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Mendes C, Loureiro T, Villela D, Bittencourt MI, Sobreira J, Bermeo D, Gomes M, Alencar D, de Castro LSS, Fock RA, Tinoco ML, Galvão H, Scapulatempo-Neto C, Schiavetti K, Senerchia AA, Gurgel MHC. Germline variant analysis from a cohort of patients with severe hypertriglyceridemia in Brazil. Mol Genet Metab Rep 2024; 40:101100. [PMID: 38933898 PMCID: PMC11201343 DOI: 10.1016/j.ymgmr.2024.101100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 05/26/2024] [Accepted: 05/28/2024] [Indexed: 06/28/2024] Open
Abstract
Hypertriglyceridemia (HTG) is a common dyslipidemia associated with an increased risk of cardiovascular disease and pancreatitis. It is well stablished that the severe cases of disease often present with an underlying genetic cause. In this study, we determined the frequency and variation spectrum of genes involved in the triglyceride metabolism in a series of Brazilian patients with severe HTG. A total of 212 patients with very high HTG, defined with fasting triglycerides (TG) ≥ 880 mg/ dL, that underwent a multi-gene panel testing were included in this research. Germline deleterious variants (i.e. Pathogenic/Likely Pathogenic (P/LP) variants) were identified in 28 out of 212 patients, reflecting an overall diagnostic yield of 13% in our cohort. Variants of unknown significance (VUS) were identified in 87 patients, and represent 80% of detected variants in this dataset. We confirm the LPL as the most frequently mutated gene in patients with severe HTG, and we had only one suspected case of familial chylomicronemia syndrome, caused by a homozygous variant in LMF1, in our cohort. Notably, we report 16 distinct and novel variants (P/LP and VUS), each of them representing a single case, not previously reported in any public databases or other studies. Our data expand our knowledge of genetic variation spectrum in patients with severe HTG in the Brazilian population, often underrepresented in public genomic databases, being also a valuable clinical resource for genetic counseling and healthcare programs in the country.
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Affiliation(s)
- Camila Mendes
- Diagnósticos da América S.A., DASA, São Paulo, SP, Brazil
| | | | - Darine Villela
- Diagnósticos da América S.A., DASA, São Paulo, SP, Brazil
| | | | | | - Diana Bermeo
- Diagnósticos da América S.A., DASA, São Paulo, SP, Brazil
| | - Mireille Gomes
- Diagnósticos da América S.A., DASA, São Paulo, SP, Brazil
| | - Dayse Alencar
- Diagnósticos da América S.A., DASA, São Paulo, SP, Brazil
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2
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Saxton S, Kontorovich AR, Wang D, Zhou B, Um SY, Lin Y, Rojas L, Tyll E, Dickinson G, Stram M, Harris CK, Gelb BD, Sampson BA, Graham JK, Tang Y. Cardiac genetic test yields and genotype-phenotype correlations from large cohort investigated by medical examiner's office. Cardiovasc Pathol 2024; 72:107654. [PMID: 38777137 DOI: 10.1016/j.carpath.2024.107654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 04/26/2024] [Accepted: 05/16/2024] [Indexed: 05/25/2024] Open
Abstract
BACKGROUND Few reports describe the yield of postmortem genetic testing from medical examiners' offices or correlate genetic test results with autopsy-confirmed phenotypes from a large cohort. OBJECTIVES To report results from cardiomyopathy- and cardiac arrhythmia-associated genetic testing in conjunction with autopsy findings of cases investigated at the United States' largest medical examiner office. METHODS Postmortem cases tested from 2015 to 2022 with a cardiomyopathy- and cardiac arrhythmia-associated gene panel were reviewed. American College of Medical Genetics and Genomics/Association for Molecular Pathology guidelines were used to classify variant pathogenicity. Correlations of pathogenic/likely pathogenic variants (P/LPVs) with cardiac pathology were evaluated. RESULTS The cohort included 1107 decedents of diverse ages and ethnicities. P/LPVs were detected in 87 (7.9%) cases, with 73 and 14 variants in cardiomyopathy and cardiac arrhythmia genes, respectively. Variants of uncertain significance were detected in 437 (39.5%) cases. The diagnostic yield (percentage of P/LPV) in decedents with cardiomyopathy (26.1%) was significantly higher than those without (P<.0001). The diagnostic yield was significantly lower in infants (0.7%) than older age groups (ranging from 1 to 74 years old, 5.7%-25.9%), which had no statistical difference between their yields. The diagnostic yields by cardiac autopsy findings were 54.0% for hypertrophic cardiomyopathy, 47.1% for arrhythmogenic cardiomyopathy, 20.0% for myocardial fibrosis, 19.0% for dilated cardiomyopathy, and 11.3% for myocarditis. Most P/LPVs were in MYBPC3, TTN, PKP2, SCN5A, MYH7, and FLNC. Ten P/LPVs were novel. CONCLUSIONS Our results support the importance of performing postmortem genetic testing on decedents of all ages with cardiomyopathy, cardiac lesions insufficient to diagnosis a specific cardiomyopathy (e.g., myocardial fibrosis), and myocarditis. Combined postmortem cardiac examination and genetic analysis are advantageous in accurately determining the underlying cause of death and informing effective clinical care of family members.
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Affiliation(s)
- Sarah Saxton
- Molecular Genetics Laboratory, New York City Office of Chief Medical Examiner, 421 East 26th Street, New York, NY, 10016
| | - Amy R Kontorovich
- Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1014, New York, NY, 10029
| | - Dawei Wang
- Molecular Genetics Laboratory, New York City Office of Chief Medical Examiner, 421 East 26th Street, New York, NY, 10016
| | - Bo Zhou
- Molecular Genetics Laboratory, New York City Office of Chief Medical Examiner, 421 East 26th Street, New York, NY, 10016
| | - Sung Yon Um
- Molecular Genetics Laboratory, New York City Office of Chief Medical Examiner, 421 East 26th Street, New York, NY, 10016
| | - Ying Lin
- Molecular Genetics Laboratory, New York City Office of Chief Medical Examiner, 421 East 26th Street, New York, NY, 10016
| | - Lisa Rojas
- Molecular Genetics Laboratory, New York City Office of Chief Medical Examiner, 421 East 26th Street, New York, NY, 10016
| | - Erin Tyll
- Molecular Genetics Laboratory, New York City Office of Chief Medical Examiner, 421 East 26th Street, New York, NY, 10016
| | - Gregory Dickinson
- Department of Forensic Pathology, New York City Office of Chief Medical Examiner, 421 East 26th Street, New York, NY, 10016
| | - Michelle Stram
- Department of Forensic Pathology, New York City Office of Chief Medical Examiner, 421 East 26th Street, New York, NY, 10016
| | - Cynthia K Harris
- Department of Forensic Pathology, New York City Office of Chief Medical Examiner, 421 East 26th Street, New York, NY, 10016
| | - Bruce D Gelb
- Mindich Child Health and Development Institute, Department of Pediatrics, and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1014, New York, NY, 10029
| | - Barbara A Sampson
- Department of Forensic Pathology, New York City Office of Chief Medical Examiner, 421 East 26th Street, New York, NY, 10016
| | - Jason K Graham
- Department of Forensic Pathology, New York City Office of Chief Medical Examiner, 421 East 26th Street, New York, NY, 10016
| | - Yingying Tang
- Molecular Genetics Laboratory, New York City Office of Chief Medical Examiner, 421 East 26th Street, New York, NY, 10016.
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3
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Fussiger H, Lima PLGSB, Souza PVS, Freua F, Husny ASE, Leão EKEA, Braga-Neto P, Kok F, Lynch DS, Saute JAM, Nóbrega PR. Clinicogenetic characterization of cerebrotendinous xanthomatosis in Brazil. Clin Genet 2024. [PMID: 39099467 DOI: 10.1111/cge.14602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 07/12/2024] [Accepted: 07/21/2024] [Indexed: 08/06/2024]
Abstract
There are few cerebrotendineous xanthomatosis (CTX) case series and observational studies including a significant number of Latin American patients. We describe a multicenter Brazilian cohort of patients with CTX highlighting their clinical phenotype, recurrent variants and assessing possible genotype-phenotype correlations. We analyzed data from all patients with clinical and molecular or biochemical diagnosis of CTX regularly followed at six genetics reference centers in Brazil between March 2020 and August 2023. We evaluated 38 CTX patients from 26 families, originating from 4 different geographical regions in Brazil. Genetic analysis identified 13 variants in the CYP27A1 gene within our population, including 3 variants that had not been previously described. The most frequent initial symptom of CTX in Brazil was cataract (27%), followed by xanthomas (24%), chronic diarrhea (13.5%), and developmental delay (13.5%). We observed that the median age at loss of ambulation correlates with the age of onset of neurological symptoms, with an average interval of 10 years (interquartile range 6.9 to 11 years). This study represents the largest CTX case series ever reported in South America. We describe phenotypic characteristics and report three new pathogenic or likely pathogenic variants.
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Affiliation(s)
- Helena Fussiger
- Graduate Program in Medicine: Medical Sciences, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | | | - Paulo V S Souza
- Neurometabolic Unit, Division of Neuromuscular Diseases, Department of Neurology and Neurosurgery, Federal University of São Paulo, São Paulo, Brazil
| | - Fernando Freua
- Clinics Hospital, Faculty of Medicine, University of Sao Paulo, São Paulo, Brazil
- Neurology Department, Beneficência Portuguesa Hospital, São Paulo, Brazil
| | - Antonette S E Husny
- Hospital Universitário Bettina Ferro de Souza, Universidade Federal do Pará, Belém, Brazil
| | - Emília K E A Leão
- University Hospital Complex Prof. Edgard Santos, Universidade Federal da Bahia, Salvador, Brazil
| | - Pedro Braga-Neto
- Division of Neurology, Federal University of Ceara, Fortaleza, Brazil
- Center of Health Sciences, State University of Ceara, Fortaleza, Brazil
| | - Fernando Kok
- Neurogenetics Unit, Department of Neurology, School of Medicine of Universidade de São Paulo, São Paulo, Brazil
| | - David S Lynch
- Department of Neuromuscular Disease, UCL Institute of Neurology, London, UK
- The Leonard Wolfson Experimental Neurology Centre, National Hospital for Neurology & Neurosurgery, London, UK
| | - Jonas A M Saute
- Graduate Program in Medicine: Medical Sciences, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
- Neurology Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
- Department of Internal Medicine, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Paulo R Nóbrega
- Division of Neurology, Federal University of Ceara, Fortaleza, Brazil
- Campus Parque Ecológico, Centro Universitário Christus, Fortaleza, Brazil
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Pak CM, Gilmore MJ, Bulkley JE, Chakraborty P, Dagan-Rosenfeld O, Foreman AKM, Gollob MH, Jenkins CL, Katz AE, Lee K, Meeks N, O'Daniel JM, Posey JE, Rego SM, Shah N, Steiner RD, Stergachis AB, Subramanian SL, Trotter T, Wallace K, Williams MS, Goddard KAB, Buchanan AH, Manickam K, Powell B, Ezzell Hunter J. Implementing evidence-based assertions of clinical actionability in the context of secondary findings: Updates from the ClinGen Actionability Working Group. Genet Med 2024; 26:101164. [PMID: 38757444 PMCID: PMC11298308 DOI: 10.1016/j.gim.2024.101164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 05/07/2024] [Accepted: 05/08/2024] [Indexed: 05/18/2024] Open
Abstract
PURPOSE The ClinGen Actionability Working Group (AWG) developed an evidence-based framework to generate actionability reports and scores of gene-condition pairs in the context of secondary findings from genome sequencing. Here we describe the expansion of the framework to include actionability assertions. METHODS Initial development of the actionability rubric was based on previously scored adult gene-condition pairs and individual expert evaluation. Rubric refinement was iterative and based on evaluation, feedback, and discussion. The final rubric was pragmatically evaluated via integration into actionability assessments for 27 gene-condition pairs. RESULTS The resulting rubric has a 4-point scale (limited, moderate, strong, and definitive) and uses the highest-scoring outcome-intervention pair of each gene-condition pair to generate a preliminary assertion. During AWG discussions, predefined criteria and factors guide discussion to produce a consensus assertion for a gene-condition pair, which may differ from the preliminary assertion. The AWG has retrospectively generated assertions for all previously scored gene-condition pairs and are prospectively asserting on gene-condition pairs under assessment, having completed over 170 adult and 188 pediatric gene-condition pairs. CONCLUSION The AWG expanded its framework to provide actionability assertions to enhance the clinical value of their resources and increase their utility as decision aids regarding return of secondary findings.
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Affiliation(s)
- Christine M Pak
- Department of Translational and Applied Genomics, Kaiser Permanente Center for Health Research, Portland, OR.
| | - Marian J Gilmore
- Department of Translational and Applied Genomics, Kaiser Permanente Center for Health Research, Portland, OR
| | - Joanna E Bulkley
- Department of Translational and Applied Genomics, Kaiser Permanente Center for Health Research, Portland, OR
| | - Pranesh Chakraborty
- Newborn Screening Ontario, Children's Hospital of Eastern Ontario, and Division of Metabolics University of Ottawa, Ottawa, ON, Canada
| | | | | | - Michael H Gollob
- Division of Cardiology, University of Toronto, Toronto, ON, Canada
| | - Charisma L Jenkins
- Department of Translational and Applied Genomics, Kaiser Permanente Center for Health Research, Portland, OR
| | - Alexander E Katz
- Division of Internal Medicine, University of Michigan, Ann Arbor, MI
| | - Kristy Lee
- Department of Genetics, University of North Carolina, Chapel Hill, NC
| | - Naomi Meeks
- Section of Genetics, Department of Pediatrics, University of Colorado, Aurora, CO
| | | | - Jennifer E Posey
- Molecular and Human Genetics Department, Baylor College of Medicine, Houston, TX
| | - Shannon M Rego
- Institute for Human Genetics, University of California, San Francisco, CA
| | - Neethu Shah
- Molecular and Human Genetics Department, Baylor College of Medicine, Houston, TX
| | - Robert D Steiner
- University of Wisconsin and Marshfield Clinic, Marshfield and Madison, WI
| | - Andrew B Stergachis
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA
| | - Sai Lakshmi Subramanian
- Molecular and Human Genetics Department, Baylor College of Medicine, Houston, TX; Roche Diagnostics, Santa Clara, CA
| | - Tracy Trotter
- Department of Pediatrics, John Muir Health, Walnut Creek, CA
| | - Kathleen Wallace
- Department of Genetics, University of North Carolina, Chapel Hill, NC
| | | | - Katrina A B Goddard
- Department of Translational and Applied Genomics, Kaiser Permanente Center for Health Research, Portland, OR
| | | | - Kandamurugu Manickam
- Department of Pediatrics, Nationwide Children's Hospital and The Ohio State University College of Medicine, Columbus, OH
| | - Bradford Powell
- Department of Genetics, University of North Carolina, Chapel Hill, NC
| | - Jessica Ezzell Hunter
- Genomics, Ethics, and Translational Research Program, RTI International, Research Triangle Park, NC
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5
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Shubina J, Tolmacheva E, Maslennikov D, Kochetkova T, Mukosey I, Sadelov I, Goltsov A, Barkov I, Ekimov A, Rogacheva M, Stupko O, Pavlova N, Kuznetsova M, Dokshukina A, Vasiliev G, Bolshakova A, Kovalskaia V, Korovko A, Pomerantseva E, Tsabai P, Buyanovskaya O, Zaretskaya N, Karetnikova N, Grebenshchikova E, Degtyareva A, Bokerija E, Kholin A, Rebrikov D, Degtyarev D, Trofimov D, Sukhih G. WES-based screening of 7,000 newborns: A pilot study in Russia. HGG ADVANCES 2024; 5:100334. [PMID: 39033325 DOI: 10.1016/j.xhgg.2024.100334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 07/17/2024] [Accepted: 07/16/2024] [Indexed: 07/23/2024] Open
Abstract
The effective implementation of whole-exome sequencing- and whole-genome sequencing-based diagnostics in the management of children affected with genetic diseases and the rapid decrease in the cost of next-generation sequencing (NGS) enables the expansion of this method to newborn genetic screening programs. Such NGS-based screening greatly increases the number of diseases that can be detected compared to conventional newborn screening, as the latter is aimed at early detection of a limited number of inborn diseases. Moreover, genetic testing provides new possibilities for family members of the proband, as many variants responsible for adult-onset conditions are inherited from the parents. However, the idea of NGS-based screening in healthy children raises issues of medical and ethical integrity as well as technical questions, including interpretation of the observed variants. Pilot studies have shown that both parents and medical professionals have moved forward and are enthused about these new possibilities. However, either the number of participants or the number of genes studied in previous investigations thus far has been limited to a few hundred, restricting the scope of potential findings. Our current study (NCT05325749) includes 7,000 apparently healthy infants born at our center between February 2021 and May 2023, who were screened for pathogenic variants in 2,350 genes. Clinically significant variants associated with early-onset diseases that can be treated, prevented, or where symptoms can be alleviated with timely introduced symptomatic therapy, were observed in 0.9% of phenotypically normal infants, 2.1% of the screened newborns were found to carry variants associated with reduced penetrance or monogenic diseases of adult-onset and/or variable expressivity, and 0.3% had chromosomal abnormalities. Here, we report our results and address questions regarding the interpretation of variants in newborns who were presumed to be healthy.
