1
|
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.
Collapse
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
| |
Collapse
|
2
|
Xue Z, Zhou A, Zhu X, Li L, Zhu H, Jin X, Wang J. NIPT-PG: empowering non-invasive prenatal testing to learn from population genomics through an incremental pan-genomic approach. Brief Bioinform 2024; 25:bbae266. [PMID: 38836702 DOI: 10.1093/bib/bbae266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 05/03/2024] [Accepted: 05/21/2024] [Indexed: 06/06/2024] Open
Abstract
Non-invasive prenatal testing (NIPT) is a quite popular approach for detecting fetal genomic aneuploidies. However, due to the limitations on sequencing read length and coverage, NIPT suffers a bottleneck on further improving performance and conducting earlier detection. The errors mainly come from reference biases and population polymorphism. To break this bottleneck, we proposed NIPT-PG, which enables the NIPT algorithm to learn from population data. A pan-genome model is introduced to incorporate variant and polymorphic loci information from tested population. Subsequently, we proposed a sequence-to-graph alignment method, which considers the read mis-match rates during the mapping process, and an indexing method using hash indexing and adjacency lists to accelerate the read alignment process. Finally, by integrating multi-source aligned read and polymorphic sites across the pan-genome, NIPT-PG obtains a more accurate z-score, thereby improving the accuracy of chromosomal aneuploidy detection. We tested NIPT-PG on two simulated datasets and 745 real-world cell-free DNA sequencing data sets from pregnant women. Results demonstrate that NIPT-PG outperforms the standard z-score test. Furthermore, combining experimental and theoretical analyses, we demonstrate the probably approximately correct learnability of NIPT-PG. In summary, NIPT-PG provides a new perspective for fetal chromosomal aneuploidies detection. NIPT-PG may have broad applications in clinical testing, and its detection results can serve as a reference for false positive samples approaching the critical threshold.
Collapse
Affiliation(s)
- Zhengfa Xue
- School of Computer Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China
- Shaanxi Engineering Research Center of Medical and Health Big Data, Xi'an Jiaotong University, Xi'an 710049, China
| | - Aifen Zhou
- Institute of Maternal and Child Health, Wuhan Children's Hospital (Wuhan Maternal and Child Health care Hospital), Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430015, China
- Department of Obstetrics, Wuhan Children's Hospital (Wuhan Maternal and Child Health care Hospital), Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430015, China
| | - Xiaoyan Zhu
- School of Computer Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China
- Shaanxi Engineering Research Center of Medical and Health Big Data, Xi'an Jiaotong University, Xi'an 710049, China
| | - Linxuan Li
- BGI Research, Shenzhen 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | | | - Xin Jin
- BGI Research, Shenzhen 518083, China
- School of Medicine, South China University of Technology, Guangzhou 510006, China
| | - Jiayin Wang
- School of Computer Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China
- Shaanxi Engineering Research Center of Medical and Health Big Data, Xi'an Jiaotong University, Xi'an 710049, China
| |
Collapse
|
3
|
Stefanov BA, Ajuh E, Allen S, Nowacki M. Eukaryotic release factor 1 from Euplotes promotes frameshifting at premature stop codons in human cells. iScience 2024; 27:109413. [PMID: 38510117 PMCID: PMC10952039 DOI: 10.1016/j.isci.2024.109413] [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: 12/07/2023] [Revised: 01/23/2024] [Accepted: 02/29/2024] [Indexed: 03/22/2024] Open
Abstract
Human physiology is highly susceptible to frameshift mutations within coding regions, and many hereditary diseases and cancers are caused by such indels. Presently, therapeutic options to counteract them are limited and, in the case of direct genome editing, risky. Here, we show that release factor 1 (eRF1) from Euplotes, an aquatic protist known for frequent +1 frameshifts in its coding regions, can enhance +1 ribosomal frameshifting at slippery heptameric sequences in human cells without an apparent requirement for an mRNA secondary structure. We further show an increase in frameshifting rate at the premature termination sequence found in the HEXA gene of Tay-Sachs disease patients, or a breast cancer cell line that harbors a tumor-driving frameshift mutation in GATA3. Although the overall increase in frameshifting would need further improvement for clinical applications, our results underscore the potential of exogenous factors, such as Eu eRF1, to increase frameshifting in human cells.
Collapse
Affiliation(s)
| | - Elvis Ajuh
- Institute of Cell Biology, University of Bern, Baltzerstrasse 4, 3012 Bern, Switzerland
| | - Sarah Allen
- Institute of Cell Biology, University of Bern, Baltzerstrasse 4, 3012 Bern, Switzerland
| | - Mariusz Nowacki
- Institute of Cell Biology, University of Bern, Baltzerstrasse 4, 3012 Bern, Switzerland
| |
Collapse
|
4
|
Durward-Akhurst SA, Marlowe JL, Schaefer RJ, Springer K, Grantham B, Carey WK, Bellone RR, Mickelson JR, McCue ME. Predicted genetic burden and frequency of phenotype-associated variants in the horse. Sci Rep 2024; 14:8396. [PMID: 38600096 PMCID: PMC11006912 DOI: 10.1038/s41598-024-57872-8] [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: 12/20/2023] [Accepted: 03/22/2024] [Indexed: 04/12/2024] Open
Abstract
Disease-causing variants have been identified for less than 20% of suspected equine genetic diseases. Whole genome sequencing (WGS) allows rapid identification of rare disease causal variants. However, interpreting the clinical variant consequence is confounded by the number of predicted deleterious variants that healthy individuals carry (predicted genetic burden). Estimation of the predicted genetic burden and baseline frequencies of known deleterious or phenotype associated variants within and across the major horse breeds have not been performed. We used WGS of 605 horses across 48 breeds to identify 32,818,945 variants, demonstrate a high predicted genetic burden (median 730 variants/horse, interquartile range: 613-829), show breed differences in predicted genetic burden across 12 target breeds, and estimate the high frequencies of some previously reported disease variants. This large-scale variant catalog for a major and highly athletic domestic animal species will enhance its ability to serve as a model for human phenotypes and improves our ability to discover the bases for important equine phenotypes.
Collapse
Affiliation(s)
- S A Durward-Akhurst
- Department of Veterinary Clinical Sciences, University of Minnesota, C339 VMC, 1353 Boyd Avenue, St. Paul, MN, 55108, USA.
| | - J L Marlowe
- Department of Veterinary Clinical Sciences, University of Minnesota, C339 VMC, 1353 Boyd Avenue, St. Paul, MN, 55108, USA
| | - R J Schaefer
- Department of Veterinary Population Medicine, University of Minnesota, 225 VMC, 1365 Gortner Avenue, St. Paul, MN, 55108, USA
| | - K Springer
- Department of Veterinary Population Medicine, University of Minnesota, 225 VMC, 1365 Gortner Avenue, St. Paul, MN, 55108, USA
| | - B Grantham
- Interval Bio LLC, 408 Stierline Road, Mountain View, CA, 94043, USA
| | - W K Carey
- Interval Bio LLC, 408 Stierline Road, Mountain View, CA, 94043, USA
| | - R R Bellone
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, CA, USA
- Population Health and Reproduction and Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - J R Mickelson
- Department of Veterinary and Biomedical Sciences, University of Minnesota, 295F Animal Science Veterinary Medicine Building, 1988 Fitch Avenue, St. Paul, MN, 55108, USA
| | - M E McCue
- Department of Veterinary Population Medicine, University of Minnesota, 225 VMC, 1365 Gortner Avenue, St. Paul, MN, 55108, USA
| |
Collapse
|
5
|
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] [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.
Collapse
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.
| |
Collapse
|
6
|
Jolfayi AG, Kohansal E, Ghasemi S, Naderi N, Hesami M, MozafaryBazargany M, Moghadam MH, Fazelifar AF, Maleki M, Kalayinia S. Exploring TTN variants as genetic insights into cardiomyopathy pathogenesis and potential emerging clues to molecular mechanisms in cardiomyopathies. Sci Rep 2024; 14:5313. [PMID: 38438525 PMCID: PMC10912352 DOI: 10.1038/s41598-024-56154-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 03/01/2024] [Indexed: 03/06/2024] Open
Abstract
The giant protein titin (TTN) is a sarcomeric protein that forms the myofibrillar backbone for the components of the contractile machinery which plays a crucial role in muscle disorders and cardiomyopathies. Diagnosing TTN pathogenic variants has important implications for patient management and genetic counseling. Genetic testing for TTN variants can help identify individuals at risk for developing cardiomyopathies, allowing for early intervention and personalized treatment strategies. Furthermore, identifying TTN variants can inform prognosis and guide therapeutic decisions. Deciphering the intricate genotype-phenotype correlations between TTN variants and their pathologic traits in cardiomyopathies is imperative for gene-based diagnosis, risk assessment, and personalized clinical management. With the increasing use of next-generation sequencing (NGS), a high number of variants in the TTN gene have been detected in patients with cardiomyopathies. However, not all TTN variants detected in cardiomyopathy cohorts can be assumed to be disease-causing. The interpretation of TTN variants remains challenging due to high background population variation. This narrative review aimed to comprehensively summarize current evidence on TTN variants identified in published cardiomyopathy studies and determine which specific variants are likely pathogenic contributors to cardiomyopathy development.
Collapse
Affiliation(s)
- Amir Ghaffari Jolfayi
- Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Erfan Kohansal
- Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Serwa Ghasemi
- Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Niloofar Naderi
- Cardiogenetic Research Center, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Mahshid Hesami
- Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | | | - Maryam Hosseini Moghadam
- Cardiogenetic Research Center, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Amir Farjam Fazelifar
- Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Majid Maleki
- Cardiogenetic Research Center, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Samira Kalayinia
- Cardiogenetic Research Center, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran.
| |
Collapse
|
7
|
Walker E, Hayes W, Bockenhauer D. Inherited non-FGF23-mediated phosphaturic disorders: A kidney-centric review. Best Pract Res Clin Endocrinol Metab 2024; 38:101843. [PMID: 38042745 DOI: 10.1016/j.beem.2023.101843] [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] [Indexed: 12/04/2023]
Abstract
Phosphate is freely filtered by the glomerulus and reabsorbed exclusively in the proximal tubule by two key transporters, NaPiIIA and NaPiIIC, encoded by SLC34A1 and SLC34A3, respectively. Regulation of these transporters occurs primarily through the hormone FGF23 and, to a lesser degree, PTH. Consequently, inherited non-FGF23 mediated phosphaturic disorders are due to generalised proximal tubular dysfunction, loss-of-function variants in SLC34A1 or SLC34A3 or excess PTH signalling. The corresponding disorders are Renal Fanconi Syndrome, Infantile Hypercalcaemia type 2, Hereditary Hypophosphataemic Rickets with Hypercalciuria and Familial Hyperparathyroidism. Several inherited forms of Fanconi renotubular syndrome (FRTS) have also been described with the underlying genes encoding for GATM, EHHADH, HNF4A and NDUFAF6. Here, we will review their pathophysiology, clinical manifestations and the implications for treatment from a kidney-centric perspective, focussing on those disorders caused by dysfunction of renal phosphate transporters. Moreover, we will highlight specific genetic aspects, as the availability of large population genetic databases has raised doubts about some of the originally proposed gene-disease associations concerning phosphate transporters or their associated proteins.
Collapse
Affiliation(s)
- Emma Walker
- Nephrology Unit, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Wesley Hayes
- Nephrology Unit, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Detlef Bockenhauer
- Nephrology Unit, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK; Department of Renal Medicine, University College London, London, UK.
| |
Collapse
|
8
|
Morimoto M, Nicoli ER, Kuptanon C, Roney JC, Serra-Vinardell J, Sharma P, Adams DR, Gallin JI, Holland SM, Rosenzweig SD, Barbot J, Ciccone C, Huizing M, Toro C, Gahl WA, Introne WJ, Malicdan MCV. Spectrum of LYST mutations in Chediak-Higashi syndrome: a report of novel variants and a comprehensive review of the literature. J Med Genet 2024; 61:212-223. [PMID: 37788905 DOI: 10.1136/jmg-2023-109420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 09/10/2023] [Indexed: 10/05/2023]
Abstract
INTRODUCTION Chediak-Higashi syndrome (CHS) is a rare autosomal recessive disorder characterised by partial oculocutaneous albinism, a bleeding diathesis, immunological dysfunction and neurological impairment. Bi-allelic loss-of-function variants in LYST cause CHS. LYST encodes the lysosomal trafficking regulator, a highly conserved 429 kDa cytoplasmic protein with an unknown function. METHODS To further our understanding of the pathogenesis of CHS, we conducted clinical evaluations on individuals with CHS enrolled in our natural history study. Using genomic DNA Sanger sequencing, we identified novel pathogenic LYST variants. Additionally, we performed an extensive literature review to curate reported LYST variants and classified these novel and reported variants according to the American College of Medical Genetics/Association for Molecular Pathology variant interpretation guidelines. RESULTS Our investigation unveiled 11 novel pathogenic LYST variants in eight patients with a clinical diagnosis of CHS, substantiated by the presence of pathognomonic giant intracellular granules. From these novel variants, together with a comprehensive review of the literature, we compiled a total of 147 variants in LYST, including 61 frameshift variants (41%), 44 nonsense variants (30%), 23 missense variants (16%), 13 splice site variants or small genomic deletions for which the coding effect is unknown (9%), 5 in-frame variants (3%) and 1 start-loss variant (1%). Notably, a genotype-phenotype correlation emerged, whereby individuals harbouring at least one missense or in-frame variant generally resulted in milder disease, while those with two nonsense or frameshift variants generally had more severe disease. CONCLUSION The identification of novel pathogenic LYST variants and improvements in variant classification will provide earlier diagnoses and improved care to individuals with CHS.
