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Scherer CR, Duquette D, Hodges PD, Macalincag M, Shin J, Young JL. 'If I Knew More… I Would Feel Less Worried': Filipino Americans' Attitudes and Knowledge of Genetic Disease, Counseling, and Testing. Public Health Genomics 2024; 27:35-44. [PMID: 38198770 DOI: 10.1159/000536173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 01/05/2024] [Indexed: 01/12/2024] Open
Abstract
INTRODUCTION The field of genetics is rapidly expanding and people are increasingly utilizing genetic testing and counseling services. However, the current literature on genetic health topics and Filipinos remains limited, as many minority populations are not adequately studied. This study describes Filipino Americans' attitudes and knowledge of genetic disease, genetic testing, and genetic counseling. To address these knowledge gaps and reduce the burden of health disparities, the informational needs of Filipino Americans regarding genetic disease and genetic services must be understood in order to better tailor these services and outreach methods. METHODS Fifteen semi-structured, qualitative interviews were held with individuals who self-identified as Filipino American between November 2022 and January 2023. Interviews were transcribed and coded using an iterative process. RESULTS Most participants were familiar with genetic disease and believed that factors such as biology, as well as cultural factors such as upbringing and food, contributed to its development. The majority of participants had previously heard of genetic testing; however, most participants either did not know much or were only familiar with ancestry direct-to-consumer genetic testing (DTC-GT). Most participants had not heard of genetic counseling and those that had heard of genetic counseling before did not understand its purpose. Overall, most participants had a positive attitude toward genetic testing and counseling. Participants identified the benefits of these services including genetic disease prevention, management, and treatment. Participants stressed the importance of educating the Filipino community and shared their ideas for how to implement outreach efforts. DISCUSSION/CONCLUSION This study found that Filipino Americans generally had a positive outlook on genetic testing and genetic counseling. We propose participant-generated ideas for outreach and education that may help inform future public health efforts that aim to educate this population about genetic disease, testing and counseling.
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Affiliation(s)
- Casey R Scherer
- Northwestern University, Feinberg School of Medicine, Graduate Program in Genetic Counseling, Chicago, Illinois, USA
| | - Debra Duquette
- Northwestern University, Feinberg School of Medicine, Graduate Program in Genetic Counseling, Chicago, Illinois, USA
| | | | - Maricar Macalincag
- Cancer Genomics Program Coordinator at Michigan Department of Health and Human Services, Lansing, Michigan, USA
| | - Jennifer Shin
- Northwestern University, Feinberg School of Medicine, Graduate Program in Genetic Counseling, Chicago, Illinois, USA
| | - Jennifer L Young
- Northwestern University, Feinberg School of Medicine, Graduate Program in Genetic Counseling, Chicago, Illinois, USA
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Brand H, Whelan CW, Duyzend M, Lemanski J, Salani M, Hao SP, Wong I, Valkanas E, Cusick C, Genetti C, Dobson L, Studwell C, Gianforcaro K, Wilkins-Haug L, Guseh S, Currall B, Gray K, Talkowski ME. High-Resolution and Noninvasive Fetal Exome Screening. N Engl J Med 2023; 389:2014-2016. [PMID: 37991862 DOI: 10.1056/nejmc2216144] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/24/2023]
Affiliation(s)
| | | | | | | | | | | | - Isaac Wong
- Massachusetts General Hospital, Boston, MA
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Robbins J, Halegoua-DeMarzio D, Basu Mallick A, Vijayvergia N, Ganetzky R, Lavu H, Giri VN, Miller J, Maley W, Shah AP, DiMeglio M, Ambelil M, Yu R, Sato T, Lefler DS. Liver Transplantation in a Woman with Mahvash Disease. N Engl J Med 2023; 389:1972-1978. [PMID: 37991855 DOI: 10.1056/nejmoa2303226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/24/2023]
Abstract
Mahvash disease is an exceedingly rare genetic disorder of glucagon signaling characterized by hyperglucagonemia, hyperaminoacidemia, and pancreatic α-cell hyperplasia. Although there is no known definitive treatment, octreotide has been used to decrease systemic glucagon levels. We describe a woman who presented to our medical center after three episodes of small-volume hematemesis. She was found to have hyperglucagonemia and pancreatic hypertrophy with genetically confirmed Mahvash disease and also had evidence of portal hypertension (recurrent portosystemic encephalopathy and variceal hemorrhage) in the absence of cirrhosis. These findings established a diagnosis of portosinusoidal vascular disease, a presinusoidal type of portal hypertension previously known as noncirrhotic portal hypertension. Liver transplantation was followed by normalization of serum glucagon and ammonia levels, reversal of pancreatic hypertrophy, and resolution of recurrent encephalopathy and bleeding varices.
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Affiliation(s)
- Justin Robbins
- From the Department of Internal Medicine (J.R., M.D.), the Division of Gastroenterology and Hepatology (D.H.-D., T.S.), the Department of Medical Oncology, Sidney Kimmel Cancer Center (A.B.M., D.S.L.), the Department of Surgery (H.L., W.M., A.P.S.), the Division of Endocrinology, Diabetes, and Metabolic Diseases (J.M.), and the Department of Pathology and Genomics (M.A.), Thomas Jefferson University, the Department of Medical Oncology, Fox Chase Cancer Center (N.V.), and the Division of Human Genetics, Children's Hospital of Philadelphia (R.G.) - all in Philadelphia; the Division of Clinical Cancer Genetics, Section of Medical Oncology, Department of Medicine, Yale School of Medicine and Yale Cancer Center, New Haven, CT (V.N.G.); and the Division of Endocrinology, Diabetes, and Metabolism, David Geffen School of Medicine at UCLA, Los Angeles (R.Y.)
| | - Dina Halegoua-DeMarzio
- From the Department of Internal Medicine (J.R., M.D.), the Division of Gastroenterology and Hepatology (D.H.-D., T.S.), the Department of Medical Oncology, Sidney Kimmel Cancer Center (A.B.M., D.S.L.), the Department of Surgery (H.L., W.M., A.P.S.), the Division of Endocrinology, Diabetes, and Metabolic Diseases (J.M.), and the Department of Pathology and Genomics (M.A.), Thomas Jefferson University, the Department of Medical Oncology, Fox Chase Cancer Center (N.V.), and the Division of Human Genetics, Children's Hospital of Philadelphia (R.G.) - all in Philadelphia; the Division of Clinical Cancer Genetics, Section of Medical Oncology, Department of Medicine, Yale School of Medicine and Yale Cancer Center, New Haven, CT (V.N.G.); and the Division of Endocrinology, Diabetes, and Metabolism, David Geffen School of Medicine at UCLA, Los Angeles (R.Y.)