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Affiliation(s)
- Jekaterina Shubina
- National Medical Research Center for Obstetrics, Gynecology, and Perinatology of the Ministry of Health of the Russian Federation, 117198 Moscow, Russia.
| | - Ekaterina Tolmacheva
- National Medical Research Center for Obstetrics, Gynecology, and Perinatology of the Ministry of Health of the Russian Federation, 117198 Moscow, Russia
| | - Dmitry Maslennikov
- National Medical Research Center for Obstetrics, Gynecology, and Perinatology of the Ministry of Health of the Russian Federation, 117198 Moscow, Russia
| | - Taisiya Kochetkova
- National Medical Research Center for Obstetrics, Gynecology, and Perinatology of the Ministry of Health of the Russian Federation, 117198 Moscow, Russia
| | - Irina Mukosey
- National Medical Research Center for Obstetrics, Gynecology, and Perinatology of the Ministry of Health of the Russian Federation, 117198 Moscow, Russia
| | - Igor Sadelov
- National Medical Research Center for Obstetrics, Gynecology, and Perinatology of the Ministry of Health of the Russian Federation, 117198 Moscow, Russia
| | - Andrey Goltsov
- National Medical Research Center for Obstetrics, Gynecology, and Perinatology of the Ministry of Health of the Russian Federation, 117198 Moscow, Russia
| | - Ilya Barkov
- National Medical Research Center for Obstetrics, Gynecology, and Perinatology of the Ministry of Health of the Russian Federation, 117198 Moscow, Russia
| | - Aleksey Ekimov
- National Medical Research Center for Obstetrics, Gynecology, and Perinatology of the Ministry of Health of the Russian Federation, 117198 Moscow, Russia
| | - Margarita Rogacheva
- National Medical Research Center for Obstetrics, Gynecology, and Perinatology of the Ministry of Health of the Russian Federation, 117198 Moscow, Russia
| | - Olga Stupko
- National Medical Research Center for Obstetrics, Gynecology, and Perinatology of the Ministry of Health of the Russian Federation, 117198 Moscow, Russia
| | - Nadezhda Pavlova
- National Medical Research Center for Obstetrics, Gynecology, and Perinatology of the Ministry of Health of the Russian Federation, 117198 Moscow, Russia
| | - Maria Kuznetsova
- National Medical Research Center for Obstetrics, Gynecology, and Perinatology of the Ministry of Health of the Russian Federation, 117198 Moscow, Russia
| | - Alina Dokshukina
- National Medical Research Center for Obstetrics, Gynecology, and Perinatology of the Ministry of Health of the Russian Federation, 117198 Moscow, Russia
| | - Grigory Vasiliev
- National Medical Research Center for Obstetrics, Gynecology, and Perinatology of the Ministry of Health of the Russian Federation, 117198 Moscow, Russia
| | - Anna Bolshakova
- National Medical Research Center for Obstetrics, Gynecology, and Perinatology of the Ministry of Health of the Russian Federation, 117198 Moscow, Russia
| | - Valeriia Kovalskaia
- National Medical Research Center for Obstetrics, Gynecology, and Perinatology of the Ministry of Health of the Russian Federation, 117198 Moscow, Russia
| | - Anastasia Korovko
- National Medical Research Center for Obstetrics, Gynecology, and Perinatology of the Ministry of Health of the Russian Federation, 117198 Moscow, Russia
| | - Ekaterina Pomerantseva
- National Medical Research Center for Obstetrics, Gynecology, and Perinatology of the Ministry of Health of the Russian Federation, 117198 Moscow, Russia
| | - Polina Tsabai
- National Medical Research Center for Obstetrics, Gynecology, and Perinatology of the Ministry of Health of the Russian Federation, 117198 Moscow, Russia
| | - Olga Buyanovskaya
- National Medical Research Center for Obstetrics, Gynecology, and Perinatology of the Ministry of Health of the Russian Federation, 117198 Moscow, Russia
| | - Nadezhda Zaretskaya
- National Medical Research Center for Obstetrics, Gynecology, and Perinatology of the Ministry of Health of the Russian Federation, 117198 Moscow, Russia
| | - Natalia Karetnikova
- National Medical Research Center for Obstetrics, Gynecology, and Perinatology of the Ministry of Health of the Russian Federation, 117198 Moscow, Russia
| | | | - Anna Degtyareva
- National Medical Research Center for Obstetrics, Gynecology, and Perinatology of the Ministry of Health of the Russian Federation, 117198 Moscow, Russia
| | - Ekaterina Bokerija
- National Medical Research Center for Obstetrics, Gynecology, and Perinatology of the Ministry of Health of the Russian Federation, 117198 Moscow, Russia
| | - Alexey Kholin
- National Medical Research Center for Obstetrics, Gynecology, and Perinatology of the Ministry of Health of the Russian Federation, 117198 Moscow, Russia
| | - Denis Rebrikov
- National Medical Research Center for Obstetrics, Gynecology, and Perinatology of the Ministry of Health of the Russian Federation, 117198 Moscow, Russia; Pirogov Russian National Research Medical University, Moscow 117997, Russia
| | - Dmitry Degtyarev
- National Medical Research Center for Obstetrics, Gynecology, and Perinatology of the Ministry of Health of the Russian Federation, 117198 Moscow, Russia
| | - Dmitriy Trofimov
- National Medical Research Center for Obstetrics, Gynecology, and Perinatology of the Ministry of Health of the Russian Federation, 117198 Moscow, Russia
| | - Gennady Sukhih
- National Medical Research Center for Obstetrics, Gynecology, and Perinatology of the Ministry of Health of the Russian Federation, 117198 Moscow, Russia
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Elfatih A, Saad C, Mifsud B, Mbarek H. Analysis of 14,392 whole genomes reveals 3.5% of Qataris carry medically actionable variants. Eur J Hum Genet 2024:10.1038/s41431-024-01656-1. [PMID: 39020067 DOI: 10.1038/s41431-024-01656-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 06/05/2024] [Accepted: 06/19/2024] [Indexed: 07/19/2024] Open
Abstract
Arabic populations are underrepresented in large genome projects; therefore, the frequency of clinically actionable variants among Arabs is largely unknown. Here, we investigated genetic variation in 14,392 whole genomes from the Qatar Genome Program (QGP) across the list of 78 actionable genes (v3.1) determined by the American College of Medical Genetics and Genomics (ACMG). Variants were categorized into one of the following groups: (1) Pathogenic (P), (2) Likely pathogenic (LP), and (3) Rare variants of uncertain significance with evidence of pathogenicity. For the classification, we used variant databases, effect predictors, and the disease-relevant phenotypes available for the cohort. Data on cardiovascular disease, cancer, and hypercholesterolemia allowed us to assess the disease-relevant phenotype association of rare missense variants. We identified 248 distinct variants in 50 ACMG genes that fulfilled our criteria to be included in one of the three groups affecting 1036 genotype-positive participants of the QGP cohort. The most frequent variants were in TTN, followed by RYR1 and ATP7B. The prevalence of reportable secondary findings was 3.5%. A further 46 heterozygous variants in six genes with an autosomal recessive mode of inheritance were detected in 200 individuals, accounting for an additional 1.4%. Altogether, they affect 5% of the population. Due to the high consanguinity rate in the QGP cohort (28% in spouses and 60% in parents), P and LP variants both in genes with dominant and recessive inheritance are important for developing better treatment options and preventive strategies in Qatar and the Arabic population of the Middle East.
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Affiliation(s)
- Amal Elfatih
- Hamad Bin Khalifa University, College of Health and Life Science, Genomics and Precision Medicine, Doha, Qatar
| | - Chadi Saad
- Qatar Genome Program, Qatar Foundation, Qatar Science and Technology Park, Innovation Center, Doha, Qatar
| | - Borbala Mifsud
- Hamad Bin Khalifa University, College of Health and Life Science, Genomics and Precision Medicine, Doha, Qatar.
- William Harvey Research Institute, Queen Mary University London, London, UK.
| | - Hamdi Mbarek
- Qatar Genome Program, Qatar Foundation, Qatar Science and Technology Park, Innovation Center, Doha, Qatar.
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7
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Xue H, Yu A, Chen L, Guo Q, Zhang L, Lin N, Chen X, Xu L, Huang H. Prenatal genetic diagnosis of fetuses with dextrocardia using whole exome sequencing in a tertiary center. Sci Rep 2024; 14:16266. [PMID: 39009665 PMCID: PMC11251054 DOI: 10.1038/s41598-024-67164-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 07/09/2024] [Indexed: 07/17/2024] Open
Abstract
To evaluate the genetic etiology of fetal dextrocardia, associated ultrasound anomalies, and perinatal outcomes, we investigated the utility of whole exome sequencing (WES) for prenatal diagnosis of dextrocardia. Fetuses with dextrocardia were prospectively collected between January 2016 and December 2022. Trio-WES was performed on fetuses with dextrocardia, following normal karyotyping and/or chromosomal microarray analysis (CMA) results. A total of 29 fetuses with dextrocardia were collected, including 27 (93.1%) diagnosed with situs inversus totalis and 2 (6.9%) with situs inversus partialis. Cardiac malformations were present in nine cases, extra-cardiac anomalies were found in seven cases, and both cardiac and extra-cardiac malformations were identified in one case. The fetal karyotypes and CMA results of 29 cases were normal. Of the 29 cases with dextrocardia, 15 underwent WES, and the other 14 cases refused. Of the 15 cases that underwent WES, clinically relevant variants were identified in 5/15 (33.3%) cases, including the diagnostic variants DNAH5, DNAH11, LRRC56, PEX10, and ZIC3, which were verified by Sanger sequencing. Of the 10 cases with non-diagnostic results via WES, eight (80%) chose to continue the pregnancies. Of the 29 fetuses with dextrocardia, 10 were terminated during pregnancy, and 19 were live born. Fetal dextrocardia is often accompanied by cardiac and extra-cardiac anomalies, and fetal dextrocardia accompanied by situs inversus is associated with a high risk of primary ciliary dyskinesia. Trio-WES is recommended following normal karyotyping and CMA results because it can improve the diagnostic utility of genetic variants of fetal dextrocardia, accurately predict fetal prognosis, and guide perinatal management and the reproductive decisions of affected families.
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Affiliation(s)
- Huili Xue
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, No. 18 Daoshan Road, Gulou District, Fuzhou City, 350001, Fujian Province, China.
| | - Aili Yu
- Reproductive Medicine Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, No. 18 Daoshan Road, Gulou District, Fuzhou City, 350001, Fujian Province, China
| | - Lingji Chen
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, No. 18 Daoshan Road, Gulou District, Fuzhou City, 350001, Fujian Province, China
| | - Qun Guo
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, No. 18 Daoshan Road, Gulou District, Fuzhou City, 350001, Fujian Province, China
| | - Lin Zhang
- Fujian Medical University, No. 88 Jiaotong Road, Cangshan District, Fuzhou City, 350001, Fujian Province, China
| | - Na Lin
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, No. 18 Daoshan Road, Gulou District, Fuzhou City, 350001, Fujian Province, China
| | - Xuemei Chen
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, No. 18 Daoshan Road, Gulou District, Fuzhou City, 350001, Fujian Province, China
| | - Liangpu Xu
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, No. 18 Daoshan Road, Gulou District, Fuzhou City, 350001, Fujian Province, China.
| | - Hailong Huang
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, No. 18 Daoshan Road, Gulou District, Fuzhou City, 350001, Fujian Province, China.
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8
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Hammer-Hansen S, Stoltze U, Bartels E, Hansen TVO, Byrjalsen A, Tybjærg-Hansen A, Juul K, Schmiegelow K, Tfelt J, Bundgaard H, Wadt K, Diness BR. Actionability and familial uptake following opportunistic genomic screening in a pediatric cancer cohort. Eur J Hum Genet 2024; 32:846-857. [PMID: 38740897 PMCID: PMC11220050 DOI: 10.1038/s41431-024-01618-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 04/02/2024] [Accepted: 04/18/2024] [Indexed: 05/16/2024] Open
Abstract
The care for patients with serious conditions is increasingly guided by genomic medicine, and genomic medicine may equally transform care for healthy individual if genomic population screening is implemented. This study examines the medical impact of opportunistic genomic screening (OGS) in a cohort of patients undergoing comprehensive genomic germline DNA testing for childhood cancer, including the impact on their relatives. Medical actionability and uptake after cascade testing in the period following disclosure of OGS results was quantified. A secondary finding was reported to 19/595 (3.2%) probands primarily in genes related to cardiovascular and lipid disorders. After a mean follow up time of 1.6 years (Interquartile range (IQR): 0.57-1.92 yrs.) only 12 (63%) of these variants were found to be medically actionable. Clinical follow up or treatment was planned in 16 relatives, and as in the probands, the prescribed treatment was primarily betablockers or cholesterol lowering therapy. No invasive procedures or implantation of medical devices were performed in probands or relatives, and no reproductive counseling was requested. After an average of 1.6 years of follow-up 2.25 relatives per family with an actionable finding had been tested. This real-world experience of OGS grants new insight into the practical implementation effects and derived health care demands of genotype-first screening. The resulting health care effect and impact on demand for genetic counseling and workup in relatives extends beyond the effect in the probands.
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Affiliation(s)
- Sophia Hammer-Hansen
- Department of Clinical Genetics, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Ulrik Stoltze
- Department of Clinical Genetics, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
- Department of Pediatric and Adolescent Medicine, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Emil Bartels
- Institute of Clinical Medicine, Faculty of Medicine, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Biochemistry, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Thomas van Overeem Hansen
- Department of Clinical Genetics, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
- Institute of Clinical Medicine, Faculty of Medicine, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Anna Byrjalsen
- Department of Clinical Genetics, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
- Department of Pediatric and Adolescent Medicine, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Anne Tybjærg-Hansen
- Institute of Clinical Medicine, Faculty of Medicine, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Biochemistry, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Klaus Juul
- Department of Pediatric and Adolescent Medicine, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Kjeld Schmiegelow
- Department of Pediatric and Adolescent Medicine, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
- Institute of Clinical Medicine, Faculty of Medicine, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Jacob Tfelt
- Institute of Clinical Medicine, Faculty of Medicine, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
- Department of Forensic Genetics, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Henning Bundgaard
- Institute of Clinical Medicine, Faculty of Medicine, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
- Department of Cardiology, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Karin Wadt
- Department of Clinical Genetics, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
- Institute of Clinical Medicine, Faculty of Medicine, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Birgitte Rode Diness
- Department of Clinical Genetics, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark.
- Institute of Clinical Medicine, Faculty of Medicine, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark.
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9
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Sun KY, Bai X, Chen S, Bao S, Zhang C, Kapoor M, Backman J, Joseph T, Maxwell E, Mitra G, Gorovits A, Mansfield A, Boutkov B, Gokhale S, Habegger L, Marcketta A, Locke AE, Ganel L, Hawes A, Kessler MD, Sharma D, Staples J, Bovijn J, Gelfman S, Di Gioia A, Rajagopal VM, Lopez A, Varela JR, Alegre-Díaz J, Berumen J, Tapia-Conyer R, Kuri-Morales P, Torres J, Emberson J, Collins R, Cantor M, Thornton T, Kang HM, Overton JD, Shuldiner AR, Cremona ML, Nafde M, Baras A, Abecasis G, Marchini J, Reid JG, Salerno W, Balasubramanian S. A deep catalogue of protein-coding variation in 983,578 individuals. Nature 2024; 631:583-592. [PMID: 38768635 PMCID: PMC11254753 DOI: 10.1038/s41586-024-07556-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 05/10/2024] [Indexed: 05/22/2024]
Abstract
Rare coding variants that substantially affect function provide insights into the biology of a gene1-3. However, ascertaining the frequency of such variants requires large sample sizes4-8. Here we present a catalogue of human protein-coding variation, derived from exome sequencing of 983,578 individuals across diverse populations. In total, 23% of the Regeneron Genetics Center Million Exome (RGC-ME) data come from individuals of African, East Asian, Indigenous American, Middle Eastern and South Asian ancestry. The catalogue includes more than 10.4 million missense and 1.1 million predicted loss-of-function (pLOF) variants. We identify individuals with rare biallelic pLOF variants in 4,848 genes, 1,751 of which have not been previously reported. From precise quantitative estimates of selection against heterozygous loss of function (LOF), we identify 3,988 LOF-intolerant genes, including 86 that were previously assessed as tolerant and 1,153 that lack established disease annotation. We also define regions of missense depletion at high resolution. Notably, 1,482 genes have regions that are depleted of missense variants despite being tolerant of pLOF variants. Finally, we estimate that 3% of individuals have a clinically actionable genetic variant, and that 11,773 variants reported in ClinVar with unknown significance are likely to be deleterious cryptic splice sites. To facilitate variant interpretation and genetics-informed precision medicine, we make this resource of coding variation from the RGC-ME dataset publicly accessible through a variant allele frequency browser.
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Affiliation(s)
| | | | - Siying Chen
- Regeneron Genetics Center, Tarrytown, NY, USA
| | - Suying Bao
- Regeneron Genetics Center, Tarrytown, NY, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Liron Ganel
- Regeneron Genetics Center, Tarrytown, NY, USA
| | | | | | | | | | | | | | | | | | | | | | - Jesús Alegre-Díaz
- Faculty of Medicine, National Autonomous University of Mexico (UNAM), Mexico City, Mexico
| | - Jaime Berumen
- Faculty of Medicine, National Autonomous University of Mexico (UNAM), Mexico City, Mexico
| | - Roberto Tapia-Conyer
- Faculty of Medicine, National Autonomous University of Mexico (UNAM), Mexico City, Mexico
| | - Pablo Kuri-Morales
- Faculty of Medicine, National Autonomous University of Mexico (UNAM), Mexico City, Mexico
- Instituto Tecnológico y de Estudios Superiores de Monterrey, Monterrey, Mexico
| | - Jason Torres
- Clinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Jonathan Emberson
- Clinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Rory Collins
- Clinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | | | | | | | | | | | | | - Mona Nafde
- Regeneron Genetics Center, Tarrytown, NY, USA
| | - Aris Baras
- Regeneron Genetics Center, Tarrytown, NY, USA
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10
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Demir O, Saglam KA, Yilmaz M, Apuhan T, Cebi AH, Turkyilmaz A. Secondary findings in genes related to cancer phenotypes in Turkish exome sequencing data from 2020 individuals. Am J Med Genet A 2024:e63806. [PMID: 38940262 DOI: 10.1002/ajmg.a.63806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 05/24/2024] [Accepted: 06/20/2024] [Indexed: 06/29/2024]
Abstract
Big data generated from exome sequencing (ES) and genome sequencing (GS) analyses can be used to detect actionable and high-penetrance variants that are not directly associated with the primary diagnosis of patients but can guide their clinical follow-up and treatment. Variants that are classified as pathogenic/likely pathogenic and are clinically significant but not directly associated with the primary diagnosis of patients are defined as secondary findings (SF). The aim of this study was to examine the frequency and variant spectrum of cancer-related SF in 2020 Turkish ES data and to discuss the importance of the presence of cancer-related SF in at-risk family members in terms of genetic counseling and follow-up. A total of 2020 patients from 2020 different families were evaluated by ES. SF were detected in 28 unrelated cases (1.38%), and variants in BRCA2 (11 patients) and MLH1 (4 patients) genes were observed most frequently. A total of 21 different variants were identified, with 4 of them (c.9919_9932del and c.3653del in the BRCA2 gene, c.2002A>G in the MSH2 gene, c.26_29del in the TMEM127 gene) being novel variations. In three different families, c.1189C>T (p.Gln397*) variation in BRCA2 gene was detected, suggesting that this may be a common variant in the Turkish population. This study represents the largest cohort conducted in the Turkish population, examining the frequency and variant spectrum of cancer-related SF. With the identification of frequent variations and the detection of novel variations, the findings of this study have contributed to the variant spectrum. Genetic testing conducted in family members is presented as real-life data, showcasing the implications in terms of counseling, monitoring, and treatment through case examples.
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Affiliation(s)
- Oguzhan Demir
- Department of Medical Genetics, Faculty of Medicine, Karadeniz Technical University, Trabzon, Turkey
| | - Kubra Adanur Saglam
- Department of Medical Genetics, Faculty of Medicine, Karadeniz Technical University, Trabzon, Turkey
| | - Mustafa Yilmaz
- Department of Medical Genetics, Faculty of Medicine, Karadeniz Technical University, Trabzon, Turkey
| | - Tuna Apuhan
- Department of Medical Genetics, Faculty of Medicine, Karadeniz Technical University, Trabzon, Turkey
| | - Alper Han Cebi
- Department of Medical Genetics, Faculty of Medicine, Karadeniz Technical University, Trabzon, Turkey
| | - Ayberk Turkyilmaz
- Department of Medical Genetics, Faculty of Medicine, Karadeniz Technical University, Trabzon, Turkey
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11
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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:S1525-1578(24)00132-6. [PMID: 38925456 DOI: 10.1016/j.jmoldx.2024.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [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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12
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Velasco HM, Bertoli-Avella A, Jaramillo CJ, Cardona DS, González LA, Vanegas MN, Arango JPV, Buitrago CA, González JAG, Marcello J, Bauer P, Moncada JE. Facing the challenges to shorten the diagnostic odyssey: first Whole Genome Sequencing experience of a Colombian cohort with suspected rare diseases. Eur J Hum Genet 2024:10.1038/s41431-024-01609-8. [PMID: 38909121 DOI: 10.1038/s41431-024-01609-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 03/04/2024] [Accepted: 04/10/2024] [Indexed: 06/24/2024] Open
Abstract
Exome and genome sequencing (ES/GS) are routinely used for the diagnosis of genetic diseases in developed countries. However, their implementation is limited in countries from Latin America. We aimed to describe the results of GS in patients with suspected rare genetic diseases in Colombia. We studied 501 patients from 22 healthcare sites from January to December 2022. GS was performed in the index cases using dried blood spots on filtercards. Ancestry analysis was performed under iAdmix. Multiomic testing was performed when needed (biomarker, enzymatic activity, RNA-seq). All tests were performed at an accredited genetic laboratory. Ethnicity prediction data confirmed that 401 patients (80%) were mainly of Amerindian origin. A genetic diagnosis was established for 142 patients with a 28.3% diagnostic yield. The highest diagnostic yield was achieved for pathologies with a metabolic component and syndromic disorders (p < 0.001). Young children had a median of 1 year of diagnostic odyssey, while the median time for adults was significantly longer (15 years). Patients with genetic syndromes have spent more than 75% of their life without a diagnosis, while for patients with neurologic and neuromuscular diseases, the time of the diagnostic odyssey tended to decrease with age. Previous testing, specifically karyotyping or chromosomal microarray were significantly associated with a longer time to reach a definitive diagnosis (p < 0.01). Furthermore, one out of five patients that had an ES before could be diagnosed by GS. The Colombian genome project is the first Latin American study reporting the experience of systematic use of diagnostic GS in rare diseases.