Collapse
Affiliation(s)
- Marie Morimoto
- NIH Undiagnosed Diseases Program, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Elena-Raluca Nicoli
- NIH Undiagnosed Diseases Program, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Chulaluck Kuptanon
- Human Biochemical Genetics Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Joseph C Roney
- Human Biochemical Genetics Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Jenny Serra-Vinardell
- Human Biochemical Genetics Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Prashant Sharma
- NIH Undiagnosed Diseases Program, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - David R Adams
- NIH Undiagnosed Diseases Program, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
- Office of the Clinical Director, National Institutes of Health, Bethesda, Maryland, USA
| | - John I Gallin
- Clinical Pathophysiology Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Steven M Holland
- Immunopathogenesis Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Sergio D Rosenzweig
- Department of Laboratory Medicine, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA
| | - Jose Barbot
- Unidade de Hematologia, Serviço de Pediatria, Centro Hospitalar do Porto, Porto, Portugal
| | - Carla Ciccone
- Human Biochemical Genetics Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Marjan Huizing
- Human Biochemical Genetics Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Camilo Toro
- NIH Undiagnosed Diseases Program, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - William A Gahl
- NIH Undiagnosed Diseases Program, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
- Human Biochemical Genetics Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Wendy J Introne
- Human Biochemical Genetics Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - May Christine V Malicdan
- NIH Undiagnosed Diseases Program, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
- Human Biochemical Genetics Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| |
Collapse
|
9
|
Zhang X, Chen Q, Li J, Luo X, Luo J, Li J, Zeng Z, Wu Y, Zhang H, Dong Y. The effectiveness of expanded carrier screening based on next-generation sequencing for severe monogenic genetic diseases. Hum Genomics 2024; 18:9. [PMID: 38297315 PMCID: PMC10829374 DOI: 10.1186/s40246-024-00577-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: 01/24/2024] [Indexed: 02/02/2024] Open
Abstract
Expanded carrier screening (ECS) based on next-generation sequencing has been the subject of few studies to estimate the effectiveness of ECS in the Chinese population. A total of 3737 individuals from Southwest China or the general Chinese population, including 1048 pairs and 1641 individuals, were analysed by ECS for 155 monogenetic diseases. An ECS panel was used to detect 147 genes and 10,449 variants in 145 autosomal recessive and 10 X-linked recessive disorders. A total of 43.27% (1617/3737) were found to be carriers of at least one of the 155 monogenetic diseases. The average number of carriers of these recessive mutations was 0.54 and ranged from 0 to 4. Of the 1048 couples, 74.81% (n = 784) were found to have at least one partner carrying more than one disease. In addition, 5.34% of the couples at risk (n = 56) were heterozygous for the same autosomal recessive disease, and 0.37% of the women (9/2440) were carriers of X-linked diseases. Our study demonstrated the clinical significance of ECS in Chinese populations and the need for a programme of familial screening for the prevention of severe recessive monogenetic diseases.
Collapse
Affiliation(s)
- Xue Zhang
- Department of Obstetrics, The First Affiliated Hospital of Chongqing Medical University, No. 1, Youyi Road, Yuanjiagang, Yuzhong District, Chongqing, 400016, People's Republic of China
| | - Qian Chen
- Department of Obstetrics, The First Affiliated Hospital of Chongqing Medical University, No. 1, Youyi Road, Yuanjiagang, Yuzhong District, Chongqing, 400016, People's Republic of China
| | - Junnan Li
- Department of Obstetrics, The First Affiliated Hospital of Chongqing Medical University, No. 1, Youyi Road, Yuanjiagang, Yuzhong District, Chongqing, 400016, People's Republic of China
| | - Xin Luo
- Department of Obstetrics, The First Affiliated Hospital of Chongqing Medical University, No. 1, Youyi Road, Yuanjiagang, Yuzhong District, Chongqing, 400016, People's Republic of China
| | - Jianyun Luo
- Department of Obstetrics, The First Affiliated Hospital of Chongqing Medical University, No. 1, Youyi Road, Yuanjiagang, Yuzhong District, Chongqing, 400016, People's Republic of China
| | - Jian Li
- Department of Obstetrics, The First Affiliated Hospital of Chongqing Medical University, No. 1, Youyi Road, Yuanjiagang, Yuzhong District, Chongqing, 400016, People's Republic of China
| | - Ziye Zeng
- Department of Obstetrics, The First Affiliated Hospital of Chongqing Medical University, No. 1, Youyi Road, Yuanjiagang, Yuzhong District, Chongqing, 400016, People's Republic of China
| | - Yan Wu
- Department of Obstetrics, The First Affiliated Hospital of Chongqing Medical University, No. 1, Youyi Road, Yuanjiagang, Yuzhong District, Chongqing, 400016, People's Republic of China
| | - Hua Zhang
- Department of Obstetrics, The First Affiliated Hospital of Chongqing Medical University, No. 1, Youyi Road, Yuanjiagang, Yuzhong District, Chongqing, 400016, People's Republic of China.
| | - Yanling Dong
- Department of Obstetrics, The First Affiliated Hospital of Chongqing Medical University, No. 1, Youyi Road, Yuanjiagang, Yuzhong District, Chongqing, 400016, People's Republic of China.
| |
Collapse
|
10
|
张 钏, 惠 玲, 周 秉, 郑 雷, 王 玉, 郝 胜, 达 振, 马 莹, 郭 金, 曹 宗, 马 旭. [Disease spectrum and pathogenic genes of inherited metabolic disorder in Gansu Province of China]. ZHONGGUO DANG DAI ER KE ZA ZHI = CHINESE JOURNAL OF CONTEMPORARY PEDIATRICS 2024; 26:67-71. [PMID: 38269462 PMCID: PMC10817745 DOI: 10.7499/j.issn.1008-8830.2308094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 12/04/2023] [Indexed: 01/26/2024]
Abstract
OBJECTIVES To investigate the disease spectrum and pathogenic genes of inherited metabolic disorder (IMD) among neonates in Gansu Province of China. METHODS A retrospective analysis was conducted on the tandem mass spectrometry data of 286 682 neonates who received IMD screening in Gansu Provincial Maternal and Child Health Hospital from January 2018 to December 2021. A genetic analysis was conducted on the neonates with positive results in tandem mass spectrometry during primary screening and reexamination. RESULTS A total of 23 types of IMD caused by 28 pathogenic genes were found in the 286 682 neonates, and the overall prevalence rate of IMD was 0.63 (1/1 593), among which phenylketonuria showed the highest prevalence rate of 0.32 (1/3 083), followed by methylmalonic acidemia (0.11, 1/8 959) and tetrahydrobiopterin deficiency (0.06, 1/15 927). In this study, 166 variants were identified in the 28 pathogenic genes, with 13 novel variants found in 9 genes. According to American College of Medical Genetics and Genomics guidelines, 5 novel variants were classified as pathogenic variants, 7 were classified as likely pathogenic variants, and 1 was classified as the variant of uncertain significance. CONCLUSIONS This study enriches the database of pathogenic gene variants for IMD and provides basic data for establishing an accurate screening and diagnosis system for IMD in this region.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | - 宗富 曹
- 国家卫生健康委科学技术研究所/国家人类遗传资源中心北京100081
| | - 旭 马
- 国家卫生健康委科学技术研究所/国家人类遗传资源中心北京100081
| |
Collapse
|
11
|
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]
|
12
|
Busnelli A, Ciani O, Caroselli S, Figliuzzi M, Poli M, Levi-Setti PE, Tarricone R, Capalbo A. Implementing preconception expanded carrier screening in a universal health care system: A model-based cost-effectiveness analysis. Genet Med 2023; 25:100943. [PMID: 37489580 DOI: 10.1016/j.gim.2023.100943] [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: 03/22/2023] [Revised: 07/17/2023] [Accepted: 07/18/2023] [Indexed: 07/26/2023] Open
Abstract
PURPOSE The limited evidence available on the cost-effectiveness (CE) of expanded carrier screening (ECS) prevents its widespread use in most countries, including Italy. Herein, we aimed to estimate the CE of 3 ECS panels (ie, American College of Medical Genetics and Genomics [ACMG] Tier 1 screening, "Focused Screening," testing 15 severe, highly penetrant conditions, and ACMG Tier 3 screening) compared with no screening, the health care model currently adopted in Italy. METHODS The reference population consisted of Italian couples seeking pregnancy with no increased personal/familial genetic risk. The CE model was developed from the perspective of the Italian universal health care system and was based on the following assumptions: 100% sensitivity of investigated screening strategies, 77% intervention rate of at-risk couples (ARCs), and no risk to conceive an affected child by risk-averse couples opting for medical interventions. RESULTS The incremental CE ratios generated by comparing each genetic screening panel with no screening were: -14,875 ± 1,208 €/life years gained (LYG) for ACMG1S, -106,863 ± 2,379 €/LYG for Focused Screening, and -47,277 ± 1,430 €/LYG for ACMG3S. ACMG1S and Focused Screening were dominated by ACMG3S. The parameter uncertainty did not significantly affect the outcome of the analyses. CONCLUSION From a universal health care system perspective, all the 3 ECS panels considered in the study would be more cost-effective than no screening.
Collapse
Affiliation(s)
- Andrea Busnelli
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele-Milan, Italy; IRCCS Humanitas Research Hospital, Rozzano-Milan, Italy.
| | - Oriana Ciani
- Center for Research on Health and Social Care Management, SDA Bocconi, Milan, Italy
| | | | | | | | - Paolo Emanuele Levi-Setti
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele-Milan, Italy; IRCCS Humanitas Research Hospital, Rozzano-Milan, Italy
| | - Rosanna Tarricone
- Center for Research on Health and Social Care Management, SDA Bocconi, Milan, Italy; Department of Social and Political Science, Bocconi University, Milan, Italy
| | | |
Collapse
|
13
|
Chen SC, Zhou XY, Li SY, Zhao MM, Huang HF, Jia J, Xu CM. Carrier burden of over 300 diseases in Han Chinese identified by expanded carrier testing of 300 couples using assisted reproductive technology. J Assist Reprod Genet 2023; 40:2157-2173. [PMID: 37450097 PMCID: PMC10440320 DOI: 10.1007/s10815-023-02876-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 06/22/2023] [Indexed: 07/18/2023] Open
Abstract
BACKGROUND Expanded carrier screening (ECS) has become a common practice for identifying carriers of monogenic diseases. However, existing large gene panels are not well-tailored to Chinese populations. In this study, ECS testing for pathogenic variants of both single-nucleotide variants (SNVs) and copy number variants (CNVs) in 330 genes implicated in 342 autosomal recessive (AR) or X-linked diseases was carried out. We assessed the differences in allele frequencies specific to the Chinese population who have used assisted reproductive technology (ART) and the important genes to screen for in this population. METHODOLOGY A total of 300 heterosexual couples were screened by our ECS panel using next-generation sequencing. A customed bioinformatic algorithm was used to analyze SNVs and CNVs. Guidelines from the American College of Medical Genetics and Genomics and the Association for Molecular Pathology were adapted for variant interpretation. Pathogenic or likely pathogenic (P/LP) SNVs located in high homology regions/deletions and duplications of one or more exons in length were independently verified with other methods. RESULTS 64.83% of the patients were identified to be carriers of at least one of 342 hereditary conditions. We identified 622 P/LP variants, 4.18% of which were flagged as CNVs. The rate of at-risk couples was 3%. A total of 149 AR diseases accounted for 64.05% of the cumulative carrier rate, and 48 diseases had a carrier rate above 1/200 in the test. CONCLUSION An expanded screening of inherited diseases by incorporating different variant types, especially CNVs, has the potential to reduce the occurrence of severe monogenic diseases in the offspring of patients using ART in China.
Collapse
Affiliation(s)
- Song-Chang Chen
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, 566 Fangxie Road, Huangpu District, Shanghai, 200001, China
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Xuan-You Zhou
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, 566 Fangxie Road, Huangpu District, Shanghai, 200001, China
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Shu-Yuan Li
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Ming-Min Zhao
- Fujungenetics Biotechnology Co., Ltd., No. 70 of Tongchuan Road, Putuo District, Shanghai, 200333, China
| | - He-Feng Huang
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, 566 Fangxie Road, Huangpu District, Shanghai, 200001, China
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200030, China
- Research Units of Embryo Original Diseases, Chinese Academy of Medical Sciences (No. 2019RU056), Shanghai, China
| | - Jia Jia
- Fujungenetics Biotechnology Co., Ltd., No. 70 of Tongchuan Road, Putuo District, Shanghai, 200333, China.
| | - Chen-Ming Xu
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, 566 Fangxie Road, Huangpu District, Shanghai, 200001, China.
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200030, China.
| |
Collapse
|
14
|
Gupta NS, Kumar P. Perspective of artificial intelligence in healthcare data management: A journey towards precision medicine. Comput Biol Med 2023; 162:107051. [PMID: 37271113 DOI: 10.1016/j.compbiomed.2023.107051] [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: 04/11/2023] [Revised: 05/06/2023] [Accepted: 05/20/2023] [Indexed: 06/06/2023]
Abstract
Mounting evidence has highlighted the implementation of big data handling and management in the healthcare industry to improve the clinical services. Various private and public companies have generated, stored, and analyzed different types of big healthcare data, such as omics data, clinical data, electronic health records, personal health records, and sensing data with the aim to move in the direction of precision medicine. Additionally, with the advancement in technologies, researchers are curious to extract the potential involvement of artificial intelligence and machine learning on big healthcare data to enhance the quality of patient's lives. However, seeking solutions from big healthcare data requires proper management, storage, and analysis, which imposes hinderances associated with big data handling. Herein, we briefly discuss the implication of big data handling and the role of artificial intelligence in precision medicine. Further, we also highlighted the potential of artificial intelligence in integrating and analyzing the big data that offer personalized treatment. In addition, we briefly discuss the applications of artificial intelligence in personalized treatment, especially in neurological diseases. Lastly, we discuss the challenges and limitations imposed by artificial intelligence in big data management and analysis to hinder precision medicine.