| | - Atrayee Basu Mallick
- From the Department of Internal Medicine (J.R., M.D.), the Division of Gastroenterology and Hepatology (D.H.-D., T.S.), the Department of Medical Oncology, Sidney Kimmel Cancer Center (A.B.M., D.S.L.), the Department of Surgery (H.L., W.M., A.P.S.), the Division of Endocrinology, Diabetes, and Metabolic Diseases (J.M.), and the Department of Pathology and Genomics (M.A.), Thomas Jefferson University, the Department of Medical Oncology, Fox Chase Cancer Center (N.V.), and the Division of Human Genetics, Children's Hospital of Philadelphia (R.G.) - all in Philadelphia; the Division of Clinical Cancer Genetics, Section of Medical Oncology, Department of Medicine, Yale School of Medicine and Yale Cancer Center, New Haven, CT (V.N.G.); and the Division of Endocrinology, Diabetes, and Metabolism, David Geffen School of Medicine at UCLA, Los Angeles (R.Y.)
| | - Namrata Vijayvergia
- From the Department of Internal Medicine (J.R., M.D.), the Division of Gastroenterology and Hepatology (D.H.-D., T.S.), the Department of Medical Oncology, Sidney Kimmel Cancer Center (A.B.M., D.S.L.), the Department of Surgery (H.L., W.M., A.P.S.), the Division of Endocrinology, Diabetes, and Metabolic Diseases (J.M.), and the Department of Pathology and Genomics (M.A.), Thomas Jefferson University, the Department of Medical Oncology, Fox Chase Cancer Center (N.V.), and the Division of Human Genetics, Children's Hospital of Philadelphia (R.G.) - all in Philadelphia; the Division of Clinical Cancer Genetics, Section of Medical Oncology, Department of Medicine, Yale School of Medicine and Yale Cancer Center, New Haven, CT (V.N.G.); and the Division of Endocrinology, Diabetes, and Metabolism, David Geffen School of Medicine at UCLA, Los Angeles (R.Y.)
| | - Rebecca Ganetzky
- From the Department of Internal Medicine (J.R., M.D.), the Division of Gastroenterology and Hepatology (D.H.-D., T.S.), the Department of Medical Oncology, Sidney Kimmel Cancer Center (A.B.M., D.S.L.), the Department of Surgery (H.L., W.M., A.P.S.), the Division of Endocrinology, Diabetes, and Metabolic Diseases (J.M.), and the Department of Pathology and Genomics (M.A.), Thomas Jefferson University, the Department of Medical Oncology, Fox Chase Cancer Center (N.V.), and the Division of Human Genetics, Children's Hospital of Philadelphia (R.G.) - all in Philadelphia; the Division of Clinical Cancer Genetics, Section of Medical Oncology, Department of Medicine, Yale School of Medicine and Yale Cancer Center, New Haven, CT (V.N.G.); and the Division of Endocrinology, Diabetes, and Metabolism, David Geffen School of Medicine at UCLA, Los Angeles (R.Y.)
| | - Harish Lavu
- From the Department of Internal Medicine (J.R., M.D.), the Division of Gastroenterology and Hepatology (D.H.-D., T.S.), the Department of Medical Oncology, Sidney Kimmel Cancer Center (A.B.M., D.S.L.), the Department of Surgery (H.L., W.M., A.P.S.), the Division of Endocrinology, Diabetes, and Metabolic Diseases (J.M.), and the Department of Pathology and Genomics (M.A.), Thomas Jefferson University, the Department of Medical Oncology, Fox Chase Cancer Center (N.V.), and the Division of Human Genetics, Children's Hospital of Philadelphia (R.G.) - all in Philadelphia; the Division of Clinical Cancer Genetics, Section of Medical Oncology, Department of Medicine, Yale School of Medicine and Yale Cancer Center, New Haven, CT (V.N.G.); and the Division of Endocrinology, Diabetes, and Metabolism, David Geffen School of Medicine at UCLA, Los Angeles (R.Y.)
| | - Veda N Giri
- From the Department of Internal Medicine (J.R., M.D.), the Division of Gastroenterology and Hepatology (D.H.-D., T.S.), the Department of Medical Oncology, Sidney Kimmel Cancer Center (A.B.M., D.S.L.), the Department of Surgery (H.L., W.M., A.P.S.), the Division of Endocrinology, Diabetes, and Metabolic Diseases (J.M.), and the Department of Pathology and Genomics (M.A.), Thomas Jefferson University, the Department of Medical Oncology, Fox Chase Cancer Center (N.V.), and the Division of Human Genetics, Children's Hospital of Philadelphia (R.G.) - all in Philadelphia; the Division of Clinical Cancer Genetics, Section of Medical Oncology, Department of Medicine, Yale School of Medicine and Yale Cancer Center, New Haven, CT (V.N.G.); and the Division of Endocrinology, Diabetes, and Metabolism, David Geffen School of Medicine at UCLA, Los Angeles (R.Y.)
| | - Jeffrey Miller
- From the Department of Internal Medicine (J.R., M.D.), the Division of Gastroenterology and Hepatology (D.H.-D., T.S.), the Department of Medical Oncology, Sidney Kimmel Cancer Center (A.B.M., D.S.L.), the Department of Surgery (H.L., W.M., A.P.S.), the Division of Endocrinology, Diabetes, and Metabolic Diseases (J.M.), and the Department of Pathology and Genomics (M.A.), Thomas Jefferson University, the Department of Medical Oncology, Fox Chase Cancer Center (N.V.), and the Division of Human Genetics, Children's Hospital of Philadelphia (R.G.) - all in Philadelphia; the Division of Clinical Cancer Genetics, Section of Medical Oncology, Department of Medicine, Yale School of Medicine and Yale Cancer Center, New Haven, CT (V.N.G.); and the Division of Endocrinology, Diabetes, and Metabolism, David Geffen School of Medicine at UCLA, Los Angeles (R.Y.)
| | - Warren Maley
- From the Department of Internal Medicine (J.R., M.D.), the Division of Gastroenterology and Hepatology (D.H.-D., T.S.), the Department of Medical Oncology, Sidney Kimmel Cancer Center (A.B.M., D.S.L.), the Department of Surgery (H.L., W.M., A.P.S.), the Division of Endocrinology, Diabetes, and Metabolic Diseases (J.M.), and the Department of Pathology and Genomics (M.A.), Thomas Jefferson University, the Department of Medical Oncology, Fox Chase Cancer Center (N.V.), and the Division of Human Genetics, Children's Hospital of Philadelphia (R.G.) - all in Philadelphia; the Division of Clinical Cancer Genetics, Section of Medical Oncology, Department of Medicine, Yale School of Medicine and Yale Cancer Center, New Haven, CT (V.N.G.); and the Division of Endocrinology, Diabetes, and Metabolism, David Geffen School of Medicine at UCLA, Los Angeles (R.Y.)
