
- Center for Cancer Biology, SA Pathology and University of South Australia, Adelaide, South Australia, Australia
| | - Sharon E Plon
- Texas Children's Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Uri Tabori
- Division of Haematology Oncology, The Hospital for Sick Children, Toronto, Ontario, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
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3
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Prendeville S, Kaur H, Ansari S, Al Qa'qa' S, Stockley TL, Lajkosz K, van der Kwast T, Cheung CC, Selvarajah S. Somatic Tumor Testing in Prostate Cancer: Experience of a Tertiary Care Center Including Pathologist-Driven Reflex Testing of Localized Tumors at Diagnosis. Mod Pathol 2024; 37:100489. [PMID: 38588883 DOI: 10.1016/j.modpat.2024.100489] [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: 11/19/2023] [Revised: 02/17/2024] [Accepted: 03/15/2024] [Indexed: 04/10/2024]
Abstract
Somatic tumor testing in prostate cancer (PCa) can guide treatment options by identifying clinically actionable variants in DNA damage repair genes, including acquired variants not detected using germline testing alone. Guidelines currently recommend performing somatic tumor testing in metastatic PCa, whereas there is no consensus on the role of testing in regional disease, and the optimal testing strategy is only evolving. This study evaluates the frequency, distribution, and pathologic correlates of somatic DNA damage repair mutations in metastatic and localized PCa following the implementation of pathologist-driven reflex testing at diagnosis. A cohort of 516 PCa samples were sequenced using a custom next-generation sequencing panel including homologous recombination repair and mismatch repair genes. Variants were classified based on the Association for Molecular Pathology/American Society of Clinical Oncology/College of American Pathologists guidelines. In total, 183 (35.5%) patients had at least one variant, which is as follows: 72 of 516 (13.9%) patients had at least 1 tier I or tier II variant, whereas 111 of 516 (21.5%) patients had a tier III variant. Tier I/II variant(s) were identified in 27% (12/44) of metastatic biopsy samples and 13% (61/472) of primary samples. Overall, 12% (62/516) of patients had at least 1 tier I/II variant in a homologous recombination repair gene, whereas 2.9% (10/516) had at least 1 tier I/II variant in a mismatch repair gene. The presence of a tier I/II variant was not significantly associated with the grade group (GG) or presence of intraductal/cribriform carcinoma in the primary tumor. Among the 309 reflex-tested hormone-naive primary tumors, tier I/II variants were identified in 10% (31/309) of cases, which is as follows: 9.2% (9/98) GG2; 9% (9/100) GG3; 9.1% (4/44) GG4; and 13.4% (9/67) GG5 cases. Our findings confirm the use of somatic tumor testing in detecting variants of clinical significance in PCa and provide insights that can inform the design of testing strategies. Pathologist-initiated reflex testing streamlines the availability of the results for clinical decision-making; however, pathologic parameters such as GG and the presence of intraductal/cribriform carcinoma may not be reliable to guide patient selection.
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Affiliation(s)
- Susan Prendeville
- Division of Anatomic Pathology, Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada.
| | - Harpreet Kaur
- Division of Genome Diagnostics, Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada
| | - Shervin Ansari
- Division of Genome Diagnostics, Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada
| | - Shifaa' Al Qa'qa'
- Division of Anatomic Pathology, Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada; Department of Pathology and Forensic Medicine, Faculty of Medicine, Al-Balqa Applied University, Al-Salt, Jordan
| | - Tracy L Stockley
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada; Division of Genome Diagnostics, Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada
| | - Katherine Lajkosz
- Department of Biostatistics, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Theodorus van der Kwast
- Division of Anatomic Pathology, Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Carol C Cheung
- Division of Anatomic Pathology, Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Shamini Selvarajah
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada; Division of Genome Diagnostics, Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada
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4
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Bouras A, Lefol C, Ruano E, Grand-Masson C, Wang Q. PMS2 or PMS2CL? Characterization of variants detected in the 3' of the PMS2 gene. Genes Chromosomes Cancer 2024; 63:e23193. [PMID: 37534630 DOI: 10.1002/gcc.23193] [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: 05/06/2023] [Revised: 07/24/2023] [Accepted: 07/25/2023] [Indexed: 08/04/2023] Open
Abstract
PMS2 germline pathogenic variants are one of the major causes for Lynch syndrome and constitutional mismatch repair deficiencies. Variant identification in the 3' region of this gene is complicated by the presence of the pseudogene PMS2CL which shares a high sequence homology with PMS2. Consequently, short-fragment screening strategies (NGS, Sanger) may fail to discriminate variant's gene localization. Using a comprehensive analysis strategy, we assessed 42 NGS-detected variants in 76 patients and found 32 localized on PMS2 while 6 on PMS2CL. Interestingly, four variants were detected in either of them in different patients. Clinical phenotype was well correlated to genotype, making it very helpful in variant assessment. Our findings emphasize the necessity of more specific complementary analyses to confirm the gene origin of each variant detected in different individuals in order to avoid variant misinterpretation. In addition, we characterized two PMS2 genomic alterations involving Alu-mediated tandem duplication and gene conversion. Those mechanisms seemed to be particularly favored in PMS2 which contribute to frequent genomic rearrangements in the 3' region of the gene.
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Affiliation(s)
- Ahmed Bouras
- Centre Léon Bérard, Laboratory of Constitutional Genetics for Frequent Cancer HCL-CLB, Lyon, France
- Inserm U1052, Centre de Recherche en Cancérologie de Lyon, Lyon, France
| | - Cedrick Lefol
- Centre Léon Bérard, Laboratory of Constitutional Genetics for Frequent Cancer HCL-CLB, Lyon, France
| | - Eric Ruano
- Centre Léon Bérard, Laboratory of Constitutional Genetics for Frequent Cancer HCL-CLB, Lyon, France
| | - Chloé Grand-Masson
- Centre Léon Bérard, Laboratory of Constitutional Genetics for Frequent Cancer HCL-CLB, Lyon, France
| | - Qing Wang
- Centre Léon Bérard, Laboratory of Constitutional Genetics for Frequent Cancer HCL-CLB, Lyon, France
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5
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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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6
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Mighton C, Shickh S, Aguda V, Krishnapillai S, Adi-Wauran E, Bombard Y. From the patient to the population: Use of genomics for population screening. Front Genet 2022; 13:893832. [PMID: 36353115 PMCID: PMC9637971 DOI: 10.3389/fgene.2022.893832] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 09/26/2022] [Indexed: 10/22/2023] Open
Abstract
Genomic medicine is expanding from a focus on diagnosis at the patient level to prevention at the population level given the ongoing under-ascertainment of high-risk and actionable genetic conditions using current strategies, particularly hereditary breast and ovarian cancer (HBOC), Lynch Syndrome (LS) and familial hypercholesterolemia (FH). The availability of large-scale next-generation sequencing strategies and preventive options for these conditions makes it increasingly feasible to screen pre-symptomatic individuals through public health-based approaches, rather than restricting testing to high-risk groups. This raises anew, and with urgency, questions about the limits of screening as well as the moral authority and capacity to screen for genetic conditions at a population level. We aimed to answer some of these critical questions by using the WHO Wilson and Jungner criteria to guide a synthesis of current evidence on population genomic screening for HBOC, LS, and FH.