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Affiliation(s)
- Harvy Mauricio Velasco
- Personalized Medicine Group, Unidad de Bioentendimiento, Bioscience Center, Ayudas Diagnósticas SURA, Medellín, Colombia.
| | | | - Carolina Jaramillo Jaramillo
- Sura Omics Science Center, Unidad de Bioentendimiento, Bioscience Center, Ayudas Diagnósticas SURA, Medellín, Colombia
| | - Danny Styvens Cardona
- Data Science Department, Bioscience Center, Ayudas Diagnósticas SURA, Medellín, Colombia
| | - Leonel Andrés González
- Personalized Medicine Group, Unidad de Bioentendimiento, Bioscience Center, Ayudas Diagnósticas SURA, Medellín, Colombia
| | - Melisa Naranjo Vanegas
- Medical Imaging & AI in Health SURA, Bioscience Center, Ayudas Diagnósticas SURA, Medellín, Colombia
| | | | - Cesar Augusto Buitrago
- Personalized Medicine Group, Unidad de Bioentendimiento, Bioscience Center, Ayudas Diagnósticas SURA, Medellín, Colombia
| | | | | | - Peter Bauer
- CENTOGENE GmbH, Rostock, Germany
- University Hospital of Rostock, Hematology, Oncology, and Palliative Medicine, Rostock, Germany
| | - Juliana Espinosa Moncada
- Sura Omics Science Center, Unidad de Bioentendimiento, Bioscience Center, Ayudas Diagnósticas SURA, Medellín, Colombia
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13
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Amer K, Soliman NA, Soror S, Gad YZ, Moustafa A, Elmonem MA, Amer M, Ragheb A, Kotb A, Taha T, Ali W, Sakr M, Ghaffar KA. Egypt Genome: Towards an African new genomic era. J Adv Res 2024:S2090-1232(24)00227-3. [PMID: 38844121 DOI: 10.1016/j.jare.2024.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 05/14/2024] [Accepted: 06/02/2024] [Indexed: 06/27/2024] Open
Abstract
BACKGROUND Studying the human genome is crucial to embrace precision medicine through tailoring treatment and prevention strategies to the unique genetic makeup and molecular information of individuals. After human genome project (1990-2003) generated the first full sequence of a human genome, there have been concerns towards Northern bias due to underrepresentation of other populations. Multiple countries have now established national genome projects aiming at the genomic knowledge that can be harnessed from their populations, which in turn can serve as a basis for their health care policies in the near future. AIM OF REVIEW The intention is to introduce the recently established Egypt Genome (EG) to delineate the genomics and genetics of both the modern and Ancient Egyptian populations. Leveraging genomic medicine to improve precision medicine strategies while building a solid foundation for large-scale genomic research capacity is the fundamental focus of EG. KEY SCIENTIFIC CONCEPTS EG generated genomic knowledge is predicted to enrich the existing human genome and to expand its diversity by studying the underrepresented African/Middle Eastern populations. The insightful impact of EG goes beyond Egypt and Africa as it fills the knowledge gaps in health and disease genomics towards improved and sustainable genomic-driven healthcare systems for better outcomes. Promoting the integration of genomics into clinical practice and spearheading the implementation of genomic-driven healthcare and precision medicine is therefore a key focus of EG. Mining into the wealth of Ancient Egyptian Genomics to delineate the genetic bridge between the contemporary and Ancient Egyptian populations is another excitingly unique area of EG to realize the global vision of human genome.
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Affiliation(s)
- Khaled Amer
- Egypt Center for Research and Regenerative Medicine (ECRRM), Cairo, Egypt.
| | - Neveen A Soliman
- Egypt Center for Research and Regenerative Medicine (ECRRM), Cairo, Egypt; Department of Pediatrics, Center of Pediatric Nephrology and Transplantation, Faculty of Medicine, Cairo University, Cairo, Egypt.
| | - Sameh Soror
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, Helwan University, Cairo, Egypt
| | - Yehia Z Gad
- Department of Medical Molecular Genetics, Human Genetics and Genome Research Institute, National Research Center, Cairo, Egypt; Ancient DNA Laboratory, National Museum of Egyptian Civilization, Egypt
| | - Ahmed Moustafa
- Department of Biology, and Bioinformatics and Integrative Genomics Lab, American University in Cairo, Cairo, Egypt
| | - Mohamed A Elmonem
- Egypt Center for Research and Regenerative Medicine (ECRRM), Cairo, Egypt; Department of Clinical and Chemical Pathology, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - May Amer
- Egypt Center for Research and Regenerative Medicine (ECRRM), Cairo, Egypt
| | - Ameera Ragheb
- Egypt Center for Research and Regenerative Medicine (ECRRM), Cairo, Egypt
| | - Amira Kotb
- Egypt Center for Research and Regenerative Medicine (ECRRM), Cairo, Egypt; Department of Clinical and Chemical Pathology, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Tarek Taha
- Egypt Center for Research and Regenerative Medicine (ECRRM), Cairo, Egypt
| | - Wael Ali
- Egypt Center for Research and Regenerative Medicine (ECRRM), Cairo, Egypt
| | - Mahmoud Sakr
- Academy of Scientific Research & Technology, Egypt
| | - Khaled Abdel Ghaffar
- Department of Oral Medicine, Periodontolgy and Diagnosis, Faculty of Dentistry, Ain Shams University, Cairo, Egypt; Ministry of Health and Population, Cairo, Egypt
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14
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Maurer MS, Miller EJ, Ruberg FL. Addressing Health Disparities-The Case for Variant Transthyretin Cardiac Amyloidosis Grows Stronger. JAMA 2024; 331:1809-1811. [PMID: 38734953 DOI: 10.1001/jama.2024.2868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 05/13/2024]
Affiliation(s)
- Mathew S Maurer
- Cardiac Amyloidosis Program, Seymour, Paul, and Gloria Milstein Division of Cardiology, Department of Medicine, Columbia University Irving Medical Center, and NewYork-Presbyterian Hospital, New York
| | - Edward J Miller
- Section of Cardiovascular Medicine, Yale School of Medicine, New Haven, Connecticut
| | - Frederick L Ruberg
- Section of Cardiovascular Medicine, Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston Medical Center, Boston, Massachusetts
- Amyloidosis Center, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts
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15
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Migliavacca MP, Sobreira J, Bermeo D, Gomes M, Alencar D, Sussuchi L, Souza CA, Silva JS, Kroll JE, Burger M, Guarischi-Sousa R, Villela D, Yamamoto GL, Milanezi F, Horigoshi N, Cesar RG, de Carvalho WB, Honjo RS, Bertola DR, Kim CA, de Souza L, Procianoy RS, Silveria RC, Rosenberg C, Giugliani R, Campana GA, Scapulatempo-Neto C, Sobreira N. Whole genome sequencing as a first-tier diagnostic test for infants in neonatal intensive care units: A pilot study in Brazil. Am J Med Genet A 2024; 194:e63544. [PMID: 38258498 DOI: 10.1002/ajmg.a.63544] [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: 12/05/2023] [Revised: 12/27/2023] [Accepted: 12/28/2023] [Indexed: 01/24/2024]
Abstract
In this pilot study, we aimed to evaluate the feasibility of whole genome sequencing (WGS) as a first-tier diagnostic test for infants hospitalized in neonatal intensive care units in the Brazilian healthcare system. The cohort presented here results from a joint collaboration between private and public hospitals in Brazil considering the initiative of a clinical laboratory to provide timely diagnosis for critically ill infants. We performed trio (proband and parents) WGS in 21 infants suspected of a genetic disease with an urgent need for diagnosis to guide medical care. Overall, the primary indication for genetic testing was dysmorphic syndromes (n = 14, 67%) followed by inborn errors of metabolism (n = 6, 29%) and skeletal dysplasias (n = 1, 5%). The diagnostic yield in our cohort was 57% (12/21) based on cases that received a definitive or likely definitive diagnostic result from WGS analysis. A total of 16 pathogenic/likely pathogenic variants and 10 variants of unknown significance were detected, and in most cases inherited from an unaffected parent. In addition, the reported variants were of different types, but mainly missense (58%) and associated with autosomal diseases (19/26); only three were associated with X-linked diseases, detected in hemizygosity in the proband an inherited from an unaffected mother. Notably, we identified 10 novel variants, absent from public genomic databases, in our cohort. Considering the entire diagnostic process, the average turnaround time from enrollment to medical report in our study was 53 days. Our findings demonstrate the remarkable utility of WGS as a diagnostic tool, elevating the potential of transformative impact since it outperforms conventional genetic tests. Here, we address the main challenges associated with implementing WGS in the medical care system in Brazil, as well as discuss the potential benefits and limitations of WGS as a diagnostic tool in the neonatal care setting.
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Affiliation(s)
| | - Joselito Sobreira
- Diagnósticos da América S.A., DASA, São Paulo, Brazil
- Hospital Infantil Sabará, São Paulo, Brazil
| | - Diana Bermeo
- Diagnósticos da América S.A., DASA, São Paulo, Brazil
| | | | - Dayse Alencar
- Diagnósticos da América S.A., DASA, São Paulo, Brazil
| | | | | | | | | | | | | | | | - Guilherme L Yamamoto
- Diagnósticos da América S.A., DASA, São Paulo, Brazil
- Instituto da Criança, Faculdade de Medicina (FMUSP), Universidade de São Paulo, São Paulo, Brazil
| | | | | | | | | | - Rachel Sayuri Honjo
- Instituto da Criança, Faculdade de Medicina (FMUSP), Universidade de São Paulo, São Paulo, Brazil
| | | | - Chong Ae Kim
- Instituto da Criança, Faculdade de Medicina (FMUSP), Universidade de São Paulo, São Paulo, Brazil
| | - Lucian de Souza
- Hospital das Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
| | | | - Rita C Silveria
- Hospital das Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
| | | | - Roberto Giugliani
- Diagnósticos da América S.A., DASA, São Paulo, Brazil
- Hospital das Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
| | | | | | - Nara Sobreira
- Diagnósticos da América S.A., DASA, São Paulo, Brazil
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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16
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Brown CM, Amendola LM, Chandrasekhar A, Hagelstrom RT, Halter G, Kesari A, Thorpe E, Perry DL, Taft RJ, Coffey AJ. A framework for the evaluation and reporting of incidental findings in clinical genomic testing. Eur J Hum Genet 2024; 32:665-672. [PMID: 38565640 PMCID: PMC11153510 DOI: 10.1038/s41431-024-01575-1] [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: 10/16/2023] [Revised: 12/29/2023] [Accepted: 02/20/2024] [Indexed: 04/04/2024] Open
Abstract
Currently, there are no widely accepted recommendations in the genomics field guiding the return of incidental findings (IFs), defined here as unexpected results that are unrelated to the indication for testing. Consequently, reporting policies for IFs among laboratories offering genomic testing are variable and may lack transparency. Herein we describe a framework developed to guide the evaluation and return of IFs encountered in probands undergoing clinical genome sequencing (cGS). The framework prioritizes clinical significance and actionability of IFs and follows a stepwise approach with stopping points at which IFs may be recommended for return or not. Over 18 months, implementation of the framework in a clinical laboratory facilitated the return of actionable IFs in 37 of 720 (5.1%) individuals referred for cGS, which is reduced to 3.1% if glucose-6-phosphate dehydrogenase (G6PD) deficiency is excluded. This framework can serve as a model to standardize reporting of IFs identified during genomic testing.
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Affiliation(s)
- Carolyn M Brown
- Medical Genomics Research, Illumina, Inc., San Diego, CA, 92122, USA.
| | - Laura M Amendola
- Medical Genomics Research, Illumina, Inc., San Diego, CA, 92122, USA
| | | | | | - Gillian Halter
- Scripps MD Anderson Cancer Center, San Diego, CA, 92121, USA
| | - Akanchha Kesari
- Medical Genomics Research, Illumina, Inc., San Diego, CA, 92122, USA
| | - Erin Thorpe
- Medical Genomics Research, Illumina, Inc., San Diego, CA, 92122, USA
| | - Denise L Perry
- Medical Genomics Research, Illumina, Inc., San Diego, CA, 92122, USA
| | - Ryan J Taft
- Medical Genomics Research, Illumina, Inc., San Diego, CA, 92122, USA
| | - Alison J Coffey
- Medical Genomics Research, Illumina, Inc., San Diego, CA, 92122, USA.
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17
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Shen C, Shen Y, Huang W, Zhang A, Zou T, Guo D, Wang H, Wu J, Hu H, Xiang M, Ye B. A novel homozygous RSPH4A variant in a family with primary ciliary dyskinesia and literature review. Front Genet 2024; 15:1364476. [PMID: 38818043 PMCID: PMC11137616 DOI: 10.3389/fgene.2024.1364476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 04/10/2024] [Indexed: 06/01/2024] Open
Abstract
Introduction: Primary ciliary dyskinesia (PCD) is a rare heterogeneous disease caused by abnormalities in motile cilia. In this case report, we first analyzed the clinical and genetic data of a proband who was suspected of having PCD on the basis of her clinical and radiological findings. Methods: Whole-exome sequencing was performed, and a variant in the RSPH4A gene was identified in the proband. Sanger sequencing was used for validation of RSPH4A variants in the proband, her sister, her daughter and her parents. Finally, the phenotypic features of the patient were analyzed, and the current literature was reviewed to better understand the gene variants in PCD related to hearing loss and the clinical manifestations of the RSPH4A variant in PCD. Results: The chief clinical symptoms of this proband included gradual mixed hearing loss, otitis media, anosmia, sinusitis, recurrent cough and infertility. Her DNA sequencing revealed a novel homozygous T to C transition at position 1321 within exon 3 of RSPH4A according to genetic testing results. This variant had never been reported before. The homozygous variant resulted in an amino acid substitution of tryptophan by arginine at position 441 (p.Trp441Arg). The same variant was also found in the proband's sister, and a heterozygous pathogenic variant was identified among immediate family members, including the proband's daughter and parents. Discussion: A literature review showed that 16 pathogenic variants in RSPH4A have been reported. Hearing loss had only been observed in patients with the RSPH4A (c.921+3_6delAAGT) splice site mutation, and the specific type of hearing loss was not described.
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Affiliation(s)
- Chenling Shen
- Department of Otolaryngology and Head and Neck Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Audiology and Speech-Language Pathology, College of Health Science and Technology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Otolaryngology and Head and Neck Surgery, Shanghai Children’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yilin Shen
- Department of Otolaryngology and Head and Neck Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Audiology and Speech-Language Pathology, College of Health Science and Technology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Weiyi Huang
- Department of Otolaryngology and Head and Neck Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Audiology and Speech-Language Pathology, College of Health Science and Technology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | | | - Tianyuan Zou
- Department of Otolaryngology and Head and Neck Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Audiology and Speech-Language Pathology, College of Health Science and Technology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Otolaryngology and Head and Neck Surgery, Shanghai Children’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Dongye Guo
- Department of Otolaryngology and Head and Neck Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Audiology and Speech-Language Pathology, College of Health Science and Technology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hao Wang
- Department of Otolaryngology and Head and Neck Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Audiology and Speech-Language Pathology, College of Health Science and Technology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jichang Wu
- Department of Otolaryngology and Head and Neck Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Audiology and Speech-Language Pathology, College of Health Science and Technology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Haixia Hu
- Department of Otolaryngology and Head and Neck Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Audiology and Speech-Language Pathology, College of Health Science and Technology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Mingliang Xiang
- Department of Otolaryngology and Head and Neck Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Audiology and Speech-Language Pathology, College of Health Science and Technology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Bin Ye
- Department of Otolaryngology and Head and Neck Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Audiology and Speech-Language Pathology, College of Health Science and Technology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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18
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Yin X, Richardson M, Laner A, Shi X, Ognedal E, Vasta V, Hansen TVO, Pineda M, Ritter D, den Dunnen JT, Hassanin E, Lyman Lin W, Borras E, Krahn K, Nordling M, Martins A, Mahmood K, Nadeau EAW, Beshay V, Tops C, Genuardi M, Pesaran T, Frayling IM, Capellá G, Latchford A, Tavtigian SV, Maj C, Plon SE, Greenblatt MS, Macrae FA, Spier I, Aretz S. Systematic large-scale application of ClinGen InSiGHT APC -specific ACMG/AMP variant classification criteria substantially alleviates the burden of variants of uncertain significance in ClinVar and LOVD databases. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.03.24306761. [PMID: 38746299 PMCID: PMC11092726 DOI: 10.1101/2024.05.03.24306761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Background Pathogenic constitutional APC variants underlie familial adenomatous polyposis, the most common hereditary gastrointestinal polyposis syndrome. To improve variant classification and resolve the interpretative challenges of variants of uncertain significance (VUS), APC-specific ACMG/AMP variant classification criteria were developed by the ClinGen-InSiGHT Hereditary Colorectal Cancer/Polyposis Variant Curation Expert Panel (VCEP). Methods A streamlined algorithm using the APC -specific criteria was developed and applied to assess all APC variants in ClinVar and the InSiGHT international reference APC LOVD variant database. Results A total of 10,228 unique APC variants were analysed. Among the ClinVar and LOVD variants with an initial classification of (Likely) Benign or (Likely) Pathogenic, 94% and 96% remained in their original categories, respectively. In contrast, 41% ClinVar and 61% LOVD VUS were reclassified into clinically actionable classes, the vast majority as (Likely) Benign. The total number of VUS was reduced by 37%. In 21 out of 36 (58%) promising APC variants that remained VUS despite evidence for pathogenicity, a data mining-driven work-up allowed their reclassification as (Likely) Pathogenic. Conclusions The application of APC -specific criteria substantially reduced the number of VUS in ClinVar and LOVD. The study also demonstrated the feasibility of a systematic approach to variant classification in large datasets, which might serve as a generalisable model for other gene-/disease-specific variant interpretation initiatives. It also allowed for the prioritization of VUS that will benefit from in-depth evidence collection. This subset of APC variants was approved by the VCEP and made publicly available through ClinVar and LOVD for widespread clinical use.
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19
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Muzurović E, Borozan S, Rizzo M. Clinical impact of genetic testing for lipid disorders. Curr Opin Cardiol 2024; 39:154-161. [PMID: 38456469 DOI: 10.1097/hco.0000000000001133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/09/2024]
Abstract
PURPOSE OF REVIEW Genetic testing is increasingly becoming a common consideration in the clinical approach of dyslipidemia patients. Advances in research in last decade and increased recognition of genetics in biological pathways modulating blood lipid levels created a gap between theoretical knowledge and its applicability in clinical practice. Therefore, it is very important to define the clinical justification of genetic testing in dyslipidemia patients. RECENT FINDINGS Clinical indications for genetic testing for most dyslipidemias are not precisely defined and there are no clearly established guideline recommendations. In patients with severe low-density lipoprotein cholesterol (LDL-C) levels, the genetic analysis can be used to guide diagnostic and therapeutic approach, while in severe hypertriglyceridemia (HTG), clinicians can rely on triglyceride level rather than a genotype along the treatment pathway. Genetic testing increases diagnostic accuracy and risk stratification, access and adherence to specialty therapies, and cost-effectiveness of cascade testing. A shared decision-making model between the provider and the patient is essential as patient values, preferences and clinical characteristics play a very strong role. SUMMARY Genetic testing for lipid disorders is currently underutilized in clinical practice. However, it should be selectively used, according to the type of dyslipidemia and when the benefits overcome costs.