| | - Ashesh P Shah
- From the Department of Internal Medicine (J.R., M.D.), the Division of Gastroenterology and Hepatology (D.H.-D., T.S.), the Department of Medical Oncology, Sidney Kimmel Cancer Center (A.B.M., D.S.L.), the Department of Surgery (H.L., W.M., A.P.S.), the Division of Endocrinology, Diabetes, and Metabolic Diseases (J.M.), and the Department of Pathology and Genomics (M.A.), Thomas Jefferson University, the Department of Medical Oncology, Fox Chase Cancer Center (N.V.), and the Division of Human Genetics, Children's Hospital of Philadelphia (R.G.) - all in Philadelphia; the Division of Clinical Cancer Genetics, Section of Medical Oncology, Department of Medicine, Yale School of Medicine and Yale Cancer Center, New Haven, CT (V.N.G.); and the Division of Endocrinology, Diabetes, and Metabolism, David Geffen School of Medicine at UCLA, Los Angeles (R.Y.)
| | - Matthew DiMeglio
- From the Department of Internal Medicine (J.R., M.D.), the Division of Gastroenterology and Hepatology (D.H.-D., T.S.), the Department of Medical Oncology, Sidney Kimmel Cancer Center (A.B.M., D.S.L.), the Department of Surgery (H.L., W.M., A.P.S.), the Division of Endocrinology, Diabetes, and Metabolic Diseases (J.M.), and the Department of Pathology and Genomics (M.A.), Thomas Jefferson University, the Department of Medical Oncology, Fox Chase Cancer Center (N.V.), and the Division of Human Genetics, Children's Hospital of Philadelphia (R.G.) - all in Philadelphia; the Division of Clinical Cancer Genetics, Section of Medical Oncology, Department of Medicine, Yale School of Medicine and Yale Cancer Center, New Haven, CT (V.N.G.); and the Division of Endocrinology, Diabetes, and Metabolism, David Geffen School of Medicine at UCLA, Los Angeles (R.Y.)
| | - Manju Ambelil
- From the Department of Internal Medicine (J.R., M.D.), the Division of Gastroenterology and Hepatology (D.H.-D., T.S.), the Department of Medical Oncology, Sidney Kimmel Cancer Center (A.B.M., D.S.L.), the Department of Surgery (H.L., W.M., A.P.S.), the Division of Endocrinology, Diabetes, and Metabolic Diseases (J.M.), and the Department of Pathology and Genomics (M.A.), Thomas Jefferson University, the Department of Medical Oncology, Fox Chase Cancer Center (N.V.), and the Division of Human Genetics, Children's Hospital of Philadelphia (R.G.) - all in Philadelphia; the Division of Clinical Cancer Genetics, Section of Medical Oncology, Department of Medicine, Yale School of Medicine and Yale Cancer Center, New Haven, CT (V.N.G.); and the Division of Endocrinology, Diabetes, and Metabolism, David Geffen School of Medicine at UCLA, Los Angeles (R.Y.)
| | - Run Yu
- From the Department of Internal Medicine (J.R., M.D.), the Division of Gastroenterology and Hepatology (D.H.-D., T.S.), the Department of Medical Oncology, Sidney Kimmel Cancer Center (A.B.M., D.S.L.), the Department of Surgery (H.L., W.M., A.P.S.), the Division of Endocrinology, Diabetes, and Metabolic Diseases (J.M.), and the Department of Pathology and Genomics (M.A.), Thomas Jefferson University, the Department of Medical Oncology, Fox Chase Cancer Center (N.V.), and the Division of Human Genetics, Children's Hospital of Philadelphia (R.G.) - all in Philadelphia; the Division of Clinical Cancer Genetics, Section of Medical Oncology, Department of Medicine, Yale School of Medicine and Yale Cancer Center, New Haven, CT (V.N.G.); and the Division of Endocrinology, Diabetes, and Metabolism, David Geffen School of Medicine at UCLA, Los Angeles (R.Y.)
| | - Takami Sato
- From the Department of Internal Medicine (J.R., M.D.), the Division of Gastroenterology and Hepatology (D.H.-D., T.S.), the Department of Medical Oncology, Sidney Kimmel Cancer Center (A.B.M., D.S.L.), the Department of Surgery (H.L., W.M., A.P.S.), the Division of Endocrinology, Diabetes, and Metabolic Diseases (J.M.), and the Department of Pathology and Genomics (M.A.), Thomas Jefferson University, the Department of Medical Oncology, Fox Chase Cancer Center (N.V.), and the Division of Human Genetics, Children's Hospital of Philadelphia (R.G.) - all in Philadelphia; the Division of Clinical Cancer Genetics, Section of Medical Oncology, Department of Medicine, Yale School of Medicine and Yale Cancer Center, New Haven, CT (V.N.G.); and the Division of Endocrinology, Diabetes, and Metabolism, David Geffen School of Medicine at UCLA, Los Angeles (R.Y.)
| | - Daniel S Lefler
- From the Department of Internal Medicine (J.R., M.D.), the Division of Gastroenterology and Hepatology (D.H.-D., T.S.), the Department of Medical Oncology, Sidney Kimmel Cancer Center (A.B.M., D.S.L.), the Department of Surgery (H.L., W.M., A.P.S.), the Division of Endocrinology, Diabetes, and Metabolic Diseases (J.M.), and the Department of Pathology and Genomics (M.A.), Thomas Jefferson University, the Department of Medical Oncology, Fox Chase Cancer Center (N.V.), and the Division of Human Genetics, Children's Hospital of Philadelphia (R.G.) - all in Philadelphia; the Division of Clinical Cancer Genetics, Section of Medical Oncology, Department of Medicine, Yale School of Medicine and Yale Cancer Center, New Haven, CT (V.N.G.); and the Division of Endocrinology, Diabetes, and Metabolism, David Geffen School of Medicine at UCLA, Los Angeles (R.Y.)