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Affiliation(s)
- Chloe Mighton
- Genomics Health Services Research Program, St. Michael’s Hospital, Unity Health Toronto, Toronto, ON, Canada
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada
| | - Salma Shickh
- Genomics Health Services Research Program, St. Michael’s Hospital, Unity Health Toronto, Toronto, ON, Canada
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada
| | - Vernie Aguda
- Genomics Health Services Research Program, St. Michael’s Hospital, Unity Health Toronto, Toronto, ON, Canada
- Centre for Medical Education, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Suvetha Krishnapillai
- Genomics Health Services Research Program, St. Michael’s Hospital, Unity Health Toronto, Toronto, ON, Canada
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada
| | - Ella Adi-Wauran
- Genomics Health Services Research Program, St. Michael’s Hospital, Unity Health Toronto, Toronto, ON, Canada
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada
| | - Yvonne Bombard
- Genomics Health Services Research Program, St. Michael’s Hospital, Unity Health Toronto, Toronto, ON, Canada
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada
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7
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Tong K, He W, He Y, Li X, Hu L, Hu H, Lu G, Lin G, Dong C, Zhang VW, Du J, Liu D. Clinical Utility of Medical Exome Sequencing: Expanded Carrier Screening for Patients Seeking Assisted Reproductive Technology in China. Front Genet 2022; 13:943058. [PMID: 36072675 PMCID: PMC9441495 DOI: 10.3389/fgene.2022.943058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 06/20/2022] [Indexed: 11/13/2022] Open
Abstract
Purpose: Expanded carrier screening (ECS) is an effective method to identify at-risk couples (ARCs) and avoid birth defects. This study aimed to reveal the carrier spectrum in the Chinese population and to delineate an expanded carrier gene panel suitable in China.Methods: Medical exome sequencing (MES), including 4,158 disease-causing genes, was offered to couples at two reproductive centers. It was initially used as a diagnostic yield for potential patients and then used for ECS. Clinical information and ECS results were retrospectively collected.Results: A total of 2,234 couples, representing 4,468 individuals, underwent MES. In total, 254 individuals showed genetic disease symptoms, and 56 of them were diagnosed with genetic diseases by MES. Overall, 94.5% of them were carriers of at least one disease-causing variant. The most prevalent genes were GJB2 for autosomal recessive disorders and G6PD for X-linked diseases. The ARC rate was 9.80%, and couples were inclined to undergo preimplantation genetic testing when diseases were classified as “profound” or “severe.”Conclusion: This study provided insight to establish a suitable ECS gene panel for the Chinese population. Disease severity significantly influenced reproductive decision-making. The results highlighted the importance of conducting ECS for couples before undergoing assisted reproductive technology.
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Affiliation(s)
- Keya Tong
- Center for Reproductive Medicine, Women and Children’s Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Human Embryo Engineering, Women and Children’s Hospital of Chongqing Medical University, Chongqing, China
| | - Wenbin He
- National Engineering and Research Center of Human Stem Cells, Changsha, China
- School of Basic Medical Science, Institute of Reproductive and Stem Cell Engineering, Central South University, Changsha, China
- Genetics Centre, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China
| | - Yao He
- Center for Reproductive Medicine, Women and Children’s Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Human Embryo Engineering, Women and Children’s Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Clinical Research Center for Reproductive Medicine, Women and Children’s Hospital of Chongqing Medical University, Chongqing, China
| | - Xiurong Li
- National Engineering and Research Center of Human Stem Cells, Changsha, China
| | - Liang Hu
- National Engineering and Research Center of Human Stem Cells, Changsha, China
| | - Hao Hu
- National Engineering and Research Center of Human Stem Cells, Changsha, China
| | - Guangxiu Lu
- National Engineering and Research Center of Human Stem Cells, Changsha, China
- School of Basic Medical Science, Institute of Reproductive and Stem Cell Engineering, Central South University, Changsha, China
- Genetics Centre, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China
| | - Ge Lin
- National Engineering and Research Center of Human Stem Cells, Changsha, China
- School of Basic Medical Science, Institute of Reproductive and Stem Cell Engineering, Central South University, Changsha, China
- Genetics Centre, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China
| | | | | | - Juan Du
- National Engineering and Research Center of Human Stem Cells, Changsha, China
- School of Basic Medical Science, Institute of Reproductive and Stem Cell Engineering, Central South University, Changsha, China
- Genetics Centre, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China
- *Correspondence: Juan Du, ; Dongyun Liu,
| | - Dongyun Liu
- Center for Reproductive Medicine, Women and Children’s Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Human Embryo Engineering, Women and Children’s Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Clinical Research Center for Reproductive Medicine, Women and Children’s Hospital of Chongqing Medical University, Chongqing, China
- *Correspondence: Juan Du, ; Dongyun Liu,
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8
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Mighton C, Lerner‐Ellis J. Principles of molecular testing for hereditary cancer. Genes Chromosomes Cancer 2022; 61:356-381. [DOI: 10.1002/gcc.23048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 04/03/2022] [Accepted: 04/06/2022] [Indexed: 11/10/2022] Open
Affiliation(s)
- Chloe Mighton
- Laboratory Medicine and Pathology, Mount Sinai Hospital, Sinai Health Toronto ON Canada
- Lunenfeld Tanenbaum Research Institute, Sinai Health Toronto ON Canada
- Genomics Health Services Research Program Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto Toronto ON Canada
- Institute of Health Policy, Management and Evaluation, Dalla Lana School of Public Health University of Toronto Toronto ON Canada
| | - Jordan Lerner‐Ellis
- Laboratory Medicine and Pathology, Mount Sinai Hospital, Sinai Health Toronto ON Canada
- Lunenfeld Tanenbaum Research Institute, Sinai Health Toronto ON Canada
- Department of Laboratory Medicine and Pathobiology University of Toronto Toronto ON Canada
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9
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Woodward ER, Green K, Burghel GJ, Bulman M, Clancy T, Lalloo F, Schlecht H, Wallace AJ, Evans DG. 30 year experience of index case identification and outcomes of cascade testing in high-risk breast and colorectal cancer predisposition genes. Eur J Hum Genet 2022; 30:413-419. [PMID: 34866136 PMCID: PMC8645350 DOI: 10.1038/s41431-021-01011-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 09/27/2021] [Accepted: 11/15/2021] [Indexed: 11/19/2022] Open
Abstract
It is 30 years since the first diagnostic cancer predisposition gene (CPG) test in the Manchester Centre for Genomic Medicine (MCGM), providing opportunities for cancer prevention, early detection and targeted treatments in index cases and at-risk family members. Here, we present time trends (1990-2020) of identification of index cases with a germline CPG variant and numbers of subsequent cascade tests, for 15 high-risk breast and gastro-intestinal tract cancer-associated CPGs: BRCA1, BRCA2, PALB2, PTEN, TP53, APC, BMPR1a, CDH1, MLH1, MSH2, MSH6, PMS2, SMAD4, STK11 and MUTYH. We recorded 2082 positive index case diagnostic screening tests, generating 3216 positive and 3140 negative family cascade (non-index) tests. This is equivalent to an average of 3.05 subsequent cascade tests per positive diagnostic index test, with 1.54 positive and 1.51 negative non-index tests per family. The CPGs with the highest numbers of non-index positive cases identified on cascade testing were BRCA1/2 (n = 1999) and the mismatch repair CPGs associated with Lynch Syndrome (n = 731). These data are important for service provision and health economic assessment of CPG diagnostic testing, in terms of cancer prevention and early detection strategies, and identifying those likely to benefit from targeted treatment strategies.
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Affiliation(s)
- Emma R Woodward
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester, M13 9WL, UK
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, M13 9PL, UK
| | - Kate Green
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester, M13 9WL, UK
| | - George J Burghel
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester, M13 9WL, UK
| | - Michael Bulman
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester, M13 9WL, UK
| | - Tara Clancy
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, M13 9PL, UK
| | - Fiona Lalloo
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester, M13 9WL, UK
| | - Helene Schlecht
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester, M13 9WL, UK
| | - Andrew J Wallace
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester, M13 9WL, UK
| | - D Gareth Evans
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester, M13 9WL, UK.
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, M13 9PL, UK.
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10
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Gibson A, Ragoonanan D, Tewari P, Petropoulos D, Rodriguez N, DiNardo C, Mahadeo KM, Khazal S. Non-myeloablative umbilical cord blood transplantation for atypical dyskeratosis congenita. Pediatr Transplant 2022; 26:e14157. [PMID: 34626046 DOI: 10.1111/petr.14157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 07/07/2021] [Accepted: 09/22/2021] [Indexed: 11/29/2022]
Abstract
BACKGROUND Short telomere syndrome (STS) in children may result in phenotypically heterogenous clinical spectrum ranging from completely asymptomatic to typical dyskeratosis congenita (DC). Patients with this cancer predisposition syndrome may have multiple organ dysfunctions including pulmonary fibrosis, liver cirrhosis, and bone marrow failure. Not all mutations in telomerase or telomere genes have been identified, and STS may pose a diagnostic and management challenge. METHODS A retrospective chart review and literature search were done for this report. RESULTS Here, we report a case of atypical DC with a heterozygous germline missense mutation in the postmeiotic segregation increased 2 (PMS2) gene, exon 5, (c.466A>G (p. Thr156Ala)). The PMS2 (a mismatch repair protein) gene is known to be an important mediator of telomere-induced aging. The patient was transfusion dependent and underwent successful umbilical cord blood transplant using a non-myeloablative regimen with alemtuzumab, fludarabine, cyclophosphamide, and total body irradiation. CONCLUSION In this case of atypical DC with a previously unreported germline missense mutation in PMS2, the patient was successfully treated with an umbilical cord blood transplant with a non-myeloablative regimen.
