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Eichten C, Kuhl A, Baker M, Kwon JM, Seroogy CM, Williams KB. Development and assessment of educational materials for spinal muscular atrophy carrier screening in the Plain community. J Genet Couns 2024. [PMID: 38197741 DOI: 10.1002/jgc4.1866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 11/26/2023] [Accepted: 12/27/2023] [Indexed: 01/11/2024]
Abstract
Spinal muscular atrophy (SMA) has been reported in both Amish and Mennonite (Plain) communities, and a higher incidence has been observed in certain Mennonite communities compared to the general population. There are several therapies for SMA, but all are most effective in pre-symptomatic newborns. To identify couples from the Wisconsin Plain community who are most likely to have a child with SMA, carrier screening is offered via mailed kits with at-home specimen collection. Our survey data about Plain families' perspectives on genetic testing suggest educational materials are needed for individuals providing informed consent with at-home specimen collection. We therefore developed a Plain population-specific educational trifold brochure about SMA carrier screening by incorporating existing medical education strategies and feedback from Plain community members and their health care providers. Along with the brochure, surveys were included in the kits to assess baseline knowledge about SMA carrier screening ("pre-education") as well as improvement in knowledge after reviewing the brochure and cultural appropriateness of the brochure ("post-education"). Fifty-five testing kits were distributed, and 26 survey pairs (pre- and post-education) were returned and analyzed (response rate 47%). Respondents had high baseline knowledge with an average of 5 of 7 questions (71%) answered correctly on the pre-education survey. Knowledge improved after reviewing the brochure as the average score increased to 6.5 of 7 questions (93%) answered correctly. Questions about risks of having an affected child after positive or negative carrier screening showed the most improvement from the pre-education to post-education surveys. Most respondents indicated the brochure was helpful, was easy to understand, and contained the right amount of information. Overall, incorporating elements of existing medical education strategies with feedback from the target population and stakeholders about appropriate language seems to be an effective method for creating beneficial, culturally responsive educational materials for the Plain population.
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Affiliation(s)
- Carly Eichten
- University of Wisconsin-Madison School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Ashley Kuhl
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Mei Baker
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
- Newborn Screening Laboratory, Wisconsin State Laboratory of Hygiene, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Jennifer M Kwon
- Department of Neurology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Christine M Seroogy
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Katie B Williams
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
- Center for Special Children, La Farge Medical Clinic - Vernon Memorial Healthcare, La Farge, Wisconsin, USA
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2
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Salame M, Bonnet C, Moctar ECM, Brahim SM, Dedy A, Vetah LA, Veten F, Hamed CT, Petit C, Houmeida A. Identification a novel pathogenic LRTOMT mutation in Mauritanian families with nonsyndromic deafness. Eur Arch Otorhinolaryngol 2023; 280:4057-4063. [PMID: 36928321 DOI: 10.1007/s00405-023-07907-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 02/27/2023] [Indexed: 03/18/2023]
Abstract
PURPOSE Although recessive mutations in GJB2 are the common genetic etiology of sensorineural hearing impairment (SNHI), variants in LRTOMT gene were also identified, mostly in Middle East and North African populations. METHODS Using Sanger sequencing we screened the exon 7 of LRTOMT in a cohort of 128 unrelated Mauritanian children with congenital deafness. RESULTS Only one biallelic missense mutation, predicted as pathogenic (c.179 T > C;p.Leu60Pro) was found at homozygous state in four families. This variant, not reported before, showed a deleterious effect by SIFT (score: 0.01) and a disease-causing effect by Mutation Taster (prob: 1). Exploration of the encoded protein 3D structure revealed a disruption from an organized α helix (in the normal protein structure) into a random conformation. Early fitting of a cochlear implant seemed to improve the audition ability of the mutation carrier. CONCLUSION Further screening using a panel of deafness genes may expose other variants underlying hearing impairment in our population.