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Benatar M, Al-Chalabi A, Crawley A, Wuu J. Reply: A new diagnostic entity must enable earlier treatment in gene carriers. Brain 2023; 146:e80-e82. [PMID: 37186590 PMCID: PMC11004921 DOI: 10.1093/brain/awad165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 05/03/2023] [Accepted: 05/05/2023] [Indexed: 05/17/2023] Open
Affiliation(s)
- Michael Benatar
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Ammar Al-Chalabi
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King’s College London, London, SE5 9RX, UK
| | | | - Joanne Wuu
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
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Chen E, Facio FM, Aradhya KW, Rojahn S, Hatchell KE, Aguilar S, Ouyang K, Saitta S, Hanson-Kwan AK, Capurro NN, Takamine E, Jamuar SS, McKnight D, Johnson B, Aradhya S. Rates and Classification of Variants of Uncertain Significance in Hereditary Disease Genetic Testing. JAMA Netw Open 2023; 6:e2339571. [PMID: 37878314 PMCID: PMC10600581 DOI: 10.1001/jamanetworkopen.2023.39571] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 09/12/2023] [Indexed: 10/26/2023] Open
Abstract
Importance Variants of uncertain significance (VUSs) are rampant in clinical genetic testing, frustrating clinicians, patients, and laboratories because the uncertainty hinders diagnoses and clinical management. A comprehensive assessment of VUSs across many disease genes is needed to guide efforts to reduce uncertainty. Objective To describe the sources, gene distribution, and population-level attributes of VUSs and to evaluate the impact of the different types of evidence used to reclassify them. Design, Setting, and Participants This cohort study used germline DNA variant data from individuals referred by clinicians for diagnostic genetic testing for hereditary disorders. Participants included individuals for whom gene panel testing was conducted between September 9, 2014, and September 7, 2022. Data were analyzed from September 1, 2022, to April 1, 2023. Main Outcomes and Measures The outcomes of interest were VUS rates (stratified by age; clinician-reported race, ethnicity, and ancestry groups; types of gene panels; and variant attributes), percentage of VUSs reclassified as benign or likely benign vs pathogenic or likely pathogenic, and enrichment of evidence types used for reclassifying VUSs. Results The study cohort included 1 689 845 individuals ranging in age from 0 to 89 years at time of testing (median age, 50 years), with 1 203 210 (71.2%) female individuals. There were 39 150 Ashkenazi Jewish individuals (2.3%), 64 730 Asian individuals (3.8%), 126 739 Black individuals (7.5%), 5539 French Canadian individuals (0.3%), 169 714 Hispanic individuals (10.0%), 5058 Native American individuals (0.3%), 2696 Pacific Islander individuals (0.2%), 4842 Sephardic Jewish individuals (0.3%), and 974 383 White individuals (57.7%). Among all individuals tested, 692 227 (41.0%) had at least 1 VUS and 535 385 (31.7%) had only VUS results. The number of VUSs per individual increased as more genes were tested, and most VUSs were missense changes (86.6%). More VUSs were observed per sequenced gene in individuals who were not from a European White population, in middle-aged and older adults, and in individuals who underwent testing for disorders with incomplete penetrance. Of 37 699 unique VUSs that were reclassified, 30 239 (80.2%) were ultimately categorized as benign or likely benign. A mean (SD) of 30.7 (20.0) months elapsed for VUSs to be reclassified to benign or likely benign, and a mean (SD) of 22.4 (18.9) months elapsed for VUSs to be reclassified to pathogenic or likely pathogenic. Clinical evidence contributed most to reclassification. Conclusions and Relevance This cohort study of approximately 1.6 million individuals highlighted the need for better methods for interpreting missense variants, increased availability of clinical and experimental evidence for variant classification, and more diverse representation of race, ethnicity, and ancestry groups in genomic databases. Data from this study could provide a sound basis for understanding the sources and resolution of VUSs and navigating appropriate next steps in patient care.
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Affiliation(s)
- Elaine Chen
- Invitae Corporation, San Francisco, California
| | | | | | | | | | | | | | - Sulagna Saitta
- Division of Clinical Genetics, Departments of Pediatrics and Obstetrics and Gynecology, David Geffen School of Medicine at UCLA, Los Angeles, California
| | | | - Nicole Nakousi Capurro
- School of Medicine, University of Valparaíso, Valparaíso, Chile
- Facultad de Medicina, Universidad Andrés Bello, Viña del Mar, Chile
| | - Eriko Takamine
- Department of Medical Genetics, Tokyo Medical and Dental University Hospital, Tokyo, Japan
| | - Saumya Shekhar Jamuar
- Genetics Service, KK Women’s and Children’s Hospital, Singapore
- SingHealth Duke-NUS Institute of Precision Medicine, Singapore
| | | | | | - Swaroop Aradhya
- Invitae Corporation, San Francisco, California
- Department of Pathology, Stanford University, Stanford, California
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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] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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.
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Maron JL, Kingsmore S, Gelb BD, Vockley J, Wigby K, Bragg J, Stroustrup A, Poindexter B, Suhrie K, Kim JH, Diacovo T, Powell CM, Trembath A, Guidugli L, Ellsworth KA, Reed D, Kurfiss A, Breeze JL, Trinquart L, Davis JM. Rapid Whole-Genomic Sequencing and a Targeted Neonatal Gene Panel in Infants With a Suspected Genetic Disorder. JAMA 2023; 330:161-169. [PMID: 37432431 PMCID: PMC10336625 DOI: 10.1001/jama.2023.9350] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 05/12/2023] [Indexed: 07/12/2023]
Abstract
Importance Genomic testing in infancy guides medical decisions and can improve health outcomes. However, it is unclear whether genomic sequencing or a targeted neonatal gene-sequencing test provides comparable molecular diagnostic yields and times to return of results. Objective To compare outcomes of genomic sequencing with those of a targeted neonatal gene-sequencing test. Design, Setting, and Participants The Genomic Medicine for Ill Neonates and Infants (GEMINI) study was a prospective, comparative, multicenter study of 400 hospitalized infants younger than 1 year of age (proband) and their parents, when available, suspected of having a genetic disorder. The study was conducted at 6 US hospitals from June 2019 to November 2021. Exposure Enrolled participants underwent simultaneous testing with genomic sequencing and a targeted neonatal gene-sequencing test. Each laboratory performed an independent interpretation of variants guided by knowledge of the patient's phenotype and returned results to the clinical care team. Change in clinical management, therapies offered, and redirection of care was provided to families based on genetic findings from either platform. Main Outcomes and Measures Primary end points were molecular diagnostic yield (participants with ≥1 pathogenic variant or variant of unknown significance), time to return of results, and clinical utility (changes in patient care). Results A molecular diagnostic variant was identified in 51% of participants (n = 204; 297 variants identified with 134 being novel). Molecular diagnostic yield of genomic sequencing was 49% (95% CI, 44%-54%) vs 27% (95% CI, 23%-32%) with the targeted gene-sequencing test. Genomic sequencing did not report 19 variants found by the targeted neonatal gene-sequencing test; the targeted gene-sequencing test did not report 164 variants identified by genomic sequencing as diagnostic. Variants unidentified by the targeted genomic-sequencing test included structural variants longer than 1 kilobase (25.1%) and genes excluded from the test (24.6%) (McNemar odds ratio, 8.6 [95% CI, 5.4-14.7]). Variant interpretation by laboratories differed by 43%. Median time to return of results was 6.1 days for genomic sequencing and 4.2 days for the targeted genomic-sequencing test; for urgent cases (n = 107) the time was 3.3 days for genomic sequencing and 4.0 days for the targeted gene-sequencing test. Changes in clinical care affected 19% of participants, and 76% of clinicians viewed genomic testing as useful or very useful in clinical decision-making, irrespective of a diagnosis. Conclusions and Relevance The molecular diagnostic yield for genomic sequencing was higher than a targeted neonatal gene-sequencing test, but the time to return of routine results was slower. Interlaboratory variant interpretation contributes to differences in molecular diagnostic yield and may have important consequences for clinical management.
