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Guha S, Reddi HV, Aarabi M, DiStefano M, Wakeling E, Dungan JS, Gregg AR. Laboratory testing for preconception/prenatal carrier screening: A technical standard of the American College of Medical Genetics and Genomics (ACMG). Genet Med 2024:101137. [PMID: 38814327 DOI: 10.1016/j.gim.2024.101137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Accepted: 04/01/2024] [Indexed: 05/31/2024] Open
Abstract
Carrier screening has historically assessed a relatively small number of autosomal recessive and X-linked conditions selected based on frequency in a specific subpopulation and association with severe morbidity or mortality. Advances in genomic technologies enable simultaneous screening of individuals for several conditions. The American College of Medical Genetics and Genomics recently published a clinical practice resource that presents a framework when offering screening for autosomal recessive and X-linked conditions during pregnancy and preconception and recommends a tier-based approach when considering the number of conditions to screen for and their frequency within the US population in general. This laboratory technical standard aims to complement the practice resource and to put forth considerations for clinical laboratories and clinicians who offer preconception/prenatal carrier screening.
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Affiliation(s)
| | - Honey V Reddi
- Department of Pathology and Laboratory Medicine, Medical College of Wisconsin, Milwaukee, WI
| | - Mahmoud Aarabi
- UPMC Medical Genetics and Genomics Laboratories, UPMC Magee-Womens Hospital, Pittsburgh, PA; Departments of Pathology and Obstetrics, Gynecology, and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | | | | | - Jeffrey S Dungan
- Department of Obstetrics and Gynecology, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Anthony R Gregg
- Department of Obstetrics and Gynecology, Prisma Health, Columbia, SC
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Chetruengchai W, Phowthongkum P, Shotelersuk V. Carrier frequency estimation of pathogenic variants of autosomal recessive and X-linked recessive mendelian disorders using exome sequencing data in 1,642 Thais. BMC Med Genomics 2024; 17:9. [PMID: 38167091 PMCID: PMC10762924 DOI: 10.1186/s12920-023-01771-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: 08/06/2023] [Accepted: 12/11/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND People with autosomal recessive disorders often were born without awareness of the carrier status of their parents. The American College of Medical Genetics and Genomics (ACMG) recommends screening 113 genes known to cause autosomal recessive and X-linked conditions in couples seeking to learn about their risk of having children with these disorders to have an appropriate reproductive plan. METHODS We analyzed the exome sequencing data of 1,642 unrelated Thai individuals to identify the pathogenic variant (PV) frequencies in genes recommended by ACMG. RESULTS In the 113 ACMG-recommended genes, 165 PV and likely PVs in 60 genes of 559 exomes (34%, 559/1642) were identified. The carrier rate was increased to 39% when glucose-6-phosphate dehydrogenase (G6PD) was added. The carrier rate was still as high as 14.7% when thalassemia and hemoglobinopathies were excluded. In addition to thalassemia, hemoglobinopathies, and G6PD deficiency, carrier frequencies of > 1% were found for Gaucher disease, primary hyperoxaluria, Pendred syndrome, and Wilson disease. Nearly 2% of the couples were at risk of having offsprings with the tested autosomal recessive conditions. CONCLUSIONS Based on the study samples, the expanded carrier screening, which specifically targeted common autosomal recessive conditions in Thai individuals, will benefit clinical outcomes, regarding preconception/prenatal genetic carrier screening.
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Affiliation(s)
- Wanna Chetruengchai
- Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok, 10330, Thailand
- Center of Excellence for Medical Genomics, Medical Genomics Cluster, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Prasit Phowthongkum
- Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok, 10330, Thailand.
- Division of Medical Genetics and Genomics, Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.
| | - Vorasuk Shotelersuk
- Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok, 10330, Thailand
- Center of Excellence for Medical Genomics, Medical Genomics Cluster, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
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Gunsel AS, Ergoren MC, Kemal H, Kafshboran HR, Cerit L, Turgay A, Duygu H. Determination of Carrier Frequency of Actionable Pathogenic Variants in Autosomal Recessive Genetic Diseases in the Turkish Cypriot Population. Genes (Basel) 2023; 14:1967. [PMID: 37895316 PMCID: PMC10606490 DOI: 10.3390/genes14101967] [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: 09/11/2023] [Revised: 10/04/2023] [Accepted: 10/19/2023] [Indexed: 10/29/2023] Open
Abstract
Whole-exome DNA sequencing is a rich source of clinically useful information for specialists, patients, and their families, as well as elucidating the genetic basis of monogenic and complex diseases in clinical diagnosis. However, interpreting and reporting variants encompassing exome and genome sequence analysis outcome data are one of the greatest challenges of the genomic era. In this study, we aimed to investigate the frequency and allele frequency spectrum of single nucleotide variants accepted as recessive disease carrier status in Turkish Cypriot exomes. The same sequencing platform and data processing line were used for the analysis of data from 100 Turkish Cypriot whole-exome sequence analysis. Identified variants were classified according to ACMG guidelines, and pathogenic variants were confirmed in other databases such as ClinVar, HGMD, Varsome, etc. Pathogenic variants were detected in 68 genes out of 100 whole-exome sequence data. The carriage rate was the highest in the CYP21A2 gene, causing 21-hydroxylase deficiency (14.70%), 11.76% in the HBB gene causing β-thalassemia, 10.29% in the BTD gene causing biotinidase deficiency, 8.82% in the CFTR gene causing cystic fibrosis, 8.82% in the RBM8A gene causing thrombocytopenia-absent radius syndrome, which is an ultra-rare disease, and 5.88% in the GAA gene causing glycogen storage disease II. The carriage of pathogenic variants in other genes causing the disease (GJB2, PAH, GALC, CYP11B2, COL4A3, HBA1, etc.) was determined as less than 5.00%. Also, the identified variations in the mentioned gene within the examined population were reported. The most prevalent mutation in North Cyprus was a missense variant (c.1360 C>T, p.Pro454Ser) detected in the CYP21A2 gene (rs6445), and the most frequently seen variant in the HBB gene was c.93-21G>A (rs35004220). We investigated reported pathogenic variants by estimating the lower and upper limits of carrier and population frequencies for autosomal recessive diseases, for which exome sequencing may reveal additional medically relevant information. Determining the lower and upper limits of these frequencies will shed light on preventive medicine practices and governmental actions.