Collapse
Affiliation(s)
- Nancy Sanjay Gupta
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University, India
| | - Pravir Kumar
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University, India.
| |
Collapse
|
15
|
Accoe D. Disclosing Reproductive Genetic Carrier Status: What about the Donor? THE AMERICAN JOURNAL OF BIOETHICS : AJOB 2023; 23:126-128. [PMID: 37339291 DOI: 10.1080/15265161.2023.2207544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/22/2023]
|
16
|
Siavrienė E, Petraitytė G, Mikštienė V, Maldžienė Ž, Sasnauskienė A, Žitkutė V, Ambrozaitytė L, Rančelis T, Utkus A, Kučinskas V, Preikšaitienė E. Molecular and Functional Characterisation of a Novel Intragenic 12q24.21 Deletion Resulting in MED13L Haploinsufficiency Syndrome. MEDICINA (KAUNAS, LITHUANIA) 2023; 59:1225. [PMID: 37512036 PMCID: PMC10385642 DOI: 10.3390/medicina59071225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 06/17/2023] [Accepted: 06/26/2023] [Indexed: 07/30/2023]
Abstract
Background and Objectives: Heterozygous pathogenic variants in the MED13L gene cause impaired intellectual development and distinctive facial features with or without cardiac defects (MIM #616789). This complex neurodevelopmental disorder is characterised by various phenotypic features, including plagiocephaly, strabismus, clubfoot, poor speech, and developmental delay. The aim of this study was to evaluate the clinical significance and consequences of a novel heterozygous intragenic MED13L deletion in a proband with clinical features of a MED13L-related disorder through extensive clinical, molecular, and functional characterisation. Materials and Methods: Combined comparative genomic hybridisation and single-nucleotide polymorphism array (SNP-CGH) was used to identify the changes in the proband's gDNA sequence (DECIPHER #430183). Intragenic MED13L deletion was specified via quantitative polymerase chain reaction (qPCR) and Sanger sequencing of the proband's cDNA sample. Western blot and bioinformatics analyses were used to investigate the consequences of this copy number variant (CNV) at the protein level. CRISPR-Cas9 technology was used for a MED13L-gene-silencing experiment in a culture of the control individual's skin fibroblasts. After the MED13L-gene-editing experiment, subsequent functional fibroblast culture analyses were performed. Results: The analysis of the proband's cDNA sample allowed for specifying the regions of the breakpoints and identifying the heterozygous deletion that spanned exons 3 to 10 of MED13L, which has not been reported previously. In silico, the deletion was predicted to result in a truncated protein NP_056150.1:p.(Val104Glyfs*5), partly altering the Med13_N domain and losing the MedPIWI and Med13_C domains. After MED13L gene editing was performed, reduced cell viability; an accelerated aging process; and inhibition of the RB1, E2F1, and CCNC gene expression were found to exist. Conclusions: Based on these findings, heterozygous intragenic 12q24.21 deletion in the affected individual resulted in MED13L haploinsufficiency due to the premature termination of protein translation, therefore leading to MED13L haploinsufficiency syndrome.
Collapse
Affiliation(s)
- Evelina Siavrienė
- Department of Human and Medical Genetics, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, 08410 Vilnius, Lithuania
| | - Gunda Petraitytė
- Department of Human and Medical Genetics, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, 08410 Vilnius, Lithuania
| | - Violeta Mikštienė
- Department of Human and Medical Genetics, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, 08410 Vilnius, Lithuania
| | - Živilė Maldžienė
- Department of Human and Medical Genetics, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, 08410 Vilnius, Lithuania
| | - Aušra Sasnauskienė
- Department of Biochemistry and Molecular Biology, Institute of Biosciences, Life Sciences Centre, Vilnius University, 10257 Vilnius, Lithuania
| | - Vilmantė Žitkutė
- Department of Biochemistry and Molecular Biology, Institute of Biosciences, Life Sciences Centre, Vilnius University, 10257 Vilnius, Lithuania
| | - Laima Ambrozaitytė
- Department of Human and Medical Genetics, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, 08410 Vilnius, Lithuania
| | - Tautvydas Rančelis
- Department of Human and Medical Genetics, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, 08410 Vilnius, Lithuania
| | - Algirdas Utkus
- Department of Human and Medical Genetics, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, 08410 Vilnius, Lithuania
| | - Vaidutis Kučinskas
- Department of Human and Medical Genetics, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, 08410 Vilnius, Lithuania
| | - Eglė Preikšaitienė
- Department of Human and Medical Genetics, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, 08410 Vilnius, Lithuania
| |
Collapse
|
17
|
Liu Y, Mao L, Huang H, Li W, Man J, Zhang W, Wang L, Li L, Sun Y, Zhai T, Guo X, Du L, Huang J, Li H, Wan Y, Wei X. Clinical diagnosis of genetic disorders at both single-nucleotide and chromosomal levels based on BGISEQ-500 platform. Hum Genome Var 2023; 10:15. [PMID: 37217505 PMCID: PMC10203365 DOI: 10.1038/s41439-023-00238-9] [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: 04/26/2022] [Revised: 02/05/2023] [Accepted: 02/19/2023] [Indexed: 05/24/2023] Open
Abstract
Most variations in the human genome refer to single-nucleotide variation (SNV), small fragment insertions and deletions, and genomic copy number variation (CNV). Many human diseases including genetic disorders are associated with variations in the genome. These disorders are often difficult to be diagnosed because of their complex clinical conditions, therefore, an effective detection method is needed to facilitate clinical diagnosis and prevent birth defects. With the development of high-throughput sequencing technology, the method of targeted sequence capture chip has been extensively used owing to its high throughput, high accuracy, fast speed, and low cost. In this study, we designed a chip that potentially captured the coding region of 3043 genes associated with 4013 monogenic diseases, with an addition of 148 chromosomal abnormalities that can be identified by targeting specific regions. To assess the efficiency, a strategy of combining the BGISEQ500 sequencing platform with the designed chip was utilized to screen variants in 63 patients. Eventually, 67 disease-associated variants were found, 31 of which were novel. The results of the evaluation test also show that this combined strategy complies with the requirements of clinical testing and has proper clinical application value.
Collapse
Affiliation(s)
- Yanqiu Liu
- Department of Genetics, Jiangxi Maternal and Child Health Hospital, 330006, Nanchang, China
| | - Liangwei Mao
- BGI-Anhui Clinical Laboratory, BGI-Shenzhen, 236000, Fuyang, China
- The State Key Laboratory of Biocatalysis and Enzyme Engineering, College of Life Sciences, Hubei University, 430062, Wuhan, China
| | - Hui Huang
- BGI Genomics, BGI-Shenzhen, 518083, Shenzhen, China
| | - Wei Li
- BGI Genomics, BGI-Shenzhen, 518083, Shenzhen, China
| | - Jianfen Man
- BGI-Wuhan Clinical Laboratory, BGI-Shenzhen, 430074, Wuhan, China
| | - Wenqian Zhang
- BGI Genomics, BGI-Shenzhen, 518083, Shenzhen, China
- BGI-Wuhan Clinical Laboratory, BGI-Shenzhen, 430074, Wuhan, China
- Department of Biology, University of Copenhagen, Copenhagen, DK-2200, Denmark
| | - Lina Wang
- BGI-Wuhan Clinical Laboratory, BGI-Shenzhen, 430074, Wuhan, China
| | - Long Li
- BGI-Wuhan Clinical Laboratory, BGI-Shenzhen, 430074, Wuhan, China
| | - Yan Sun
- BGI Genomics, BGI-Shenzhen, 518083, Shenzhen, China
| | - Teng Zhai
- BGI Genomics, BGI-Shenzhen, 518083, Shenzhen, China
| | - Xueqin Guo
- BGI-Wuhan Clinical Laboratory, BGI-Shenzhen, 430074, Wuhan, China
| | - Lique Du
- BGI-Wuhan Clinical Laboratory, BGI-Shenzhen, 430074, Wuhan, China
| | - Jin Huang
- BGI-Wuhan Clinical Laboratory, BGI-Shenzhen, 430074, Wuhan, China
| | - Hao Li
- BGI-Anhui Clinical Laboratory, BGI-Shenzhen, 236000, Fuyang, China
| | - Yang Wan
- Department of Obstetrics and Gynecology, Fuyang People's Hospital, 236000, Fuyang, China.
| | - Xiaoming Wei
- BGI-Wuhan Clinical Laboratory, BGI-Shenzhen, 430074, Wuhan, China.
| |
Collapse
|
18
|
Fang Y, Li J, Zhang M, Cheng Y, Wang C, Zhu J. Clinical application value of expanded carrier screening in the population of childbearing age. Eur J Med Res 2023; 28:151. [PMID: 37031186 PMCID: PMC10082524 DOI: 10.1186/s40001-023-01112-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 03/30/2023] [Indexed: 04/10/2023] Open
Abstract
OBJECTIVE The objective of this study was to explore the clinical utility of the implementation of expanded carrier screening (ECS) in Chinese population of childbearing age. MATERIALS AND METHODS Based on capillary electrophoresis, a first-generation sequencing technology, a prospective screening study of carriers of 15 single-gene diseases was carried out in 327 subjects in Anhui Province, including 84 couples and 159 women of childbearing age, the disease carrier rate, types of screened pathogenic genes, and incidence of both partners carrying the same pathogenic genes were summarized and analyzed. RESULTS In 320 people with normal phenotypes who underwent ECS for 15 genetic diseases and 7 spouses who underwent targeted gene sequencing, 65 carriers of at least one disease were detected, with a total carrier rate of 20.31% (65/320). Among the 65 carriers, 81.54% (53/65) carried one genetic variant, 16.92% (11/65) carried two genetic variants, and 1.54% (1/65) carried three genetic variants. In this study, the three diseases with the highest carrier rates were hereditary deafness (8.13%, 26/320), Wilson's disease (4.06%, 13/320), and phenylketonuria (3.13%, 10/320). One high-risk couple (1.19%, 1/84) was detected. CONCLUSIONS It has certain clinical application value to implement ECS in the population of childbearing age in China.
Collapse
Affiliation(s)
- Yuqin Fang
- Affiliated Maternity and Child Health Hospital of Anhui Medical University, Hefei, China
- Maternity and Child Health Hospital of Anhui Province, Hefei, China
| | - Jingran Li
- Maternity and Child Health Hospital of Anhui Province, Hefei, China
| | - Miaomiao Zhang
- Maternity and Child Health Hospital of Anhui Province, Hefei, China
| | - Yuan Cheng
- Maternity and Child Health Hospital of Anhui Province, Hefei, China
| | - Chaohong Wang
- Maternity and Child Health Hospital of Anhui Province, Hefei, China
| | - Jiansheng Zhu
- Affiliated Maternity and Child Health Hospital of Anhui Medical University, Hefei, China.
- Maternity and Child Health Hospital of Anhui Province, Hefei, China.
| |
Collapse
|
19
|
Saldarriaga JF, López JE, Díaz-García L, Montoya-Ruiz C. Changes in Lolium perenne L. rhizosphere microbiome during phytoremediation of Cd- and Hg-contaminated soils. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:49498-49511. [PMID: 36781665 PMCID: PMC10104932 DOI: 10.1007/s11356-023-25501-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 01/18/2023] [Indexed: 04/16/2023]
Abstract
The contamination of soil and water by metals such as mercury (Hg) and cadmium (Cd) has been increasing in recent years, because of anthropogenic activities such as mining and agriculture, respectively. In this work, the changes in the rhizosphere microbiome of Lolium perenne L. during the phytoremediation of soils contaminated with Hg and Cd were evaluated. For this, two soil types were sampled, one inoculated with mycorrhizae and one without. The soils were contaminated with Hg and Cd, and L. perenne seeds were sown and harvested after 30 days. To assess changes in the microbiome, DNA isolation tests were performed, for which samples were subjected to two-step PCR amplification with specific 16S rDNA V3-V4 primers (337F and 805R). With mycorrhizae, changes had been found in the absorption processes of metals and a new distribution. While with respect to microorganisms, families such as the Enterobacteriaceae have been shown to have biosorption and efflux effects on metals such as Hg and Cd. Mycorrhizae then improve the efficiency of removal and allow the plant to better distribute the absorbed concentrations. Overall, L. perenne is a species with a high potential for phytoremediation of Cd- and Hg-contaminated soils in the tropics. Inoculation with mycorrhizae modifies the phytoremediation mechanisms of the plant and the composition of microorganisms in the rhizosphere. Mycorrhizal inoculation and changes in the microbiome were associated with increased plant tolerance to Cd and Hg. Microorganism-assisted phytoremediation is an appropriate alternative for L. perenne.
Collapse
Affiliation(s)
- Juan F Saldarriaga
- Dept. of Civil and Environmental Engineering, Universidad de los Andes, Carrera 1Este, #19A-40, 111711, Bogotá, Colombia.
| | - Julián E López
- Facultad de Arquitectura E Ingeniería, Institución Universitaria Colegio Mayor de Antioquia, Carrera 78 # 65 - 46, 050034, Medellín, Colombia
| | - Laura Díaz-García
- Department of Chemical & Biological Engineering and Advanced Biomanufacturing Centre, University of Sheffield, Sir Robert Hadfield Building, Mappin Street, Sheffield, S1 3JD, UK
| | - Carolina Montoya-Ruiz
- Facultad de Ciencias, Universidad Nacional de Colombia, Sede Medellín Calle, 59A #63-20, 050034, Medellín, Colombia
| |
Collapse
|
20
|
Rink BD. Informed consent for expanded carrier screening: Past, present, and future. Prenat Diagn 2023; 43:489-495. [PMID: 36636969 DOI: 10.1002/pd.6310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 12/01/2022] [Accepted: 01/08/2023] [Indexed: 01/14/2023]
Abstract
History, law, bioethics, and geocultural influences all have impacted the modern application of informed consent. It is a complex, multilayered process to communicate information and obtain voluntary patient permission before a health care intervention. Lack of provider education about genetic disorders, complexities of advanced genomic technologies, limited time during patient encounters, and low health literacy within a population all represent challenges to effective communication. There is no consensus on how informed consent in reproductive genetics is optimally obtained. Expanded carrier screening (ECS) is purposed to simultaneously test for a large list of diseases in a pan-ethnic manner. The increased use of ECS is driven by advances in genomic technologies, decreased cost, an improved understanding of single gene disorders, and in support of reproductive autonomy. Academic organizations recommend pretest counseling when patients consider ECS, yet best practice is not established. Ongoing research is needed to determine how optimally implement informed consent given the increased complexity of ECS.