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Affiliation(s)
- Malak Salame
- Unité de Recherche sur les Biomarqueurs dans la Population Mauritanienne, UNA-FST, Nouakchott, Mauritania
| | - Crystel Bonnet
- Institut de l'AuditionInstitut Pasteur, Inserm, Paris, France
| | - Ely Cheikh Mohamed Moctar
- Division of Otolaryngology, Department of Surgery, University of California, San Diego, 9500 Gilman Drive, Mail Code 0666, La Jolla, CA, 92093, USA
| | - Selma Mohamed Brahim
- Unité de Recherche sur les Biomarqueurs dans la Population Mauritanienne, UNA-FST, Nouakchott, Mauritania
- Centre National d'Oncologie (CNO), Unité de Recherche et d'Enseignement, Nouakchott, Mauritania
| | - Abdallahi Dedy
- Centre Hospitalier National de Nouakchott (CHN), Nouakchott, Mauritania
| | | | - Fatimetou Veten
- Unité de Recherche sur les Biomarqueurs dans la Population Mauritanienne, UNA-FST, Nouakchott, Mauritania
| | | | - Christine Petit
- Institut de l'AuditionInstitut Pasteur, Inserm, Paris, France
- Collège de France, Paris, France
| | - Ahmed Houmeida
- Unité de Recherche sur les Biomarqueurs dans la Population Mauritanienne, UNA-FST, Nouakchott, Mauritania.
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Kerr SM, Cowan E, Klaric L, Bell C, O'Sullivan D, Buchanan D, Grzymski JJ, van Hout CV, Tzoneva G, Shuldiner AR, Wilson JF, Miedzybrodzka Z. Clinical case study meets population cohort: identification of a BRCA1 pathogenic founder variant in Orcadians. Eur J Hum Genet 2023; 31:588-595. [PMID: 36927983 PMCID: PMC10172333 DOI: 10.1038/s41431-023-01297-w] [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: 08/02/2022] [Revised: 12/20/2022] [Accepted: 01/18/2023] [Indexed: 03/18/2023] Open
Abstract
We multiply ascertained the BRCA1 pathogenic missense variant c.5207T > C; p.Val1736Ala (V1736A) in clinical investigation of breast and ovarian cancer families from Orkney in the Northern Isles of Scotland, UK. We sought to investigate the frequency and clinical relevance of this variant in those of Orcadian ancestry as an exemplar of the value of population cohorts in clinical care, especially in isolated populations. Oral history and birth, marriage and death registrations indicated genealogical linkage of the clinical cases to ancestors from the Isle of Westray, Orkney. Further clinical cases were identified through targeted testing for V1736A in women of Orcadian ancestry attending National Health Service (NHS) genetic clinics for breast and ovarian cancer family risk assessments. The variant segregates with female breast and ovarian cancer in clinically ascertained cases. Separately, exome sequence data from 2088 volunteer participants with three or more Orcadian grandparents, in the ORCADES research cohort, was interrogated to estimate the population prevalence of V1736A in Orcadians. The effects of the variant were assessed using Electronic Health Record (EHR) linkage. Twenty out of 2088 ORCADES research volunteers (~1%) carry V1736A, with a common haplotype around the variant. This allele frequency is ~480-fold higher than in UK Biobank participants. Cost-effectiveness of population screening for BRCA1 founder pathogenic variants has been demonstrated at a carrier frequency below the ~1% observed here. Thus we suggest that Orcadian women should be offered testing for the BRCA1 V1736A founder pathogenic variant, starting with those with known Westray ancestry.
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Affiliation(s)
- Shona M Kerr
- MRC Human Genetics Unit, University of Edinburgh, Institute of Genetics and Cancer, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK
| | - Emma Cowan
- Department of Medical Genetics, Ashgrove House, NHS Grampian, Aberdeen, AB25 2ZA, UK
| | - Lucija Klaric
- MRC Human Genetics Unit, University of Edinburgh, Institute of Genetics and Cancer, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK
| | - Christine Bell
- Department of Medical Genetics, Ashgrove House, NHS Grampian, Aberdeen, AB25 2ZA, UK
| | - Dawn O'Sullivan
- Department of Medical Genetics, Ashgrove House, NHS Grampian, Aberdeen, AB25 2ZA, UK
| | - David Buchanan
- MRC Human Genetics Unit, University of Edinburgh, Institute of Genetics and Cancer, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK
| | - Joseph J Grzymski
- Center for Genomic Medicine, Desert Research Institute, Reno, NV, USA
- Renown Health, Reno, NV, USA
| | - Cristopher V van Hout
- Regeneron Genetics Center, Tarrytown, NY, USA
- Laboratorio Internacional de Investigatión sobre el Genoma Humano, Campus Juriquilla de la Universidad Nacional Autónoma de México, Querétaro, Querétaro, 76230, México
| | | | | | - James F Wilson
- MRC Human Genetics Unit, University of Edinburgh, Institute of Genetics and Cancer, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Teviot Place, Edinburgh, EH8 9AG, UK
| | - Zosia Miedzybrodzka
- Department of Medical Genetics, Ashgrove House, NHS Grampian, Aberdeen, AB25 2ZA, UK.