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Affiliation(s)
- Jill L. Maron
- Women and Infants Hospital of Rhode Island, Providence
| | - Stephen Kingsmore
- Rady Children’s Institute for Genomic Medicine, San Diego, California
| | - Bruce D. Gelb
- Mindich Child Health and Development Institute and Departments of Pediatrics and Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Jerry Vockley
- University of Pittsburgh Medical Center Children’s Hospital, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Kristen Wigby
- Rady Children’s Institute for Genomic Medicine, San Diego, California
- Department of Pediatrics, University of California San Diego, San Diego
| | - Jennifer Bragg
- Mindich Child Health and Development Institute and Departments of Pediatrics and Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Annemarie Stroustrup
- Division of Neonatology, Department of Pediatrics, Cohen Children’s Medical Center at Northwell Health, New Hyde Park, New York, New York
| | - Brenda Poindexter
- Children’s Healthcare of Atlanta, Department of Pediatrics, Emory University, Atlanta, Georgia
| | - Kristen Suhrie
- Indiana University School of Medicine, Department of Pediatrics and Medical and Molecular Genetics, Indianapolis
| | - Jae H. Kim
- Perinatal Institute, Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Thomas Diacovo
- University of Pittsburgh Medical Center Children’s Hospital, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Cynthia M. Powell
- University of North Carolina Children’s Research Institute, University of North Carolina Children’s Hospital, Chapel Hill
| | - Andrea Trembath
- University of North Carolina Children’s Research Institute, University of North Carolina Children’s Hospital, Chapel Hill
| | - Lucia Guidugli
- Rady Children’s Institute for Genomic Medicine, San Diego, California
| | | | - Dallas Reed
- Department of Pediatrics, Tufts Medical Center, Boston, Massachusetts
| | - Anne Kurfiss
- Department of Pediatrics, Tufts Medical Center, Boston, Massachusetts
| | - Janis L. Breeze
- Tufts Clinical and Translational Science Institute, Tufts University, and Institute for Clinical Research and Health Policy Studies, Tufts Medical Center, Boston, Massachusetts
| | - Ludovic Trinquart
- Tufts Clinical and Translational Science Institute, Tufts University, and Institute for Clinical Research and Health Policy Studies, Tufts Medical Center, Boston, Massachusetts
| | - Jonathan M. Davis
- Department of Pediatrics, Tufts Medical Center, Boston, Massachusetts
- Tufts Clinical and Translational Science Institute, Tufts University, and Institute for Clinical Research and Health Policy Studies, Tufts Medical Center, Boston, Massachusetts
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Wright CF, Campbell P, Eberhardt RY, Aitken S, Perrett D, Brent S, Danecek P, Gardner EJ, Chundru VK, Lindsay SJ, Andrews K, Hampstead J, Kaplanis J, Samocha KE, Middleton A, Foreman J, Hobson RJ, Parker MJ, Martin HC, FitzPatrick DR, Hurles ME, Firth HV. Genomic Diagnosis of Rare Pediatric Disease in the United Kingdom and Ireland. N Engl J Med 2023; 388:1559-1571. [PMID: 37043637 PMCID: PMC7614484 DOI: 10.1056/nejmoa2209046] [Citation(s) in RCA: 38] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
BACKGROUND Pediatric disorders include a range of highly penetrant, genetically heterogeneous conditions amenable to genomewide diagnostic approaches. Finding a molecular diagnosis is challenging but can have profound lifelong benefits. METHODS We conducted a large-scale sequencing study involving more than 13,500 families with probands with severe, probably monogenic, difficult-to-diagnose developmental disorders from 24 regional genetics services in the United Kingdom and Ireland. Standardized phenotypic data were collected, and exome sequencing and microarray analyses were performed to investigate novel genetic causes. We developed an iterative variant analysis pipeline and reported candidate variants to clinical teams for validation and diagnostic interpretation to inform communication with families. Multiple regression analyses were performed to evaluate factors affecting the probability of diagnosis. RESULTS A total of 13,449 probands were included in the analyses. On average, we reported 1.0 candidate variant per parent-offspring trio and 2.5 variants per singleton proband. Using clinical and computational approaches to variant classification, we made a diagnosis in approximately 41% of probands (5502 of 13,449). Of 3599 probands in trios who received a diagnosis by clinical assertion, approximately 76% had a pathogenic de novo variant. Another 22% of probands (2997 of 13,449) had variants of uncertain significance in genes that were strongly linked to monogenic developmental disorders. Recruitment in a parent-offspring trio had the largest effect on the probability of diagnosis (odds ratio, 4.70; 95% confidence interval [CI], 4.16 to 5.31). Probands were less likely to receive a diagnosis if they were born extremely prematurely (i.e., 22 to 27 weeks' gestation; odds ratio, 0.39; 95% CI, 0.22 to 0.68), had in utero exposure to antiepileptic medications (odds ratio, 0.44; 95% CI, 0.29 to 0.67), had mothers with diabetes (odds ratio, 0.52; 95% CI, 0.41 to 0.67), or were of African ancestry (odds ratio, 0.51; 95% CI, 0.31 to 0.78). CONCLUSIONS Among probands with severe, probably monogenic, difficult-to-diagnose developmental disorders, multimodal analysis of genomewide data had good diagnostic power, even after previous attempts at diagnosis. (Funded by the Health Innovation Challenge Fund and Wellcome Sanger Institute.).