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Affiliation(s)
- Emir Muzurović
- Department of Internal Medicine, Endocrinology Section, Clinical Centre of Montenegro
- Faculty of Medicine, University of Montenegro, Podgorica, Montenegro
| | - Sanja Borozan
- Department of Internal Medicine, Endocrinology Section, Clinical Centre of Montenegro
- Faculty of Medicine, University of Montenegro, Podgorica, Montenegro
| | - Manfredi Rizzo
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties, University of Palermo, Palermo, Italy
- Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
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20
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Lee JS, Cho EH, Kim B, Hong J, Kim YG, Kim Y, Jang JH, Lee ST, Kong SY, Lee W, Shin S, Song EY. Clinical Practice Guideline for Blood-based Circulating Tumor DNA Assays. Ann Lab Med 2024; 44:195-209. [PMID: 38221747 PMCID: PMC10813828 DOI: 10.3343/alm.2023.0389] [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: 10/02/2023] [Revised: 12/06/2023] [Accepted: 01/06/2024] [Indexed: 01/16/2024] Open
Abstract
Circulating tumor DNA (ctDNA) has emerged as a promising tool for various clinical applications, including early diagnosis, therapeutic target identification, treatment response monitoring, prognosis evaluation, and minimal residual disease detection. Consequently, ctDNA assays have been incorporated into clinical practice. In this review, we offer an in-depth exploration of the clinical implementation of ctDNA assays. Notably, we examined existing evidence related to pre-analytical procedures, analytical components in current technologies, and result interpretation and reporting processes. The primary objective of this guidelines is to provide recommendations for the clinical utilization of ctDNA assays.
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Affiliation(s)
- Jee-Soo Lee
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Eun Hye Cho
- Department of Laboratory Medicine, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Boram Kim
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | | | - Young-gon Kim
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Yoonjung Kim
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Ja-Hyun Jang
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Seung-Tae Lee
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Korea
- Dxome Co. Ltd., Seongnam, Korea
| | - Sun-Young Kong
- Department of Laboratory Medicine, National Cancer Center, Goyang, Korea
| | - Woochang Lee
- Department of Laboratory Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Saeam Shin
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Eun Young Song
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
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21
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Thomson KL, Jiang C, Richardson E, Westphal DS, Burkard T, Wolf CM, Vatta M, Harrison SM, Ingles J, Bezzina CR, Kroncke BM, Vandenberg JI, Ng CA. Clinical interpretation of KCNH2 variants using a robust PS3/BS3 functional patch-clamp assay. HGG ADVANCES 2024; 5:100270. [PMID: 38219013 PMCID: PMC10840334 DOI: 10.1016/j.xhgg.2024.100270] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 01/07/2024] [Accepted: 01/08/2024] [Indexed: 01/15/2024] Open
Abstract
Long QT syndrome (LQTS), caused by the dysfunction of cardiac ion channels, increases the risk of sudden death in otherwise healthy young people. For many variants in LQTS genes, there is insufficient evidence to make a definitive genetic diagnosis. We have established a robust functional patch-clamp assay to facilitate classification of missense variants in KCNH2, one of the key LQTS genes. A curated set of 30 benign and 30 pathogenic missense variants were used to establish the range of normal and abnormal function. The extent to which variants reduced protein function was quantified using Z scores, the number of standard deviations from the mean of the normalized current density of the set of benign variant controls. A Z score of -2 defined the threshold for abnormal loss of function, which corresponds to 55% wild-type function. More extreme Z scores were observed for variants with a greater loss-of-function effect. We propose that the Z score for each variant can be used to inform the application and weighting of abnormal and normal functional evidence criteria (PS3 and BS3) within the American College of Medical Genetics and Genomics variant classification framework. The validity of this approach was demonstrated using a series of 18 KCNH2 missense variants detected in a childhood onset LQTS cohort, where the level of function assessed using our assay correlated to the Schwartz score (a scoring system used to quantify the probability of a clinical diagnosis of LQTS) and the length of the corrected QT (QTc) interval.
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Affiliation(s)
- Kate L Thomson
- Oxford Genetics Laboratories, Churchill Hospital, Oxford, UK
| | - Connie Jiang
- Faculty of Medicine and Health, UNSW Sydney, Kensington, NSW, Australia; Mark Cowley Lidwill Research Program in Cardiac Electrophysiology, Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia
| | - Ebony Richardson
- Centre for Population Genomics, Garvan Institute of Medical Research and UNSW Sydney, Sydney, NSW, Australia; Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Dominik S Westphal
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine and Health, Technical University of Munich, Munich, Germany; Department of Internal Medicine I, Klinikum Rechts der Isar, School of Medicine and Health, Technical University of Munich, Munich, Germany; European Reference Network for Rare, Low Prevalence and Complex Diseases of the Heart: ERN GUARD-Heart
| | - Tobias Burkard
- Department of Congenital Heart Disease and Pediatric Cardiology, German Heart Center Munich, Technical University of Munich, School of Medicine and Health, Munich, Germany
| | - Cordula M Wolf
- European Reference Network for Rare, Low Prevalence and Complex Diseases of the Heart: ERN GUARD-Heart; Department of Congenital Heart Disease and Pediatric Cardiology, German Heart Center Munich, Technical University of Munich, School of Medicine and Health, Munich, Germany; DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, Munich, Germany
| | | | | | - Jodie Ingles
- Centre for Population Genomics, Garvan Institute of Medical Research and UNSW Sydney, Sydney, NSW, Australia; Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Connie R Bezzina
- European Reference Network for Rare, Low Prevalence and Complex Diseases of the Heart: ERN GUARD-Heart; Department of Experimental Cardiology, Amsterdam Cardiovascular Sciences, University of Amsterdam, Amsterdam UMC, Amsterdam, the Netherlands
| | - Brett M Kroncke
- Vanderbilt Center for Arrhythmia Research and Therapeutics, Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jamie I Vandenberg
- Mark Cowley Lidwill Research Program in Cardiac Electrophysiology, Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia; School of Clinical Medicine, UNSW Sydney, Darlinghurst, NSW, Australia.
| | - Chai-Ann Ng
- Mark Cowley Lidwill Research Program in Cardiac Electrophysiology, Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia; School of Clinical Medicine, UNSW Sydney, Darlinghurst, NSW, Australia.
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22
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Aamer W, Al-Maraghi A, Syed N, Gandhi GD, Aliyev E, Al-Kurbi AA, Al-Saei O, Kohailan M, Krishnamoorthy N, Palaniswamy S, Al-Malki K, Abbasi S, Agrebi N, Abbaszadeh F, Akil ASAS, Badii R, Ben-Omran T, Lo B, Mokrab Y, Fakhro KA. Burden of Mendelian disorders in a large Middle Eastern biobank. Genome Med 2024; 16:46. [PMID: 38584274 PMCID: PMC11000384 DOI: 10.1186/s13073-024-01307-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 02/19/2024] [Indexed: 04/09/2024] Open
Abstract
BACKGROUND Genome sequencing of large biobanks from under-represented ancestries provides a valuable resource for the interrogation of Mendelian disease burden at world population level, complementing small-scale familial studies. METHODS Here, we interrogate 6045 whole genomes from Qatar-a Middle Eastern population with high consanguinity and understudied mutational burden-enrolled at the national Biobank and phenotyped for 58 clinically-relevant quantitative traits. We examine a curated set of 2648 Mendelian genes from 20 panels, annotating known and novel pathogenic variants and assessing their penetrance and impact on the measured traits. RESULTS We find that 62.5% of participants are carriers of at least 1 known pathogenic variant relating to recessive conditions, with homozygosity observed in 1 in 150 subjects (0.6%) for which Peninsular Arabs are particularly enriched versus other ancestries (5.8-fold). On average, 52.3 loss-of-function variants were found per genome, 6.5 of which affect a known Mendelian gene. Several variants annotated in ClinVar/HGMD as pathogenic appeared at intermediate frequencies in this cohort (1-3%), highlighting Arab founder effect, while others have exceedingly high frequencies (> 5%) prompting reconsideration as benign. Furthermore, cumulative gene burden analysis revealed 56 genes having gene carrier frequency > 1/50, including 5 ACMG Tier 3 panel genes which would be candidates for adding to newborn screening in the country. Additionally, leveraging 58 biobank traits, we systematically assess the impact of novel/rare variants on phenotypes and discover 39 candidate large-effect variants associating with extreme quantitative traits. Furthermore, through rare variant burden testing, we discover 13 genes with high mutational load, including 5 with impact on traits relevant to disease conditions, including metabolic disorder and type 2 diabetes, consistent with the high prevalence of these conditions in the region. CONCLUSIONS This study on the first phase of the growing Qatar Genome Program cohort provides a comprehensive resource from a Middle Eastern population to understand the global mutational burden in Mendelian genes and their impact on traits in seemingly healthy individuals in high consanguinity settings.
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Affiliation(s)
- Waleed Aamer
- Department of Human Genetics, Sidra Medicine, Doha, Qatar
| | | | - Najeeb Syed
- Applied Bioinformatics Core, Sidra Medicine, Doha, Qatar
| | | | - Elbay Aliyev
- Department of Human Genetics, Sidra Medicine, Doha, Qatar
| | | | - Omayma Al-Saei
- Department of Human Genetics, Sidra Medicine, Doha, Qatar
| | | | | | | | | | - Saleha Abbasi
- Department of Human Genetics, Sidra Medicine, Doha, Qatar
| | - Nourhen Agrebi
- Department of Human Genetics, Sidra Medicine, Doha, Qatar
| | | | | | - Ramin Badii
- Diagnostic Genomic Division, Hamad Medical Corporation, Doha, Qatar
| | - Tawfeg Ben-Omran
- Section of Clinical and Metabolic Genetics, Department of pediatrics, Hamad Medical Corporation, Doha, Qatar
- Department of Pediatric, Weill Cornell Medical College, Doha, Qatar
- Division of Genetic & Genomics Medicine, Sidra Medicine, Doha, Qatar
| | - Bernice Lo
- Department of Human Genetics, Sidra Medicine, Doha, Qatar
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Younes Mokrab
- Department of Human Genetics, Sidra Medicine, Doha, Qatar.
- Department of Genetic Medicine, Weill Cornell Medicine-Qatar, Doha, Qatar.
- College of Health Sciences, Qatar University, Doha, Qatar.
| | - Khalid A Fakhro
- Department of Human Genetics, Sidra Medicine, Doha, Qatar.
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar.
- Department of Genetic Medicine, Weill Cornell Medicine-Qatar, Doha, Qatar.
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23
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Chen LS, Yu CW, Li WJ, Hsieh WC, Li YP. Carrier screening for present disease prevalence and recessive genetic disorder in Taiwanese population. J Hum Genet 2024; 69:115-118. [PMID: 38135707 DOI: 10.1038/s10038-023-01212-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 11/07/2023] [Accepted: 12/04/2023] [Indexed: 12/24/2023]
Abstract
Carrier screening is important to people have a higher prevalence of severe recessive or X-linked genetic conditions. This study is aimed that the frequency and uncertain nature of genetic variants was identified in Taiwanese population, providing individuals with information at risk of inherited diseases and their heritability to newborns. A total of 480 subjects receiving genetic counseling with no family history of inherited disorders were recruited into a cohort from 2018 to 2022. Next-generation sequencing (NGS) panel for autosomal dominant (AD), autosomal recessive (AR) and X-linked diseases was sequenced to assess disease prevalence and carrier frequency for the targeted diseases. Publicly available NGS datasets were analyzed following a tier-based system and ACMG recommendation. 5.3% of subjects showed the presence of variants for genetic disorder, and 2.3% of them were determined with AD. 14 of subjects with pathogenic variants were carriers for AR. The inherited genes were LDLR for AD disorders and AR disorders included GAA and ATP7B. 21.6% of subjects had highest carrier frequency of GJB2 gene. 0.5% of subjects had highest frequency of GJB6 for AR condition. In conclusions, the variants in LDLR, GAA and ATP7B genes were identified in Taiwanese population, indicating individuals had higher risk of Pompe disease, Wilson's disease and familial hypercholesterolemia. Taiwanese individuals carrying GJB2 and GJB6 had the considerable risk of hearing loss passing to their offspring.
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Affiliation(s)
- Li Shan Chen
- Department of Obstetrics and Gynecology, Shin Kong Wu Ho Su Memorial Hospital, Taipei, Taiwan
| | - Cheng Wei Yu
- Department of Obstetrics and Gynecology, Shin Kong Wu Ho Su Memorial Hospital, Taipei, Taiwan
| | - Wei Jiun Li
- Department of Obstetrics and Gynecology, Shin Kong Wu Ho Su Memorial Hospital, Taipei, Taiwan
| | - Wen Chi Hsieh
- Department of Obstetrics and Gynecology, Shin Kong Wu Ho Su Memorial Hospital, Taipei, Taiwan
| | - Yi Ping Li
- Department of Obstetrics and Gynecology, Shin Kong Wu Ho Su Memorial Hospital, Taipei, Taiwan.
- Department of Obstetrics and Gynecology, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan.
- School of Medicine, Fu Jen Catholic University, New Taipei City, Taiwan.
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24
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Krenn M, Wagner M, Zulehner G, Weng R, Jäger F, Keritam O, Sener M, Brücke C, Milenkovic I, Langer A, Buchinger D, Habersam R, Mayerhanser K, Brugger M, Brunet T, Jacob M, Graf E, Berutti R, Cetin H, Hoefele J, Winkelmann J, Zimprich F, Rath J. Next-generation sequencing and comprehensive data reassessment in 263 adult patients with neuromuscular disorders: insights into the gray zone of molecular diagnoses. J Neurol 2024; 271:1937-1946. [PMID: 38127101 PMCID: PMC10972933 DOI: 10.1007/s00415-023-12101-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 11/03/2023] [Accepted: 11/04/2023] [Indexed: 12/23/2023]
Abstract
BACKGROUND Neuromuscular disorders (NMDs) are heterogeneous conditions with a considerable fraction attributed to monogenic defects. Despite the advancements in genomic medicine, many patients remain without a diagnosis. Here, we investigate whether a comprehensive reassessment strategy improves the diagnostic outcomes. METHODS We analyzed 263 patients with NMD phenotypes that underwent diagnostic exome or genome sequencing at our tertiary referral center between 2015 and 2023. We applied a comprehensive reassessment encompassing variant reclassification, re-phenotyping and NGS data reanalysis. Multivariable logistic regression was performed to identify predictive factors associated with a molecular diagnosis. RESULTS Initially, a molecular diagnosis was identified in 53 cases (20%), while an additional 23 (9%) had findings of uncertain significance. Following comprehensive reassessment, the diagnostic yield increased to 23%, revealing 44 distinct monogenic etiologies. Reasons for newly obtained molecular diagnoses were variant reclassifications in 7 and NGS data reanalysis in 3 cases including one recently described disease-gene association (DNAJB4). Male sex reduced the odds of receiving a molecular diagnosis (OR 0.42; 95%CI 0.21-0.82), while a positive family history (OR 5.46; 95%CI 2.60-11.76) and a myopathy phenotype (OR 2.72; 95%CI 1.11-7.14) increased the likelihood. 7% were resolved through targeted genetic testing or classified as acquired etiologies. CONCLUSION Our findings reinforce the use of NGS in NMDs of suspected monogenic origin. We show that a comprehensive reassessment enhances diagnostic accuracy. However, one needs to be aware that genetic diagnoses are often made with uncertainty and can even be downgraded based on new evidence.
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Affiliation(s)
- Martin Krenn
- Department of Neurology, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | - Matias Wagner
- Institute of Human Genetics, Klinikum Rechts Der Isar, School of Medicine, Technical University of Munich, Munich, Germany
- Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany
| | - Gudrun Zulehner
- Department of Neurology, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | - Rosa Weng
- Department of Neurology, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | - Fiona Jäger
- Department of Neurology, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | - Omar Keritam
- Department of Neurology, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | - Merve Sener
- Department of Neurology, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | - Christof Brücke
- Department of Neurology, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | - Ivan Milenkovic
- Department of Neurology, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | - Agnes Langer
- Department of Neurology, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | - Dominic Buchinger
- Department of Neurology, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | - Richard Habersam
- Department of Neurology, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | - Katharina Mayerhanser
- Institute of Human Genetics, Klinikum Rechts Der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Melanie Brugger
- Institute of Human Genetics, Klinikum Rechts Der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Theresa Brunet
- Institute of Human Genetics, Klinikum Rechts Der Isar, School of Medicine, Technical University of Munich, Munich, Germany
- Department of Pediatric Neurology, Developmental Medicine and Social Pediatrics, Dr. Von Hauner's Children's Hospital, University of Munich, Munich, Germany
| | - Maureen Jacob
- Institute of Human Genetics, Klinikum Rechts Der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Elisabeth Graf
- Institute of Human Genetics, Klinikum Rechts Der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Riccardo Berutti
- Institute of Human Genetics, Klinikum Rechts Der Isar, School of Medicine, Technical University of Munich, Munich, Germany
- Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany
| | - Hakan Cetin
- Department of Neurology, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | - Julia Hoefele
- Institute of Human Genetics, Klinikum Rechts Der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Juliane Winkelmann
- Institute of Human Genetics, Klinikum Rechts Der Isar, School of Medicine, Technical University of Munich, Munich, Germany
- Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany
| | - Fritz Zimprich
- Department of Neurology, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | - Jakob Rath
- Department of Neurology, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria.
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria.
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Oladayo AM, Prochaska S, Busch T, Adeyemo WL, Gowans LJ, Eshete M, Awotoye W, Sule V, Alade A, Adeyemo AA, Mossey PA, Prince A, Murray JC, Butali A. Parents and Provider Perspectives on the Return of Genomic Findings for Cleft Families in Africa. AJOB Empir Bioeth 2024; 15:133-146. [PMID: 38236653 PMCID: PMC11153024 DOI: 10.1080/23294515.2024.2302993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/21/2024]
Abstract
BACKGROUND Inadequate knowledge among health care providers (HCPs) and parents of affected children limits the understanding and utility of secondary genetic findings (SFs) in under-represented populations in genomics research. SFs arise from deep DNA sequencing done for research or diagnostic purposes and may burden patients and their families despite their potential health importance. This study aims to evaluate the perspective of both groups regarding SFs and their choices in the return of results from genetic testing in the context of orofacial clefts. METHODS Using an online survey, we evaluated the experiences of 252 HCPs and 197 parents across participating cleft clinics in Ghana and Nigeria toward the return of SFs across several domains. RESULTS Only 1.6% of the HCPs felt they had an expert understanding of when and how to incorporate genomic medicine into practice, while 50.0% agreed that all SFs should be returned to patients. About 95.4% of parents were willing to receive all the information from genetic testing (including SFs), while the majority cited physicians as their primary information source (64%). CONCLUSIONS Overall, parents and providers were aware that genetic testing could help in the clinical management of diseases. However, they cited a lack of knowledge about genomic medicine, uncertain clinical utility, and lack of available learning resources as barriers. The knowledge gained from this study will assist with developing guidelines and policies to guide providers on the return of SFs in sub-Saharan Africa and across the continent.