- Medical Genetics Group, School of Medicine, Medical Sciences, Nutrition and Dentistry, University of Aberdeen, Polwarth Building, Aberdeen, AB25 2ZD, UK.
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4
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Williams KB, Lasarev MR, Baker M, Seroogy CM. Cross-sectional survey on genetic testing utilization and perceptions in Wisconsin Amish and Mennonite communities. J Community Genet 2023; 14:41-49. [PMID: 36385695 PMCID: PMC9947211 DOI: 10.1007/s12687-022-00621-z] [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: 02/10/2022] [Accepted: 11/07/2022] [Indexed: 11/18/2022] Open
Abstract
Amish and Mennonite (Plain) communities have increased prevalence of many recessively inherited disorders due to founder variants that can be identified using next-generation sequencing (NGS). We assessed newborn screening (NBS) utilization, prior genetic testing, and perceptions of genetic testing among Wisconsin Plain communities to guide implementation and utilization of a population-specific NGS gene panel testing. A mailed paper survey (N = 959) of demographics, NBS utilization, prior genetic testing, and preferences for categorical genetic disorder and defined clinical context testing was developed. Overall response rate was 39% (N = 378; 183 Amish, 193 Mennonite; 2 not Amish/Mennonite). Mennonites were more likely to respond in favor of carrier screening for metabolic disorders and other surgical conditions and less likely to respond in favor of asymptomatic testing for neurologic disorders and lethal disorders compared to Amish. Reported utilization of NBS was positively associated with stated interest in genetic testing for an asymptomatic child. Reported prior genetic testing was positively associated with stated interest in carrier screening and negatively associated with testing a symptomatic child. Although Plain community members share many common outward characteristics, our survey responses suggest diversity in their views of genetic testing and support laboratory methods that can be flexible to varied needs of individuals.
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Affiliation(s)
- Katie B. Williams
- Center for Special Children, La Farge Medical Clinic - Vernon Memorial Healthcare, 206 North Mill Street, La Farge, WI 54639 USA ,Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, WI USA
| | - Michael R. Lasarev
- Department of Biostatistics and Medical Informatics, University of Wisconsin School of Medicine and Public Health, Madison, WI USA
| | - Mei Baker
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, WI USA ,Wisconsin State Laboratory of Hygiene, University of Wisconsin School of Medicine and Public Health, Madison, WI USA ,Center for Human Genomics and Precision Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI USA
| | - Christine M. Seroogy
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, WI USA
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Österlund T, Filges S, Johansson G, Ståhlberg A. UMIErrorCorrect and UMIAnalyzer: Software for Consensus Read Generation, Error Correction, and Visualization Using Unique Molecular Identifiers. Clin Chem 2022; 68:1425-1435. [PMID: 36031761 DOI: 10.1093/clinchem/hvac136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 07/08/2022] [Indexed: 11/14/2022]
Abstract
BACKGROUND Targeted sequencing using unique molecular identifiers (UMIs) enables detection of rare variant alleles in challenging applications, such as cell-free DNA analysis from liquid biopsies. Standard bioinformatics pipelines for data processing and variant calling are not adapted for deep-sequencing data containing UMIs, are inflexible, and require multistep workflows or dedicated computing resources. METHODS We developed a bioinformatics pipeline using Python and an R package for data analysis and visualization. To validate our pipeline, we analyzed cell-free DNA reference material with known mutant allele frequencies (0%, 0.125%, 0.25%, and 1%) and public data sets. RESULTS We developed UMIErrorCorrect, a bioinformatics pipeline for analyzing sequencing data containing UMIs. UMIErrorCorrect only requires fastq files as inputs and performs alignment, UMI clustering, error correction, and variant calling. We also provide UMIAnalyzer, a graphical user interface, for data mining, visualization, variant interpretation, and report generation. UMIAnalyzer allows the user to adjust analysis parameters and study their effect on variant calling. We demonstrated the flexibility of UMIErrorCorrect by analyzing data from 4 different targeted sequencing protocols. We also show its ability to detect different mutant allele frequencies in standardized cell-free DNA reference material. UMIErrorCorrect outperformed existing pipelines for targeted UMI sequencing data in terms of variant detection sensitivity. CONCLUSIONS UMIErrorCorrect and UMIAnalyzer are comprehensive and customizable bioinformatics tools that can be applied to any type of library preparation protocol and enrichment chemistry using UMIs. Access to simple, generic, and open-source bioinformatics tools will facilitate the implementation of UMI-based sequencing approaches in basic research and clinical applications.