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Affiliation(s)
- Caroline F. Wright
- Department of Clinical and Biomedical Sciences, University of Exeter Medical School, RILD Building, Royal Devon & Exeter Hospital, Barrack Road, Exeter UK, EX2 5DW
| | - Patrick Campbell
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SA
- Cambridge University Hospitals Foundation Trust, Addenbrooke’s Hospital, Cambridge UK, CB2 0QQ
| | - Ruth Y. Eberhardt
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SA
| | - Stuart Aitken
- MRC Human Genetics Unit, Institute of Genetic and Cancer, University of Edinburgh, Edinburgh UK, EH4 2XU
| | - Daniel Perrett
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SA
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SD
| | - Simon Brent
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SA
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SD
| | - Petr Danecek
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SA
| | - Eugene J. Gardner
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SA
| | - V. Kartik Chundru
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SA
| | - Sarah J. Lindsay
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SA
| | - Katrina Andrews
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SA
| | - Juliet Hampstead
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SA
| | - Joanna Kaplanis
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SA
| | - Kaitlin E. Samocha
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SA
| | - Anna Middleton
- Wellcome Connecting Science, Wellcome Genome Campus, Hinxton, Cambridge, UK, CB10 1SA
| | - Julia Foreman
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SA
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SD
| | - Rachel J. Hobson
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SA
| | - Michael J. Parker
- Wellcome Centre for Ethics and Humanities/Ethox Centre, Oxford Population Health, University of Oxford, Big Data Institute, Old Road Campus, Oxford, UK, OX3 7LF
| | - Hilary C. Martin
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SA
| | - David R. FitzPatrick
- MRC Human Genetics Unit, Institute of Genetic and Cancer, University of Edinburgh, Edinburgh UK, EH4 2XU
| | - Matthew E. Hurles
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SA
| | - Helen V. Firth
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SA
- Cambridge University Hospitals Foundation Trust, Addenbrooke’s Hospital, Cambridge UK, CB2 0QQ
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Alarcón Garavito GA, Moniz T, Déom N, Redin F, Pichini A, Vindrola-Padros C. The implementation of large-scale genomic screening or diagnostic programmes: A rapid evidence review. Eur J Hum Genet 2023; 31:282-295. [PMID: 36517584 PMCID: PMC9995480 DOI: 10.1038/s41431-022-01259-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 11/17/2022] [Accepted: 11/22/2022] [Indexed: 12/15/2022] Open
Abstract
Genomic healthcare programmes, both in a research and clinical context, have demonstrated a pivotal opportunity to prevent, diagnose, and treat rare diseases. However, implementation factors could increase overall costs and affect uptake. As well, uncertainties remain regarding effective training, guidelines and legislation. The purpose of this rapid evidence review was to draw together the available global evidence on the implementation of genomic testing programmes, particularly on population-based screening and diagnostic programmes implemented at the national level, to understand the range of factors influencing implementation. This review involved a search of terms related to genomics, implementation and health care. The search was limited to peer-reviewed articles published between 2017-2022 and found in five databases. The review included thirty articles drawing on sixteen countries. A wide range of factors was cited as critical to the successful implementation of genomics programmes. These included having policy frameworks, regulations, guidelines; clinical decision support tools; access to genetic counselling; and education and training for healthcare staff. The high costs of implementing and integrating genomics into healthcare were also often barriers to stakeholders. National genomics programmes are complex and require the generation of evidence and addressing implementation challenges. The findings from this review highlight that there is a strong emphasis on addressing genomic education and engagement among varied stakeholders, including the general public, policymakers, and governments. Articles also emphasised the development of appropriate policies and regulatory frameworks to govern genomic healthcare, with a focus on legislation that regulates the collection, storage, and sharing of personal genomic data.
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Affiliation(s)
| | - Thomas Moniz
- Rapid Research Evaluation and Appraisal Lab (RREAL), University College London, 43-45 Foley Street, W1W 7TY, London, UK
| | - Noémie Déom
- Rapid Research Evaluation and Appraisal Lab (RREAL), University College London, 43-45 Foley Street, W1W 7TY, London, UK
| | - Federico Redin
- Rapid Research Evaluation and Appraisal Lab (RREAL), University College London, 43-45 Foley Street, W1W 7TY, London, UK
| | | | - Cecilia Vindrola-Padros
- Rapid Research Evaluation and Appraisal Lab (RREAL), University College London, 43-45 Foley Street, W1W 7TY, London, UK.
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10
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Kaiser J. Sequencing projects will screen 200,000 newborns for disease. Science 2022; 378:1159. [PMID: 36520905 DOI: 10.1126/science.adg2858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
U.K. and New York City efforts face cost and ethical issues.
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11
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Chada AR, Crawford S, Hipp HS, Kawwass JF. Trends and outcomes for preimplantation genetic testing for monogenic disorders in the United States, 2014-2018. Fertil Steril 2022; 118:1190-1193. [PMID: 36241429 DOI: 10.1016/j.fertnstert.2022.08.854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 08/18/2022] [Accepted: 08/22/2022] [Indexed: 01/13/2023]
Affiliation(s)
- Anisha R Chada
- Department of Gynecology & Obstetrics, Emory University School of Medicine, Atlanta, Georgia.
| | - Sara Crawford
- Department of Mathematics and Computer Science, University of Mount Union, Alliance, Ohio
| | - Heather S Hipp
- Division of Reproductive Endocrinology and Infertility, Department of Gynecology and Obstetrics, Emory University, Atlanta, Georgia
| | - Jennifer F Kawwass
- Division of Reproductive Endocrinology and Infertility, Department of Gynecology and Obstetrics, Emory University, Atlanta, Georgia
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12
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O'Dowd A. Advanced diagnosis and personalised treatment: the clinical geneticist. BMJ 2022; 377:o1160. [PMID: 35609898 DOI: 10.1136/bmj.o1160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Abstract
The advent of high-throughput sequencing has facilitated genotype-phenotype correlations in congenital diseases. This has provided molecular diagnosis and benefited patient management but has also revealed substantial phenotypic heterogeneity. Although distinct neuroinflammatory diseases are scarce among the several thousands of established congenital diseases, elements of neuroinflammation are increasingly recognized in a substantial proportion of inborn errors of immunity, where it may even dominate the clinical picture at initial presentation. Although each disease entity is rare, they collectively can constitute a significant proportion of neuropediatric patients in tertiary care and may occasionally also explain adult neurology patients. We focus this review on the signs and symptoms of neuroinflammation that have been reported in association with established pathogenic variants in immune genes and suggest the following subdivision based on proposed underlying mechanisms: autoinflammatory disorders, tolerance defects, and immunodeficiency disorders. The large group of autoinflammatory disorders is further subdivided into IL-1β-mediated disorders, NF-κB dysregulation, type I interferonopathies, and hemophagocytic syndromes. We delineate emerging pathogenic themes underlying neuroinflammation in monogenic diseases and describe the breadth of the clinical spectrum to support decisions to screen for a genetic diagnosis and encourage further research on a neglected phenomenon.