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Affiliation(s)
- Aziz Suat Gunsel
- Department of Cardiology, Faculty of Medicine, Near East University, Nicosia 99138, Cyprus; (A.S.G.); (H.K.); (L.C.); (H.D.)
| | - Mahmut Cerkez Ergoren
- Department of Medical Genetics, Faculty of Medicine, Near East University, Nicosia 99138, Cyprus;
- Laboratory of Medical Genetics, Near East University Hospital, Near East University, Nicosia 99138, Cyprus;
| | - Hatice Kemal
- Department of Cardiology, Faculty of Medicine, Near East University, Nicosia 99138, Cyprus; (A.S.G.); (H.K.); (L.C.); (H.D.)
| | | | - Levent Cerit
- Department of Cardiology, Faculty of Medicine, Near East University, Nicosia 99138, Cyprus; (A.S.G.); (H.K.); (L.C.); (H.D.)
| | - Ayla Turgay
- Laboratory of Medical Genetics, Near East University Hospital, Near East University, Nicosia 99138, Cyprus;
| | - Hamza Duygu
- Department of Cardiology, Faculty of Medicine, Near East University, Nicosia 99138, Cyprus; (A.S.G.); (H.K.); (L.C.); (H.D.)
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Chui MMC, Mak CCY, Yu MHC, Wong SYY, Lun KS, Yung TC, Kwong AKY, Chow PC, Chung BHY. Evaluating High-Confidence Genes in Conotruncal Cardiac Defects by Gene Burden Analyses. J Am Heart Assoc 2023; 12:e028226. [PMID: 36789878 PMCID: PMC10111484 DOI: 10.1161/jaha.122.028226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Background In nonsyndromic conotruncal cardiac defects, the use of next-generation sequencing for clinical diagnosis is increasingly adopted, but gene-disease associations in research are only partially translated to diagnostic panels, suggesting a need for evidence-based consensus. Methods and Results In an exome data set of 245 patients with conotruncal cardiac defects, we performed burden analysis on a high-confidence congenital heart disease gene list (n=132) with rare (<0.01%) and ultrarare (absent in the Genome Aggregation Database) protein-altering variants. Overall, we confirmed an excess of rare variants compared with ethnicity-matched controls and identified 2 known genes (GATA6, NOTCH1) and 4 candidate genes supported by the literature (ANKRD11, DOCK6, NPHP4, and STRA6). Ultrarare variant analysis was performed in combination with 3 other published studies (n=1451) and identified 3 genes (FLT4, NOTCH1, TBX1) to be significant, whereas a subgroup analysis involving 391 Chinese subjects identified only GATA6 as significant. Conclusions We suggest that these significant genes in our rare and ultrarare burden analyses warrant prioritization for clinical testing implied for rare inherited and de novo variants. Additionally, associations on ClinVar for these genes were predominantly variants of uncertain significance. Therefore, a more stringent assessment of gene-disease associations in a larger and ethnically diverse cohort is required to be prudent for future curation of conotruncal cardiac defect genes.