Collapse
Affiliation(s)
- Britton D Rink
- Director Clinical Genetics Mount Carmel Health Systems, Division of Genetic and Genomic Medicine Nationwide Children's Hospital, Columbus, Ohio, USA
| |
Collapse
|
21
|
Clevenger SK, Brandt JS, Khan SP, Shingala P, Carrick J, Aluwalia R, Heiman GA, Ashkinadze E. Rate of manifesting carriers and other unexpected findings on carrier screening. Prenat Diagn 2023; 43:117-125. [PMID: 36529847 DOI: 10.1002/pd.6289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 12/08/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022]
Abstract
OBJECTIVES To ascertain the rate of unexpected findings on carrier screening (CS) and assess whether implications are disclosed to patients. METHODS We performed a retrospective observational study of subjects who had CS after pre-test counseling from a licensed genetic counselor at a large tertiary care center. We quantified the rate of unexpected finding on CS, defined as manifesting carriers (MCs), genotypes predicting phenotype, and chromosome abnormalities. We determined how often patients were informed of implications. We performed subgroup analyses by type of unexpected finding and calculated odds ratios (OR) and 95% confidence intervals (CI) for carrier testing methodology (genotype) and number of genes tested. RESULTS A total of 4685 patients had CS over the selected time frame. Of those patients, 412 patients (8.8%) had one unexpected finding and 29 patients (0.6%) had two or more findings. In total, 466 unexpected findings were identified, including 437 MC conditions, 23 genotypes predicting phenotype, and 6 chromosome abnormalities. Patients were informed of the implications for MCs, genotypes predicting phenotype, and chromosome abnormalities in 27.6%, 91.3%, and 100% of cases, respectively. More unexpected findings were detected with sequencing compared to genotyping (OR 2.21 and 95% CI 1.76-2.76) and with ≥200 gene panels compared to <200 gene panels (OR 1.79 and 95% CI 1.47-2.17). CONCLUSION This study highlights that nondisclosure of unexpected findings on CS is common and underscores the need for further research to improve post-test counseling and follow-up.
Collapse
Affiliation(s)
- Sydney K Clevenger
- Oncology Support Services, Morristown Medical Center, Morristown, New Jersey, USA.,Rutgers University Genetic Counseling Master's Program, Piscataway, New Jersey, USA
| | - Justin S Brandt
- Division of Maternal-Fetal Medicine, Department of Obstetrics, Gynecology, and Reproductive Sciences, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey, USA
| | - Shama P Khan
- Division of Maternal-Fetal Medicine, Department of Obstetrics, Gynecology, and Reproductive Sciences, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey, USA
| | - Pranali Shingala
- Division of Maternal-Fetal Medicine, Department of Obstetrics, Gynecology, and Reproductive Sciences, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey, USA
| | - Jillian Carrick
- Department of Genetics and the Human Genetics Institute of New Jersey, Rutgers, the State University of New Jersey, Piscataway, New Jersey, USA
| | - Ruchi Aluwalia
- Department of Genetics and the Human Genetics Institute of New Jersey, Rutgers, the State University of New Jersey, Piscataway, New Jersey, USA
| | - Gary A Heiman
- Rutgers University Genetic Counseling Master's Program, Piscataway, New Jersey, USA.,Department of Genetics and the Human Genetics Institute of New Jersey, Rutgers, the State University of New Jersey, Piscataway, New Jersey, USA
| | - Elena Ashkinadze
- Rutgers University Genetic Counseling Master's Program, Piscataway, New Jersey, USA.,Division of Maternal-Fetal Medicine, Department of Obstetrics, Gynecology, and Reproductive Sciences, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey, USA
| |
Collapse
|
22
|
Vintschger E, Kraemer D, Joset P, Horn AHC, Rauch A, Sticht H, Bachmann-Gagescu R. Challenges for the implementation of next generation sequencing-based expanded carrier screening: Lessons learned from the ciliopathies. Eur J Hum Genet 2022:10.1038/s41431-022-01267-8. [PMID: 36550190 PMCID: PMC10400553 DOI: 10.1038/s41431-022-01267-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 11/18/2022] [Accepted: 12/09/2022] [Indexed: 12/24/2022] Open
Abstract
Next generation sequencing (NGS) can detect carrier status for rare recessive disorders, informing couples about their reproductive risk. The recent ACMG recommendations support offering NGS-based carrier screening (NGS-CS) in an ethnic and population-neutral manner for all genes that have a carrier frequency >1/200 (based on GnomAD). To evaluate current challenges for NGS-CS, we focused on the ciliopathies, a well-studied group of rare recessive disorders. We analyzed 118 ciliopathy genes by whole exome sequencing in ~400 healthy local individuals and ~1000 individuals from the UK1958-birth cohort. We found 20% of healthy individuals (1% of couples) to be carriers of reportable variants in a ciliopathy gene, while 50% (4% of couples) carry variants of uncertain significance (VUS). This large proportion of VUS is partly explained by the limited utility of the ACMG/AMP variant-interpretation criteria in healthy individuals, where phenotypic match or segregation criteria cannot be used. Most missense variants are thus classified as VUS and not reported, which reduces the negative predictive value of the screening test. We show how gene-specific variation patterns and structural protein information can help prioritize variants most likely to be disease-causing, for (future) functional assays. Even when considering only strictly pathogenic variants, the observed carrier frequency is substantially higher than expected based on estimated disease prevalence, challenging the 1/200 carrier frequency cut-off proposed for choice of genes to screen. Given the challenges linked to variant interpretation in healthy individuals and the uncertainties about true carrier frequencies, genetic counseling must clearly disclose these limitations of NGS-CS.
Collapse
Affiliation(s)
- Ella Vintschger
- Institute of Medical Genetics, University of Zurich, 8952, Schlieren, Switzerland
| | - Dennis Kraemer
- Institute of Medical Genetics, University of Zurich, 8952, Schlieren, Switzerland
| | - Pascal Joset
- Institute of Medical Genetics, University of Zurich, 8952, Schlieren, Switzerland.,Institute of Medical Genetics and Pathology, University Hospital Basel, 4031, Basel, Switzerland
| | - Anselm H C Horn
- Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054, Erlangen, Germany.,Praeclare Clinical Research Priority Program of the Medical Faculty, University of Zurich, Zurich, Switzerland
| | - Anita Rauch
- Institute of Medical Genetics, University of Zurich, 8952, Schlieren, Switzerland.,Praeclare Clinical Research Priority Program of the Medical Faculty, University of Zurich, Zurich, Switzerland
| | - Heinrich Sticht
- Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054, Erlangen, Germany
| | - Ruxandra Bachmann-Gagescu
- Institute of Medical Genetics, University of Zurich, 8952, Schlieren, Switzerland. .,Praeclare Clinical Research Priority Program of the Medical Faculty, University of Zurich, Zurich, Switzerland. .,Department of Molecular Life Sciences, University of Zurich, 8057, Zurich, Switzerland.
| |
Collapse
|
23
|
Abulí A, Costa-Roger M, Codina-Solà M, Valenzuela I, Leno-Colorado J, Rovira-Moreno E, Cueto-González A, Fernández-Álvarez P, García-Arumí E, Cuscó I, Tizzano EF. Experience using singleton exome sequencing of probands as an approach to preconception carrier screening in consanguineous couples. J Med Genet 2022; 60:540-546. [PMID: 36600615 DOI: 10.1136/jmg-2022-108607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 10/05/2022] [Indexed: 12/13/2022]
Abstract
BACKGROUND Consanguineous couples have an increased risk of severe diseases in offspring due to autosomal recessive disorders. Exome sequencing (ES) offers the possibility of extensive preconception carrier screening (PCS) in consanguineous couples who may be at risk of rare genetic disorders. METHODS We retrospectively analysed ES data from 65 probands affected with rare genetic disorders born from consanguineous couples. We explored diagnostic yield and carrier status for recessive disorders. RESULTS The overall diagnostic yield in a singleton approach was 53.8%, mostly recessive variants. In a hypothetical exome-based PCS, only 11.7% of these causative rare variants would have been missed in the filtering process. Carrier screening for recessive conditions allowed the identification of at least one additional pathogenic or likely pathogenic variant in 85.7% of the probands, being the majority with a gene carrier frequency <1 in 200. In addition, considering only clinically actionable conditions, we estimated that 12.3% of our close consanguineous couples may be at risk for an additional recessive disease. CONCLUSIONS Our results demonstrate that ES outperforms panel-based screening in a PCS context in consanguineous couples and could potentially increase their reproductive autonomy and facilitate informed decision-making.
Collapse
Affiliation(s)
- Anna Abulí
- Department of Clinical and Molecular Genetics, Hospital Universitari Vall d'Hebron, Barcelona, Spain .,Medicine Genetics Group Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
| | - Mar Costa-Roger
- Department of Clinical and Molecular Genetics, Hospital Universitari Vall d'Hebron, Barcelona, Spain.,Medicine Genetics Group Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
| | - Marta Codina-Solà
- Department of Clinical and Molecular Genetics, Hospital Universitari Vall d'Hebron, Barcelona, Spain.,Medicine Genetics Group Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
| | - Irene Valenzuela
- Department of Clinical and Molecular Genetics, Hospital Universitari Vall d'Hebron, Barcelona, Spain.,Medicine Genetics Group Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
| | - Jordi Leno-Colorado
- Department of Clinical and Molecular Genetics, Hospital Universitari Vall d'Hebron, Barcelona, Spain.,Medicine Genetics Group Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
| | - Eulàlia Rovira-Moreno
- Department of Clinical and Molecular Genetics, Hospital Universitari Vall d'Hebron, Barcelona, Spain.,Medicine Genetics Group Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
| | - Anna Cueto-González
- Department of Clinical and Molecular Genetics, Hospital Universitari Vall d'Hebron, Barcelona, Spain.,Medicine Genetics Group Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
| | - Paula Fernández-Álvarez
- Department of Clinical and Molecular Genetics, Hospital Universitari Vall d'Hebron, Barcelona, Spain.,Medicine Genetics Group Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
| | - Elena García-Arumí
- Department of Clinical and Molecular Genetics, Hospital Universitari Vall d'Hebron, Barcelona, Spain.,Medicine Genetics Group Vall d'Hebron Research Institute (VHIR), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Barcelona, Spain
| | - Ivon Cuscó
- Department of Clinical and Molecular Genetics, Hospital Universitari Vall d'Hebron, Barcelona, Spain.,Medicine Genetics Group Vall d'Hebron Research Institute (VHIR), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Barcelona, Spain
| | - Eduardo F Tizzano
- Department of Clinical and Molecular Genetics, Hospital Universitari Vall d'Hebron, Barcelona, Spain.,Medicine Genetics Group Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
| |
Collapse
|
24
|
Nikfar A, Mansouri M, Chiti H, Abhari GF, Parsamanesh N. Cockayne syndrome in an Iranian pedigree with a homozygous missense variant in the ERCC6 gene. GENE REPORTS 2022. [DOI: 10.1016/j.genrep.2022.101665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
|
25
|
LILLEY CULLENM, DELILLE MINERVE, MIRZA KAMRANM, PARILLA MEGAN. Toward a More Just System of Care in Molecular Pathology. Milbank Q 2022; 100:1192-1242. [PMID: 36454130 PMCID: PMC9836258 DOI: 10.1111/1468-0009.12587] [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: 02/02/2022] [Revised: 05/09/2022] [Accepted: 06/23/2022] [Indexed: 12/02/2022] Open
Abstract
Policy Points American health care policy must be critically assessed to establish the role it plays in sustaining and alleviating the health disparities that currently exist in molecular genetic testing. It is critical to understand the economic and sociocultural influences that drive patients to undergo or forgo molecular testing, especially in marginalized patient populations. A multipronged solution with actions necessary from multiple stakeholders is required to reduce the cost of health care, rebalance regional disparities, encourage physician engagement, reduce data bias, and earn patients' trust. CONTEXT The health status of a population is greatly influenced by both biological processes and external factors. For years, minority and low socioeconomic patient populations have faced worse outcomes and poorer health in the United States. Experts have worked extensively to understand the issues and find solutions to alleviate this disproportionate burden of disease. As a result, there have been some improvements and successes, but wide gaps still exist. Diagnostic molecular genetic testing and so-called personalized medicine are just now being integrated into the current American health care system. The way in which these tests are integrated can either exacerbate or reduce health disparities. METHODS We provide case scenarios-loosely based on real-life patients-so that nonexperts can see the impacts of complex policy decisions and unintentional biases in technology without needing to understand all the intricacies. We use data to explain these findings from an extensive literature search examining both peer-reviewed and gray literature. FINDINGS Access to diagnostic molecular genetic testing is not equitable or sufficient, owing to at least five major factors: (1) cost to the patient, (2) location, (3) lack of provider buy-in, (4) data-set bias, and (5) lack of public trust. CONCLUSIONS Molecular genetic pathology can be made more equitable with the concerted efforts of multiple stakeholders. Confronting the five major factors identified here may help us usher in a new era of precision medicine without its discriminatory counterpart.
Collapse
Affiliation(s)
| | | | - KAMRAN M. MIRZA
- Loyola University Chicago, Strich School of Medicine
- Loyola Medical Center
| | - MEGAN PARILLA
- Loyola University Chicago, Strich School of Medicine
- Loyola Medical Center
| |
Collapse
|
26
|
Dapas M, Dunaif A. Deconstructing a Syndrome: Genomic Insights Into PCOS Causal Mechanisms and Classification. Endocr Rev 2022; 43:927-965. [PMID: 35026001 PMCID: PMC9695127 DOI: 10.1210/endrev/bnac001] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Indexed: 01/16/2023]
Abstract
Polycystic ovary syndrome (PCOS) is among the most common disorders in women of reproductive age, affecting up to 15% worldwide, depending on the diagnostic criteria. PCOS is characterized by a constellation of interrelated reproductive abnormalities, including disordered gonadotropin secretion, increased androgen production, chronic anovulation, and polycystic ovarian morphology. It is frequently associated with insulin resistance and obesity. These reproductive and metabolic derangements cause major morbidities across the lifespan, including anovulatory infertility and type 2 diabetes (T2D). Despite decades of investigative effort, the etiology of PCOS remains unknown. Familial clustering of PCOS cases has indicated a genetic contribution to PCOS. There are rare Mendelian forms of PCOS associated with extreme phenotypes, but PCOS typically follows a non-Mendelian pattern of inheritance consistent with a complex genetic architecture, analogous to T2D and obesity, that reflects the interaction of susceptibility genes and environmental factors. Genomic studies of PCOS have provided important insights into disease pathways and have indicated that current diagnostic criteria do not capture underlying differences in biology associated with different forms of PCOS. We provide a state-of-the-science review of genetic analyses of PCOS, including an overview of genomic methodologies aimed at a general audience of non-geneticists and clinicians. Applications in PCOS will be discussed, including strengths and limitations of each study. The contributions of environmental factors, including developmental origins, will be reviewed. Insights into the pathogenesis and genetic architecture of PCOS will be summarized. Future directions for PCOS genetic studies will be outlined.