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Affiliation(s)
- Abimbola M Oladayo
- Department Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, USA
- Iowa Institute of Oral Health Research, University of Iowa, Iowa City, IA, USA
| | - Sydney Prochaska
- Department of Global Health, College of Public Health, University of Iowa, Iowa City, IA, USA
| | - Tamara Busch
- Iowa Institute of Oral Health Research, University of Iowa, Iowa City, IA, USA
| | - Wasiu L. Adeyemo
- Department of Oral and Maxillofacial Surgery, University of Lagos
| | - Lord J.J. Gowans
- Department of Biochemistry and Biotechnology, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Mekonen Eshete
- Addis Ababa University, School of Medicine, Department of Surgery, Addis Ababa, Ethiopia
| | - Waheed Awotoye
- Department Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, USA
- Iowa Institute of Oral Health Research, University of Iowa, Iowa City, IA, USA
| | - Veronica Sule
- Department of Operative Dentistry, College of Dentistry, University of Iowa, Iowa City, IA, USA
| | - Azeez Alade
- Department Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, USA
- Iowa Institute of Oral Health Research, University of Iowa, Iowa City, IA, USA
| | | | - Peter A. Mossey
- Department of Orthodontics, University of Dundee, Dundee, UK
| | | | | | - Azeez Butali
- Department Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, USA
- Iowa Institute of Oral Health Research, University of Iowa, Iowa City, IA, USA
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26
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Dangoni GD, Teixeira ACB, da Costa SS, Scliar MO, Carvalho LML, Silva LN, Novak EM, Vince CSC, Maschietto MC, Sugayama SMM, Odone-Filho V, Krepischi ACV. Germline mutations in cancer predisposition genes among pediatric patients with cancer and congenital anomalies. Pediatr Res 2024; 95:1346-1355. [PMID: 38182823 DOI: 10.1038/s41390-023-03000-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 11/08/2023] [Accepted: 12/20/2023] [Indexed: 01/07/2024]
Abstract
BACKGROUND Childhood cancer has a poorly known etiology, and investigating the underlying genetic background may provide novel insights. A recognized association exists between non-chromosomal birth defects and childhood cancer susceptibility. METHODS We performed whole-exome sequencing and chromosomal microarray analysis in a cohort of childhood cancer (22 individuals, 50% with congenital anomalies) to unravel deleterious germline variants. RESULTS A diagnostic yield of 14% was found, encompassing heterozygous variants in bona fide dominant Cancer Predisposition Genes (CPGs). Considering candidate and recessive CPGs harboring monoallelic variants, which were also deemed to play a role in the phenotype, the yield escalated to 45%. Most of the deleterious variants were mapped in genes not conventionally linked to the patient's tumor type. Relevant findings were detected in 55% of the syndromic individuals, mostly variants potentially underlying both phenotypes. CONCLUSION We uncovered a remarkable prevalence of germline deleterious CPG variants, highlighting the significance of a comprehensive genetic analysis in pediatric cancer, especially when coupled with additional clinical signs. Moreover, our findings emphasized the potential for oligogenic inheritance, wherein multiple genes synergistically increase cancer risk. Lastly, our investigation unveiled potentially novel genotype-phenotype associations, such as SETD5 in neuroblastoma, KAT6A in gliomas, JAG1 in hepatoblastomas, and TNFRSF13B in Langerhans cell histiocytosis. IMPACT Novel gene-phenotype associations and candidate genes for pediatric cancer were unraveled, such as KAT6A in gliomas, SETD5 in neuroblastoma, JAG1 in hepatoblastomas, and TNFRSF13B in Langerhans cell histiocytosis. Our analysis revealed a high frequency of deleterious germline variants, particularly in cases accompanied by additional clinical signs, highlighting the importance of a comprehensive genetic evaluation in childhood cancer. Our findings also underscored the potential for oligogenic inheritance in pediatric cancer risk. Understanding the cancer etiology is crucial for genetic counseling, often influencing therapeutic decisions and offering valuable insights into molecular targets for the development of oncological therapies.
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Affiliation(s)
- Gustavo D Dangoni
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
| | - Anne Caroline B Teixeira
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
| | - Silvia S da Costa
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
| | - Marília O Scliar
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
| | - Laura M L Carvalho
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
| | - Luciana N Silva
- Department of Pediatrics, Instituto de Tratamento do Câncer Infantil (ITACI), Faculty of Medicine, University of São Paulo, São Paulo, SP, Brazil
| | - Estela M Novak
- Department of Pediatrics, Instituto de Tratamento do Câncer Infantil (ITACI), Faculty of Medicine, University of São Paulo, São Paulo, SP, Brazil
| | | | | | - Sofia M M Sugayama
- Department of Pediatrics, Instituto de Tratamento do Câncer Infantil (ITACI), Faculty of Medicine, University of São Paulo, São Paulo, SP, Brazil
| | - Vicente Odone-Filho
- Department of Pediatrics, Instituto de Tratamento do Câncer Infantil (ITACI), Faculty of Medicine, University of São Paulo, São Paulo, SP, Brazil
| | - Ana Cristina V Krepischi
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil.
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27
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Amiel J, Héron D, Isidor B. [Exome, genome and incidental findings]. Med Sci (Paris) 2024; 40:377-380. [PMID: 38651963 DOI: 10.1051/medsci/2024029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024] Open
Affiliation(s)
- Jeanne Amiel
- Service de Médecine génomique des maladies rares, hôpital Necker-Enfants Malades, Paris
| | - Delphine Héron
- UF de génétique clinique, APHP Sorbonne Université, hôpital Pitié-Salpêtrière, Paris
| | - Bertrand Isidor
- Service de génétique médicale, unité de génétique clinique, CHU de Nantes - Hôtel Dieu, Nantes
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28
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Ohmoto A, Hayashi N, Takahashi S, Ueki A. Current prospects of hereditary adrenal tumors: towards better clinical management. Hered Cancer Clin Pract 2024; 22:4. [PMID: 38532453 DOI: 10.1186/s13053-024-00276-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Accepted: 03/14/2024] [Indexed: 03/28/2024] Open
Abstract
Adrenocortical carcinoma (ACC) and pheochromocytoma/paraganglioma (PPGL) are two rare types of adrenal gland malignancies. Regarding hereditary tumors, some patients with ACC are associated with with Li-Fraumeni syndrome (LFS), and those with PPGL with multiple endocrine neoplasia type 2. Recent studies have expanded this spectrum to include other types of hereditary tumors, such as Lynch syndrome or familial adenomatous polyposis. Individuals harboring germline TP53 pathogenic variants that cause LFS have heterogeneous phenotypes depending on the respective variant type. As an example, R337H variant found in Brazilian is known as low penetrant. While 50-80% of pediatric ACC patients harbored a LFS, such a strong causal relationship is not observed in adult patients, which suggests different pathophysiologies between the two populations. As for PPGL, because multiple driver genes, such as succinate dehydrogenase (SDH)-related genes, RET, NF1, and VHL have been identified, universal multi-gene germline panel testing is warranted as a comprehensive and cost-effective approach. PPGL pathogenesis is divided into three molecular pathways (pseudohypoxia, Wnt signaling, and kinase signaling), and this classification is expected to result in personalized medicine based on genomic profiles. It remains unknown whether clinical characteristics differ between cases derived from genetic predisposition syndromes and sporadic cases, or whether the surveillance strategy should be changed depending on the genetic background or whether it should be uniform. Close cooperation among medical genomics experts, endocrinologists, oncologists, and early investigators is indispensable for improving the clinical management for multifaceted ACC and PPGL.
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Affiliation(s)
- Akihiro Ohmoto
- Division of Medical Oncology, Cancer Institute Hospital of Japanese Foundation for Cancer Research, Tokyo, 1358550, Japan.
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, 417 East 68th Street, New York, NY, 10065, USA.
| | - Naomi Hayashi
- Division of Genomic Medicine, Cancer Institute Hospital of Japanese Foundation for Cancer Research, Tokyo, 1358550, Japan
- Division of Clinical Genetic Oncology, Cancer Institute Hospital of Japanese Foundation for Cancer Research, Tokyo, 1358550, Japan
| | - Shunji Takahashi
- Division of Medical Oncology, Cancer Institute Hospital of Japanese Foundation for Cancer Research, Tokyo, 1358550, Japan
- Division of Genomic Medicine, Cancer Institute Hospital of Japanese Foundation for Cancer Research, Tokyo, 1358550, Japan
| | - Arisa Ueki
- Division of Clinical Genetic Oncology, Cancer Institute Hospital of Japanese Foundation for Cancer Research, Tokyo, 1358550, Japan
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Ruberg FL, Maurer MS. Cardiac Amyloidosis Due to Transthyretin Protein: A Review. JAMA 2024; 331:778-791. [PMID: 38441582 PMCID: PMC11167454 DOI: 10.1001/jama.2024.0442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/07/2024]
Abstract
Importance Systemic amyloidosis from transthyretin (ATTR) protein is the most common type of amyloidosis that causes cardiomyopathy. Observations Transthyretin (TTR) protein transports thyroxine (thyroid hormone) and retinol (vitamin A) and is synthesized predominantly by the liver. When the TTR protein misfolds, it can form amyloid fibrils that deposit in the heart causing heart failure, heart conduction block, or arrhythmia such as atrial fibrillation. The biological processes by which amyloid fibrils form are incompletely understood but are associated with aging and, in some patients, affected by inherited variants in the TTR genetic sequence. ATTR amyloidosis results from misfolded TTR protein deposition. ATTR can occur in association with normal TTR genetic sequence (wild-type ATTR) or with abnormal TTR genetic sequence (variant ATTR). Wild-type ATTR primarily manifests as cardiomyopathy while ATTR due to a genetic variant manifests as cardiomyopathy and/or polyneuropathy. Approximately 50 000 to 150 000 people in the US have heart failure due to ATTR amyloidosis. Without treatment, heart failure due to ATTR amyloidosis is associated with a median survival of approximately 5 years. More than 130 different inherited genetic variants in TTR exist. The most common genetic variant is Val122Ile (pV142I), an allele with an origin in West African countries, that is present in 3.4% of African American individuals in the US or approximately 1.5 million persons. The diagnosis can be made using serum free light chain assay and immunofixation electrophoresis to exclude light chain amyloidosis combined with cardiac nuclear scintigraphy to detect radiotracer uptake in a pattern consistent with amyloidosis. Loop diuretics, such as furosemide, torsemide, and bumetanide, are the primary treatment for fluid overload and symptomatic relief of patients with ATTR heart failure. An ATTR-directed therapy that inhibited misfolding of the TTR protein (tafamidis, a protein stabilizer), compared with placebo, reduced mortality from 42.9% to 29.5%, reduced hospitalizations from 0.7/year to 0.48/year, and was most effective when administered early in disease course. Conclusions and Relevance ATTR amyloidosis causes cardiomyopathy in up to approximately 150 000 people in the US and tafamidis is the only currently approved therapy. Tafamidis slowed progression of ATTR amyloidosis and improved survival and prevented hospitalization, compared with placebo, in people with ATTR-associated cardiomyopathy.
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Affiliation(s)
- Frederick L Ruberg
- Section of Cardiovascular Medicine, Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston Medical Center, Boston, Massachusetts
- Amyloidosis Center, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts
| | - Mathew S Maurer
- Cardiac Amyloidosis Program, Seymour, Paul, and Gloria Milstein Division of Cardiology, Department of Medicine, Columbia University Irving Medical Center, and NewYork-Presbyterian Hospital, New York
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30
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Rosenblum LS, Auger SM, Zhu H, Zhou Z, Xin W, Reiner J, Wolf Z, Leach NT. Prenatal Testing for Variants in Genes Associated with Hereditary Cancer Risk: Laboratory Experience and Considerations. J Mol Diagn 2024; 26:202-212. [PMID: 38171482 DOI: 10.1016/j.jmoldx.2023.12.002] [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: 04/05/2023] [Revised: 10/29/2023] [Accepted: 12/11/2023] [Indexed: 01/05/2024] Open
Abstract
Prenatal molecular genetic testing for familial variants that cause inherited disorders has been performed for decades and is accepted as standard of care. However, the spectrum of genes considered for prenatal testing is expanding because of genetic testing for hereditary cancer risk (HCR) and inclusion of conditions with associated cancer risk in carrier screening panels. A few of these disorders, such as ataxia telangiectasia and Bloom syndrome, include increased cancer risk as part of the phenotype, already meet professional guidelines for prenatal testing, and may be associated with increased cancer risk in heterozygous carriers. In addition, recent studies implicate heterozygosity for variants in lysosomal storage disease genes in HCR etiology. Currently, there is no specific professional guidance regarding prenatal testing for HCR. To determine the prevalence of such testing, we reviewed 1345 consecutive prenatal specimens received in our laboratory for familial variant-specific testing and identified 65 (4.8%) with a known or likely HCR component, plus 210 (15.6%) for lysosomal storage disease. These specimens were classified into five distinct categories for clarity and to enable evaluation. Our experience assessing prenatal specimens for variants associated with HCR, with or without a constitutional phenotype, provides metrics for and contributes to the points to consider in prenatal testing for HCR.
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Affiliation(s)
- Lynne S Rosenblum
- Molecular Diagnostics Laboratory, Labcorp, Westborough, Massachusetts.
| | - Stephanie M Auger
- Molecular Diagnostics Laboratory, Labcorp, Westborough, Massachusetts
| | - Hui Zhu
- Molecular Diagnostics Laboratory, Labcorp, Westborough, Massachusetts
| | - Zhaoqing Zhou
- Molecular Diagnostics Laboratory, Labcorp, Westborough, Massachusetts
| | - Winnie Xin
- Molecular Diagnostics Laboratory, Labcorp, Westborough, Massachusetts
| | - Jennifer Reiner
- Molecular Diagnostics Laboratory, Labcorp, Westborough, Massachusetts
| | - Zena Wolf
- Molecular Diagnostics Laboratory, Labcorp, Westborough, Massachusetts
| | - Natalia T Leach
- Molecular Diagnostics Laboratory, Labcorp, Westborough, Massachusetts
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31
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Nolan J, Buchanan J, Taylor J, Almeida J, Bedenham T, Blair E, Broadgate S, Butler S, Cazeaux A, Craft J, Cranston T, Crawford G, Forrest J, Gabriel J, George E, Gillen D, Haeger A, Hastings Ward J, Hawkes L, Hodgkiss C, Hoffman J, Jones A, Karpe F, Kasperaviciute D, Kovacs E, Leigh S, Limb E, Lloyd-Jani A, Lopez J, Lucassen A, McFarlane C, O'Rourke AW, Pond E, Sherman C, Stewart H, Thomas E, Thomas S, Thomas T, Thomson K, Wakelin H, Walker S, Watson M, Williams E, Ormondroyd E. Secondary (additional) findings from the 100,000 Genomes Project: Disease manifestation, health care outcomes, and costs of disclosure. Genet Med 2024; 26:101051. [PMID: 38131308 DOI: 10.1016/j.gim.2023.101051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 12/15/2023] [Accepted: 12/15/2023] [Indexed: 12/23/2023] Open
Abstract
PURPOSE The UK 100,000 Genomes Project offered participants screening for additional findings (AFs) in genes associated with familial hypercholesterolemia (FH) or hereditary cancer syndromes including breast/ovarian cancer (HBOC), Lynch, familial adenomatous polyposis, MYH-associated polyposis, multiple endocrine neoplasia (MEN), and von Hippel-Lindau. Here, we report disclosure processes, manifestation of AF-related disease, outcomes, and costs. METHODS An observational study in an area representing one-fifth of England. RESULTS Data were collected from 89 adult AF recipients. At disclosure, among 57 recipients of a cancer-predisposition-associated AF and 32 recipients of an FH-associated AF, 35% and 88%, respectively, had personal and/or family history evidence of AF-related disease. During post-disclosure investigations, 4 cancer-AF recipients had evidence of disease, including 1 medullary thyroid cancer. Six women with an HBOC AF, 3 women with a Lynch syndrome AF, and 2 individuals with a MEN AF elected for risk-reducing surgery. New hyperlipidemia diagnoses were made in 6 FH-AF recipients and treatment (re-)initiated for 7 with prior hyperlipidemia. Generating and disclosing AFs in this region cost £1.4m; £8680 per clinically significant AF. CONCLUSION Generation and disclosure of AFs identifies individuals with and without personal or familial evidence of disease and prompts appropriate clinical interventions. Results can inform policy toward secondary findings.
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Affiliation(s)
- Joshua Nolan
- Radcliffe Department of Medicine, University of Oxford, United Kingdom
| | - James Buchanan
- Health Economics Research Centre, University of Oxford, United Kingdom
| | - John Taylor
- Oxford Genetic Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Joao Almeida
- Genomics England, United Kingdom Department of Health and Social Care, United Kingdom
| | - Tina Bedenham
- Oxford Genetic Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Edward Blair
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Suzanne Broadgate
- Oxford Genetic Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Samantha Butler
- Birmingham Women's and Children's Hospitals NHS Foundation Trust, Birmingham, United Kingdom
| | - Angela Cazeaux
- University Hospitals Southampton NHS Foundation Trust, Southampton, United Kingdom
| | - Judith Craft
- Oxford Genetic Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Treena Cranston
- Oxford Genetic Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Gillian Crawford
- University Hospitals Southampton NHS Foundation Trust, Southampton, United Kingdom
| | - Jamie Forrest
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom; University of Manchester, Manchester, United Kingdom
| | - Jessica Gabriel
- Oxford Genetic Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Elaine George
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
| | - Donna Gillen
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
| | - Ash Haeger
- Oxford Genetic Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | | | - Lara Hawkes
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Claire Hodgkiss
- Oxford Genetic Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Jonathan Hoffman
- Birmingham Women's and Children's Hospitals NHS Foundation Trust, Birmingham, United Kingdom
| | - Alan Jones
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
| | - Fredrik Karpe
- Radcliffe Department of Medicine, University of Oxford, United Kingdom; NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom
| | - Dalia Kasperaviciute
- Genomics England, United Kingdom Department of Health and Social Care, United Kingdom
| | - Erika Kovacs
- University Hospitals Southampton NHS Foundation Trust, Southampton, United Kingdom
| | - Sarah Leigh
- Genomics England, United Kingdom Department of Health and Social Care, United Kingdom
| | - Elizabeth Limb
- Population Health Research Institute, St George's University of London, London, United Kingdom
| | - Anjali Lloyd-Jani
- Oxford Genetic Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Javier Lopez
- Genomics England, United Kingdom Department of Health and Social Care, United Kingdom
| | - Anneke Lucassen
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom; Centre for Personalised Medicine, Nuffield Department of Medicine, University of Oxford, United Kingdom
| | - Carlos McFarlane
- Birmingham Women's and Children's Hospitals NHS Foundation Trust, Birmingham, United Kingdom
| | - Anthony W O'Rourke
- Oxford Genetic Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Emily Pond
- University Hospitals Southampton NHS Foundation Trust, Southampton, United Kingdom
| | - Catherine Sherman
- University Hospitals Southampton NHS Foundation Trust, Southampton, United Kingdom
| | - Helen Stewart
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Ellen Thomas
- Genomics England, United Kingdom Department of Health and Social Care, United Kingdom
| | - Simon Thomas
- University Hospitals Southampton NHS Foundation Trust, Southampton, United Kingdom
| | - Tessy Thomas
- University Hospitals Southampton NHS Foundation Trust, Southampton, United Kingdom
| | - Kate Thomson
- Oxford Genetic Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Hannah Wakelin
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Susan Walker
- Genomics England, United Kingdom Department of Health and Social Care, United Kingdom
| | - Melanie Watson
- University Hospitals Southampton NHS Foundation Trust, Southampton, United Kingdom
| | - Eleanor Williams
- Genomics England, United Kingdom Department of Health and Social Care, United Kingdom
| | - Elizabeth Ormondroyd
- Radcliffe Department of Medicine, University of Oxford, United Kingdom; NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom.