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Affiliation(s)
- Amber Gibson
- Department of Pediatrics, Children's Cancer Hospital, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Dristhi Ragoonanan
- Department of Pediatrics, Children's Cancer Hospital, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Priti Tewari
- Department of Pediatrics, Pediatric Stem Cell Transplantation and Cellular Therapy, CARTOX Program, Children's Cancer Hospital, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Demetrios Petropoulos
- Department of Pediatrics, Pediatric Stem Cell Transplantation and Cellular Therapy, CARTOX Program, Children's Cancer Hospital, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Nidra Rodriguez
- Division of Hematology, Department of Pediatrics, Mc Govern Medical School, The University of Texas Health Science Center, Houston, Texas, USA
| | - Courtney DiNardo
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Kris M Mahadeo
- Department of Pediatrics, Pediatric Stem Cell Transplantation and Cellular Therapy, CARTOX Program, Children's Cancer Hospital, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Sajad Khazal
- Department of Pediatrics, Pediatric Stem Cell Transplantation and Cellular Therapy, CARTOX Program, Children's Cancer Hospital, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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11
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Hirsch S, Dikow N, Pfister SM, Pajtler KW. Cancer predisposition in pediatric neuro-oncology-practical approaches and ethical considerations. Neurooncol Pract 2021; 8:526-538. [PMID: 34594567 DOI: 10.1093/nop/npab031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
A genetic predisposition to tumor development can be identified in up to 10% of pediatric patients with central nervous system (CNS) tumors. For some entities, the rate of an underlying predisposition is even considerably higher. In recent years, population-based approaches have helped to further delineate the role of cancer predisposition in pediatric oncology. Investigations for cancer predisposition syndrome (CPS) can be guided by clinical signs and family history leading to directed testing of specific genes. The increasingly adopted molecular analysis of tumor and often parallel blood samples with multi-gene panel, whole-exome, or whole-genome sequencing identifies additional patients with or without clinical signs. Diagnosis of a genetic predisposition may put an additional burden on affected families. However, information on a given cancer predisposition may be critical for the patient as potentially influences treatment decisions and may offer the patient and healthy carriers the chance to take part in intensified surveillance programs aiming at early tumor detection. In this review, we discuss some of the practical and ethical challenges resulting from the widespread use of new diagnostic techniques and the most important CPS that may manifest with brain tumors in childhood.
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Affiliation(s)
- Steffen Hirsch
- Hopp-Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Institute of Human Genetics, Heidelberg University Hospital, Heidelberg, Germany
| | - Nicola Dikow
- Institute of Human Genetics, Heidelberg University Hospital, Heidelberg, Germany
| | - Stefan M Pfister
- Hopp-Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Kristian W Pajtler
- Hopp-Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany.,Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
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12
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Tang J, Tan M, Deng Y, Tang H, Shi H, Li M, Ma W, Li J, Dai H, Li J, Zhou S, Li X, Wei F, Ma X, Luo L. Two Novel Pathogenic Variants of TJP2 Gene and the Underlying Molecular Mechanisms in Progressive Familial Intrahepatic Cholestasis Type 4 Patients. Front Cell Dev Biol 2021; 9:661599. [PMID: 34504838 PMCID: PMC8421653 DOI: 10.3389/fcell.2021.661599] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 07/09/2021] [Indexed: 12/13/2022] Open
Abstract
Progressive familial intrahepatic cholestasis (PFIC) is an autosomal recessive inherited disease that accounts for 10%-15% childhood cholestasis and could lead to infant disability or death. There are three well-established types of PFIC (1-3), caused by mutations in the ATP8B1, ABCB11, and ABCB4 genes. Biallelic pathogenic variants in the tight junction protein 2 gene (TJP2) were newly reported as a cause for PFIC type 4; however, only a limited number of patients and undisputable variants have been reported for TJP2, and the underlying mechanism for PFIC 4 remains poorly understood. To explore the diagnostic yield of TJP2 analysis in suspected PFIC patients negative for the PFIC1-3 mutation, we designed a multiplex polymerase chain reaction-based next-generation sequencing method to analyze TJP2 gene variants in 267 PFIC patients and identified biallelic rare variants in three patients, including three known pathogenic variants and two novel variants in three patients. By using CRISPR-cas9 technology, we demonstrated that TJP2 c.1202A > G was pathogenic at least partially by increasing the expression and nuclear localization of TJP2 protein. With the minigene assay, we showed that TJP2 c.2668-11A > G was a new pathogenic variant by inducing abnormal splicing of TJP2 gene and translation of prematurely truncated TJP2 protein. Furthermore, knockdown of TJP2 protein by siRNA technology led to inhibition of cell proliferation, induction of apoptosis, dispersed F-actin, and disordered microfilaments in LO2 and HepG2celles. Global gene expression profiling of TJP2 knockdown LO2 cells and HepG2 cells identified the dysregulated genes involved in the regulation of actin cytoskeleton. Microtubule cytoskeleton genes were significantly downregulated in TJP2 knockdown cells. The results of this study demonstrate that TJP2 c.1202A > G and TJP2 c.2668-11A > G are two novel pathogenic variants and the cytoskeleton-related functions and pathways might be potential molecular pathogenesis for PFIC.
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Affiliation(s)
- Jia Tang
- NHC Key Laboratory of Male Reproduction and Genetics, Guangdong Provincial Reproductive Science Institute (Guangdong Provincial Fertility Hospital), Guangzhou, China
- Department of Medical Imaging Center, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, China
- Medical Genetics Center, Jiangmen Maternity and Child Health Care Hospital, Jiangmen, China
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
| | - Meihua Tan
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- BGI Genomics Co., Ltd., Shenzhen, China
| | - Yihui Deng
- Department of Medical Imaging Center, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, China
| | - Hui Tang
- Department of Medical Imaging Center, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, China
| | - Haihong Shi
- Medical Genetics Center, Jiangmen Maternity and Child Health Care Hospital, Jiangmen, China
| | - Mingzhen Li
- NHC Key Laboratory of Male Reproduction and Genetics, Guangdong Provincial Reproductive Science Institute (Guangdong Provincial Fertility Hospital), Guangzhou, China
| | - Wei Ma
- Department of Biology, School of Basic Medicine, Jiamusi University, Jiamusi, China
| | - Jia Li
- BGI Genomics Co., Ltd., Shenzhen, China
| | - Hongzheng Dai
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
| | - Jianli Li
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
| | - Shengmei Zhou
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, CA, United States
| | - Xu Li
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
| | - Fengxiang Wei
- Longgang District Maternity & Child Healthcare Hospital of Shenzhen City, Shenzhen, China
| | - Xiaofen Ma
- Department of Medical Imaging of Guangdong Second Provincial General Hospital, Guangzhou, China
| | - Liangping Luo
- Department of Medical Imaging Center, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, China
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13
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Claes KBM, Rosseel T, De Leeneer K. Dealing with Pseudogenes in Molecular Diagnostics in the Next Generation Sequencing Era. Methods Mol Biol 2021; 2324:363-381. [PMID: 34165726 DOI: 10.1007/978-1-0716-1503-4_22] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Presence of pseudogenes is a dreadful issue in next generation sequencing (NGS), because their contamination can interfere with the detection of variants in the genuine gene and generate false positive and false negative variants.In this chapter we focus on issues related to the application of NGS strategies for analysis of genes with pseudogenes in a clinical setting. The degree to which a pseudogene impacts the ability to accurately detect and map variants in its parent gene depends on the degree of similarity (homology) with the parent gene itself. Hereby, target enrichment and mapping strategies are crucial factors to avoid "contaminating" pseudogene sequences. For target enrichment, we describe advantages and disadvantages of PCR- and capture-based strategies. For mapping strategies, we discuss crucial parameters that need to be considered to accurately distinguish sequences of functional genes from pseudogenic sequences. Finally, we discuss some examples of genes associated with Mendelian disorders, for which interesting NGS approaches are described to avoid interference with pseudogene sequences.