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Affiliation(s)
- Martin M C Chui
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, LKS Faculty of Medicine The University of Hong Kong Hong Kong SAR China
| | - Christopher C Y Mak
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, LKS Faculty of Medicine The University of Hong Kong Hong Kong SAR China
| | - Mullin H C Yu
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, LKS Faculty of Medicine The University of Hong Kong Hong Kong SAR China
| | - Sandra Y Y Wong
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, LKS Faculty of Medicine The University of Hong Kong Hong Kong SAR China
| | - Kin-Shing Lun
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, LKS Faculty of Medicine The University of Hong Kong Hong Kong SAR China.,Department of Paediatrics and Adolescent Medicine The Hong Kong Children's Hospital Hong Kong SAR China
| | - Tak-Cheung Yung
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, LKS Faculty of Medicine The University of Hong Kong Hong Kong SAR China.,Department of Paediatrics and Adolescent Medicine The Hong Kong Children's Hospital Hong Kong SAR China
| | - Anna K Y Kwong
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, LKS Faculty of Medicine The University of Hong Kong Hong Kong SAR China
| | - Pak-Cheong Chow
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, LKS Faculty of Medicine The University of Hong Kong Hong Kong SAR China.,Department of Paediatrics and Adolescent Medicine The Hong Kong Children's Hospital Hong Kong SAR China
| | - Brian H Y Chung
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, LKS Faculty of Medicine The University of Hong Kong Hong Kong SAR China.,Department of Paediatrics and Adolescent Medicine The Hong Kong Children's Hospital Hong Kong SAR China.,Department of Paediatrics and Adolescent Medicine Queen Mary Hospital Hong Kong SAR China
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Park S, Jang SS, Lee S, Kim M, Sim H, Jeon H, Hong SE, Lee J, Lee J, Jeon EY, Lee J, Lee CR, Kim SY, Kim MJ, Yoon JG, Lim BC, Kim WJ, Kim KJ, Ko JM, Cho A, Lee JS, Choi M, Chae JH. Systematic analysis of inheritance pattern determination in genes that cause rare neurodevelopmental diseases. Front Genet 2022; 13:990015. [PMID: 36212160 PMCID: PMC9533195 DOI: 10.3389/fgene.2022.990015] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 08/23/2022] [Indexed: 01/09/2023] Open
Abstract
Despite recent advancements in our understanding of genetic etiology and its molecular and physiological consequences, it is not yet clear what genetic features determine the inheritance pattern of a disease. To address this issue, we conducted whole exome sequencing analysis to characterize genetic variants in 1,180 Korean patients with neurological symptoms. The diagnostic yield for definitive pathogenic variant findings was 50.8%, after including 33 cases (5.9%) additionally diagnosed by reanalysis. Of diagnosed patients, 33.4% carried inherited variants. At the genetic level, autosomal recessive-inherited genes were characterized by enrichments in metabolic process, muscle organization and metal ion homeostasis pathways. Transcriptome and interactome profiling analyses revealed less brain-centered expression and fewer protein-protein interactions for recessive genes. The majority of autosomal recessive genes were more tolerant of variation, and functional prediction scores of recessively-inherited variants tended to be lower than those of dominantly-inherited variants. Additionally, we were able to predict the rates of carriers for recessive variants. Our results showed that genes responsible for neurodevelopmental disorders harbor different molecular mechanisms and expression patterns according to their inheritance patterns. Also, calculated frequency rates for recessive variants could be utilized to pre-screen rare neurodevelopmental disorder carriers.
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Affiliation(s)
- Soojin Park
- Department of Pediatrics, Seoul National University College of Medicine, Seoul National University Children’s Hospital, Seoul, South Korea
| | - Se Song Jang
- Department of Pediatrics, Seoul National University College of Medicine, Seoul National University Children’s Hospital, Seoul, South Korea
| | - Seungbok Lee
- Department of Pediatrics, Seoul National University College of Medicine, Seoul National University Children’s Hospital, Seoul, South Korea,Department of Genomic Medicine, Seoul National University Hospital, Seoul, South Korea
| | - Minsoo Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
| | - Hyungtai Sim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
| | - Hyeongseok Jeon
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
| | - Sung Eun Hong
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
| | - Jean Lee
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
| | - Jeongeun Lee
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
| | - Eun Young Jeon
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
| | - Jeongha Lee
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
| | - Cho-Rong Lee
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
| | - Soo Yeon Kim
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, South Korea
| | - Man Jin Kim
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, South Korea,Rare Disease Center, Seoul National University Hospital, Seoul, South Korea
| | - Jihoon G. Yoon
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, South Korea
| | - Byung Chan Lim
- Department of Pediatrics, Seoul National University College of Medicine, Seoul National University Children’s Hospital, Seoul, South Korea
| | - Woo Joong Kim
- Department of Pediatrics, Seoul National University College of Medicine, Seoul National University Children’s Hospital, Seoul, South Korea
| | - Ki Joong Kim
- Department of Pediatrics, Seoul National University College of Medicine, Seoul National University Children’s Hospital, Seoul, South Korea
| | - Jung Min Ko
- Department of Pediatrics, Seoul National University College of Medicine, Seoul National University Children’s Hospital, Seoul, South Korea
| | - Anna Cho
- Department of Pediatrics, Seoul National University Bundang Hospital, Seongnam, South Korea
| | - Jin Sook Lee
- Department of Pediatrics, Seoul National University Hospital Child Cancer and Rare Disease Administration, Seoul National University Children’s Hospital, Seoul, South Korea
| | - Murim Choi
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea,*Correspondence: Murim Choi, ; Jong-Hee Chae,
| | - Jong-Hee Chae
- Department of Pediatrics, Seoul National University College of Medicine, Seoul National University Children’s Hospital, Seoul, South Korea,Department of Genomic Medicine, Seoul National University Hospital, Seoul, South Korea,*Correspondence: Murim Choi, ; Jong-Hee Chae,
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