Collapse
Affiliation(s)
- Matthew Dapas
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Andrea Dunaif
- Division of Endocrinology, Diabetes and Bone Disease, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| |
Collapse
|
27
|
Van Steijvoort E, Peeters H, Vandecruys H, Verguts J, Peeraer K, Matthijs G, Borry P. Exploring informed choice in preconception reproductive genetic carrier screening by using a modified Multidimensional Measure of Informed Choice. PATIENT EDUCATION AND COUNSELING 2022; 105:3313-3318. [PMID: 35906131 DOI: 10.1016/j.pec.2022.07.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 06/08/2022] [Accepted: 07/21/2022] [Indexed: 06/15/2023]
Abstract
OBJECTIVES To explore informed choice in reproductive genetic carrier screening (RGCS). METHODS Women visiting a gynaecologist practice in Flanders (Belgium) were asked to consider participation in a study where RGCS was offered for free to them and their male partner. A modified Multidimensional Measure of Informed Choice was used to determine whether couples who opted for RGCS made an informed choice. In addition, we assessed risk perception, feelings towards RGCS, anxiety and decisional conflict. RESULTS Most participants (82 %, n = 63/77) made an informed choice with regard to RGCS according to our modified MMIC. Thirteen participants made an uninformed choice due to insufficient knowledge and one participant because of insufficient knowledge and value-inconsistency. Anxiety scores were elevated for three participants. Two participants presented with decisional conflict. CONCLUSION Our results show high rates of informed choice among non-pregnant couples who were offered RGCS in a research study and received up to 30 min of pre-test counseling. PRACTICE IMPLICATIONS Limited resources outside a research context may impact informed choice. Pre-test counselling initiatives for RGCS should ideally be organized in such a way that information can be provided at multiple time points to avoid information overload and to allow for a reflection period.
Collapse
Affiliation(s)
- Eva Van Steijvoort
- Department of Public Health and Primary Care, KU Leuven, Leuven, Belgium.
| | - Hilde Peeters
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Hilde Vandecruys
- Department of Gynaecology and Obstetrics, Jessa Ziekenhuis, Hasselt, Belgium
| | - Jasper Verguts
- Department of Gynaecology and Obstetrics, Jessa Ziekenhuis, Hasselt, Belgium
| | - Karen Peeraer
- Department of Development and Regeneration, KU Leuven, Leuven, Belgium
| | - Gert Matthijs
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Pascal Borry
- Department of Public Health and Primary Care, KU Leuven, Leuven, Belgium
| |
Collapse
|
28
|
Capalbo A, Gabbiato I, Caroselli S, Picchetta L, Cavalli P, Lonardo F, Bianca S, Giardina E, Zuccarello D. Considerations on the use of carrier screening testing in human reproduction: comparison between recommendations from the Italian Society of Human Genetics and other international societies. J Assist Reprod Genet 2022; 39:2581-2593. [PMID: 36370240 PMCID: PMC9722986 DOI: 10.1007/s10815-022-02653-3] [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: 09/24/2022] [Accepted: 10/31/2022] [Indexed: 11/15/2022] Open
Abstract
PURPOSE Carrier screening (CS) is a term used to describe a genetic test performed on individuals without family history of genetic disorders, to investigate the carrier status for pathogenic variants associated with multiple recessive conditions. The advent of next-generation sequencing enabled simultaneous CS for an increasing number of conditions; however, a consensus on which diseases to include in gene panels and how to best develop the provision of CS is far to be reached. Therefore, the provision of CS is jeopardized and inconsistent and requires solving several important issues. METHODS In 2020, the Italian Society of Human Genetics (SIGU) established a working group composed of clinical and laboratory geneticists from public and private fields to elaborate a document to define indications and best practice of CS provision for couples planning a pregnancy. RESULTS Hereby, we present the outcome of the Italian working group's activity and compare it with previously published international recommendations (American College of Medical Genetics and Genomics (ACMG), American College of Obstetricians and Gynecologists (ACOG), and Royal Australian and New Zealand College of Obstetricians and Gynaecologists (RANZCOG)). We determine a core message on genetic counseling and nine main subject categories to explore, spanning from goals and execution to technical scientific, ethical, and socio-economic topics. Moreover, a level of agreement on the most critical points is discussed using a 5-point agreement scale, demonstrating a high level of consensus among the four societies. CONCLUSIONS This document is intended to provide genetic and healthcare professionals involved in human reproduction with guidance regarding the clinical implementation of CS.
Collapse
Affiliation(s)
| | - Ilaria Gabbiato
- Department of Lab Medicine, Unit of Clinical Genetics and Epidemiology University Hospital of Padova, Padua, Italy
| | | | | | | | - Fortunato Lonardo
- UOSD Genetica Medica, AORN "San Pio" - P.O. "G. Rummo", Benevento, Italy
| | | | - Emiliano Giardina
- Laboratorio Di Medicina Genomica - UILDM Università Degli Studi Di Roma "Tor Vergata", Fondazione Santa Lucia-IRCCS, Rome, Italy
| | - Daniela Zuccarello
- Department of Lab Medicine, Unit of Clinical Genetics and Epidemiology University Hospital of Padova, Padua, Italy
| |
Collapse
|
29
|
Van Steijvoort E, Devolder H, Geysen I, Van Epperzeel S, Peeters H, Peeraer K, Matthijs G, Borry P. Knowledge, attitudes and preferences regarding reproductive genetic carrier screening among reproductive-aged men and women in Flanders (Belgium). Eur J Hum Genet 2022; 30:1255-1261. [PMID: 35304601 PMCID: PMC9626621 DOI: 10.1038/s41431-022-01082-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 01/12/2022] [Accepted: 02/24/2022] [Indexed: 02/04/2023] Open
Abstract
Through carrier screening couples at-risk of conceiving a child with an autosomal recessive or X-linked condition can be identified prior to conception. The aim of this study was to assess knowledge, attitudes and preferences regarding reproductive genetic carrier screening (RGCS) among reproductive-aged men and women in Flanders (Belgium). Women and men of reproductive age visiting their pharmacist were invited to answer a self-administered questionnaire. Prior to filling in the questionnaire, participants were asked to read an information leaflet explaining some key concepts about RGCS. Our sample included 387 individuals of reproductive age, of which 68.5% were female and 31.5% were male. Most of the participants were below 34 years old (72.9%), didn't have children (68.6%) and were currently in a relationship (69.1%). Offering RGCS to couples that want to have children was found acceptable by 86% of participants. However, fewer participants would consider RGCS for themselves in the future (61%). We observed a positive correlation between attitude score/knowledge score and the intention to have RGCS. Half of the participants (50.9%) preferred the disclosure of individual test results. Most of participants indicated that RGCS should be offered through the gynecologist (81.1%), followed by the GP (71.5%) and the Centre for Human Genetics (64.8%). About 68.9% of participants were willing to pay out-of-pocket for an RGCS test. We recommend that RGCS should ideally be implemented through a tailored implementation strategy whereby individual needs and preferences can be taken into account.
Collapse
Affiliation(s)
- Eva Van Steijvoort
- Department of Public Health and Primary Care, Centre for Biomedical Ethics and Law, KU Leuven, Leuven, Belgium.
| | - Heleen Devolder
- Department of Public Health and Primary Care, Centre for Biomedical Ethics and Law, KU Leuven, Leuven, Belgium
| | - Inne Geysen
- Department of Public Health and Primary Care, Centre for Biomedical Ethics and Law, KU Leuven, Leuven, Belgium
| | - Silke Van Epperzeel
- Department of Public Health and Primary Care, Centre for Biomedical Ethics and Law, KU Leuven, Leuven, Belgium
| | - Hilde Peeters
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Karen Peeraer
- Department of Development and Regeneration, Woman and Child, KU Leuven, Leuven, Belgium
| | - Gert Matthijs
- Department of Human Genetics, Laboratory for Molecular Diagnosis, KU Leuven, Leuven, Belgium
| | - Pascal Borry
- Department of Public Health and Primary Care, Centre for Biomedical Ethics and Law, KU Leuven, Leuven, Belgium
| |
Collapse
|
30
|
The Australian Reproductive Genetic Carrier Screening Project (Mackenzie's Mission): Design and Implementation. J Pers Med 2022; 12:jpm12111781. [PMID: 36579509 PMCID: PMC9698511 DOI: 10.3390/jpm12111781] [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: 09/16/2022] [Revised: 10/17/2022] [Accepted: 10/20/2022] [Indexed: 01/01/2023] Open
Abstract
Reproductive genetic carrier screening (RGCS) provides people with information about their chance of having children with autosomal recessive or X-linked genetic conditions, enabling informed reproductive decision-making. RGCS is recommended to be offered to all couples during preconception or in early pregnancy. However, cost and a lack of awareness may prevent access. To address this, the Australian Government funded Mackenzie’s Mission—the Australian Reproductive Genetic Carrier Screening Project. Mackenzie’s Mission aims to assess the acceptability and feasibility of an easily accessible RGCS program, provided free of charge to the participant. In study Phase 1, implementation needs were mapped, and key study elements were developed. In Phase 2, RGCS is being offered by healthcare providers educated by the study team. Reproductive couples who provide consent are screened for over 1200 genes associated with >750 serious, childhood-onset genetic conditions. Those with an increased chance result are provided comprehensive genetic counseling support. Reproductive couples, recruiting healthcare providers, and study team members are also invited to complete surveys and/or interviews. In Phase 3, a mixed-methods analysis will be undertaken to assess the program outcomes, psychosocial implications and implementation considerations alongside an ongoing bioethical analysis and a health economic evaluation. Findings will inform the implementation of an ethically robust RGCS program.
Collapse
|
31
|
Edwards S, Laing N. Genetic Counselling Needs for Reproductive Genetic Carrier Screening: A Scoping Review. J Pers Med 2022; 12:1699. [PMID: 36294838 PMCID: PMC9605645 DOI: 10.3390/jpm12101699] [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: 07/25/2022] [Revised: 10/03/2022] [Accepted: 10/08/2022] [Indexed: 11/17/2022] Open
Abstract
Reproductive genetic carrier screening provides individuals and couples with information regarding their risk of having a child affected by an autosomal recessive or X-linked recessive genetic condition. This information allows them the opportunity to make reproductive decisions in line with their own beliefs and values. Traditionally, carrier screening has been accessed by family members of affected individuals. In recent years, improvements to accessibility and updates to recommendations suggest that all women planning or in early pregnancy should be offered reproductive genetic carrier screening. As uptake moves towards the population scale, how can the genetic counselling needs of such large-scale screening be met? A scoping review of the literature was performed to ascertain what the genetic counselling needs of reproductive genetic carrier screening are, and what future research is needed. Four broad themes were identified in the existing literature: (1) The offer-when and in what context to offer screening; (2) Information-the importance of and what to include in education, and pre- and post-test counselling; (3) Who and how-who the genetic counselling is performed by and how; (4) Personalization-how do we find the balance between standardized and individualized approaches? Based on the existing literature, we present a set of recommendations for consideration in implementing population-scale reproductive genetic carrier screening as well as suggested areas for future research.
Collapse
Affiliation(s)
- Samantha Edwards
- Harry Perkins Institute of Medical Research and Centre for Medical Research, University of Western Australia, QEII Medical Centre, Nedlands, WA 6009, Australia
| | | |
Collapse
|
32
|
Yang L, Xu Y, Xia J, Yan H, Ding C, Shi Q, Wu Y, Liu P, Pan J, Zeng Y, Zhang Y, Chen F, Jiang H, Xu Y, Li W, Zhou C, Gao Y. Simultaneous detection of genomic imbalance in patients receiving preimplantation genetic testing for monogenic diseases (PGT-M). Front Genet 2022; 13:976131. [PMID: 36246639 PMCID: PMC9559864 DOI: 10.3389/fgene.2022.976131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 08/31/2022] [Indexed: 11/23/2022] Open
Abstract
Background: Preimplantation genetic test for monogenic disorders (PGT-M) has been used to select genetic disease-free embryos for implantation during in vitro fertilization (IVF) treatment. However, embryos tested by PGT-M have risks of harboring chromosomal aneuploidy. Hence, a universal method to detect monogenic diseases and genomic imbalances is required. Methods: Here, we report a novel PGT-A/M procedure allowing simultaneous detection of monogenic diseases and genomic imbalances in one experiment. Library was prepared in a special way that multiplex polymerase chain reaction (PCR) was integrated into the process of whole genome amplification. The resulting library was used for one-step low-pass whole genome sequencing (WGS) and high-depth target enrichment sequencing (TES). Results: The TAGs-seq PGT-A/M was first validated with genomic DNA (gDNA) and the multiple displacement amplification (MDA) products of a cell line. Over 90% of sequencing reads covered the whole-genome region with around 0.3–0.4 × depth, while around 5.4%–7.3% of reads covered target genes with >10000 × depth. Then, for clinical validation, 54 embryos from 8 women receiving PGT-M of β-thalassemia were tested by the TAGs-seq PGT-A/M. In each embryo, an average of 20.0 million reads with 0.3 × depth of the whole-genome region was analyzed for genomic imbalance, while an average of 0.9 million reads with 11260.0 × depth of the target gene HBB were analyzed for β-thalassemia. Eventually, 18 embryos were identified with genomic imbalance with 81.1% consistency to karyomapping results. 10 embryos contained β-thalassemia with 100% consistency to conventional PGT-M method. Conclusion: TAGs-seq PGT-A/M simultaneously detected genomic imbalance and monogenic disease in embryos without dramatic increase of sequencing data output.