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D'Gama AM, Hills S, Douglas J, Young V, Genetti CA, Wojcik MH, Feldman HA, Yu TW, G Parker M, Agrawal PB. Implementation of rapid genomic sequencing in safety-net neonatal intensive care units: protocol for the VIrtual GenOme CenteR (VIGOR) proof-of-concept study. BMJ Open 2024; 14:e080529. [PMID: 38320840 PMCID: PMC10859977 DOI: 10.1136/bmjopen-2023-080529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 01/17/2024] [Indexed: 02/15/2024] Open
Abstract
INTRODUCTION Rapid genomic sequencing (rGS) in critically ill infants with suspected genetic disorders has high diagnostic and clinical utility. However, rGS has primarily been available at large referral centres with the resources and expertise to offer state-of-the-art genomic care. Critically ill infants from racial and ethnic minority and/or low-income populations disproportionately receive care in safety-net and/or community settings lacking access to state-of-the-art genomic care, contributing to unacceptable health equity gaps. VIrtual GenOme CenteR is a 'proof-of-concept' implementation science study of an innovative delivery model for genomic care in safety-net neonatal intensive care units (NICUs). METHODS AND ANALYSIS We developed a virtual genome centre at a referral centre to remotely support safety-net NICU sites predominantly serving racial and ethnic minority and/or low-income populations and have limited to no access to rGS. Neonatal providers at each site receive basic education about genomic medicine from the study team and identify eligible infants. The study team enrols eligible infants (goal n of 250) and their parents and follows families for 12 months. Enrolled infants receive rGS, the study team creates clinical interpretive reports to guide neonatal providers on interpreting results, and neonatal providers return results to families. Data is collected via (1) medical record abstraction, (2) surveys, interviews and focus groups with neonatal providers and (3) surveys and interviews with families. We aim to examine comprehensive implementation outcomes based on the Proctor Implementation Framework using a mixed methods approach. ETHICS AND DISSEMINATION This study is approved by the institutional review board of Boston Children's Hospital (IRB-P00040496) and participating sites. Participating families are required to provide electronic written informed consent and neonatal provider consent is implied through the completion of surveys. The results will be disseminated via peer-reviewed publications and data will be made accessible per National Institutes of Health (NIH) policies. TRIAL REGISTRATION NUMBER NCT05205356/clinicaltrials.gov.
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Affiliation(s)
- Alissa M D'Gama
- Division of Newborn Medicine, Department of Pediatrics, Boston Children's Hospital, Boston, Massachusetts, USA
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | - Sonia Hills
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Jessica Douglas
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Vanessa Young
- Division of Newborn Medicine, Department of Pediatrics, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Casie A Genetti
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, Massachusetts, USA
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Monica H Wojcik
- Division of Newborn Medicine, Department of Pediatrics, Harvard Medical School, Boston Children's Hospital, Boston, Massachusetts, USA
- Division of Genetics and Genomics, Department of Pediatrics, Harvard Medical School, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Henry A Feldman
- Division of Newborn Medicine, Department of Pediatrics, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Timothy W Yu
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, Massachusetts, USA
| | | | - Pankaj B Agrawal
- Division of Neonatology, Department of Pediatrics, University of Miami Miller School of Medicine, Miami, Florida, USA
- Jackson Health System, Holtz Children's Hospital, Miami, Florida, USA
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Koster R, Schipper LJ, Giesbertz NAA, van Beek D, Mendeville M, Samsom KG, Rosenberg EH, Hogervorst FBL, Roepman P, Boelens MC, Bosch LJW, van den Berg JG, Meijer GA, Voest EE, Cuppen E, Ruijs MWG, van Wezel T, van der Kolk L, Monkhorst K. Impact of genetic counseling strategy on diagnostic yield and workload for genome-sequencing-based tumor diagnostics. Genet Med 2024; 26:101032. [PMID: 38006283 DOI: 10.1016/j.gim.2023.101032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 11/17/2023] [Accepted: 11/19/2023] [Indexed: 11/26/2023] Open
Abstract
PURPOSE Genome sequencing (GS) enables comprehensive molecular analysis of tumors and identification of hereditary cancer predisposition. According to guidelines, directly determining pathogenic germline variants (PGVs) requires pretest genetic counseling, which is cost-ineffective. Referral for genetic counseling based on tumor variants alone could miss relevant PGVs and/or result in unnecessary referrals. METHODS We validated GS for detection of germline variants and simulated 3 strategies using paired tumor-normal GS data of 937 metastatic patients. In strategy-1, genetic counseling before tumor testing allowed direct PGV analysis. In strategy-2 and -3, germline testing and referral for post-test genetic counseling is based on tumor variants using Dutch (strategy-2) or Europen Society for Medical Oncology (ESMO) Precision Medicine Working Group (strategy-3) guidelines. RESULTS In strategy-1, PGVs would be detected in 50 patients (number-needed-to counsel; NTC = 18.7). In strategy-2, 86 patients would have been referred for genetic counseling and 43 would have PGVs (NTC = 2). In strategy-3, 94 patients would have been referred for genetic counseling and 32 would have PGVs (NTC = 2.9). Hence, 43 and 62 patients, respectively, were unnecessarily referred based on a somatic variant. CONCLUSION Both post-tumor test counseling strategies (2 and 3) had significantly lower NTC, and strategy-2 had the highest PGV yield. Combining pre-tumor test mainstreaming and post-tumor test counseling may maximize the clinically relevant PGV yield and minimize unnecessary referrals.
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Affiliation(s)
- Roelof Koster
- The Netherlands Cancer Institute, Amsterdam, The Netherlands.
| | - Luuk J Schipper
- The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | | | | | - Kris G Samsom
- The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | | | - Paul Roepman
- Hartwig Medical Foundation, Amsterdam, The Netherlands
| | | | - Linda J W Bosch
- The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | - Gerrit A Meijer
- The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Emile E Voest
- The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Edwin Cuppen
- Hartwig Medical Foundation, Amsterdam, The Netherlands
| | | | - Tom van Wezel
- The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | - Kim Monkhorst
- The Netherlands Cancer Institute, Amsterdam, The Netherlands.
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Roberts AM, DiStefano MT, Riggs ER, Josephs KS, Alkuraya FS, Amberger J, Amin M, Berg JS, Cunningham F, Eilbeck K, Firth HV, Foreman J, Hamosh A, Hay E, Leigh S, Martin CL, McDonagh EM, Perrett D, Ramos EM, Robinson PN, Rath A, Sant DW, Stark Z, Whiffin N, Rehm HL, Ware JS. Toward robust clinical genome interpretation: Developing a consistent terminology to characterize Mendelian disease-gene relationships-allelic requirement, inheritance modes, and disease mechanisms. Genet Med 2024; 26:101029. [PMID: 37982373 PMCID: PMC11039201 DOI: 10.1016/j.gim.2023.101029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 11/09/2023] [Accepted: 11/12/2023] [Indexed: 11/21/2023] Open
Abstract
PURPOSE The terminology used for gene-disease curation and variant annotation to describe inheritance, allelic requirement, and both sequence and functional consequences of a variant is currently not standardized. There is considerable discrepancy in the literature and across clinical variant reporting in the derivation and application of terms. Here, we standardize the terminology for the characterization of disease-gene relationships to facilitate harmonized global curation and to support variant classification within the ACMG/AMP framework. METHODS Terminology for inheritance, allelic requirement, and both structural and functional consequences of a variant used by Gene Curation Coalition members and partner organizations was collated and reviewed. Harmonized terminology with definitions and use examples was created, reviewed, and validated. RESULTS We present a standardized terminology to describe gene-disease relationships, and to support variant annotation. We demonstrate application of the terminology for classification of variation in the ACMG SF 2.0 genes recommended for reporting of secondary findings. Consensus terms were agreed and formalized in both Sequence Ontology (SO) and Human Phenotype Ontology (HPO) ontologies. Gene Curation Coalition member groups intend to use or map to these terms in their respective resources. CONCLUSION The terminology standardization presented here will improve harmonization, facilitate the pooling of curation datasets across international curation efforts and, in turn, improve consistency in variant classification and genetic test interpretation.
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Affiliation(s)
- Angharad M Roberts
- National Heart and Lung Institute and MRC London Institute of Medical Sciences, Imperial College London, London, United Kingdom; Dept of Medical Genetics, Great Ormond Street Hospital, Great Ormond Street, London, United Kingdom.
| | - Marina T DiStefano
- Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
| | | | - Katherine S Josephs
- National Heart and Lung Institute and MRC London Institute of Medical Sciences, Imperial College London, London, United Kingdom; Royal Brompton and Harefield Hospitals, Guy's and St. Thomas' NHS Foundation Trust, London, United Kingdom
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, KFSHRC, Riyadh, Saudi Arabia
| | - Joanna Amberger
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | | | - Jonathan S Berg
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Fiona Cunningham
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Karen Eilbeck
- Department of Biomedical Informatics, University of Utah, Salt Lake City, UT
| | - Helen V Firth
- Dept of Medical Genetics, Cambridge University Hospitals, Cambridge, United Kingdom; Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Julia Foreman
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Ada Hamosh
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Eleanor Hay
- Dept of Medical Genetics, Great Ormond Street Hospital, Great Ormond Street, London, United Kingdom
| | - Sarah Leigh
- Genomics England, Queen Mary University of London, Dawson Hall, London, United Kingdom
| | | | - Ellen M McDonagh
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom; Open Targets, Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Daniel Perrett
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Erin M Ramos
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | | | - Ana Rath
- INSERM, US14-Orphanet, Paris, France
| | - David W Sant
- Department of Biomedical Informatics, University of Utah, Salt Lake City, UT
| | - Zornitza Stark
- Australian Genomics, Melbourne 3052, Australia; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne 3052, Australia; University of Melbourne, Melbourne 3052, Australia
| | - Nicola Whiffin
- Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Big Data Institute and Wellcome Centre for Human Genetics, University of Oxford, United Kingdom
| | - Heidi L Rehm
- Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
| | - James S Ware
- National Heart and Lung Institute and MRC London Institute of Medical Sciences, Imperial College London, London, United Kingdom; Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Royal Brompton and Harefield Hospitals, Guy's and St. Thomas' NHS Foundation Trust, London, United Kingdom
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Mitchell LA, Jivani K, Young MA, Jacobs C, Willis AM. Systematic review of the uptake and outcomes from returning secondary findings to adult participants in research genomic testing. J Genet Couns 2024. [PMID: 38197527 DOI: 10.1002/jgc4.1865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 12/06/2023] [Accepted: 12/09/2023] [Indexed: 01/11/2024]
Abstract
The increasing use of genomic sequencing in research means secondary findings (SF) is more frequently detected and becoming a more pressing issue for researchers. This is reflected by the recent publication of multiple guidelines on this issue, calling for researchers to have a plan for managing SF prior to commencing their research. A deeper understanding of participants' experiences and outcomes from receiving SF is needed to ensure that the return of SF is conducted ethically and with adequate support. This review focuses on the uptake and outcomes of receiving actionable SF for research participants. This review included studies from January 2010 to January 2023. Databases searched included Medline, Embase, PsycINFO, and Scopus. Of the 3903 studies identified, 29 were included in the analysis. The uptake of SF ranged between 20% and 97%, and outcomes were categorized into psychological, clinical, lifestyle and behavioral, and family outcomes. The results indicate there is minimal psychological impact from receiving SF. Almost all participants greatly valued receiving SF. These findings highlight considerations for researchers when returning results, including the importance of involving genetic health professionals in consenting, results return process, and ensuring continuity of care by engaging healthcare providers.
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Affiliation(s)
- Lucas A Mitchell
- Clinical Translation and Engagement Platform, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
- School of Clinical Medicine, St Vincent's Healthcare Clinical Campus, Faculty of Medicine and Health, UNSW Sydney, Sydney, New South Wales, Australia
| | - Karishma Jivani
- Graduate School of Health, University of Technology Sydney, Ultimo, New South Wales, Australia
| | - Mary-Anne Young
- Clinical Translation and Engagement Platform, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
- School of Clinical Medicine, St Vincent's Healthcare Clinical Campus, Faculty of Medicine and Health, UNSW Sydney, Sydney, New South Wales, Australia
| | - Chris Jacobs
- Graduate School of Health, University of Technology Sydney, Ultimo, New South Wales, Australia
| | - Amanda M Willis
- Clinical Translation and Engagement Platform, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
- School of Clinical Medicine, St Vincent's Healthcare Clinical Campus, Faculty of Medicine and Health, UNSW Sydney, Sydney, New South Wales, Australia
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Wiley LK, Shortt JA, Roberts ER, Lowery J, Kudron E, Lin M, Mayer D, Wilson M, Brunetti TM, Chavan S, Phang TL, Pozdeyev N, Lesny J, Wicks SJ, Moore ET, Morgenstern JL, Roff AN, Shalowitz EL, Stewart A, Williams C, Edelmann MN, Hull M, Patton JT, Axell L, Ku L, Lee YM, Jirikowic J, Tanaka A, Todd E, White S, Peterson B, Hearst E, Zane R, Greene CS, Mathias R, Coors M, Taylor M, Ghosh D, Kahn MG, Brooks IM, Aquilante CL, Kao D, Rafaels N, Crooks KR, Hess S, Barnes KC, Gignoux CR. Building a vertically integrated genomic learning health system: The biobank at the Colorado Center for Personalized Medicine. Am J Hum Genet 2024; 111:11-23. [PMID: 38181729 PMCID: PMC10806731 DOI: 10.1016/j.ajhg.2023.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 11/30/2023] [Accepted: 12/01/2023] [Indexed: 01/07/2024] Open
Abstract
Precision medicine initiatives across the globe have led to a revolution of repositories linking large-scale genomic data with electronic health records, enabling genomic analyses across the entire phenome. Many of these initiatives focus solely on research insights, leading to limited direct benefit to patients. We describe the biobank at the Colorado Center for Personalized Medicine (CCPM Biobank) that was jointly developed by the University of Colorado Anschutz Medical Campus and UCHealth to serve as a unique, dual-purpose research and clinical resource accelerating personalized medicine. This living resource currently has more than 200,000 participants with ongoing recruitment. We highlight the clinical, laboratory, regulatory, and HIPAA-compliant informatics infrastructure along with our stakeholder engagement, consent, recontact, and participant engagement strategies. We characterize aspects of genetic and geographic diversity unique to the Rocky Mountain region, the primary catchment area for CCPM Biobank participants. We leverage linked health and demographic information of the CCPM Biobank participant population to demonstrate the utility of the CCPM Biobank to replicate complex trait associations in the first 33,674 genotyped individuals across multiple disease domains. Finally, we describe our current efforts toward return of clinical genetic test results, including high-impact pathogenic variants and pharmacogenetic information, and our broader goals as the CCPM Biobank continues to grow. Bringing clinical and research interests together fosters unique clinical and translational questions that can be addressed from the large EHR-linked CCPM Biobank resource within a HIPAA- and CLIA-certified environment.
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Affiliation(s)
- Laura K Wiley
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; Department of Biomedical Informatics, University of Colorado School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Jonathan A Shortt
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; Department of Biomedical Informatics, University of Colorado School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Emily R Roberts
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Jan Lowery
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; University of Colorado Cancer Center, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; Department of Community and Behavioral Health, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Elizabeth Kudron
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; Department of Biomedical Informatics, University of Colorado School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Meng Lin
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; Department of Biomedical Informatics, University of Colorado School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - David Mayer
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; Department of Biomedical Informatics, University of Colorado School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Melissa Wilson
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; Department of Biomedical Informatics, University of Colorado School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Tonya M Brunetti
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Sameer Chavan
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Tzu L Phang
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Nikita Pozdeyev
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; Department of Biomedical Informatics, University of Colorado School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Joseph Lesny
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Stephen J Wicks
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Ethan T Moore
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Joshua L Morgenstern
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Alanna N Roff
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Elise L Shalowitz
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Adrian Stewart
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Cole Williams
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Michelle N Edelmann
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Madelyne Hull
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - J Tacker Patton
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Lisen Axell
- CU Cancer Center, Hereditary Cancer Clinic, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Lisa Ku
- CU Cancer Center, Hereditary Cancer Clinic, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Yee Ming Lee
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; Department of Clinical Pharmacy, University of Colorado Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | | | | | - Emily Todd
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; UCHealth, Aurora, CO 80045, USA
| | | | - Brett Peterson
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | | | - Richard Zane
- UCHealth, Aurora, CO 80045, USA; University of Colorado School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Casey S Greene
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; Department of Biomedical Informatics, University of Colorado School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Rasika Mathias
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Marilyn Coors
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Matthew Taylor
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; Division of Cardiology, University of Colorado School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Debashis Ghosh
- Department of Biostatistics and Informatics, Colorado School of Public Health, Aurora, CO 80045, USA
| | - Michael G Kahn
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Ian M Brooks
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; Department of Biomedical Informatics, University of Colorado School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Christina L Aquilante
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; Department of Pharmaceutical Sciences, University of Colorado Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - David Kao
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; Division of Cardiology, University of Colorado School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; CARE Innovation Center, UCHealth, Aurora, CO 80045, USA
| | - Nicholas Rafaels
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Kristy R Crooks
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; Department of Pathology, University of Colorado School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | | | - Kathleen C Barnes
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
| | - Christopher R Gignoux
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; Department of Biomedical Informatics, University of Colorado School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
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Gold NB, Nadel A, Green RC. Ready or not, genomic screening of fetuses is already here. Genet Med 2024; 26:101008. [PMID: 37860970 PMCID: PMC10842943 DOI: 10.1016/j.gim.2023.101008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 10/12/2023] [Accepted: 10/13/2023] [Indexed: 10/21/2023] Open
Affiliation(s)
- Nina B Gold
- Division of Medical Genetics and Metabolism, Massachusetts General Hospital for Children, Boston, MA; Harvard Medical School, Boston, MA.
| | - Allan Nadel
- Harvard Medical School, Boston, MA; Department of Obstetrics and Gynecology, Massachusetts General Hospital, Boston, MA
| | - Robert C Green
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA; Ariadne Labs, Boston, MA; Department of Medicine, Harvard Medical School, Boston, MA; Broad Institute, Boston, MA
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Guo F, Liu R, Pan Y, Collins C, Bean L, Ma Z, Mathur A, Da Silva C, Nallamilli B, Guruju N, Chen-Deutsch X, Yousaf R, Chin E, Balciuniene J, Hegde M. Evidence from 2100 index cases supports genome sequencing as a first-tier genetic test. Genet Med 2024; 26:100995. [PMID: 37838930 DOI: 10.1016/j.gim.2023.100995] [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: 03/16/2023] [Revised: 10/04/2023] [Accepted: 10/06/2023] [Indexed: 10/16/2023] Open
Abstract
PURPOSE Genome sequencing (GS) is one of the most comprehensive assays that interrogate single-nucleotide variants, copy number variants, mitochondrial variants, repeat expansions, and structural variants in a single assay. Despite the clear technical superiority, the full clinical utility of GS has yet to be determined. METHODS We systematically evaluated 2100 clinical GS index cases performed in our laboratory to explore the diagnostic yield of GS as first-tier and as follow-up testing. RESULTS The overall diagnostic yield was 28% (585/2100). The diagnostic yield for GS as the first-tier test was 26% (294/1146). Among cases with prior non-diagnostic genetic tests, GS provided a diagnosis for 27% (247/910) of cases, including 56 cases with prior exome sequencing (ES). Although re-analysis of previous ES might have resolved the diagnosis in 29 cases, diagnoses for 27 cases would have been missed because of the technical inferiority of ES. Moreover, GS further disclosed additional genetic etiology in 3 out of 44 cases with existing partial diagnosis. CONCLUSION We present the largest-to-date GS data set of a clinically heterogeneous cohort from a single clinical laboratory. Our data demonstrate that GS should be considered as the first-tier genetic test that has the potential to shorten the diagnostic odyssey.
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Affiliation(s)
- Fen Guo
- Revvity Omics, Pittsburgh, PA.