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Affiliation(s)
| | - Toon Rosseel
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Kim De Leeneer
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
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14
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Ramirez NJ, Posadas-Cantera S, Caballero-Oteyza A, Camacho-Ordonez N, Grimbacher B. There is no gene for CVID - novel monogenetic causes for primary antibody deficiency. Curr Opin Immunol 2021; 72:176-185. [PMID: 34153571 DOI: 10.1016/j.coi.2021.05.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 05/27/2021] [Accepted: 05/28/2021] [Indexed: 12/25/2022]
Abstract
'There is no gene for fate' (citation from the movie 'GATTACA') - and there is no gene for CVID. Common Variable ImmunoDeficiency (CVID) is the most prevalent primary immunodeficiency in humans. CVID is characterized by an increased susceptibility to infections, hypogammaglobulinemia, reduced switched memory B cell numbers in peripheral blood and a defective response to vaccination, often complicated by autoimmune and autoinflammatory conditions. However, as soon as a genetic diagnosis has been made in a patient with CVID, the diagnosis must be changed to the respective genetic cause (www.esid.org). Therefore, there are genetic causes for primary antibody deficiencies, but not for CVID. Primary antibody deficiencies (PADs) are a heterogeneous group of disorders. Several attempts have been made to gain further insights into the pathogenesis of PAD, using unbiased approaches such as whole exome or genome sequencing. Today, in just about 35% of cases with PAD, monogenic mutations (including those in the gene TNFRSF13B) can be identified in a set of 68 genes [1•]. These mutations occur either sporadically or are inherited and do explain an often complex phenotype. In our review, we not only discuss gene defects identified in PAD patients previously diagnosed with CVID and/or CVID-like disorders such as IKZF1, CTNNBL1, TNFSF13 and BACH2, but also genetic defects which were initially described in non-CVID patients but have later also been observed in patients with PAD such as PLCG2, PIK3CG, PMS2, RNF31, KMT2D, STAT3. We also included interesting genetic defects in which the pathophysiology suggests a close relation to other known defects of the adaptive immune response, such as DEF6, SAMD9 and SAMD9L, and hence a CVID-like phenotype may be observed in the future. However, alternative mechanisms most likely add to the development of an antibody-deficient phenotype, such as polygenic origins, epigenetic changes, and/or environmental factors.
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Affiliation(s)
- Neftali J Ramirez
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center, Faculty of Medicine, Albert-Ludwigs-University of Freiburg, Freiburg, Germany; Integrated Research Training Group (IRTG) Medical Epigenetics, Collaborative Research Centre 992, Freiburg, Germany; Faculty of Biology, Albert-Ludwigs-University of Freiburg, Germany
| | - Sara Posadas-Cantera
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center, Faculty of Medicine, Albert-Ludwigs-University of Freiburg, Freiburg, Germany
| | - Andrés Caballero-Oteyza
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center, Faculty of Medicine, Albert-Ludwigs-University of Freiburg, Freiburg, Germany; RESIST - Cluster of Excellence 2155 to Hanover Medical School, Satellite Center Freiburg, Freiburg, Germany
| | - Nadezhda Camacho-Ordonez
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center, Faculty of Medicine, Albert-Ludwigs-University of Freiburg, Freiburg, Germany; Faculty of Biology, Albert-Ludwigs-University of Freiburg, Germany
| | - Bodo Grimbacher
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center, Faculty of Medicine, Albert-Ludwigs-University of Freiburg, Freiburg, Germany; DZIF - German Center for Infection Research, Satellite Center Freiburg, Freiburg, Germany; CIBSS - Centre for Integrative Biological Signalling Studies, Albert-Ludwigs University, Freiburg, Germany; RESIST - Cluster of Excellence 2155 to Hanover Medical School, Satellite Center Freiburg, Freiburg, Germany.
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15
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Zampieri S, Cattarossi S, Pavan E, Barbato A, Fiumara A, Peruzzo P, Scarpa M, Ciana G, Dardis A. Accurate Molecular Diagnosis of Gaucher Disease Using Clinical Exome Sequencing as a First-Tier Test. Int J Mol Sci 2021; 22:ijms22115538. [PMID: 34073924 PMCID: PMC8197298 DOI: 10.3390/ijms22115538] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 05/18/2021] [Accepted: 05/20/2021] [Indexed: 11/16/2022] Open
Abstract
Gaucher disease (GD) is an autosomal recessive lysosomal disorder due to beta-glucosidase gene (GBA) mutations. The molecular diagnosis of GD is complicated by the presence of recombinant alleles originating from a highly homologous pseudogene. Clinical exome sequencing (CES) is a rapid genetic approach for identifying disease-causing mutations. However, copy number variation and recombination events are poorly detected, and further investigations are required to avoid mis-genotyping. The aim of this work was to set-up an integrated strategy for GD patients genotyping using CES as a first-line test. Eight patients diagnosed with GD were analyzed by CES. Five patients were fully genotyped, while three were revealed to be homozygous for mutations that were not confirmed in the parents. Therefore, MLPA (multiplex ligation-dependent probe amplification) and specific long-range PCR were performed, and two recombinant alleles, one of them novel, and one large deletion were identified. Furthermore, an MLPA assay performed in one family resulted in the identification of an additional novel mutation (p.M124V) in a relative, in trans with the known p.N409S mutation. In conclusion, even though CES has become extensively used in clinical practice, our study emphasizes the importance of a comprehensive molecular strategy to provide proper GBA genotyping and genetic counseling.
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Affiliation(s)
- Stefania Zampieri
- Regional Coordinator Centre for Rare Diseases, University Hospital of Udine, 33100 Udine, Italy
| | - Silvia Cattarossi
- Regional Coordinator Centre for Rare Diseases, University Hospital of Udine, 33100 Udine, Italy
| | - Eleonora Pavan
- Regional Coordinator Centre for Rare Diseases, University Hospital of Udine, 33100 Udine, Italy
| | - Antonio Barbato
- Department of Clinical Medicine and Surgery, Federico II University Hospital, 80131 Naples, Italy
| | - Agata Fiumara
- Pediatric Unit, Regional Referral Center for Inherited Metabolic Disease, University of Catania, 95123 Catania, Italy
| | - Paolo Peruzzo
- Regional Coordinator Centre for Rare Diseases, University Hospital of Udine, 33100 Udine, Italy
| | - Maurizio Scarpa
- Regional Coordinator Centre for Rare Diseases, University Hospital of Udine, 33100 Udine, Italy
| | - Giovanni Ciana
- Regional Coordinator Centre for Rare Diseases, University Hospital of Udine, 33100 Udine, Italy
| | - Andrea Dardis
- Regional Coordinator Centre for Rare Diseases, University Hospital of Udine, 33100 Udine, Italy
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16
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O'Connor LP, Lebastchi AH, Fasaye GA, Dikoglu E, Daneshvar MA, Ahdoot M, Merino MJ, Pinto PA. 'Case of the Month' from the National Cancer Institute, Bethesda, MD, USA: investigating genetic aberrations in a patient with high-risk prostate cancer. BJU Int 2021; 127:171-174. [PMID: 33547722 DOI: 10.1111/bju.15273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Luke P O'Connor
- Center for Cancer Research, Urologic Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Amir H Lebastchi
- Center for Cancer Research, Urologic Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Grace-Ann Fasaye
- Center for Cancer Research, Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Esra Dikoglu
- Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Michael A Daneshvar
- Center for Cancer Research, Urologic Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Michael Ahdoot
- Center for Cancer Research, Urologic Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Maria J Merino
- Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Peter A Pinto
- Center for Cancer Research, Urologic Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
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17
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Diagnosis of Lynch Syndrome and Strategies to Distinguish Lynch-Related Tumors from Sporadic MSI/dMMR Tumors. Cancers (Basel) 2021; 13:cancers13030467. [PMID: 33530449 PMCID: PMC7865821 DOI: 10.3390/cancers13030467] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 01/19/2021] [Accepted: 01/22/2021] [Indexed: 02/07/2023] Open
Abstract
Simple Summary Microsatellite instability (MSI) is a hallmark of Lynch syndrome (LS)-related tumors but is not specific, as most of MSI/mismatch repair-deficient (dMMR) tumors are sporadic. Therefore, the identification of MSI/dMMR requires additional diagnostic tools to identify LS. In this review, we address the hallmarks of LS and present recent advances in diagnostic and screening strategies to identify LS patients. We also discuss the pitfalls associated with current strategies, which should be taken into account in order to improve the diagnosis of LS. Abstract Microsatellite instability (MSI) is a hallmark of Lynch syndrome (LS)-related tumors but is not specific to it, as approximately 80% of MSI/mismatch repair-deficient (dMMR) tumors are sporadic. Methods leading to the diagnosis of LS have considerably evolved in recent years and so have tumoral tests for LS screening and for the discrimination of LS-related to MSI-sporadic tumors. In this review, we address the hallmarks of LS, including the clinical, histopathological, and molecular features. We present recent advances in diagnostic and screening strategies to identify LS patients. We also discuss the pitfalls associated with the current strategies, which should be taken into account to improve the diagnosis of LS and avoid inappropriate clinical management.