Collapse
Affiliation(s)
- Lin Yang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- BGI-Shenzhen, Shenzhen, China
| | - Yan Xu
- Reproductive Medicine Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Reproductive Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Jun Xia
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- BGI-Shenzhen, Shenzhen, China
| | | | - Chenhui Ding
- Reproductive Medicine Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Reproductive Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | | | | | | | - Jiafu Pan
- Reproductive Medicine Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Reproductive Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yanhong Zeng
- Reproductive Medicine Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Reproductive Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | | | | | | | - Yanwen Xu
- Reproductive Medicine Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Reproductive Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- *Correspondence: Yanwen Xu, ; Wei Li, ; Canquan Zhou, ; Ya Gao,
| | - Wei Li
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
- Hebei Industrial Technology Research Institute of Genomics in Maternal and Child Health, Shijiazhuang, China
- *Correspondence: Yanwen Xu, ; Wei Li, ; Canquan Zhou, ; Ya Gao,
| | - Canquan Zhou
- Reproductive Medicine Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Reproductive Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- *Correspondence: Yanwen Xu, ; Wei Li, ; Canquan Zhou, ; Ya Gao,
| | - Ya Gao
- BGI-Shenzhen, Shenzhen, China
- Shenzhen Engineering Laboratory for Birth Defects Screening, Shenzhen, China
- *Correspondence: Yanwen Xu, ; Wei Li, ; Canquan Zhou, ; Ya Gao,
| |
Collapse
|
33
|
Kingsmore SF, Smith LD, Kunard CM, Bainbridge M, Batalov S, Benson W, Blincow E, Caylor S, Chambers C, Del Angel G, Dimmock DP, Ding Y, Ellsworth K, Feigenbaum A, Frise E, Green RC, Guidugli L, Hall KP, Hansen C, Hobbs CA, Kahn SD, Kiel M, Van Der Kraan L, Krilow C, Kwon YH, Madhavrao L, Le J, Lefebvre S, Mardach R, Mowrey WR, Oh D, Owen MJ, Powley G, Scharer G, Shelnutt S, Tokita M, Mehtalia SS, Oriol A, Papadopoulos S, Perry J, Rosales E, Sanford E, Schwartz S, Tran D, Reese MG, Wright M, Veeraraghavan N, Wigby K, Willis MJ, Wolen AR, Defay. T. A genome sequencing system for universal newborn screening, diagnosis, and precision medicine for severe genetic diseases. Am J Hum Genet 2022; 109:1605-1619. [PMID: 36007526 PMCID: PMC9502059 DOI: 10.1016/j.ajhg.2022.08.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/01/2022] [Indexed: 12/31/2022] Open
Abstract
Newborn screening (NBS) dramatically improves outcomes in severe childhood disorders by treatment before symptom onset. In many genetic diseases, however, outcomes remain poor because NBS has lagged behind drug development. Rapid whole-genome sequencing (rWGS) is attractive for comprehensive NBS because it concomitantly examines almost all genetic diseases and is gaining acceptance for genetic disease diagnosis in ill newborns. We describe prototypic methods for scalable, parentally consented, feedback-informed NBS and diagnosis of genetic diseases by rWGS and virtual, acute management guidance (NBS-rWGS). Using established criteria and the Delphi method, we reviewed 457 genetic diseases for NBS-rWGS, retaining 388 (85%) with effective treatments. Simulated NBS-rWGS in 454,707 UK Biobank subjects with 29,865 pathogenic or likely pathogenic variants associated with 388 disorders had a true negative rate (specificity) of 99.7% following root cause analysis. In 2,208 critically ill children with suspected genetic disorders and 2,168 of their parents, simulated NBS-rWGS for 388 disorders identified 104 (87%) of 119 diagnoses previously made by rWGS and 15 findings not previously reported (NBS-rWGS negative predictive value 99.6%, true positive rate [sensitivity] 88.8%). Retrospective NBS-rWGS diagnosed 15 children with disorders that had been undetected by conventional NBS. In 43 of the 104 children, had NBS-rWGS-based interventions been started on day of life 5, the Delphi consensus was that symptoms could have been avoided completely in seven critically ill children, mostly in 21, and partially in 13. We invite groups worldwide to refine these NBS-rWGS conditions and join us to prospectively examine clinical utility and cost effectiveness.
Collapse
Affiliation(s)
- Stephen F. Kingsmore
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA,Keck Graduate Institute, Claremont, CA 91711, USA,Corresponding author
| | - Laurie D. Smith
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA
| | | | - Matthew Bainbridge
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA
| | - Sergey Batalov
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA
| | - Wendy Benson
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA
| | - Eric Blincow
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA
| | - Sara Caylor
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA
| | - Christina Chambers
- Department of Pediatrics, University of California San Diego, San Diego, CA 92093, USA
| | | | - David P. Dimmock
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA
| | - Yan Ding
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA
| | - Katarzyna Ellsworth
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA
| | - Annette Feigenbaum
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA,Department of Pediatrics, University of California San Diego, San Diego, CA 92093, USA
| | - Erwin Frise
- Fabric Genomics, Inc., Oakland, CA 94612, USA
| | - Robert C. Green
- Mass General Brigham, Broad Institute, Ariadne Labs and Harvard Medical School, Boston, MA 02115, USA
| | - Lucia Guidugli
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA
| | | | - Christian Hansen
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA
| | - Charlotte A. Hobbs
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA
| | | | - Mark Kiel
- Genomenon Inc., Ann Arbor, MI 48108, USA
| | - Lucita Van Der Kraan
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA
| | | | - Yong H. Kwon
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA
| | - Lakshminarasimha Madhavrao
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA
| | - Jennie Le
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA
| | | | - Rebecca Mardach
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA,Department of Pediatrics, University of California San Diego, San Diego, CA 92093, USA
| | | | - Danny Oh
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA
| | - Mallory J. Owen
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA
| | | | - Gunter Scharer
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA
| | | | - Mari Tokita
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA
| | | | - Albert Oriol
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA
| | | | - James Perry
- Rady Children’s Hospital, San Diego, CA 92123, USA,Department of Pediatrics, University of California San Diego, San Diego, CA 92093, USA
| | - Edwin Rosales
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA
| | - Erica Sanford
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA
| | | | - Duke Tran
- Illumina, Inc., San Diego, CA 92122, USA
| | | | - Meredith Wright
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA
| | - Narayanan Veeraraghavan
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA
| | - Kristen Wigby
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA,Department of Pediatrics, University of California San Diego, San Diego, CA 92093, USA
| | - Mary J. Willis
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA
| | | | - Thomas Defay.
- Alexion, Astra Zeneca Rare Disease, Boston, MA 02210, USA
| |
Collapse
|
34
|
Abstract
Genetic diseases disrupt the functionality of an infant's genome during fetal-neonatal adaptation and represent a leading cause of neonatal and infant mortality in the United States. Due to disease acuity, gene locus and allelic heterogeneity, and overlapping and diverse clinical phenotypes, diagnostic genome sequencing in neonatal intensive care units has required the development of methods to shorten turnaround times and improve genomic interpretation. From 2012 to 2021, 31 clinical studies documented the diagnostic and clinical utility of first-tier rapid or ultrarapid whole-genome sequencing through cost-effective identification of pathogenic genomic variants that change medical management, suggest new therapeutic strategies, and refine prognoses. Genomic diagnosis also permits prediction of reproductive recurrence risk for parents and surviving probands. Using implementation science and quality improvement, deployment of a genomic learning healthcare system will contribute to a reduction of neonatal and infant mortality through the integration of genome sequencing into best-practice neonatal intensive care.
Collapse
Affiliation(s)
- Stephen F. Kingsmore
- Rady Children’s Hospital Institute for Genomic Medicine, Rady Children’s Hospital-San Diego
| | - F. Sessions Cole
- Division of Newborn Medicine, Edward Mallinckrodt Department of Pediatrics, Washington University School of Medicine in St. Louis
| |
Collapse
|
35
|
Tong K, He W, He Y, Li X, Hu L, Hu H, Lu G, Lin G, Dong C, Zhang VW, Du J, Liu D. Clinical Utility of Medical Exome Sequencing: Expanded Carrier Screening for Patients Seeking Assisted Reproductive Technology in China. Front Genet 2022; 13:943058. [PMID: 36072675 PMCID: PMC9441495 DOI: 10.3389/fgene.2022.943058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 06/20/2022] [Indexed: 11/13/2022] Open
Abstract
Purpose: Expanded carrier screening (ECS) is an effective method to identify at-risk couples (ARCs) and avoid birth defects. This study aimed to reveal the carrier spectrum in the Chinese population and to delineate an expanded carrier gene panel suitable in China.Methods: Medical exome sequencing (MES), including 4,158 disease-causing genes, was offered to couples at two reproductive centers. It was initially used as a diagnostic yield for potential patients and then used for ECS. Clinical information and ECS results were retrospectively collected.Results: A total of 2,234 couples, representing 4,468 individuals, underwent MES. In total, 254 individuals showed genetic disease symptoms, and 56 of them were diagnosed with genetic diseases by MES. Overall, 94.5% of them were carriers of at least one disease-causing variant. The most prevalent genes were GJB2 for autosomal recessive disorders and G6PD for X-linked diseases. The ARC rate was 9.80%, and couples were inclined to undergo preimplantation genetic testing when diseases were classified as “profound” or “severe.”Conclusion: This study provided insight to establish a suitable ECS gene panel for the Chinese population. Disease severity significantly influenced reproductive decision-making. The results highlighted the importance of conducting ECS for couples before undergoing assisted reproductive technology.
Collapse
Affiliation(s)
- Keya Tong
- Center for Reproductive Medicine, Women and Children’s Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Human Embryo Engineering, Women and Children’s Hospital of Chongqing Medical University, Chongqing, China
| | - Wenbin He
- National Engineering and Research Center of Human Stem Cells, Changsha, China
- School of Basic Medical Science, Institute of Reproductive and Stem Cell Engineering, Central South University, Changsha, China
- Genetics Centre, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China
| | - Yao He
- Center for Reproductive Medicine, Women and Children’s Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Human Embryo Engineering, Women and Children’s Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Clinical Research Center for Reproductive Medicine, Women and Children’s Hospital of Chongqing Medical University, Chongqing, China
| | - Xiurong Li
- National Engineering and Research Center of Human Stem Cells, Changsha, China
| | - Liang Hu
- National Engineering and Research Center of Human Stem Cells, Changsha, China
| | - Hao Hu
- National Engineering and Research Center of Human Stem Cells, Changsha, China
| | - Guangxiu Lu
- National Engineering and Research Center of Human Stem Cells, Changsha, China
- School of Basic Medical Science, Institute of Reproductive and Stem Cell Engineering, Central South University, Changsha, China
- Genetics Centre, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China
| | - Ge Lin
- National Engineering and Research Center of Human Stem Cells, Changsha, China
- School of Basic Medical Science, Institute of Reproductive and Stem Cell Engineering, Central South University, Changsha, China
- Genetics Centre, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China
| | | | | | - Juan Du
- National Engineering and Research Center of Human Stem Cells, Changsha, China
- School of Basic Medical Science, Institute of Reproductive and Stem Cell Engineering, Central South University, Changsha, China
- Genetics Centre, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China
- *Correspondence: Juan Du, ; Dongyun Liu,
| | - Dongyun Liu
- Center for Reproductive Medicine, Women and Children’s Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Human Embryo Engineering, Women and Children’s Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Clinical Research Center for Reproductive Medicine, Women and Children’s Hospital of Chongqing Medical University, Chongqing, China
- *Correspondence: Juan Du, ; Dongyun Liu,
| |
Collapse
|
36
|
Boonsawat P, Horn AHC, Steindl K, Baumer A, Joset P, Kraemer D, Bahr A, Ivanovski I, Cabello EM, Papik M, Zweier M, Oneda B, Sirleto P, Burkhardt T, Sticht H, Rauch A. Assessing clinical utility of preconception expanded carrier screening regarding residual risk for neurodevelopmental disorders. NPJ Genom Med 2022; 7:45. [PMID: 35906228 PMCID: PMC9338263 DOI: 10.1038/s41525-022-00316-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 07/15/2022] [Indexed: 11/10/2022] Open
Abstract
The magnitude of clinical utility of preconception expanded carrier screening (ECS) concerning its potential to reduce the risk of affected offspring is unknown. Since neurodevelopmental disorders (NDDs) in their offspring is a major concern of parents-to-be, we addressed the question of residual risk by assessing the risk-reduction potential for NDDs in a retrospective study investigating ECS with different criteria for gene selection and definition of pathogenicity. We used exome sequencing data from 700 parents of children with NDDs and blindly screened for carrier-alleles in up to 3046 recessive/X-linked genes. Depending on variant pathogenicity thresholds and gene content, NDD-risk-reduction potential was up to 43.5% in consanguineous, and 5.1% in nonconsanguineous couples. The risk-reduction-potential was compromised by underestimation of pathogenicity of missense variants (false-negative-rate 4.6%), inherited copy-number variants and compound heterozygosity of one inherited and one de novo variant (0.9% each). Adherence to the ACMG recommendations of restricting ECS to high-frequency genes in nonconsanguineous couples would more than halve the detectable inherited NDD-risk. Thus, for optimized clinical utility of ECS, screening in recessive/X-linked genes regardless of their frequency (ACMG Tier-4) and sensible pathogenicity thresholds should be considered for all couples seeking ECS.
Collapse
Affiliation(s)
| | - Anselm H C Horn
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland.,Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Katharina Steindl
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Alessandra Baumer
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Pascal Joset
- Medical Genetics, University Hospital Basel, Basel, Switzerland
| | - Dennis Kraemer
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Angela Bahr
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Ivan Ivanovski
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Elena M Cabello
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Michael Papik
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Markus Zweier
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Beatrice Oneda
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Pietro Sirleto
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Tilo Burkhardt
- University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Heinrich Sticht
- Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Anita Rauch
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland. .,University Children's Hospital Zurich, University of Zurich, Zurich, Switzerland.
| |
Collapse
|
37
|
Polyzos NP, Ayoubi JM, Pirtea P. General infertility workup in times of high assisted reproductive technology efficacy. Fertil Steril 2022; 118:8-18. [PMID: 35725122 DOI: 10.1016/j.fertnstert.2022.05.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 05/05/2022] [Accepted: 05/12/2022] [Indexed: 11/04/2022]
Abstract
The assessments of oocyte quality and quantity and endocrine profile have traditionally been the cornerstone of the general workup of couples with infertility. Over the years, several clinical, hormonal, and functional biomarkers have been adopted to assess ovarian function and identify endocrine disorders before assisted reproductive technology. Furthermore, the genetic workup of patients has drastically changed, introducing novel markers. This not only allowed the prediction of response to ovarian stimulation but also contributed toward the development of a safer and more efficient management of women undergoing assisted reproductive technology. The scope of this review is to provide an overview of the current and novel strategies adopted for the assessment of ovarian function and ovulatory and endocrine disorders in women planning to conceive. Furthermore, it aims to provide an insight in the role of novel genetic biomarkers and use of expanded carrier screening as part of preliminary workup of women with infertility.