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Affiliation(s)
- Hannes Lindahl
- Clinical Immunology and Transfusion Medicine, Karolinska University Hospital, Stockholm, Sweden
- Center for Molecular Medicine, Department of Clinical Neuroscience, Karolinska Institute, Karolinska University Hospital, Stockholm, Sweden
| | - Yenan T. Bryceson
- Clinical Immunology and Transfusion Medicine, Karolinska University Hospital, Stockholm, Sweden
- Center for Hematology and Regenerative Medicine, Department of Medicine, Karolinska Institute, Karolinska University Hospital Huddinge, Stockholm, Sweden
- Brogelmann Research Laboratory, Department of Clinical Sciences, University of Bergen, Bergen, Norway
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14
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Brunet AA, Harvey AR, Carvalho LS. Primary and Secondary Cone Cell Death Mechanisms in Inherited Retinal Diseases and Potential Treatment Options. Int J Mol Sci 2022; 23:ijms23020726. [PMID: 35054919 PMCID: PMC8775779 DOI: 10.3390/ijms23020726] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 01/05/2022] [Accepted: 01/05/2022] [Indexed: 12/13/2022] Open
Abstract
Inherited retinal diseases (IRDs) are a leading cause of blindness. To date, 260 disease-causing genes have been identified, but there is currently a lack of available and effective treatment options. Cone photoreceptors are responsible for daylight vision but are highly susceptible to disease progression, the loss of cone-mediated vision having the highest impact on the quality of life of IRD patients. Cone degeneration can occur either directly via mutations in cone-specific genes (primary cone death), or indirectly via the primary degeneration of rods followed by subsequent degeneration of cones (secondary cone death). How cones degenerate as a result of pathological mutations remains unclear, hindering the development of effective therapies for IRDs. This review aims to highlight similarities and differences between primary and secondary cone cell death in inherited retinal diseases in order to better define cone death mechanisms and further identify potential treatment options.
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Affiliation(s)
- Alicia A. Brunet
- Centre for Ophthalmology and Visual Sciences, The University of Western Australia, 35 Stirling Hwy, Crawley, WA 6009, Australia;
- Lions Eye Institute Ltd., 2 Verdun St, Nedlands, WA 6009, Australia
- Correspondence: ; Tel.: +61-423-359-714
| | - Alan R. Harvey
- School of Human Sciences, The University of Western Australia, 35 Stirling Hwy, Crawley, WA 6009, Australia;
- Perron Institute for Neurological and Translational Science, 8 Verdun St, Nedlands, WA 6009, Australia
| | - Livia S. Carvalho
- Centre for Ophthalmology and Visual Sciences, The University of Western Australia, 35 Stirling Hwy, Crawley, WA 6009, Australia;
- Lions Eye Institute Ltd., 2 Verdun St, Nedlands, WA 6009, Australia
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15
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Mohan P, Lemoine J, Trotter C, Rakova I, Billings P, Peacock S, Kao C, Wang Y, Xia F, Eng CM, Benn P. Clinical experience with non-invasive prenatal screening for single-gene disorders. Ultrasound Obstet Gynecol 2022; 59:33-39. [PMID: 34358384 PMCID: PMC9302116 DOI: 10.1002/uog.23756] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 07/29/2021] [Accepted: 08/02/2021] [Indexed: 05/10/2023]
Abstract
OBJECTIVE To assess the performance of a non-invasive prenatal screening test (NIPT) for a panel of dominant single-gene disorders (SGD) with a combined population incidence of 1 in 600. METHODS Cell-free fetal DNA isolated from maternal plasma samples accessioned from 14 April 2017 to 27 November 2019 was analyzed by next-generation sequencing, targeting 30 genes, to look for pathogenic or likely pathogenic variants implicated in 25 dominant conditions. The conditions included Noonan spectrum disorders, skeletal disorders, craniosynostosis syndromes, Cornelia de Lange syndrome, Alagille syndrome, tuberous sclerosis, epileptic encephalopathy, SYNGAP1-related intellectual disability, CHARGE syndrome, Sotos syndrome and Rett syndrome. NIPT-SGD was made available as a clinical service to women with a singleton pregnancy at ≥ 9 weeks' gestation, with testing on maternal and paternal genomic DNA to assist in interpretation. A minimum of 4.5% fetal fraction was required for test interpretation. Variants identified in the mother were deemed inconclusive with respect to fetal carrier status. Confirmatory prenatal or postnatal diagnostic testing was recommended for all screen-positive patients and follow-up information was requested. The screen-positive rates with respect to the clinical indication for testing were evaluated. RESULTS A NIPT-SGD result was available for 2208 women, of which 125 (5.7%) were positive. Elevated test-positive rates were observed for referrals with a family history of a disorder on the panel (20/132 (15.2%)) or a primary indication of fetal long-bone abnormality (60/178 (33.7%)), fetal craniofacial abnormality (6/21 (28.6%)), fetal lymphatic abnormality (20/150 (13.3%)) or major fetal cardiac defect (4/31 (12.9%)). For paternal age ≥ 40 years as a sole risk factor, the test-positive rate was 2/912 (0.2%). Of the 125 positive cases, follow-up information was available for 67 (53.6%), with none classified as false-positive. No false-negative cases were identified. CONCLUSIONS NIPT can assist in the early detection of a set of SGD, particularly when either abnormal ultrasound findings or a family history is present. Additional clinical studies are needed to evaluate the optimal design of the gene panel, define target populations and assess patient acceptability. NIPT-SGD offers a safe and early prenatal screening option. © 2021 The Authors. Ultrasound in Obstetrics & Gynecology published by John Wiley & Sons Ltd on behalf of International Society of Ultrasound in Obstetrics and Gynecology.
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Affiliation(s)
| | | | | | | | | | | | | | - Y. Wang
- Baylor GeneticsHoustonTXUSA
- Baylor College of MedicineHoustonTXUSA
| | - F. Xia
- Baylor GeneticsHoustonTXUSA
- Baylor College of MedicineHoustonTXUSA
| | - C. M. Eng
- Baylor GeneticsHoustonTXUSA
- Baylor College of MedicineHoustonTXUSA
| | - P. Benn
- Department of Genetics and Genome SciencesUniversity of Connecticut Health CenterFarmingtonCTUSA
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Long-Read Sequencing Could Increase Diagnosis Rates. Am J Med Genet A 2021; 185:3526-7. [PMID: 34784116 DOI: 10.1002/ajmg.a.61711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Affiliation(s)
| | - Eric D Green
- National Human Genome Research Institute, Bethesda, Maryland, USA
| | - Teri Manolio
- National Human Genome Research Institute, Bethesda, Maryland, USA
| | | | - David Curtis
- UCL Genetics Institute, University College London, UK
- Centre for Psychiatry, Queen Mary University of London, UK
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18
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Schon K. Whole genome sequencing helps pinpoint a genetic diagnosis for patients. BMJ 2021; 375:n2680. [PMID: 34732386 DOI: 10.1136/bmj.n2680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
- Katherine Schon
- University of Cambridge & Cambridge University Hospitals NHS Trust
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19
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Abstract
Clinical characterization of a patient phenotype has been the quintessential approach for elucidating a differential diagnosis and a hypothesis to explore a potential clinical diagnosis. This has resulted in a language of medicine and a semantic ontology, with both specialty- and subspecialty-specific lexicons, that can be challenging to translate and interpret. There is no 'Rosetta Stone' of clinical medicine such as the genetic code that can assist translation and interpretation of the language of genetics. Nevertheless, the information content embodied within a clinical diagnosis can guide management, therapeutic intervention, and potentially prognostic outlook of disease enabling anticipatory guidance for patients and families. Clinical genomics is now established firmly in medical practice. The granularity and informative content of a personal genome is immense. Yet, we are limited in our utility of much of that personal genome information by the lack of functional characterization of the overwhelming majority of computationally annotated genes in the haploid human reference genome sequence. Whereas DNA and the genetic code have provided a 'Rosetta Stone' to translate genetic variant information, clinical medicine, and clinical genomics provide the context to understand human biology and disease. A path forward will integrate deep phenotyping, such as available in a clinical synopsis in the Online Mendelian Inheritance in Man (OMIM) entries, with personal genome analyses.