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18
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Kassem N, Stout LA, Hunter C, Schneider B, Radovich M. Precision Prevention: The Current State and Future of Genomically Guided Cancer Prevention. JCO Precis Oncol 2020; 4:96-108. [PMID: 35050732 DOI: 10.1200/po.19.00278] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The identification of cancer-predisposing germline variants has potentially substantial clinical impact for patients and their families. Although management guidelines have been proposed for some genes, guidelines for other genes are lacking. This review focuses on the current surveillance and management guidelines for the most common hereditary cancer syndromes and discusses some of the most pivotal studies supporting the available guidelines. We also highlight the gaps in the identification of germline carriers, the cascade testing of at-risk relatives, and the challenges impeding the proper follow-up and optimal management of pathogenic germline carriers. The anticipated surge in the number of identified germline carriers, deficient management guidelines, poor cascade testing uptake, and long-term follow-up necessitate the development of multidisciplinary clinics as an obligatory step toward the improvement of cancer prevention.
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Affiliation(s)
- Nawal Kassem
- Indiana University School of Medicine, Indianapolis, IN.,Indiana University Health Precision Genomics, Indianapolis, IN
| | - Leigh Anne Stout
- Indiana University School of Medicine, Indianapolis, IN.,Indiana University Health Precision Genomics, Indianapolis, IN
| | - Cynthia Hunter
- Indiana University School of Medicine, Indianapolis, IN.,Indiana University Health Precision Genomics, Indianapolis, IN
| | - Bryan Schneider
- Indiana University School of Medicine, Indianapolis, IN.,Indiana University Health Precision Genomics, Indianapolis, IN
| | - Milan Radovich
- Indiana University School of Medicine, Indianapolis, IN.,Indiana University Health Precision Genomics, Indianapolis, IN
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19
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Resolving misalignment interference for NGS-based clinical diagnostics. Hum Genet 2020; 140:477-492. [PMID: 32915251 DOI: 10.1007/s00439-020-02216-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Accepted: 07/31/2020] [Indexed: 01/18/2023]
Abstract
Next-generation sequencing (NGS) is an incredibly useful tool for genetic disease diagnosis. However, the most commonly used bioinformatics methods for analyzing sequence reads insufficiently discriminate genomic regions with extensive sequence identity, such as gene families and pseudogenes, complicating diagnostics. This problem has been recognized for specific genes, including many involved in human disease, and diagnostic labs must perform additional costly steps to guarantee accurate diagnosis in these cases. Here we report a new data analysis method based on the comparison of read depth between highly homologous regions to identify misalignment. Analyzing six clinically important genes-CYP21A2, GBA, HBA1/2, PMS2, and SMN1-each exhibiting misalignment issues related to homology, we show that our technique can correctly identify potential misalignment events and be used to make appropriate calls. Combined with long-range PCR and/or MLPA orthogonal testing, our clinical laboratory can improve variant calling with minimal additional cost. We propose an accurate and cost-efficient NGS testing procedure that will benefit disease diagnostics, carrier screening, and research-based population studies.
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20
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Akras Z, Bungo B, Leach BH, Marquard J, Ahluwalia M, Carraway H, Grivas P, Sohal DP, Funchain P. Primer on Hereditary Cancer Predisposition Genes Included Within Somatic Next-Generation Sequencing Panels. JCO Precis Oncol 2019; 3:1-11. [DOI: 10.1200/po.18.00258] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
PURPOSE It has been estimated that 5% to 10% of cancers are due to hereditary causes. Recent data sets indicate that the incidence of hereditary cancer may be as high as 17.5% in patients with cancer, and a notable subset is missed if screening is solely by family history and current syndrome-based testing guidelines. Identification of germline variants has implications for both patients and their families. There is currently no comprehensive overview of cancer susceptibility genes or inclusion of these genes in commercially available somatic testing. We aimed to summarize genes linked to hereditary cancer and the somatic and germline panels that include such genes. METHODS Germline predisposition genes were chosen if commercially available for testing. Penetrance was defined as low, moderate, or high according to whether the gene conferred a 0% to 20%, 20% to 50%, or 50% to 100% lifetime risk of developing the cancer or, when percentages were not available, was estimated on the basis of existing literature descriptions. RESULTS We identified a total of 89 genes linked to hereditary cancer predisposition, and we summarized these genes alphabetically and by organ system. We considered four germline and six somatic commercially available panel tests and quantified the coverage of germline genes across them. Comparison between the number of genes that had germline importance and the number of genes included in somatic testing showed that many but not all germline genes are tested by frequently used somatic panels. CONCLUSION The inclusion of cancer-predisposing genes in somatic variant testing panels makes incidental germline findings likely. Although somatic testing can be used to screen for germline variants, this strategy is inadequate for comprehensive screening. Access to genetic counseling is essential for interpretation of germline implications of somatic testing and implementation of appropriate screening and follow-up.
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21
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Jansen AML, Tops CMJ, Ruano D, van Eijk R, Wijnen JT, Ten Broeke S, Nielsen M, Hes FJ, van Wezel T, Morreau H. The complexity of screening PMS2 in DNA isolated from formalin-fixed paraffin-embedded material. Eur J Hum Genet 2019; 28:333-338. [PMID: 31616036 DOI: 10.1038/s41431-019-0527-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 09/19/2019] [Accepted: 09/27/2019] [Indexed: 11/09/2022] Open
Abstract
Germline variants in the DNA mismatch repair (MMR) gene PMS2 cause 1-14% of all Lynch Syndrome cancers. Correct variant analysis of PMS2 is complex due to the presence of multiple pseudogenes and the occurrence of gene conversion. The analysis complexity increases in highly fragmented DNA from formalin-fixed paraffin-embedded (FFPE) tissue. Here we describe a reliable approach to detect true PMS2 variants in fragmented DNA. A custom NGS panel designed for FFPE tissue was used targeting four MMR genes, POLE and POLD1. Amplicon design for PMS2 was based on the position of paralogous sequence variants (PSVs) that distinguish PMS2 from its pseudogenes. PMS2 variants in exons 1-11 can be correctly curated based on this information. For exons 12-15 this is less reliable as these undergo gene conversion. Using this method, we screened PMS2 variants in 125 MMR-deficient tumors. Of the 125 tumors tested, six were unexplained MMR-deficient tumors with solitary PMS2 protein expression loss. In these six tumors two unclassified variants (class 3) and five variants likely affecting function (class 4/5) were detected in PMS2. One microsatellite unstable tumor with positive staining for all MMR proteins was found to carry a frameshift PMS2 variant (class 5). No class 4 or class 5 PMS2 variants were detected in tumors with other patterns of MMR protein expression loss.
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Affiliation(s)
- Anne M L Jansen
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands.,Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Carli M J Tops
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Dina Ruano
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Ronald van Eijk
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Juul T Wijnen
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Sanne Ten Broeke
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Maartje Nielsen
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Frederik J Hes
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Tom van Wezel
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Hans Morreau
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands.