Collapse
Affiliation(s)
- Nikolaos P Polyzos
- Department of Obstetrics, Gynecology and Reproductive Medicine, Dexeus University Hospital, Barcelona, Spain; Faculty of Medicine and Health Sciences, Ghent University (UZ Gent), Gent, Belgium.
| | - Jean Marc Ayoubi
- Department of Obstetrics, Gynecology and Reproductive Medicine, Hospital Foch-Faculté de Medicine Paris Ouest (UVSQ), Suresnes, France
| | - Paul Pirtea
- Department of Obstetrics, Gynecology and Reproductive Medicine, Hospital Foch-Faculté de Medicine Paris Ouest (UVSQ), Suresnes, France
| |
Collapse
|
38
|
Schmidtke J, Krawczak M. Carrier detection probabilities for autosomal recessive variants in unrelated and consanguineous couples - an evaluation of the 86 genes of the ACMG 'Tier 3' panel. J Community Genet 2022; 13:399-401. [PMID: 35661981 PMCID: PMC9314508 DOI: 10.1007/s12687-022-00593-0] [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: 03/29/2022] [Accepted: 05/19/2022] [Indexed: 11/30/2022] Open
Abstract
Carrier screening for autosomal recessive variants has become a cornerstone of community and public health genetics. While the first carrier screening programs were confined to conditions with relatively high prevalence, and hence well-known carrier frequency, the number of candidate genes has increased greatly since the advent of high-throughput DNA sequencing technologies. The epidemiological database of the ensuing gene panels is mostly sparse, and judgement of their performance is, therefore, anything but straightforward. We therefore derived estimates of the carrier detection probabilities among non-consanguineous and consanguineous couples as expected using the ‘Tier 3’ carrier screening gene panel recently recommended by the American College of Medical Genetics (ACMG). For non-Finnish Europeans, the respective estimate for unrelated couples equals 0.63%, implying that the ACMG Tier 3 panel accounts for over 90% of the genetic load for autosomal recessive diseases in this population. Among the offspring of first cousins, the corresponding incidence is expected to be tenfold higher, an increase still consistent with previous estimates of the overall risk of birth defects for this type of mating. Our considerations are intended to aid the implementation of carrier screening programs and to provide additional support to reproductive counselling and to obtaining informed consent.
Collapse
Affiliation(s)
- Jörg Schmidtke
- Medizinische Hochschule Hannover, Carl-Neuberg-Strasse 1, 30625, Hannover, Germany. .,Amedes MVZ Wagnerstibbe, Georgstrasse 50, 30159, Hannover, Germany.
| | - Michael Krawczak
- Institute of Medical Informatics and Statistics, Kiel University, University Medical Centre Schleswig-Holstein Campus Kiel, Brunswiker Strasse 10, 24105, Kiel, Germany
| |
Collapse
|
39
|
Raz A, Timmermans S, Eyal G, Brothers K, Minari J. Challenges for precision public health communication in the era of genomic medicine. Genet Med 2022; 24:1814-1820. [PMID: 35657379 DOI: 10.1016/j.gim.2022.05.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 05/12/2022] [Accepted: 05/13/2022] [Indexed: 11/18/2022] Open
Abstract
Although still in the early stages of development, the advent of fast, high-output, and cost-effective next-generation DNA sequencing technology is moving precision medicine into public health. Before this shift toward next-generation sequencing in public health settings, individual patients met geneticists after showing symptoms and through limited family screening. In the new era of precision public health, everyone is a possible participant in genetic sequencing, simply by being born (newborn screening), by donating blood (biobanking), or through population screening. These initiatives are increasingly offered to individuals throughout their life and more individuals are encountering opportunities to use DNA sequencing. This article raises awareness of these growing areas and calls for different models of public engagement and communication about genomics, including screening asymptomatic populations, obtaining consent for unspecified and unforeseen future uses of genomic data, and managing variants of uncertain significance. Given that such communication challenges loom large, established norms of practice in genomic medicine and research should be reconsidered.
Collapse
Affiliation(s)
- Aviad Raz
- Department of Sociology & Anthropology, Ben-Gurion University of the Nagev, Beersheba, Israel.
| | | | - Gil Eyal
- Precision Medicine & Society Program, Department of Sociology, Columbia University, New York, NY
| | - Kyle Brothers
- Department of Pediatrics, School of Medicine, University of Louisville, Louisville, KY
| | - Jusaku Minari
- Uehiro Research Division for iPS Cell Ethics, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| |
Collapse
|
40
|
Field MA. Bioinformatic Challenges Detecting Genetic Variation in Precision Medicine Programs. Front Med (Lausanne) 2022; 9:806696. [PMID: 35463004 PMCID: PMC9024231 DOI: 10.3389/fmed.2022.806696] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 03/21/2022] [Indexed: 11/13/2022] Open
Abstract
Precision medicine programs to identify clinically relevant genetic variation have been revolutionized by access to increasingly affordable high-throughput sequencing technologies. A decade of continual drops in per-base sequencing costs means it is now feasible to sequence an individual patient genome and interrogate all classes of genetic variation for < $1,000 USD. However, while advances in these technologies have greatly simplified the ability to obtain patient sequence information, the timely analysis and interpretation of variant information remains a challenge for the rollout of large-scale precision medicine programs. This review will examine the challenges and potential solutions that exist in identifying predictive genetic biomarkers and pharmacogenetic variants in a patient and discuss the larger bioinformatic challenges likely to emerge in the future. It will examine how both software and hardware development are aiming to overcome issues in short read mapping, variant detection and variant interpretation. It will discuss the current state of the art for genetic disease and the remaining challenges to overcome for complex disease. Success across all types of disease will require novel statistical models and software in order to ensure precision medicine programs realize their full potential now and into the future.
Collapse
Affiliation(s)
- Matt A. Field
- Centre for Tropical Bioinformatics and Molecular Biology, College of Public Health, Medical and Veterinary Science, James Cook University, Cairns, QLD, Australia
- Immunogenomics Lab, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
- *Correspondence: Matt A. Field
| |
Collapse
|
41
|
Van Steijvoort E, Demuynck R, Peeters H, Vandecruys H, Verguts J, Peeraer K, Matthijs G, Borry P. Reasons affecting the uptake of reproductive genetic carrier screening among nonpregnant reproductive-aged women in Flanders (Belgium). J Genet Couns 2022; 31:1043-1053. [PMID: 35385167 DOI: 10.1002/jgc4.1575] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 02/26/2022] [Accepted: 03/05/2022] [Indexed: 11/07/2022]
Abstract
Reproductive genetic carrier screening (RGCS) allows to identify couples who have an increased likelihood of conceiving a child affected with an autosomal recessive or X-linked monogenic condition. Multiple studies have reported on a wide and fragmented set of reasons to accept or decline RGCS. Only a few studies have been performed to assess the uptake of RGCS. Nonpregnant women visiting their gynecologist were invited to complete a questionnaire assessing perceived susceptibility, the acceptability of offering RGCS, attitudes, the intention to participate in RGCS, reasons to accept or decline RGCS, and sociodemographic characteristics. Women who showed the intention to have RGCS were asked to consider a free RGCS offer. Most women (n = 127) were between 25 and 34 years old (60%), in a relationship (91%), and wanted to have children (65%). Study participants had positive attitudes towards RGCS and the intention to consider RGCS in the future. Reasons to accept RGCS were being able to share genetic information with children or relatives (n = 104/127, 82%), to prevent the birth of a child affected with a hereditary condition (n = 103/127, 81%), and/or to know the chance of conceiving a child with a hereditary condition (n = 102/127, 80%). Reasons for declining RGCS were the possible concerns that could arise when receiving test results (n = 27/127, 21%), having no family history of hereditary disorders (n = 19/127, 15%), and not wanting to take action based on test results (n = 13/127, 10%). Among test intenders that met the inclusion criteria, 53% decided to participate in RGCS together with their male reproductive partner. More in-depth research on the decision-making process behind the choice to accept or decline an RGCS offer would be highly valuable to make sure couples are making informed reproductive choices.
Collapse
Affiliation(s)
- Eva Van Steijvoort
- Department of Public Health and Primary Care, KU Leuven, Leuven, Belgium
| | - Remke Demuynck
- Department of Public Health and Primary Care, KU Leuven, Leuven, Belgium
| | - Hilde Peeters
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Hilde Vandecruys
- Department of Gynecology and Obstetrics, Jessa Ziekenhuis Hasselt, Hasselt, Belgium
| | - Jasper Verguts
- Department of Gynecology and Obstetrics, Jessa Ziekenhuis Hasselt, Hasselt, Belgium
| | - Karen Peeraer
- Department of Development and Regeneration, KU Leuven, Leuven, Belgium
| | - Gert Matthijs
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Pascal Borry
- Department of Public Health and Primary Care, KU Leuven, Leuven, Belgium
| |
Collapse
|
42
|
Current Updates on Expanded Carrier Screening: New Insights in the Omics Era. Medicina (B Aires) 2022; 58:medicina58030455. [PMID: 35334631 PMCID: PMC8951681 DOI: 10.3390/medicina58030455] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 03/18/2022] [Accepted: 03/19/2022] [Indexed: 11/28/2022] Open
Abstract
Genetic carrier screening has been successfully used over the last decades to identify individuals at risk of transmitting specific DNA variants to their newborns, thus having an affected child. Traditional testing has been offered based on familial and/or ethnic backgrounds. The development of high-throughput technologies, such as next-generations sequencing, able to allow the study of large genomic regions in a time and cost-affordable way, has moved carrier screening toward a more comprehensive and extensive approach, i.e., expanded carrier screening (ECS). ECS simultaneously analyses several disease-related genes and better estimates individuals’ carrier status. Indeed, it is not influenced by ethnicity and is not limited to a subset of mutations that may arise from poor information in some populations. Moreover, if couples carry out ECS before conceiving a baby, it allows them to obtain a complete estimation of their genetic risk and the possibility to make an informed decision regarding their reproductive life. Despite these advantages, some weakness still exists regarding, for example, the number of genes and the kind of diseases to be analyzed and the interpretation and communication of the obtained results. Once these points are fixed, it is expectable that ECS will become an ever more frequent practice in clinical settings.
Collapse
|
43
|
Courage C, Koehler U, Kleinle S, Neuhann T, Holinski-Feder E, Abicht A. Präkonzeptionsscreening. GYNAKOLOGISCHE ENDOKRINOLOGIE 2022. [DOI: 10.1007/s10304-021-00434-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
44
|
Kotecha UH, Mistri M, Rayabarapu P, Shah P, Shah N. The diagnostic utility of exome-based carrier screening in families with a positive family history. Am J Med Genet A 2022; 188:1323-1333. [PMID: 34997808 DOI: 10.1002/ajmg.a.62633] [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: 04/27/2021] [Revised: 10/15/2021] [Accepted: 12/26/2021] [Indexed: 11/09/2022]
Abstract
Identification of disease-causing variants in families with a history of a suspected recessive disorder is essential for appropriate counseling and reproductive decision making. The present case series depicts the utility of whole exome-based phenotypes-driven carrier analysis in 14 families with a positive family history. A phenotype-based analysis revealed a putative diagnostic yield of 71.4%. Proband sample, though insufficient, was available in only one family, which allowed the diagnosis to be confirmed. In the remaining nine families, despite the detection of heterozygous pathogenic/likely pathogenic variants, only a putative diagnosis was possible due to incomplete proband phenotyping as well as nonavailability of proband samples. We describe the youngest known patient homozygous for a likely pathogenic variant in PPP1R21. He is currently asymptomatic at 7 days of life and has a simplified gyral pattern on neuroimaging. The case series, though small, captures the challenges in the diagnosis of genetic disorders in low to middle income countries with in-equitable health care access. It reinforces the significance of detailed phenotyping in the proband as well as the importance of DNA storage for a conclusive diagnosis. A recurring post-test counseling challenge was risk ascertainment and reproductive decision making in subsequent pregnancies if the detected pathogenic/likely pathogenic variants are co-inherited, in families with a putative diagnosis. When opted for, prenatal testing in such a scenario would be limited in its ability to comment on the fetal status with respect to the disorder in the proband.
Collapse
Affiliation(s)
| | - Mehul Mistri
- Neuberg Centre for Genomic Medicine, Ahmedabad, India
| | | | - Parth Shah
- Neuberg Centre for Genomic Medicine, Ahmedabad, India
| | - Nidhi Shah
- Neuberg Centre for Genomic Medicine, Ahmedabad, India
| |
Collapse
|
45
|
Calcagno M, D'Agata R, Breveglieri G, Borgatti M, Bellassai N, Gambari R, Spoto G. Nanoparticle-Enhanced Surface Plasmon Resonance Imaging Enables the Ultrasensitive Detection of Non-Amplified Cell-Free Fetal DNA for Non-Invasive Prenatal Testing. Anal Chem 2021; 94:1118-1125. [PMID: 34964602 PMCID: PMC8771635 DOI: 10.1021/acs.analchem.1c04196] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
![]()
Although many potential
applications in early clinical diagnosis
have been proposed, the use of a surface plasmon resonance imaging
(SPRI) technique for non-invasive prenatal diagnostic approaches based
on maternal blood analysis is confined. Here, we report a nanoparticle-enhanced
SPRI strategy for a non-invasive prenatal fetal sex determination
based on the detection of a Y-chromosome specific sequence (single-gene
SRY) in cell-free fetal DNA from maternal plasma. The SPR assay proposed
here allows for detection of male DNA in mixtures of 2.5 aM male and
female genomic DNAs with no preliminary amplification of the DNA target
sequence, thus establishing an analytical protocol that does not require
costly, time-consuming, and prone to sample contamination PCR-based
procedures. Afterward, the developed protocol was successfully applied
to reveal male cell-free fetal DNA in the plasma of pregnant women
at different gestational ages, including early gestational ages. This
approach would pave the way for the establishment of faster and cost-effective
non-invasive prenatal testing.