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Deutsche Gesellschaft für Humangenetik e.V. (GfH). MED GENET-BERLIN 2023; 35:313-321. [PMID: 38841542 PMCID: PMC11006314 DOI: 10.1515/medgen-2023-2060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2024]
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40
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Balasar Ö, Başdemirci M. Assessment of whole-exome sequencing results in neurogenetic diseases. J Hum Genet 2023; 68:797-804. [PMID: 37524782 DOI: 10.1038/s10038-023-01185-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 06/22/2023] [Accepted: 07/19/2023] [Indexed: 08/02/2023]
Abstract
Neurogenetic diseases are rare genetic diseases in which neurological findings are prominent. Whole exome sequencing (WES) has led to great advances in the understanding of the causes of neurogenetic diseases. Etiological research ends with the WES method in many patients. This etiological research is called a "diagnostic odyssey" for many families. Here, we present the results of 168 patients who were previously undiagnosed and underwent WES with the suspicion of neurogenetic disease. A total of 168 cases, 94 males and 74 females, with suspected undiagnosed neurogenetic disease were included in the study. We presented the WES results of the patients. The mean age of patients at the time of WES request was 11 years (range 0.25-68 years). Seventy percent (n = 117) of the patients were born from consanguineous marriage. Most of the patients were children (n = 145). Patients were grouped according to age at the time of examination. Patients younger than 18 years of age at the time of examination were classified as children, otherwise adults. Seventy-eight patients had either a pathogenic variant or a likely pathogenic variant so the diagnostic rate for WES in our cohort was %46. Our experience showing the high diagnostic rate of WES, supports its use in undiagnosed neurogenetic diseases. It also affects medical treatment, prognosis and family planning by enabling early diagnosis in patients.
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Affiliation(s)
- Özgür Balasar
- Department of Medical Genetics, Konya City Hospital, Konya, Turkey.
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41
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Sun KY, Bai X, Chen S, Bao S, Kapoor M, Zhang C, Backman J, Joseph T, Maxwell E, Mitra G, Gorovits A, Mansfield A, Boutkov B, Gokhale S, Habegger L, Marcketta A, Locke A, Kessler MD, Sharma D, Staples J, Bovijn J, Gelfman S, Gioia AD, Rajagopal V, Lopez A, Varela JR, Alegre J, Berumen J, Tapia-Conyer R, Kuri-Morales P, Torres J, Emberson J, Collins R, Cantor M, Thornton T, Kang HM, Overton J, Shuldiner AR, Cremona ML, Nafde M, Baras A, Abecasis G, Marchini J, Reid JG, Salerno W, Balasubramanian S. A deep catalog of protein-coding variation in 985,830 individuals. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.09.539329. [PMID: 37214792 PMCID: PMC10197621 DOI: 10.1101/2023.05.09.539329] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Coding variants that have significant impact on function can provide insights into the biology of a gene but are typically rare in the population. Identifying and ascertaining the frequency of such rare variants requires very large sample sizes. Here, we present the largest catalog of human protein-coding variation to date, derived from exome sequencing of 985,830 individuals of diverse ancestry to serve as a rich resource for studying rare coding variants. Individuals of African, Admixed American, East Asian, Middle Eastern, and South Asian ancestry account for 20% of this Exome dataset. Our catalog of variants includes approximately 10.5 million missense (54% novel) and 1.1 million predicted loss-of-function (pLOF) variants (65% novel, 53% observed only once). We identified individuals with rare homozygous pLOF variants in 4,874 genes, and for 1,838 of these this work is the first to document at least one pLOF homozygote. Additional insights from the RGC-ME dataset include 1) improved estimates of selection against heterozygous loss-of-function and identification of 3,459 genes intolerant to loss-of-function, 83 of which were previously assessed as tolerant to loss-of-function and 1,241 that lack disease annotations; 2) identification of regions depleted of missense variation in 457 genes that are tolerant to loss-of-function; 3) functional interpretation for 10,708 variants of unknown or conflicting significance reported in ClinVar as cryptic splice sites using splicing score thresholds based on empirical variant deleteriousness scores derived from RGC-ME; and 4) an observation that approximately 3% of sequenced individuals carry a clinically actionable genetic variant in the ACMG SF 3.1 list of genes. We make this important resource of coding variation available to the public through a variant allele frequency browser. We anticipate that this report and the RGC-ME dataset will serve as a valuable reference for understanding rare coding variation and help advance precision medicine efforts.
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Affiliation(s)
| | | | - Siying Chen
- Regeneron Genetics Center, Tarrytown, NY, USA
| | - Suying Bao
- Regeneron Genetics Center, Tarrytown, NY, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | - Adam Locke
- Regeneron Genetics Center, Tarrytown, NY, USA
| | | | | | | | | | | | | | | | | | | | - Jesus Alegre
- Experimental Research Unit from the Faculty of Medicine (UIME), National Autonomous University of Mexico (UNAM)
| | - Jaime Berumen
- Experimental Research Unit from the Faculty of Medicine (UIME), National Autonomous University of Mexico (UNAM)
| | - Roberto Tapia-Conyer
- Experimental Research Unit from the Faculty of Medicine (UIME), National Autonomous University of Mexico (UNAM)
| | - Pablo Kuri-Morales
- Experimental Research Unit from the Faculty of Medicine (UIME), National Autonomous University of Mexico (UNAM)
| | - Jason Torres
- Clinical Trial Service Unit & Epidemiological Studies Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Jonathan Emberson
- Clinical Trial Service Unit & Epidemiological Studies Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
- MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Rory Collins
- Clinical Trial Service Unit & Epidemiological Studies Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | | | | | | | | | | | | | | | | | - Mona Nafde
- Regeneron Genetics Center, Tarrytown, NY, USA
| | - Aris Baras
- Regeneron Genetics Center, Tarrytown, NY, USA
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42
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Vassy JL, Brunette CA, Lebo MS, MacIsaac K, Yi T, Danowski ME, Alexander NVJ, Cardellino MP, Christensen KD, Gala M, Green RC, Harris E, Jones NE, Kerman BJ, Kraft P, Kulkarni P, Lewis ACF, Lubitz SA, Natarajan P, Antwi AA. The GenoVA study: Equitable implementation of a pragmatic randomized trial of polygenic-risk scoring in primary care. Am J Hum Genet 2023; 110:1841-1852. [PMID: 37922883 PMCID: PMC10645559 DOI: 10.1016/j.ajhg.2023.10.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 10/03/2023] [Accepted: 10/03/2023] [Indexed: 11/07/2023] Open
Abstract
Polygenic risk scores (PRSs) hold promise for disease risk assessment and prevention. The Genomic Medicine at Veterans Affairs (GenoVA) Study is addressing three main challenges to the clinical implementation of PRSs in preventive care: defining and determining their clinical utility, implementing them in time-constrained primary care settings, and countering their potential to exacerbate healthcare disparities. The study processes used to test patients, report their PRS results to them and their primary care providers (PCPs), and promote the use of those results in clinical decision-making are modeled on common practices in primary care. The following diseases were chosen for their prevalence and familiarity to PCPs: coronary artery disease; type 2 diabetes; atrial fibrillation; and breast, colorectal, and prostate cancers. A randomized clinical trial (RCT) design and primary outcome of time-to-new-diagnosis of a target disease bring methodological rigor to the question of the clinical utility of PRS implementation. The study's pragmatic RCT design enhances its relevance to how PRS might reasonably be implemented in primary care. Steps the study has taken to promote health equity include the thoughtful handling of genetic ancestry in PRS construction and reporting and enhanced recruitment strategies to address underrepresentation in research participation. To date, enhanced recruitment efforts have been both necessary and successful: participants of underrepresented race and ethnicity groups have been less likely to enroll in the study than expected but ultimately achieved proportional representation through targeted efforts. The GenoVA Study experience to date offers insights for evaluating the clinical utility of equitable PRS implementation in adult primary care.
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Affiliation(s)
- Jason L Vassy
- VA Boston Healthcare System, Boston, MA, USA; Division of General Internal Medicine and Primary Care, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA; Ariadne Labs, Boston, MA, USA.
| | - Charles A Brunette
- VA Boston Healthcare System, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Matthew S Lebo
- Harvard Medical School, Boston, MA, USA; Laboratory for Molecular Medicine, Mass General Brigham, Boston, MA, USA; Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | | | - Thomas Yi
- VA Boston Healthcare System, Boston, MA, USA
| | | | - Nicholas V J Alexander
- VA Boston Healthcare System, Boston, MA, USA; Bucharest University Emergency Hospital, Bucharest, Romania; Bucharest University of Economic Studies, Bucharest, Romania
| | | | - Kurt D Christensen
- Harvard Medical School, Boston, MA, USA; Department of Population Medicine, Harvard Pilgrim Health Care Institute, Boston, MA, USA
| | - Manish Gala
- Harvard Medical School, Boston, MA, USA; Division of Gastroenterology and Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Robert C Green
- Harvard Medical School, Boston, MA, USA; Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA; Ariadne Labs, Boston, MA, USA; Department of Medicine (Genetics), Mass General Brigham, Boston, MA, USA
| | | | - Natalie E Jones
- VA Boston Healthcare System, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Benjamin J Kerman
- Division of General Internal Medicine and Primary Care, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Peter Kraft
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | | | - Anna C F Lewis
- Department of Medicine (Genetics), Mass General Brigham, Boston, MA, USA; Edmond and Lily Safra Center for Ethics, Harvard University, Boston, MA, USA
| | - Steven A Lubitz
- Demoulas Center for Cardiac Arrhythmias, Massachusetts General Hospital, Boston, MA, USA; Novartis Institutes for BioMedical Research, Novartis, Basel, Basel-Stadt, Switzerland
| | - Pradeep Natarajan
- Harvard Medical School, Boston, MA, USA; Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
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43
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Kim Y, Kim JM, Cho HW, Park HY, Park MH. Frequency of actionable secondary findings in 7472 Korean genomes derived from the National Project of Bio Big Data pilot study. Hum Genet 2023; 142:1561-1569. [PMID: 37728764 PMCID: PMC10602966 DOI: 10.1007/s00439-023-02592-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 08/14/2023] [Indexed: 09/21/2023]
Abstract
Exome and genome sequencing (ES/GS) in genetic medicine and research leads to discovering genomic secondary findings (SFs) unrelated to the purpose of the primary test. There is a lack of agreement to return the SF results for individuals undergoing the test. The aim of this study is to investigate the frequency of actionable secondary findings using GS data obtained from the rare disease study and the Korean Genome and Epidemiology Study (KoGES) in the National Project of Bio Big Data pilot study. Pathogenic (P) or likely pathogenic (LP) variants of 78 SF genes recommended by the American College of Medical Genetics and Genomics (ACMG) were screened in the rare disease study and KoGES. The pathogenicity of SF gene variants was determined according to the ACMG interpretation. The overall SF rate was 3.75% for 280 individuals with 298 P/LP variants of 41 ACMG SF genes which were identified among 7472 study participants. The frequencies of genes associated with cardiovascular, cancer, and miscellaneous phenotypes were 2.17%, 1.22%, and 0.58%, respectively. The most frequent SF gene was TTN followed by BRCA2. The frequency of actionable SFs among participants with rare disease and general population participants in the Korean population presented here will assist in reporting results of medically actionable SFs in genomic medicine.
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Affiliation(s)
- Youngjun Kim
- Division of Genome Science, Department of Precision Medicine, National Institute of Health, Cheongju, Republic of Korea
| | - Jeong-Min Kim
- Division of Genome Science, Department of Precision Medicine, National Institute of Health, Cheongju, Republic of Korea
| | - Hye-Won Cho
- Division of Genome Science, Department of Precision Medicine, National Institute of Health, Cheongju, Republic of Korea
| | - Hyun-Young Park
- Department of Precision Medicine, National Institute of Health, Cheongju, Republic of Korea.
| | - Mi-Hyun Park
- Division of Genome Science, Department of Precision Medicine, National Institute of Health, Cheongju, Republic of Korea.
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44
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Brennenstuhl H, Schaaf CP. [Genomic newborn screening-research approaches, challenges, and opportunities]. Bundesgesundheitsblatt Gesundheitsforschung Gesundheitsschutz 2023; 66:1232-1242. [PMID: 37831095 PMCID: PMC10622372 DOI: 10.1007/s00103-023-03777-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 09/12/2023] [Indexed: 10/14/2023]
Abstract
The application of high-throughput sequencing methods for population-based genomic newborn screening offers numerous opportunities for improving population health. The use of genome-based sequencing technology holds potential to enable the diagnosis of virtually any genetic disorder at an early stage and offers great flexibility when it comes to selection and expansion of target diseases. National and international efforts are therefore being made to investigate the ethical, legal, social, psychological, and technical aspects of genomic newborn screening. In addition to the many opportunities, there are numerous challenges and questions that remain to be answered: When and how should legal guardians be informed about such screening? Which diseases should be screened for? How should incidental findings or identification of a genetic predisposition be dealt with? Should data be stored long term and if so, how can this be done securely? Provided there is an appropriate regulatory framework and a transparent consent process, genomic newborn screening has the potential to fundamentally change the way in which we screen for congenital diseases. However, there is still much to be done. To achieve understanding and acceptance of genomic newborn screening amongst all stakeholders and thus to maximize its benefits for the population, a public discourse on the possibilities and limitations of genomic newborn screening is of critical importance. This article aims to provide an overview of the innovative technical developments in the field of human genetics, describe national and international approaches, and discuss challenges and opportunities of genomic newborn screening development.
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Affiliation(s)
- Heiko Brennenstuhl
- Institut für Humangenetik, Universität Heidelberg, Heidelberg, Baden-Württemberg, Deutschland
| | - Christian P Schaaf
- Institut für Humangenetik, Universität Heidelberg, Heidelberg, Baden-Württemberg, Deutschland.
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45
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Smith HS, Bonkowski ES, Hickingbotham MR, Pereira S, May T, Guerrini CJ. Clinically Indicated Genomic Sequencing of Children in Foster Care: Legal and Ethical Issues. J Pediatr 2023; 262:113612. [PMID: 37468037 PMCID: PMC10792112 DOI: 10.1016/j.jpeds.2023.113612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 07/03/2023] [Accepted: 07/11/2023] [Indexed: 07/21/2023]
Abstract
There are approximately 400 000 children in foster care in the US, approximately one-half of whom have chronic health problems and approximately 10% of whom have complex healthcare needs. Given the increasing relevance of genomic sequencing to guide clinical care for children with rare, chronic, and undiagnosed conditions, it may be an important component of diagnostic evaluation for children in foster care. Clinically indicated genomic sequencing may provide information that has health implications for children in foster care, as well as for their biological parents and other relatives. Whether and how genomic sequencing results impact legal decision making and family court outcomes is not yet well-understood. We describe scenarios that highlight legal, ethical, and policy issues surrounding genomic sequencing for children in foster care using 3 cases adapted from real-world events. Together, these cases highlight important yet underexplored issues that arise when genomic information has legal relevance in family court and ethical implications for child and family well-being. As genomic sequencing becomes more routine for the general pediatric population, additional research is needed to better understand its impacts on children and other stakeholders within the foster care system.
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Affiliation(s)
- Hadley Stevens Smith
- Department of Population Medicine, Precision Medicine Translational Research (PROMoTeR) Center, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA.
| | - Emily S Bonkowski
- St. Jude Children's Research Hospital, Memphis, TN; University of Washington Institute for Public Health Genetics, Seattle, WA
| | - Madison R Hickingbotham
- Department of Population Medicine, Precision Medicine Translational Research (PROMoTeR) Center, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA
| | - Stacey Pereira
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX
| | - Thomas May
- Department of Medical Education and Clinical Sciences, Washington State University, Pullman, WA
| | - Christi J Guerrini
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX
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46
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Koyama S, Wang Y, Paruchuri K, Uddin MM, Cho SMJ, Urbut SM, Haidermota S, Hornsby WE, Green RC, Daly MJ, Neale BM, Ellinor PT, Smoller JW, Lebo MS, Karlson EW, Martin AR, Natarajan P. Decoding Genetics, Ancestry, and Geospatial Context for Precision Health. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.10.24.23297096. [PMID: 37961173 PMCID: PMC10635180 DOI: 10.1101/2023.10.24.23297096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Mass General Brigham, an integrated healthcare system based in the Greater Boston area of Massachusetts, annually serves 1.5 million patients. We established the Mass General Brigham Biobank (MGBB), encompassing 142,238 participants, to unravel the intricate relationships among genomic profiles, environmental context, and disease manifestations within clinical practice. In this study, we highlight the impact of ancestral diversity in the MGBB by employing population genetics, geospatial assessment, and association analyses of rare and common genetic variants. The population structures captured by the genetics mirror the sequential immigration to the Greater Boston area throughout American history, highlighting communities tied to shared genetic and environmental factors. Our investigation underscores the potency of unbiased, large-scale analyses in a healthcare-affiliated biobank, elucidating the dynamic interplay across genetics, immigration, structural geospatial factors, and health outcomes in one of the earliest American sites of European colonization.
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Affiliation(s)
- Satoshi Koyama
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Ying Wang
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kaavya Paruchuri
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Md Mesbah Uddin
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - So Mi J. Cho
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Integrative Research Center for Cerebrovascular and Cardiovascular Diseases, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Sarah M. Urbut
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Sara Haidermota
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Whitney E. Hornsby
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Robert C. Green
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Department of Medicine (Genetics), MassGeneralBrigham, Boston, MA, USA
- Broad Institute and Ariadne Labs, Boston, MA, USA
| | - Mark J. Daly
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Institute for Molecular Medicine Finland (FIMM), Finland
- University of Helsinki, Helsinki, Finland
| | - Benjamin M. Neale
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Patrick T. Ellinor
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Jordan W. Smoller
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Center for Precision Psychiatry, Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
| | - Matthew S. Lebo
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Mass General Brigham Personalized Medicine, Cambridge, MA, USA
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, USA
| | - Elizabeth W. Karlson
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Mass General Brigham Personalized Medicine, Cambridge, MA, USA
- Division of Rheumatology, Inflammation and Immunity, Department of Medicine, Brigham and Women’s Hospital., Boston, MA, USA
| | - Alicia R. Martin
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Pradeep Natarajan
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
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47
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Josephs KS, Roberts AM, Theotokis P, Walsh R, Ostrowski PJ, Edwards M, Fleming A, Thaxton C, Roberts JD, Care M, Zareba W, Adler A, Sturm AC, Tadros R, Novelli V, Owens E, Bronicki L, Jarinova O, Callewaert B, Peters S, Lumbers T, Jordan E, Asatryan B, Krishnan N, Hershberger RE, Chahal CAA, Landstrom AP, James C, McNally EM, Judge DP, van Tintelen P, Wilde A, Gollob M, Ingles J, Ware JS. Beyond gene-disease validity: capturing structured data on inheritance, allelic requirement, disease-relevant variant classes, and disease mechanism for inherited cardiac conditions. Genome Med 2023; 15:86. [PMID: 37872640 PMCID: PMC10594882 DOI: 10.1186/s13073-023-01246-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 10/12/2023] [Indexed: 10/25/2023] Open
Abstract
BACKGROUND As the availability of genomic testing grows, variant interpretation will increasingly be performed by genomic generalists, rather than domain-specific experts. Demand is rising for laboratories to accurately classify variants in inherited cardiac condition (ICC) genes, including secondary findings. METHODS We analyse evidence for inheritance patterns, allelic requirement, disease mechanism and disease-relevant variant classes for 65 ClinGen-curated ICC gene-disease pairs. We present this information for the first time in a structured dataset, CardiacG2P, and assess application in genomic variant filtering. RESULTS For 36/65 gene-disease pairs, loss of function is not an established disease mechanism, and protein truncating variants are not known to be pathogenic. Using the CardiacG2P dataset as an initial variant filter allows for efficient variant prioritisation whilst maintaining a high sensitivity for retaining pathogenic variants compared with two other variant filtering approaches. CONCLUSIONS Access to evidence-based structured data representing disease mechanism and allelic requirement aids variant filtering and analysis and is a pre-requisite for scalable genomic testing.