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22
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Okkels H, Lagerstedt-Robinsson K, Wikman FP, Hansen TVO, Lolas I, Lindberg LJ, Krarup HB. Detection of PMS2 Mutations by Screening Hereditary Nonpolyposis Colon Cancer Families from Denmark and Sweden. Genet Test Mol Biomarkers 2019; 23:688-695. [PMID: 31433215 DOI: 10.1089/gtmb.2018.0316] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Background and Aims: Hereditary nonpolyposis colon cancer (HNPCC) and Lynch syndrome (LS) are characterized by defects in the mismatch repair (MMR) system, which protects the integrity of the genome. Pathogenic variants in four MMR genes (MLH1, MSH2, MSH6, and PMS2) are responsible for LS, an autosomal, dominant hereditary disease that occurs with a frequency of 2-5% among all colorectal cancer cases. It has been estimated that ∼2-5% of all pathogenic variants found in the four MMR genes in LS cases are detected in the PMS2 gene. An overview of detected variants is presented here. Materials and Methods: Long-range (LR) PMS2 polymerase chain reaction (PCR) and PMS2 multiplex ligation probe amplification (MLPA) assays were used to detect PMS2 variants in ∼1500 probands. In a subset of the probands, pathogenic PMS2 variants were detected by next-generation sequencing, and all detected variants were confirmed by LR-PCR combined with an MLPA assay. Results: A summary of PMS2 mutation analyses performed on colon cancer patients from molecular diagnostic laboratories in Denmark and Sweden is presented. By screening ∼1500 HNPCC probands, a total of 40 different PMS2 variants were detected in 71 probands (5%); 20 variants were classified as pathogenic (C5), 2 variants as likely pathogenic (C4), 15 variants as variants of unknown significance (VUSs) (C3), 1 variant as likely benign (C2), and 2 variants as benign (C1). In total, 22/71 (31%) of the probands carried a pathogenic sequence variant. Among the probands with isolated loss of pPMS2 expression, the fraction of pathogenic variants was 20/35 (55%). Conclusions: Approximately 5% of the probands found in the Danish and Swedish populations presented here carried a PMS2 variant. In this study, six novel pathogenic variants and seven VUSs are reported.
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Affiliation(s)
- Henrik Okkels
- Section of Molecular Diagnostics, Department of Clinical Chemistry, Aalborg University Hospital, Aalborg, Denmark
| | - Kristina Lagerstedt-Robinsson
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Friedrik P Wikman
- Department of Molecular Medicine (MOMA), Århus University Hospital, Århus, Denmark
| | - Thomas V O Hansen
- Department of Clinical Genetics, University Hospital of Copenhagen, Copenhagen, Denmark.,Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Ihab Lolas
- Section of Molecular Diagnostics, Department of Clinical Chemistry, Aalborg University Hospital, Aalborg, Denmark
| | - Lars Joachim Lindberg
- The Danish HNPCC Registry, Clinical Research Centre, Copenhagen University Hospital, Hvidovre, Denmark
| | - Henrik B Krarup
- Section of Molecular Diagnostics, Department of Clinical Chemistry, Aalborg University Hospital, Aalborg, Denmark
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23
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Chiang T, Liu X, Wu TJ, Hu J, Sedlazeck FJ, White S, Schaid D, Andrade MD, Jarvik GP, Crosslin D, Stanaway I, Carrell DS, Connolly JJ, Hakonarson H, Groopman EE, Gharavi AG, Fedotov A, Bi W, Leduc MS, Murdock DR, Jiang Y, Meng L, Eng CM, Wen S, Yang Y, Muzny DM, Boerwinkle E, Salerno W, Venner E, Gibbs RA. Atlas-CNV: a validated approach to call single-exon CNVs in the eMERGESeq gene panel. Genet Med 2019; 21:2135-2144. [PMID: 30890783 PMCID: PMC6752313 DOI: 10.1038/s41436-019-0475-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 02/25/2019] [Indexed: 12/24/2022] Open
Abstract
PURPOSE To provide a validated method to confidently identify exon-containing copy-number variants (CNVs), with a low false discovery rate (FDR), in targeted sequencing data from a clinical laboratory with particular focus on single-exon CNVs. METHODS DNA sequence coverage data are normalized within each sample and subsequently exonic CNVs are identified in a batch of samples, when the target log2 ratio of the sample to the batch median exceeds defined thresholds. The quality of exonic CNV calls is assessed by C-scores (Z-like scores) using thresholds derived from gold standard samples and simulation studies. We integrate an ExonQC threshold to lower FDR and compare performance with alternate software (VisCap). RESULTS Thirteen CNVs were used as a truth set to validate Atlas-CNV and compared with VisCap. We demonstrated FDR reduction in validation, simulation, and 10,926 eMERGESeq samples without sensitivity loss. Sixty-four multiexon and 29 single-exon CNVs with high C-scores were assessed by Multiplex Ligation-dependent Probe Amplification (MLPA). CONCLUSION Atlas-CNV is validated as a method to identify exonic CNVs in targeted sequencing data generated in the clinical laboratory. The ExonQC and C-score assignment can reduce FDR (identification of targets with high variance) and improve calling accuracy of single-exon CNVs respectively. We propose guidelines and criteria to identify high confidence single-exon CNVs.
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Affiliation(s)
- Theodore Chiang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.
| | - Xiuping Liu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Tsung-Jung Wu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Jianhong Hu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | | | - Daniel Schaid
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Mariza de Andrade
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Gail P Jarvik
- University of Washington Medical Center, Seattle, WA, USA
| | - David Crosslin
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
| | - Ian Stanaway
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
| | - David S Carrell
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
| | | | | | - Emily E Groopman
- Department of Medicine, Division of Nephrology, Columbia University, New York, NY, USA
| | - Ali G Gharavi
- Department of Medicine, Division of Nephrology, Columbia University, New York, NY, USA
| | - Alexander Fedotov
- Irving Institute for Clinical and Translational Research, Columbia University, New York, NY, USA
| | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics Laboratories, 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
| | - Yunyun Jiang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Linyan Meng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics Laboratories, Houston, TX, USA
| | - Christine M Eng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics Laboratories, Houston, TX, USA
| | - Shu Wen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics Laboratories, Houston, TX, USA
| | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics Laboratories, Houston, TX, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Eric Boerwinkle
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.,UTHealth School of Public Health, Houston, TX, USA
| | - William Salerno
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 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.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
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24
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Evaluation for Genetic Disorders in the Absence of a Clinical Indication for Testing. J Mol Diagn 2019; 21:3-12. [DOI: 10.1016/j.jmoldx.2018.09.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 08/29/2018] [Accepted: 09/17/2018] [Indexed: 01/01/2023] Open
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25
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Gould GM, Grauman PV, Theilmann MR, Spurka L, Wang IE, Melroy LM, Chin RG, Hite DH, Chu CS, Maguire JR, Hogan GJ, Muzzey D. Detecting clinically actionable variants in the 3' exons of PMS2 via a reflex workflow based on equivalent hybrid capture of the gene and its pseudogene. BMC MEDICAL GENETICS 2018; 19:176. [PMID: 30268105 PMCID: PMC6162901 DOI: 10.1186/s12881-018-0691-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 09/20/2018] [Indexed: 12/14/2022]
Abstract
Background Hereditary cancer screening (HCS) for germline variants in the 3′ exons of PMS2, a mismatch repair gene implicated in Lynch syndrome, is technically challenging due to homology with its pseudogene PMS2CL. Sequences of PMS2 and PMS2CL are so similar that next-generation sequencing (NGS) of short fragments—common practice in multigene HCS panels—may identify the presence of a variant but fail to disambiguate whether its origin is the gene or the pseudogene. Molecular approaches utilizing longer DNA fragments, such as long-range PCR (LR-PCR), can definitively localize variants in PMS2, yet applying such testing to all samples can have logistical and economic drawbacks. Methods To address these drawbacks, we propose and characterize a reflex workflow for variant discovery in the 3′ exons of PMS2. We cataloged the natural variation in PMS2 and PMS2CL in 707 samples and designed hybrid-capture probes to enrich the gene and pseudogene with equal efficiency. For PMS2 exon 11, NGS reads were aligned, filtered using gene-specific variants, and subject to standard diploid variant calling. For PMS2 exons 12–15, the NGS reads were permissively aligned to PMS2, and variant calling was performed with the expectation of observing four alleles (i.e., tetraploid calling). In this reflex workflow, short-read NGS identifies potentially reportable variants that are then subject to disambiguation via LR-PCR-based testing. Results Applying short-read NGS screening to 299 HCS samples and cell lines demonstrated >99% analytical sensitivity and >99% analytical specificity for single-nucleotide variants (SNVs) and short insertions and deletions (indels), as well as >96% analytical sensitivity and >99% analytical specificity for copy-number variants. Importantly, 92% of samples had resolved genotypes from short-read NGS alone, with the remaining 8% requiring LR-PCR reflex. Conclusion Our reflex workflow mitigates the challenges of screening in PMS2 and serves as a guide for clinical laboratories performing multigene HCS. To facilitate future exploration and testing of PMS2 variants, we share the raw and processed LR-PCR data from commercially available cell lines, as well as variant frequencies from a diverse patient cohort. Electronic supplementary material The online version of this article (10.1186/s12881-018-0691-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Peter V Grauman
- Counsyl, 180 Kimball Way, South San Francisco, CA, 94080, USA
| | | | - Lindsay Spurka
- Counsyl, 180 Kimball Way, South San Francisco, CA, 94080, USA
| | - Irving E Wang
- Counsyl, 180 Kimball Way, South San Francisco, CA, 94080, USA
| | - Laura M Melroy
- Counsyl, 180 Kimball Way, South San Francisco, CA, 94080, USA
| | - Robert G Chin
- Counsyl, 180 Kimball Way, South San Francisco, CA, 94080, USA
| | - Dustin H Hite
- Counsyl, 180 Kimball Way, South San Francisco, CA, 94080, USA
| | - Clement S Chu
- Counsyl, 180 Kimball Way, South San Francisco, CA, 94080, USA
| | - Jared R Maguire
- Counsyl, 180 Kimball Way, South San Francisco, CA, 94080, USA
| | - Gregory J Hogan
- Counsyl, 180 Kimball Way, South San Francisco, CA, 94080, USA
| | - Dale Muzzey
- Counsyl, 180 Kimball Way, South San Francisco, CA, 94080, USA.