Collapse
Affiliation(s)
- Marzia Calcagno
- Department of Chemical Sciences, University of Catania, Viale Andrea Doria, 6, 95125 Catania, Italy
| | - Roberta D'Agata
- Department of Chemical Sciences, University of Catania, Viale Andrea Doria, 6, 95125 Catania, Italy
| | - Giulia Breveglieri
- Department of Life Sciences and Biotechnology, University of Ferrara, Via Fossato di Mortara 74, 44121 Ferrara, Italy
| | - Monica Borgatti
- Department of Life Sciences and Biotechnology, University of Ferrara, Via Fossato di Mortara 74, 44121 Ferrara, Italy
| | - Noemi Bellassai
- Department of Chemical Sciences, University of Catania, Viale Andrea Doria, 6, 95125 Catania, Italy
| | - Roberto Gambari
- Department of Life Sciences and Biotechnology, University of Ferrara, Via Fossato di Mortara 74, 44121 Ferrara, Italy
| | - Giuseppe Spoto
- Department of Chemical Sciences, University of Catania, Viale Andrea Doria, 6, 95125 Catania, Italy.,INBB, Istituto Nazionale di Biostrutture e Biosistemi, Viale Delle Medaglie D'Oro, 305, 00136 Roma, Italy
| |
Collapse
|
46
|
Laing NG, Ong RW, Ravenscroft G. Genetic neuromuscular disorders: what is the best that we can do? Neuromuscul Disord 2021; 31:1081-1089. [PMID: 34736628 DOI: 10.1016/j.nmd.2021.07.007] [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: 06/30/2021] [Accepted: 07/12/2021] [Indexed: 11/17/2022]
Abstract
The major advances in genetic neuromuscular disorders in the last 30 years have been: (a) identification of the genetic basis for hundreds of these disorders, (b) through knowing the genes, understanding their pathobiology and (c) subsequent implementation of evidence-based treatments for some of the disorders. New genomic technologies are providing precision diagnosis, mode of inheritance and likely prognosis for more patients than ever before. Parents of children with a genetic diagnosis can then use preimplantation or prenatal diagnosis to avoid having further affected children if they wish. But is this the best we can do for genetic neuromuscular disorders? Since the 1980s, it has been argued it would be better to identify Duchenne muscular dystrophy carrier mothers, rather than diagnose their affected sons. Carrier screening for recessive disorders can identify couples with a high chance of having affected children. It allows couples reproductive choice and can prevent infant morbidity and mortality and significant distress for families. Professional bodies in many countries now recommend prospective parents should be informed about carrier screening. Implementing and funding expensive therapies increases the cost-effectiveness of carrier screening, increasing its attractiveness to governments. Best practice for genetic neuromuscular disorders should include equitable access to carrier screening.
Collapse
Affiliation(s)
- Nigel G Laing
- QEII Medical Centre, Neurogenetic Diseases Group, Harry Perkins Institute of Medical Research and University of Western Australia, 6 Verdun Street, Nedlands, Western Australia 6009, Australia; Neurogenetic Unit, Department of Diagnostic Genomics, PathWest Laboratory Medicine, West Australian Department of Health, QEII Medical Centre, Nedlands, Western Australia 6009, Australia.
| | - Royston W Ong
- QEII Medical Centre, Neurogenetic Diseases Group, Harry Perkins Institute of Medical Research and University of Western Australia, 6 Verdun Street, Nedlands, Western Australia 6009, Australia
| | - Gianina Ravenscroft
- QEII Medical Centre, Neurogenetic Diseases Group, Harry Perkins Institute of Medical Research and University of Western Australia, 6 Verdun Street, Nedlands, Western Australia 6009, Australia; School of Biomedical Sciences, University of Western Australia, Nedlands, Western Australia 6009, Australia
| |
Collapse
|
47
|
Wang T, Bahrampour M, Byrnes J, Scuffham P, Kirk E, Downes M. Economic evaluation of reproductive carrier screening for recessive genetic conditions: a systematic review. Expert Rev Pharmacoecon Outcomes Res 2021; 22:197-206. [PMID: 34643123 DOI: 10.1080/14737167.2022.1993063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
INTRODUCTION Autosomal recessive (AR) and x-linked (XL) conditions are rare but collectively common which impact millions of people globally on morbidity, mortality and costs. Advanced medical technologies allow prospective parents to make informed reproductive decisions to avoid having affected children. Economic evaluations targeting on reproductive carrier screening (RCS) for AR and/or XL conditions have been conducted, but there has not been a systematic review in this area. AREAS COVERED A systematic search of economic evaluations for RCS was undertaken using the following databases - EMBASE, MEDLINE and SCOPUS. The search strategy was designed to capture full economic evaluations related to RCS since 1990. This review followed the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) strategy. The included 23 studies adopted various types of methodologies to conduct economic evaluations. The majority of studies examined a single condition. The various clinical strategies and screened conditions caused the different cost-effectiveness conclusions in the published studies. EXPERT OPINION Establishing a validated and practical clinical strategy of RCS and investigating the cost-effectiveness of multiple conditions in one economic evaluation are critical for implementing RCS in the future. Further economic evaluations are essential to provide evidence-based practice for decision-makers.
Collapse
Affiliation(s)
- Tianjiao Wang
- Centre for Applied Health Economics, School of Medicine and Dentistry, Griffith University, Nathan, Australia.,Menzies Health Institute Queensland, Griffith University, Gold Coast, Australia
| | - Mina Bahrampour
- Centre for Applied Health Economics, School of Medicine and Dentistry, Griffith University, Nathan, Australia.,Menzies Health Institute Queensland, Griffith University, Gold Coast, Australia
| | - Joshua Byrnes
- Centre for Applied Health Economics, School of Medicine and Dentistry, Griffith University, Nathan, Australia.,Menzies Health Institute Queensland, Griffith University, Gold Coast, Australia
| | - Paul Scuffham
- Centre for Applied Health Economics, School of Medicine and Dentistry, Griffith University, Nathan, Australia.,Menzies Health Institute Queensland, Griffith University, Gold Coast, Australia
| | - Edwin Kirk
- Centre for Clinical Genetics, Sydney Children's Hospital Randwick, Randwick, Australia.,School of Women's and Children's Health, University of New South Wales, Randwick, Australia.,New South Wales Health Pathology Randwick Genomics Laboratory, Randwick, Australia
| | - Martin Downes
- Centre for Applied Health Economics, School of Medicine and Dentistry, Griffith University, Nathan, Australia.,Menzies Health Institute Queensland, Griffith University, Gold Coast, Australia
| |
Collapse
|
48
|
Jéru I. Genetics of lipodystrophy syndromes. Presse Med 2021; 50:104074. [PMID: 34562561 DOI: 10.1016/j.lpm.2021.104074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 08/24/2021] [Accepted: 09/15/2021] [Indexed: 12/11/2022] Open
Abstract
Lipodystrophic syndromes (LS) constitute a clinically and genetically heterogeneous group of diseases characterized by a loss of adipose tissue. These syndromes are usually associated with metabolic complications, which are determinant for morbidity and mortality. The classical forms of LS include partial, generalized, and progeroid lipodystrophies. They are usually due to defects in proteins playing a key role in adipogenesis and adipocyte functions. More recently, systemic disorders combining lipodystrophy and multiple organ dysfunction have been described, including autoinflammatory syndromes, mitochondrial disorders, as well as other complex entities. To date, more than thirty genes have been implicated in the monogenic forms of LS, but the majority of them remain genetically-unexplained. The associated pathophysiological mechanisms also remain to be clarified in many instances. Next generation sequencing-based approaches allow simultaneous testing of multiple genes and have become crucial to speed up the identification of new disease-causing genes. The challenge for geneticists is now the interpretation of the amount of available genetic data, generated especially by exome and whole-genome sequencing. International recommendations on the interpretation and classification of variants have been set up and are regularly reassessed. Very close collaboration between geneticists, clinicians, and researchers will be necessary to make rapid progress in understanding the molecular and cellular basis of these diseases, and to promote personalized medicine.
Collapse
Affiliation(s)
- Isabelle Jéru
- Laboratoire commun de Biologie et Génétique Moléculaires, Hôpital Saint-Antoine, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France; Sorbonne Université-Inserm UMRS_938, Centre de Recherche Saint-Antoine (CRSA), Paris 75012, France.
| |
Collapse
|
49
|
Newborn screening with targeted sequencing: a multicenter investigation and a pilot clinical study in China. J Genet Genomics 2021; 49:13-19. [PMID: 34474183 DOI: 10.1016/j.jgg.2021.08.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 08/10/2021] [Accepted: 08/12/2021] [Indexed: 12/13/2022]
Abstract
Different newborn screening (NBS) programs have been practiced in many countries since the 1960s. It is of considerable interest whether next-generation sequencing is applicable in NBS. We have developed a panel of 465 causative genes for 596 early-onset, relatively high incidence, and potentially actionable severe inherited diseases in our Newborn Screening with Targeted Sequencing (NESTS) program to screen 11,484 babies in 8 Women and Children's hospitals nationwide in China retrospectively. The positive rate from preliminary screening of NESTS was 7.85% (902/11,484). With 45.89% (414/902) follow-up of preliminary positive cases, the overall clinically confirmative diagnosis rate of monogenic disorders was 12.07% (50/414), estimating an average of 0.95% (7.85% × 12.07%) clinical diagnosis rate, suggesting that monogenic disorders account for a considerable proportion of birth defects. The disease/gene spectrum varied in different regions of China. NESTS was implemented in a hospital by screening 3923 newborns to evaluate its clinical application. The turn-around time of a primary report, including the sequencing period of < 7 days, was within 11 days by our automatic interpretation pipeline. Our results suggest that NESTS is feasible and cost-effective as a first-tier NBS program, which will change the status of current clinical practice of NBS in China.
Collapse
|
50
|
Dorval G, Jeanpierre C, Morinière V, Tournant C, Bessières B, Attié-Bittach T, Amiel J, Spaggari E, Ville Y, Merieau E, Gubler MC, Saunier S, Heidet L. Cystic kidney diseases associated with mutations in phosphomannomutase 2 promotor: a large spectrum of phenotypes. Pediatr Nephrol 2021; 36:2361-2369. [PMID: 33580824 DOI: 10.1007/s00467-021-04953-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 12/24/2020] [Accepted: 01/15/2021] [Indexed: 12/12/2022]
Abstract
BACKGROUND Co-occurrence of polycystic kidney disease and hyperinsulinemic hypoglycemia has been reported in children in a few families associated with a variant in the promotor of the PMM2 gene, at position -167 upstream of the coding sequence. PMM2 encodes phosphomannomutase 2, a key enzyme in N-glycosylation. While biallelic coding PMM2 mutations are involved in congenital disorder of glycosylation CDG1A, that particular variant in the promoter of the gene, either in the homozygous state or associated with a mutation in the coding exons of the gene, is thought to restrict the N-glycosylation defect to the kidney and the pancreas. METHODS Targeted exome sequencing of a panel of genes involved in monogenic kidney diseases. RESULTS We identified a PMM2 variant at position -167 associated with a pathogenic PMM2 variant in the coding exons in 3 families, comprising 6 cases affected with a cystic kidney disease. The spectrum of phenotypes was very broad, from extremely enlarged fetal cystic kidneys in the context of a COACH-like syndrome, to isolated cystic kidney disease with small kidneys, slowly progressing toward kidney failure in adulthood. Hypoglycemia was reported only in one case. CONCLUSION These data show that the PMM2 promotor variation, in trans of a PMM2 coding mutation, is associated with a wide spectrum of kidney phenotypes, and is not always associated with extra-renal symptoms. When present, extra-renal defects may include COACH-like syndrome. These data prompt screening of PMM2 in unresolved cases of fetal hyperechogenic/cystic kidneys as well as in cystic kidney disease in children and adults. Graphical Abstract.
Collapse
Affiliation(s)
- Guillaume Dorval
- APHP, Service de Génétique moléculaire, Hôpital universitaire Necker-Enfants malades, F-75015, Paris, France
- Laboratory of Hereditary Kidney Diseases, Université de Paris, Imagine Institute, INSERM UMR 1163, F-75015, Paris, France
| | - Cécile Jeanpierre
- Laboratory of Hereditary Kidney Diseases, Université de Paris, Imagine Institute, INSERM UMR 1163, F-75015, Paris, France
| | - Vincent Morinière
- APHP, Service de Génétique moléculaire, Hôpital universitaire Necker-Enfants malades, F-75015, Paris, France
| | - Carole Tournant
- APHP, Service de Génétique moléculaire, Hôpital universitaire Necker-Enfants malades, F-75015, Paris, France
| | - Bettina Bessières
- APHP, Embryofœtopathologie, Service d'Histologie-Embryologie-Cytogénétique, Hôpital universitaire Necker-Enfants malades, F-75015, Paris, France
| | - Tania Attié-Bittach
- APHP, Embryofœtopathologie, Service d'Histologie-Embryologie-Cytogénétique, Hôpital universitaire Necker-Enfants malades, F-75015, Paris, France
- Université de Paris, Imagine Institute, INSERM UMR 1163, F-75015, Paris, France
| | - Jeanne Amiel
- Université de Paris, Imagine Institute, INSERM UMR 1163, F-75015, Paris, France
- APHP, Service de Génétique, Hôpital universitaire Necker-Enfants malades, F-75015, Paris, France
| | - Emmanuel Spaggari
- APHP, Service d'Obstétrique et Médecine fœtale, Hôpital universitaire Necker-Enfants malades, F-75015, Paris, France
| | - Yves Ville
- APHP, Service d'Obstétrique et Médecine fœtale, Hôpital universitaire Necker-Enfants malades, F-75015, Paris, France
- EA 7328, Université de Paris, Paris, France
| | - Elodie Merieau
- Service de Néphrologie pédiatrique, Hôpital universitaire de Tours, Tours, France
| | - Marie-Claire Gubler
- Laboratory of Hereditary Kidney Diseases, Université de Paris, Imagine Institute, INSERM UMR 1163, F-75015, Paris, France
| | - Sophie Saunier
- Laboratory of Hereditary Kidney Diseases, Université de Paris, Imagine Institute, INSERM UMR 1163, F-75015, Paris, France
| | - Laurence Heidet
- Laboratory of Hereditary Kidney Diseases, Université de Paris, Imagine Institute, INSERM UMR 1163, F-75015, Paris, France.
- APHP, Service de Néphrologie pédiatrique, Centre de Référence MARHEA, Hôpital universitaire Necker-Enfants malades, 149 rue de Sèvres, F-75015, Paris, France.
| |
Collapse
|