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Affiliation(s)
- Katherine S Josephs
- National Heart and Lung Institute, Imperial College London, Du Cane Road, London, W12 0NN, UK
- Royal Brompton and Harefield Hospitals, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Angharad M Roberts
- National Heart and Lung Institute, Imperial College London, Du Cane Road, London, W12 0NN, UK
- Great Ormond Street Hospital, NHS Foundation Trust, London, UK
| | - Pantazis Theotokis
- National Heart and Lung Institute, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Roddy Walsh
- Amsterdam University Medical Centre, University of Amsterdam, Heart Center, Department of Experimental Cardiology, Amsterdam Cardiovascular Sciences, Amsterdam, The Netherlands
| | | | - Matthew Edwards
- Clinical Genetics & Genomics Lab, Royal Brompton and Harefield Hospitals, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Andrew Fleming
- Clinical Genetics & Genomics Lab, Royal Brompton and Harefield Hospitals, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Courtney Thaxton
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jason D Roberts
- Population Health Research Institute, McMaster University, and Hamilton Health Sciences, Hamilton, Ontario, Canada
| | - Melanie Care
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
- Division of Cardiology, Toronto General Hospital, Toronto, Canada
| | - Wojciech Zareba
- Clinical Cardiovascular Research Center, University of Rochester, Rochester, NY, USA
| | - Arnon Adler
- Division of Cardiology, Peter Munk Cardiac Centre, University Health Network and Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | | | - Rafik Tadros
- Cardiovascular Genetics Center, Montreal Heart Institute, and Faculty of Medicine, Université de Montréal, Montreal, Canada
| | - Valeria Novelli
- Unit of Immunology and Functional Genomics, Centro Cardiologico Monzino IRCCS, Milano, Italy
| | - Emma Owens
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Lucas Bronicki
- Department of Pathology and Laboratory Medicine, University of Ottawa, Ottawa, Ontario, Canada
- Department of Genetics, CHEO, Ottawa, Ontario, Canada
| | - Olga Jarinova
- Department of Pathology and Laboratory Medicine, University of Ottawa, Ottawa, Ontario, Canada
- Department of Genetics, CHEO, Ottawa, Ontario, Canada
| | - Bert Callewaert
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Stacey Peters
- Department of Cardiology and Genomic Medicine, Royal Melbourne Hospital, Melbourne, Australia
- University of Melbourne, Melbourne, Australia
| | - Tom Lumbers
- Barts Health & University College London Hospitals NHS Trusts, London, UK
- Institute of Health Informatics, University College London, London, UK
| | - Elizabeth Jordan
- Divisions of Human Genetics and Cardiovascular Medicine, The Ohio State University, Columbus, OH, USA
| | - Babken Asatryan
- Department of Cardiology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Neesha Krishnan
- Centre for Population Genomics, Garvan Institute of Medical Research, and UNSW Sydney, Sydney, Australia
| | - Ray E Hershberger
- Divisions of Human Genetics and Cardiovascular Medicine, The Ohio State University, Columbus, OH, USA
| | - C Anwar A Chahal
- Center for Inherited Cardiovascular Diseases, WellSpan Health, Lancaster, PA, USA
- Cardiac Electrophysiology and Inherited Cardiovascular Diseases, Cardiovascular Division, Hospital of the University of Pennsylvania, Philadelphia, PA, USA
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN, USA
- Barts Heart Centre, St Bartholomew's Hospital, Barts Health NHS Trust, London, UK
| | - Andrew P Landstrom
- Department of Pediatrics and Cell Biology, Duke University School of Medicine, Durham, NC, USA
| | - Cynthia James
- Johns Hopkins Center for Inherited Heart Diseases, Department of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Elizabeth M McNally
- Center for Genetic Medicine, Dept of Medicine (Cardiology), Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Daniel P Judge
- Medical University of South Carolina, Charleston, SC, USA
| | - Peter van Tintelen
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Arthur Wilde
- Department of Cardiology, Amsterdam UMC location University of Amsterdam, Meibergdreef 9, Amsterdam, the Netherlands
- Amsterdam Cardiovascular Sciences, Heart Failure and Arrhythmias, Amsterdam UMC location University of Amsterdam, Amsterdam, the Netherlands
| | - Michael Gollob
- Inherited Arrhythmia and Cardiomyopathy Program, Division of Cardiology, University of Toronto, Toronto, ON, Canada
| | - Jodie Ingles
- Centre for Population Genomics, Garvan Institute of Medical Research, and UNSW Sydney, Sydney, Australia
| | - James S Ware
- National Heart and Lung Institute, Imperial College London, Du Cane Road, London, W12 0NN, UK.
- Royal Brompton and Harefield Hospitals, Guy's and St Thomas' NHS Foundation Trust, London, UK.
- MRC London Institute of Medical Sciences, Imperial College London, London, UK.
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48
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Menzel M, Ossowski S, Kral S, Metzger P, Horak P, Marienfeld R, Boerries M, Wolter S, Ball M, Neumann O, Armeanu-Ebinger S, Schroeder C, Matysiak U, Goldschmid H, Schipperges V, Fürstberger A, Allgäuer M, Eberhardt T, Niewöhner J, Blaumeiser A, Ploeger C, Haack TB, Tay TKY, Kelemen O, Pauli T, Kirchner M, Kluck K, Ott A, Renner M, Admard J, Gschwind A, Lassmann S, Kestler H, Fend F, Illert AL, Werner M, Möller P, Seufferlein TTW, Malek N, Schirmacher P, Fröhling S, Kazdal D, Budczies J, Stenzinger A. Multicentric pilot study to standardize clinical whole exome sequencing (WES) for cancer patients. NPJ Precis Oncol 2023; 7:106. [PMID: 37864096 PMCID: PMC10589320 DOI: 10.1038/s41698-023-00457-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 09/26/2023] [Indexed: 10/22/2023] Open
Abstract
A growing number of druggable targets and national initiatives for precision oncology necessitate broad genomic profiling for many cancer patients. Whole exome sequencing (WES) offers unbiased analysis of the entire coding sequence, segmentation-based detection of copy number alterations (CNAs), and accurate determination of complex biomarkers including tumor mutational burden (TMB), homologous recombination repair deficiency (HRD), and microsatellite instability (MSI). To assess the inter-institution variability of clinical WES, we performed a comparative pilot study between German Centers of Personalized Medicine (ZPMs) from five participating institutions. Tumor and matched normal DNA from 30 patients were analyzed using custom sequencing protocols and bioinformatic pipelines. Calling of somatic variants was highly concordant with a positive percentage agreement (PPA) between 91 and 95% and a positive predictive value (PPV) between 82 and 95% compared with a three-institution consensus and full agreement for 16 of 17 druggable targets. Explanations for deviations included low VAF or coverage, differing annotations, and different filter protocols. CNAs showed overall agreement in 76% for the genomic sequence with high wet-lab variability. Complex biomarkers correlated strongly between institutions (HRD: 0.79-1, TMB: 0.97-0.99) and all institutions agreed on microsatellite instability. This study will contribute to the development of quality control frameworks for comprehensive genomic profiling and sheds light onto parameters that require stringent standardization.
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Affiliation(s)
- Michael Menzel
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- Center for Personalized Medicine (ZPM), Heidelberg, Germany
| | - Stephan Ossowski
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- Center for Personalized Medicine (ZPM), Tübingen, Germany
- Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen, Tübingen, Germany
| | - Sebastian Kral
- Institute for Surgical Pathology, Medical Center, University of Freiburg, Freiburg, Germany
- Center for Personalized Medicine (ZPM), Freiburg, Germany
| | - Patrick Metzger
- Center for Personalized Medicine (ZPM), Freiburg, Germany
- Institute of Medical Bioinformatics and Systems Medicine (IBSM), Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Peter Horak
- Center for Personalized Medicine (ZPM), Heidelberg, Germany
- Division of Translational Medical Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Ralf Marienfeld
- Institute of Pathology, University Hospital Ulm, Ulm, Germany
- Center for Personalized Medicine (ZPM), Ulm, Germany
| | - Melanie Boerries
- Center for Personalized Medicine (ZPM), Freiburg, Germany
- Institute of Medical Bioinformatics and Systems Medicine (IBSM), Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Comprehensive Cancer Center Freiburg (CCCF), Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK) Partner Site Freiburg, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Steffen Wolter
- Institute for Surgical Pathology, Medical Center, University of Freiburg, Freiburg, Germany
- Center for Personalized Medicine (ZPM), Freiburg, Germany
| | - Markus Ball
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- Center for Personalized Medicine (ZPM), Heidelberg, Germany
| | - Olaf Neumann
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- Center for Personalized Medicine (ZPM), Heidelberg, Germany
| | - Sorin Armeanu-Ebinger
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- Center for Personalized Medicine (ZPM), Tübingen, Germany
| | - Christopher Schroeder
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- Center for Personalized Medicine (ZPM), Tübingen, Germany
| | - Uta Matysiak
- Institute for Surgical Pathology, Medical Center, University of Freiburg, Freiburg, Germany
- Center for Personalized Medicine (ZPM), Freiburg, Germany
| | - Hannah Goldschmid
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- Center for Personalized Medicine (ZPM), Heidelberg, Germany
| | - Vincent Schipperges
- Center for Personalized Medicine (ZPM), Freiburg, Germany
- Institute of Medical Bioinformatics and Systems Medicine (IBSM), Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Axel Fürstberger
- Institute of Pathology, University Hospital Ulm, Ulm, Germany
- Center for Personalized Medicine (ZPM), Ulm, Germany
- Institute of Medical Systems Biology, Ulm University, Ulm, Germany
| | - Michael Allgäuer
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- Center for Personalized Medicine (ZPM), Heidelberg, Germany
| | - Timo Eberhardt
- Institute of Pathology, University Hospital Ulm, Ulm, Germany
- Center for Personalized Medicine (ZPM), Ulm, Germany
| | - Jakob Niewöhner
- Institute of Pathology, University Hospital Ulm, Ulm, Germany
| | - Andreas Blaumeiser
- Center for Personalized Medicine (ZPM), Freiburg, Germany
- Institute of Medical Bioinformatics and Systems Medicine (IBSM), Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK) Partner Site Freiburg, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Carolin Ploeger
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- Center for Personalized Medicine (ZPM), Heidelberg, Germany
| | - Tobias Bernd Haack
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- Center for Personalized Medicine (ZPM), Tübingen, Germany
| | - Timothy Kwang Yong Tay
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- Center for Personalized Medicine (ZPM), Heidelberg, Germany
- Department of Anatomical Pathology, Singapore General Hospital, Singapore, Singapore
| | - Olga Kelemen
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- Center for Personalized Medicine (ZPM), Tübingen, Germany
| | - Thomas Pauli
- Center for Personalized Medicine (ZPM), Freiburg, Germany
- Institute of Medical Bioinformatics and Systems Medicine (IBSM), Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Martina Kirchner
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- Center for Personalized Medicine (ZPM), Heidelberg, Germany
| | - Klaus Kluck
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- Center for Personalized Medicine (ZPM), Heidelberg, Germany
| | - Alexander Ott
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- Center for Personalized Medicine (ZPM), Tübingen, Germany
| | - Marcus Renner
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- Center for Personalized Medicine (ZPM), Heidelberg, Germany
- Division of Translational Medical Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Jakob Admard
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- Center for Personalized Medicine (ZPM), Tübingen, Germany
| | - Axel Gschwind
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- Center for Personalized Medicine (ZPM), Tübingen, Germany
| | - Silke Lassmann
- Institute for Surgical Pathology, Medical Center, University of Freiburg, Freiburg, Germany
- Center for Personalized Medicine (ZPM), Freiburg, Germany
| | - Hans Kestler
- Institute of Pathology, University Hospital Ulm, Ulm, Germany
- Center for Personalized Medicine (ZPM), Ulm, Germany
| | - Falko Fend
- Institute of Pathology and Neuropathology, University Hospital Tübingen, Tübingen, Germany
| | - Anna Lena Illert
- Department of Medicine I, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79085, Freiburg, Germany
- Medical Department for Hematology and Oncology, Klinikum Rechts der Isar, Technische Universität München, 80333, Munich, Germany
- German Cancer Consortium (DKTK) Partner Site Munich, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Martin Werner
- Institute for Surgical Pathology, Medical Center, University of Freiburg, Freiburg, Germany
- Center for Personalized Medicine (ZPM), Freiburg, Germany
- German Cancer Consortium (DKTK) Partner Site Freiburg, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Peter Möller
- Institute of Pathology, University Hospital Ulm, Ulm, Germany
| | | | - Nisar Malek
- Center for Personalized Medicine (ZPM), Tübingen, Germany
- Department of Internal Medicine I, University Hospital Tübingen, Tübingen, Germany
| | - Peter Schirmacher
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- Center for Personalized Medicine (ZPM), Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Stefan Fröhling
- Center for Personalized Medicine (ZPM), Heidelberg, Germany
- Division of Translational Medical Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Daniel Kazdal
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- Center for Personalized Medicine (ZPM), Heidelberg, Germany
| | - Jan Budczies
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany.
- Center for Personalized Medicine (ZPM), Heidelberg, Germany.
- German Cancer Consortium (DKTK), Heidelberg, Germany.
| | - Albrecht Stenzinger
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany.
- Center for Personalized Medicine (ZPM), Heidelberg, Germany.
- German Cancer Consortium (DKTK), Heidelberg, Germany.
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49
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Gold JI, Madhavan S, Park J, Zouk H, Perez E, Strong A, Drivas TG, Karaa A, Yudkoff M, Rader D, Green RC, Gold NB. Phenotypes of undiagnosed adults with actionable OTC and GLA variants. HGG ADVANCES 2023; 4:100226. [PMID: 37593415 PMCID: PMC10428110 DOI: 10.1016/j.xhgg.2023.100226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 07/21/2023] [Indexed: 08/19/2023] Open
Abstract
Inherited metabolic disorders (IMDs) are variably expressive, complicating identification of affected individuals. A genotype-first approach can identify individuals at risk for morbidity and mortality from undiagnosed IMDs and can lead to protocols that improve clinical detection, counseling, and management. Using data from 57,340 participants in two hospital biobanks, we assessed the frequency and phenotypes of individuals with pathogenic/likely pathogenic variants (PLPVs) in two IMD genes: GLA, associated with Fabry disease, and OTC, associated with ornithine transcarbamylase deficiency. Approximately 1 in 19,100 participants harbored an undiagnosed PLPV in GLA or OTC. We identified three individuals (2 male, 1 female) with PLPVs in GLA, all of whom were undiagnosed, and three individuals (3 female) with PLPVs in OTC, two of whom were undiagnosed. All three individuals with PLPVs in GLA (100%) had symptoms suggestive of mild Fabry disease, and one individual (14.2%) had an ischemic stroke at age 33, likely indicating the presence of classic disease. No individuals with PLPVs in OTC had documented hyperammonemia despite exposure to catabolic states, but all (100%) had chronic symptoms suggestive of attenuated disease, including mood disorders and migraines. Our findings suggest that GLA and OTC variants identified via a genotype-first approach are of high penetrance and that population screening of these genes can be used to facilitate stepwise phenotyping and appropriate care.
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Affiliation(s)
- Jessica I. Gold
- Division of Human Genetics, Department of Pediatrics, Children’s Hospital of Philadelphia; Philadelphia, PA, USA
| | - Sarina Madhavan
- Harvard Medical School, Boston, MA, USA
- Harvard Business School, Cambridge, MA, USA
| | - Joseph Park
- Department of Genetics, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Hana Zouk
- Harvard Medical School, Boston, MA, USA
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Emma Perez
- Mass General Brigham Personalized Medicine, Cambridge MA, USA
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | - Alanna Strong
- Division of Human Genetics, Department of Pediatrics, Children’s Hospital of Philadelphia; Philadelphia, PA, USA
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Theodore G. Drivas
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Amel Karaa
- Massachusetts General Hospital for Children, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Marc Yudkoff
- Division of Human Genetics, Department of Pediatrics, Children’s Hospital of Philadelphia; Philadelphia, PA, USA
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Daniel Rader
- Department of Genetics, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Regeneron Genetics Center
- Division of Human Genetics, Department of Pediatrics, Children’s Hospital of Philadelphia; Philadelphia, PA, USA
- Harvard Medical School, Boston, MA, USA
- Harvard Business School, Cambridge, MA, USA
- Department of Genetics, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
- Mass General Brigham Personalized Medicine, Cambridge MA, USA
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Massachusetts General Hospital for Children, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Broad Institute, Boston, MA, USA
- Ariadne Labs, Boston, MA, USA
| | - Penn Medicine BioBank
- Division of Human Genetics, Department of Pediatrics, Children’s Hospital of Philadelphia; Philadelphia, PA, USA
- Harvard Medical School, Boston, MA, USA
- Harvard Business School, Cambridge, MA, USA
- Department of Genetics, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
- Mass General Brigham Personalized Medicine, Cambridge MA, USA
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Massachusetts General Hospital for Children, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Broad Institute, Boston, MA, USA
- Ariadne Labs, Boston, MA, USA
| | - Robert C. Green
- Harvard Medical School, Boston, MA, USA
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA
- Broad Institute, Boston, MA, USA
- Ariadne Labs, Boston, MA, USA
| | - Nina B. Gold
- Massachusetts General Hospital for Children, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
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50
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Chin HL, Lam JCM, Christopher D, Michelle PL, Junrong BY. Challenges associated with the identification of germline variants on myeloid malignancy genomic profiling-a Singaporean experience. Front Oncol 2023; 13:1182639. [PMID: 37860182 PMCID: PMC10582742 DOI: 10.3389/fonc.2023.1182639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 09/07/2023] [Indexed: 10/21/2023] Open
Abstract
Genomic profiling to identify myeloid-malignancy-related gene mutations is routinely performed for patients with suspected or definite myeloid malignancies. The most common specimen types in our experience are peripheral blood and bone marrow aspirates. Although primarily intended to identify somatic mutations, not infrequently, potentially clinically significant germline variants are also identified. Confirmation of the germline status of these variants is typically performed by hair follicle or skin fibroblast testing. If the germline variant is classified as a pathogenic or likely pathogenic variant and occurs in a gene known to be associated with a disease relevant to the patient's phenotype (for example, the identification of a DDX41 pathogenic variant in an individual with acute myeloid leukemia), the management algorithm is typically quite straightforward. Challenging situations may occur such as when the germline variant is classified as a pathogenic or likely pathogenic variant and occurs in a gene not known to be associated with the patient's phenotype/presenting complaint. We have encountered several such challenging cases in which potentially clinically significant germline variants were identified on the initial genomic profiling of peripheral blood or bone marrow aspirate. In this article, we present these cases and discuss the genetic counseling and management approaches.
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Affiliation(s)
- Hui-Lin Chin
- Khoo Teck Puat National University Children's Medical Institute, Department of Paediatrics, National University Hospital, Singapore, Singapore
- Department of Paediatrics, National University of Singapore, Singapore, Singapore
| | - Joyce Ching Mei Lam
- Children’s Blood and Cancer Centre, KK Women’s and Children’s Hospital, Singapore, Singapore
- Duke-National University of Singapore (NUS) Medical School, Singapore, Singapore
| | - Dheepa Christopher
- Department of Haematology, Tan Tock Seng Hospital, Singapore, Singapore
- Department of Laboratory Medicine, Khoo Teck Puat Hospital, Singapore, Singapore
| | - Poon Limei Michelle
- Department of Haematology-Oncology, National University Cancer Institute, National University Hospital, Singapore, Singapore
| | - Benedict Yan Junrong
- Department of Laboratory Medicine, National University Hospital, Singapore, Singapore
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