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26
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Herman DS, Smith C, Liu C, Vaughn CP, Palaniappan S, Pritchard CC, Shirts BH. Efficient Detection of Copy Number Mutations in PMS2 Exons with a Close Homolog. J Mol Diagn 2018; 20:512-521. [PMID: 29792936 DOI: 10.1016/j.jmoldx.2018.03.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 03/23/2018] [Indexed: 01/25/2023] Open
Abstract
Detection of 3' PMS2 copy-number mutations that cause Lynch syndrome is difficult because of highly homologous pseudogenes. To improve the accuracy and efficiency of clinical screening for these mutations, we developed a new method to analyze standard capture-based, next-generation sequencing data to identify deletions and duplications in PMS2 exons 9 to 15. The approach captures sequences using PMS2 targets, maps sequences randomly among regions with equal mapping quality, counts reads aligned to homologous exons and introns, and flags read count ratios outside of empirically derived reference ranges. The method was trained on 1352 samples, including 8 known positives, and tested on 719 samples, including 17 known positives. Clinical implementation of the first version of this method detected new mutations in the training (N = 7) and test (N = 2) sets that had not been identified by our initial clinical testing pipeline. The described final method showed complete sensitivity in both sample sets and false-positive rates of 5% (training) and 7% (test), dramatically decreasing the number of cases needing additional mutation evaluation. This approach leveraged the differences between gene and pseudogene to distinguish between PMS2 and PMS2CL copy-number mutations. These methods enable efficient and sensitive Lynch syndrome screening for 3' PMS2 copy-number mutations and may be applied similarly to other genomic regions with highly homologous pseudogenes.
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Affiliation(s)
- Daniel S Herman
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Laboratory Medicine, University of Washington, Seattle, Washington.
| | - Christina Smith
- Department of Laboratory Medicine, University of Washington, Seattle, Washington
| | - Chang Liu
- Department of Laboratory Medicine, University of Washington, Seattle, Washington
| | | | - Selvi Palaniappan
- Department of Clinical Genomics, Ambry Genetics, Aliso Viejo, California
| | - Colin C Pritchard
- Department of Laboratory Medicine, University of Washington, Seattle, Washington
| | - Brian H Shirts
- Department of Laboratory Medicine, University of Washington, Seattle, Washington
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27
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Kerkhof J, Schenkel LC, Reilly J, McRobbie S, Aref-Eshghi E, Stuart A, Rupar CA, Adams P, Hegele RA, Lin H, Rodenhiser D, Knoll J, Ainsworth PJ, Sadikovic B. Clinical Validation of Copy Number Variant Detection from Targeted Next-Generation Sequencing Panels. J Mol Diagn 2017; 19:905-920. [DOI: 10.1016/j.jmoldx.2017.07.004] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 06/13/2017] [Accepted: 07/31/2017] [Indexed: 01/05/2023] Open
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28
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Screening for germline mutations in mismatch repair genes in patients with Lynch syndrome by next generation sequencing. Fam Cancer 2017; 17:387-394. [DOI: 10.1007/s10689-017-0043-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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29
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Yohe S, Thyagarajan B. Review of Clinical Next-Generation Sequencing. Arch Pathol Lab Med 2017; 141:1544-1557. [PMID: 28782984 DOI: 10.5858/arpa.2016-0501-ra] [Citation(s) in RCA: 203] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
CONTEXT - Next-generation sequencing (NGS) is a technology being used by many laboratories to test for inherited disorders and tumor mutations. This technology is new for many practicing pathologists, who may not be familiar with the uses, methodology, and limitations of NGS. OBJECTIVE - To familiarize pathologists with several aspects of NGS, including current and expanding uses; methodology including wet bench aspects, bioinformatics, and interpretation; validation and proficiency; limitations; and issues related to the integration of NGS data into patient care. DATA SOURCES - The review is based on peer-reviewed literature and personal experience using NGS in a clinical setting at a major academic center. CONCLUSIONS - The clinical applications of NGS will increase as the technology, bioinformatics, and resources evolve to address the limitations and improve quality of results. The challenge for clinical laboratories is to ensure testing is clinically relevant, cost-effective, and can be integrated into clinical care.
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Affiliation(s)
- Sophia Yohe
- From the Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis
| | - Bharat Thyagarajan
- From the Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis
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30
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Zampieri S, Cattarossi S, Bembi B, Dardis A. GBA Analysis in Next-Generation Era: Pitfalls, Challenges, and Possible Solutions. J Mol Diagn 2017; 19:733-741. [PMID: 28727984 DOI: 10.1016/j.jmoldx.2017.05.005] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 04/21/2017] [Accepted: 05/19/2017] [Indexed: 01/11/2023] Open
Abstract
Mutations in the gene encoding the lysosomal enzyme acid β-glucosidase (GBA) are responsible for Gaucher disease and represent the main genetic risk factor for developing Parkinson disease. In past years, next-generation sequencing (NGS) technology has been applied for the molecular analysis of the GBA gene, both as a single gene or as part of gene panels. However, the presence of complex gene-pseudogene rearrangements, resulting from the presence of a highly homologous pseudogene (GBAP1) located downstream of the GBA gene, makes NGS analysis of GBA challenging. Therefore, adequate strategies should be adopted to avoid misdetection of GBA recombinant mutations. Here, we validated a strategy for the identification of GBA mutations using parallel massive sequencing and provide an overview of the major drawbacks encountered during GBA analysis by NGS. We implemented a NGS workflow, using a set of 38 patients with Gaucher disease carrying different GBA alleles identified previously by Sanger sequencing. As expected, the presence of the pseudogene significantly affected data output. However, the combination of specific procedures for the library preparation and data analysis resulted in maximal repeatability and reproducibility, and a robust performance with 97% sensitivity and 100% specificity. In conclusion, the pipeline described here represents a useful approach to deal with GBA sequencing using NGS technology.
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Affiliation(s)
- Stefania Zampieri
- Regional Coordinator Centre for Rare Diseases, Academic Hospital Santa Maria della Misericordia, Udine, Italy
| | - Silvia Cattarossi
- Regional Coordinator Centre for Rare Diseases, Academic Hospital Santa Maria della Misericordia, Udine, Italy
| | - Bruno Bembi
- Regional Coordinator Centre for Rare Diseases, Academic Hospital Santa Maria della Misericordia, Udine, Italy
| | - Andrea Dardis
- Regional Coordinator Centre for Rare Diseases, Academic Hospital Santa Maria della Misericordia, Udine, Italy.