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Affiliation(s)
- Tobias Österlund
- Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Region Västra Götaland, Gothenburg, Sweden.,Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden.,Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Stefan Filges
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Gustav Johansson
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden.,Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden.,SiMSen Diagnostics AB, Gothenburg, Sweden
| | - Anders Ståhlberg
- Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Region Västra Götaland, Gothenburg, Sweden.,Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden.,Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
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6
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Lynch MT, Maloney KA, Pollin TI, Streeten EA, Puffenberger EG, Strauss KA, Shuldiner AR, Mitchell BD. Impact of parental relatedness on reproductive outcomes among the Old Order Amish of Lancaster County. Am J Med Genet A 2022; 188:2119-2128. [PMID: 35442562 DOI: 10.1002/ajmg.a.62757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 02/01/2022] [Accepted: 03/18/2022] [Indexed: 11/06/2022]
Abstract
Genetically isolated populations that arise due to recent bottleneck events have reduced genetic variation reflecting the common set of founders. Increased genetic relatedness among members of isolated populations puts them at increased risk for some recessive disorders that are rare in outbred populations. To assess the burden on reproductive health, we compared frequencies of adverse reproductive outcomes between Amish couples who were both heterozygous carriers of a highly penetrant pathogenic or likely pathogenic variant and noncarrier couples from the same Amish community. In addition, we evaluated whether overall genetic relatedness of parents was associated with reproductive outcomes. Of the 1824 couples included in our study, 11.1% were at risk of producing a child with an autosomal recessive disorder. Carrier couples reported a lower number of miscarriages compared to noncarrier couples (p = 0.02), although the number of stillbirths (p = 0.3), live births (p = 0.9), and number of pregnancies (p = 0.9) did not differ significantly between groups. In contrast, higher overall relatedness between spouses was positively correlated with number of live births (p < 0.0001), pregnancies (p < 0.0001), and stillbirths (p = 0.03), although not with the number of miscarriages (p = 0.4). These results highlight a complex association between relatedness of parents and reproductive health outcomes in this community.
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Affiliation(s)
- Megan T Lynch
- Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA.,Department of Medicine Baltimore, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Kristin A Maloney
- Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA.,Department of Medicine Baltimore, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Toni I Pollin
- Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA.,Department of Medicine Baltimore, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Elizabeth A Streeten
- Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA.,Department of Medicine Baltimore, University of Maryland School of Medicine, Baltimore, Maryland, USA
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- Regeneron Genetics Center LLC, Tarrytown, New York, USA
| | | | - Braxton D Mitchell
- Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA.,Department of Medicine Baltimore, University of Maryland School of Medicine, Baltimore, Maryland, USA.,Geriatrics Research and Education Clinical Center, Baltimore Veterans Administration Medical Center, Baltimore, Maryland, USA
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7
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DInur-Schejter Y, Stepensky P. Social determinants of health and primary immunodeficiency. Ann Allergy Asthma Immunol 2021; 128:12-18. [PMID: 34628007 DOI: 10.1016/j.anai.2021.10.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Revised: 10/01/2021] [Accepted: 10/04/2021] [Indexed: 12/15/2022]
Abstract
OBJECTIVE Inborn errors of immunity (IEI) are rare genetic conditions affecting the immune system. The rate of IEI and their presentation, course, and treatment are all affected by a multitude of social determinants, eventually affecting prognosis. This review summarizes the current knowledge of the social determinants affecting infectious susceptibility, genetic predisposition, diagnosis, and treatment of IEI. DATA SOURCES PubMed. STUDY SELECTIONS Search terms included "consanguinity," "social determinants," and "founder effect." Further studies were selected based on relevant citations. RESULTS Changes in climate and human behavior have modulated the spread of disease vectors and infectious organisms. Consanguinity increases the rate of autosomal recessive conditions, changes the distribution, and affects the severity of IEI. Access to sophisticated genetic and immunologic diagnostic modalities affects genetic counseling and timely diagnosis. Effective genetic counseling should address to the patient's genetic background and ethical code. Access to appropriate and timely treatment of immunodeficiencies is scarce in some regions of the world. CONCLUSION High consanguinity rate and reduced access to prophylactic measures increase the burden of immunodeficiencies in many low- and medium-income countries. Furthermore, poor access to diagnostic and treatment modalities in these regions adversely affects patients' prognosis. Increased awareness among health care professionals and the public and increased collaboration with Western countries aid in diagnosis of these conditions. Further advancements require improved public funding to the prevention, diagnosis, and treatment of IEI.