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31
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Germline Mutations in MLH1 Leading to Isolated Loss of PMS2 Expression in Lynch Syndrome: Implications for Diagnostics in the Clinic. Am J Surg Pathol 2017; 41:861-864. [DOI: 10.1097/pas.0000000000000827] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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32
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Rey JM, Ducros V, Pujol P, Wang Q, Buisine MP, Aissaoui H, Maudelonde T, Olschwang S. Improving Mutation Screening in Patients with Colorectal Cancer Predisposition Using Next-Generation Sequencing. J Mol Diagn 2017; 19:589-601. [PMID: 28502729 DOI: 10.1016/j.jmoldx.2017.04.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 03/03/2017] [Accepted: 04/10/2017] [Indexed: 12/25/2022] Open
Abstract
Identification of genetic alterations is important for family risk assessment in colorectal cancers. Next-generation sequencing (NGS) technologies provide useful tools for single-nucleotide and copy number variation (CNV) identification in many genes and samples simultaneously. Herein, we present the validation of current Multiplicom MASTR designs of mismatch repair combined to familial adenomatous polyposis genes in a single PCR reamplification test for eight DNA samples simultaneously on a MiSeq apparatus. Blood samples obtained from 224 patients were analyzed. We correctly identified the 97 mutations selected among 48 samples tested in a validation cohort. PMS2 NGS analysis of the eight positive controls identified single-nucleotide variations not detected with targeted referent methods. As NGS method could not discriminate if some of them were assigned to PMS2 or pseudogenes, only CNV analysis with multiplex ligand probe-dependent amplification confirmation was retained for clinical use. Twenty-seven new variants of unknown significance, 21 disease-causing variants, and two CNVs were detected among the 176 patient samples analyzed in diagnosis routine. MUTYH disease-causing mutations were identified in two patient samples assessed for mismatch repair testing, confirming that this method facilitates accurate and rapid individual risk assessments. In one sample, the MUTYH mutation was associated with a MSH6 disease-causing mutation, suggesting that this method is helpful to identify additional cancer risk modifiers and provides a useful tool to optimize clinical issues.
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Affiliation(s)
- Jean-Marc Rey
- Laboratoire de Biopathologie Cellulaire et Tissulaire des Tumeurs, Arnaud de Villeneuve Hospital, Montpellier, France.
| | - Vincent Ducros
- Laboratoire de Biopathologie Cellulaire et Tissulaire des Tumeurs, Arnaud de Villeneuve Hospital, Montpellier, France
| | - Pascal Pujol
- Oncogenetic Department, Arnaud de Villeneuve Hospital, Montpellier, France
| | - Qing Wang
- Laboratoire de Génétique Constitutionnelle des Cancers Fréquents, Léon Bérard Center, Lyon, France
| | - Marie-Pierre Buisine
- Laboratoire de Biochimie et Biologie Moléculaire, Oncologie et Génétique Moléculaire, Center de Biologie Pathologie, CHRU Lille, Lille, France
| | | | - Thierry Maudelonde
- Laboratoire de Biopathologie Cellulaire et Tissulaire des Tumeurs, Arnaud de Villeneuve Hospital, Montpellier, France; Montpellier University, EA2415, Institut Universitaire de Recherche Clinique, Montpellier, France
| | - Sylviane Olschwang
- INSERM UMR_S910, Aix-Marseille University, Ramsay Générale de Santé Clairval Hospital, Marseille, France
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33
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van der Klift HM, Mensenkamp AR, Drost M, Bik EC, Vos YJ, Gille HJJP, Redeker BEJW, Tiersma Y, Zonneveld JBM, García EG, Letteboer TGW, Olderode-Berends MJW, van Hest LP, van Os TA, Verhoef S, Wagner A, van Asperen CJ, Ten Broeke SW, Hes FJ, de Wind N, Nielsen M, Devilee P, Ligtenberg MJL, Wijnen JT, Tops CMJ. Comprehensive Mutation Analysis of PMS2 in a Large Cohort of Probands Suspected of Lynch Syndrome or Constitutional Mismatch Repair Deficiency Syndrome. Hum Mutat 2016; 37:1162-1179. [PMID: 27435373 DOI: 10.1002/humu.23052] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 07/06/2016] [Accepted: 07/07/2016] [Indexed: 01/01/2023]
Abstract
Monoallelic PMS2 germline mutations cause 5%-15% of Lynch syndrome, a midlife cancer predisposition, whereas biallelic PMS2 mutations cause approximately 60% of constitutional mismatch repair deficiency (CMMRD), a rare childhood cancer syndrome. Recently improved DNA- and RNA-based strategies are applied to overcome problematic PMS2 mutation analysis due to the presence of pseudogenes and frequent gene conversion events. Here, we determined PMS2 mutation detection yield and mutation spectrum in a nationwide cohort of 396 probands. Furthermore, we studied concordance between tumor IHC/MSI (immunohistochemistry/microsatellite instability) profile and mutation carrier state. Overall, we found 52 different pathogenic PMS2 variants explaining 121 Lynch syndrome and nine CMMRD patients. In vitro mismatch repair assays suggested pathogenicity for three missense variants. Ninety-one PMS2 mutation carriers (70%) showed isolated loss of PMS2 in their tumors, for 31 (24%) no or inconclusive IHC was available, and eight carriers (6%) showed discordant IHC (presence of PMS2 or loss of both MLH1 and PMS2). Ten cases with isolated PMS2 loss (10%; 10/97) harbored MLH1 mutations. We confirmed that recently improved mutation analysis provides a high yield of PMS2 mutations in patients with isolated loss of PMS2 expression. Application of universal tumor prescreening methods will however miss some PMS2 germline mutation carriers.
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Affiliation(s)
- Heleen M van der Klift
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands. .,Department of Human Genetics, Leiden University Medical Centre, Leiden, The Netherlands.
| | - Arjen R Mensenkamp
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Mark Drost
- Department of Human Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Elsa C Bik
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Yvonne J Vos
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Hans J J P Gille
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
| | - Bert E J W Redeker
- Department of Clinical Genetics, Academic Medical Centre, Amsterdam, The Netherlands
| | - Yvonne Tiersma
- Department of Human Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - José B M Zonneveld
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Encarna Gómez García
- Department of Clinical Genetics, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Tom G W Letteboer
- Department of Medical Genetics, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Maran J W Olderode-Berends
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Liselotte P van Hest
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
| | - Theo A van Os
- Department of Clinical Genetics, Academic Medical Centre, Amsterdam, The Netherlands
| | - Senno Verhoef
- Netherlands Cancer Institute, Amsterdam, The Netherlands.,Clinical Genetics Service, Saint Mary's Hospital, Central Manchester University Hospitals NHS Foundation Trust, Manchester, United Kingdom
| | - Anja Wagner
- Department of Clinical Genetics, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Christi J van Asperen
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Sanne W Ten Broeke
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Frederik J Hes
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Niels de Wind
- Department of Human Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Maartje Nielsen
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Peter Devilee
- Department of Human Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Marjolijn J L Ligtenberg
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Juul T Wijnen
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands.,Department of Human Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Carli M J Tops
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
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Abou Tayoun AN, Krock B, Spinner NB. Sequencing-based diagnostics for pediatric genetic diseases: progress and potential. Expert Rev Mol Diagn 2016; 16:987-99. [PMID: 27388938 DOI: 10.1080/14737159.2016.1209411] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
INTRODUCTION The last two decades have witnessed revolutionary changes in clinical diagnostics, fueled by the Human Genome Project and advances in high throughput, Next Generation Sequencing (NGS). We review the current state of sequencing-based pediatric diagnostics, associated challenges, and future prospects. AREAS COVERED We present an overview of genetic disease in children, review the technical aspects of Next Generation Sequencing and the strategies to make molecular diagnoses for children with genetic disease. We discuss the challenges of genomic sequencing including incomplete current knowledge of variants, lack of data about certain genomic regions, mosaicism, and the presence of regions with high homology. Expert commentary: NGS has been a transformative technology and the gap between the research and clinical communities has never been so narrow. Therapeutic interventions are emerging based on genomic findings and the applications of NGS are progressing to prenatal genetics, epigenomics and transcriptomics.
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Affiliation(s)
- Ahmad N Abou Tayoun
- a Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine , The Children's Hospital of Philadelphia , Philadelphia , PA , USA.,b The Perelman School of Medicine , The University of Pennsylvania , Philadelphia , PA , USA
| | - Bryan Krock
- a Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine , The Children's Hospital of Philadelphia , Philadelphia , PA , USA.,b The Perelman School of Medicine , The University of Pennsylvania , Philadelphia , PA , USA
| | - Nancy B Spinner
- a Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine , The Children's Hospital of Philadelphia , Philadelphia , PA , USA.,b The Perelman School of Medicine , The University of Pennsylvania , Philadelphia , PA , USA
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