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Affiliation(s)
- Yael DInur-Schejter
- Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel; Department of Bone Marrow Transplantation and Cancer Immunotherapy, Hadassah Ein Kerem Medical Center, Jerusalem, Israel.
| | - Polina Stepensky
- Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel; Department of Bone Marrow Transplantation and Cancer Immunotherapy, Hadassah Ein Kerem Medical Center, Jerusalem, Israel
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Chen Y, Fang B, Hu X, Guo R, Guo J, Fang K, Ni J, Li W, Qian S, Hao C. Identification and functional analysis of novel SLC25A19 variants causing thiamine metabolism dysfunction syndrome 4. Orphanet J Rare Dis 2021; 16:403. [PMID: 34587972 PMCID: PMC8480130 DOI: 10.1186/s13023-021-02028-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 09/19/2021] [Indexed: 11/10/2022] Open
Abstract
Background Thiamine metabolism dysfunction syndrome 4 (THMD4, OMIM #613710) is an autosomal recessive inherited disease caused by the deficiency of SLC25A19 that encodes the mitochondrial thiamine pyrophosphate (TPP) transporter. This disorder is characterized by bilateral striatal degradation and progressive polyneuropathy with the onset of fever of unknown origin. The limited number of reported cases and lack of functional annotation of related gene variants continue to limit diagnosis. Results We report three cases of encephalopathy from two unrelated pedigrees with basal ganglia signal changes after fever of unknown origin. To distinguish this from other types of encephalopathy, such as acute necrotizing encephalopathy, exome sequencing was performed, and four novel heterozygous variations, namely, c.169G>A (p.Ala57Thr), c.383C>T (p.Ala128Val), c.76G>A (p.Gly26Arg), and c.745T>A (p.Phe249Ile), were identified in SLC25A19. All variants were confirmed using Sanger sequencing. To determine the pathogenicity of these variants, functional studies were performed. We found that mitochondrial TPP levels were significantly decreased in the presence of SLC25A19 variants, indicating that TPP transport activities of mutated SLC25A19 proteins were impaired. Thus, combining clinical phenotype, genetic analysis, and functional studies, these variants were deemed as likely pathogenic. Conclusions Exome sequencing analysis enables molecular diagnosis as well as provides potential etiology. Further studies will enable the elucidation of SLC25A19 protein function. Our investigation supplied key molecular evidence for the precise diagnosis of and clinical decision-making for a rare disease.
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Affiliation(s)
- Yuanying Chen
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute, MOE Key Laboratory of Major Diseases in Children, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China.,Henan Key Laboratory of Pediatric Inherited and Metabolic Diseases, Henan Children's Hospital, Zhengzhou Hospital of Beijing Children's Hospital, Zhengzhou, China
| | - Boliang Fang
- Pediatric Intensive Care Unit, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China
| | - Xuyun Hu
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute, MOE Key Laboratory of Major Diseases in Children, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China.,Henan Key Laboratory of Pediatric Inherited and Metabolic Diseases, Henan Children's Hospital, Zhengzhou Hospital of Beijing Children's Hospital, Zhengzhou, China
| | - Ruolan Guo
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute, MOE Key Laboratory of Major Diseases in Children, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China.,Henan Key Laboratory of Pediatric Inherited and Metabolic Diseases, Henan Children's Hospital, Zhengzhou Hospital of Beijing Children's Hospital, Zhengzhou, China
| | - Jun Guo
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute, MOE Key Laboratory of Major Diseases in Children, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China.,Henan Key Laboratory of Pediatric Inherited and Metabolic Diseases, Henan Children's Hospital, Zhengzhou Hospital of Beijing Children's Hospital, Zhengzhou, China
| | - Kenan Fang
- Pediatric Intensive Care Unit, Luoyang Maternal and Child Health Hospital, Luoyang, China
| | - Jingwen Ni
- Pediatric Intensive Care Unit, Luoyang Maternal and Child Health Hospital, Luoyang, China
| | - Wei Li
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute, MOE Key Laboratory of Major Diseases in Children, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China.,Henan Key Laboratory of Pediatric Inherited and Metabolic Diseases, Henan Children's Hospital, Zhengzhou Hospital of Beijing Children's Hospital, Zhengzhou, China
| | - Suyun Qian
- Pediatric Intensive Care Unit, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China.
| | - Chanjuan Hao
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute, MOE Key Laboratory of Major Diseases in Children, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China. .,Henan Key Laboratory of Pediatric Inherited and Metabolic Diseases, Henan Children's Hospital, Zhengzhou Hospital of Beijing Children's Hospital, Zhengzhou, China.
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9
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Puffenberger EG. Mendelian disease research in the Plain populations of Lancaster County, Pennsylvania. Am J Med Genet A 2021; 185:3322-3333. [PMID: 34532947 DOI: 10.1002/ajmg.a.62489] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 07/30/2021] [Accepted: 08/05/2021] [Indexed: 11/07/2022]
Abstract
Founder populations have long contributed to our knowledge of rare disease genes and phenotypes. From the pioneering work of Dr. Victor McKusick to today, research in these groups has shed light on rare recessive phenotypes, expanded the clinical spectrum of disease, and facilitated disease gene identification. Current clinical and research studies in these special groups augment the wealth of knowledge already gained, provide new insights into emerging problems such as variant interpretation and reduced penetrance, and contribute to the development of novel therapies for rare genetic diseases. Clinical developments over the past 30 years have altered the fundamental relationship with the Lancaster Plain communities: research has become more collaborative, and the knowledge imparted by these studies is now being harnessed to provide cutting-edge translational medicine to the very community of vulnerable individuals who need it most.
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10
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Lynch MT, Maloney KA, Pollin TI, Streeten EA, Xu H, Shuldiner AR, Van Hout CV, Gonzaga-Jauregui C, Mitchell BD. The burden of pathogenic variants in clinically actionable genes in a founder population. Am J Med Genet A 2021; 185:3476-3484. [PMID: 34467620 DOI: 10.1002/ajmg.a.62472] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 08/06/2021] [Accepted: 08/10/2021] [Indexed: 11/10/2022]
Abstract
Founder populations may be enriched with certain genetic variants of high clinical impact compared to nonfounder populations due to bottleneck events and genetic drift. Using exome sequencing (ES), we quantified the load of pathogenic variants that may be clinically actionable in 6136 apparently healthy adults living in the Lancaster, PA Old Order Amish settlement. We focused on variants in 78 genes deemed clinically actionable by the American College of Medical Genetics and Genomics (ACMG) or Geisinger's MyCode Health Initiative. ES revealed 3191 total variants among these genes including 480 nonsynonymous variants. After quality control and filtering, we applied the ACMG/AMP guidelines for variant interpretation and classified seven variants, across seven genes, as either pathogenic or likely pathogenic. Through genetic drift, all seven variants, are highly enriched in the Amish compared to nonfounder populations. In total, 14.7% of Lancaster Amish individuals carry at least one of these variants, largely explained by the 13% who harbor a copy of a single variant in APOB. Other studies report combined frequencies of pathogenic/likely pathogenic (P/LP) variants in actionable genes between 2.0% and 6.2% in outbred populations. The Amish population harbors fewer actionable variants compared to similarly characterized nonfounder populations but have a higher frequency of each variant identified, offering opportunities for efficient and cost-effective targeted precision medicine.
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Affiliation(s)
- Megan T Lynch
- Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA.,Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Kristin A Maloney
- Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA.,Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Toni I Pollin
- Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA.,Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Elizabeth A Streeten
- Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA.,Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Huichun Xu
- Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA.,Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
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- Regeneron Genetics Center LLC, Tarrytown, New York, USA
| | | | | | | | - Braxton D Mitchell
- Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA.,Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA.,Baltimore Veterans Administration Medical Center Geriatrics Research and Education Clinical Center, Baltimore, Maryland, USA
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