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Affiliation(s)
- James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
- Texas Children's Hospital, Houston, Texas, USA
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Abstract
Reproductive genetic screening has introduced the possibility for pregnant women to learn, during the pregnancy or sometimes earlier, about the likelihood of their baby being affected with certain genetic conditions. As medicine progresses, the options afforded by this early information have expanded. This has led to a shifting paradigm in prenatal screening, wherein the early knowledge is seen as useful not solely for its inherent value to the pregnant woman, but also as enabling an expansion of conditions whose identification may allow early intervention and clinical impact. This article discusses this paradigm against the backdrop of prenatal genetic screening that is available today.
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21
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ACMG Releases Guidelines for Exome and Genome Sequencing for Pediatric Patients. Am J Med Genet A 2021; 185:3185-6. [PMID: 34655171 DOI: 10.1002/ajmg.a.61706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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22
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Katakura Y, Kimura T, Kusano T, Tatsumi F, Iwamoto Y, Sanada J, Fushimi Y, Shimoda M, Kohara K, Nakanishi S, Kaku K, Mune T, Kaneto H. Case Report: A Variety of Immune-Related Adverse Events Triggered by Immune Checkpoint Inhibitors in a Subject With Malignant Melanoma: Destructive Thyroiditis, Aseptic Meningitis and Isolated ACTH Deficiency. Front Endocrinol (Lausanne) 2021; 12:722586. [PMID: 34712202 PMCID: PMC8547604 DOI: 10.3389/fendo.2021.722586] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 09/20/2021] [Indexed: 11/16/2022] Open
Abstract
Recently, immune checkpoint inhibitors have been drawing much attention as cancer immunotherapy, but it has been shown that various immune-related adverse events (irAEs) are induced by immune checkpoint inhibitors in various organs, which has become one of the serious issues at present. A 58-year-old Japanese male with malignant melanoma was treated with nivolumab and/or ipilimumab. During the period of treatment, he suffered from various irAEs. Firstly, about 1 month after starting nivolumab monotherapy, destructive thyroiditis was induced, and so we started replacement therapy with levothyroxine. Secondly, about 1 month after starting nivolumab and ipilimumab combination therapy, aseptic meningitis was induced. We stopped both drugs and started steroid therapy with prednisolone. Finally, about 9 months after restarting nivolumab, isolated adrenocorticotropic hormone (ACTH) deficiency was induced, and so we started replacement therapy with hydrocortisone. Taken together, we should bear in mind the possibility of a variety of irAEs when we use immune checkpoint inhibitors.
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Affiliation(s)
| | - Tomohiko Kimura
- Department of Diabetes, Endocrinology and Metabolism, Kawasaki Medical School, Kurashiki, Japan
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23
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Hurvitz N, Azmanov H, Kesler A, Ilan Y. Establishing a second-generation artificial intelligence-based system for improving diagnosis, treatment, and monitoring of patients with rare diseases. Eur J Hum Genet 2021; 29:1485-1490. [PMID: 34276056 PMCID: PMC8484657 DOI: 10.1038/s41431-021-00928-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/06/2021] [Accepted: 06/16/2021] [Indexed: 02/07/2023] Open
Abstract
Patients with rare diseases are a major challenge for healthcare systems. These patients face three major obstacles: late diagnosis and misdiagnosis, lack of proper response to therapies, and absence of valid monitoring tools. We reviewed the relevant literature on first-generation artificial intelligence (AI) algorithms which were designed to improve the management of chronic diseases. The shortage of big data resources and the inability to provide patients with clinical value limit the use of these AI platforms by patients and physicians. In the present study, we reviewed the relevant literature on the obstacles encountered in the management of patients with rare diseases. Examples of currently available AI platforms are presented. The use of second-generation AI-based systems that are patient-tailored is presented. The system provides a means for early diagnosis and a method for improving the response to therapies based on clinically meaningful outcome parameters. The system may offer a patient-tailored monitoring tool that is based on parameters that are relevant to patients and caregivers and provides a clinically meaningful tool for follow-up. The system can provide an inclusive solution for patients with rare diseases and ensures adherence based on clinical responses. It has the potential advantage of not being dependent on large datasets and is a dynamic system that adapts to ongoing changes in patients' disease and response to therapy.
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Affiliation(s)
- Noa Hurvitz
- Faculty of Medicine, Department of Medicine, Hebrew University, Hadassah Medical Center, Jerusalem, Israel
| | - Henny Azmanov
- Faculty of Medicine, Department of Medicine, Hebrew University, Hadassah Medical Center, Jerusalem, Israel
| | - Asa Kesler
- Faculty of Medicine, Department of Medicine, Hebrew University, Hadassah Medical Center, Jerusalem, Israel
| | - Yaron Ilan
- Faculty of Medicine, Department of Medicine, Hebrew University, Hadassah Medical Center, Jerusalem, Israel.
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24
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Kolosov N, Daly MJ, Artomov M. Prioritization of disease genes from GWAS using ensemble-based positive-unlabeled learning. Eur J Hum Genet 2021; 29:1527-1535. [PMID: 34276057 PMCID: PMC8484264 DOI: 10.1038/s41431-021-00930-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 05/23/2021] [Accepted: 06/21/2021] [Indexed: 02/07/2023] Open
Abstract
A primary challenge in understanding disease biology from genome-wide association studies (GWAS) arises from the inability to directly implicate causal genes from association data. Integration of multiple-omics data sources potentially provides important functional links between associated variants and candidate genes. Machine-learning is well-positioned to take advantage of a variety of such data and provide a solution for the prioritization of disease genes. Yet, classical positive-negative classifiers impose strong limitations on the gene prioritization procedure, such as a lack of reliable non-causal genes for training. Here, we developed a novel gene prioritization tool-Gene Prioritizer (GPrior). It is an ensemble of five positive-unlabeled bagging classifiers (Logistic Regression, Support Vector Machine, Random Forest, Decision Tree, Adaptive Boosting), that treats all genes of unknown relevance as an unlabeled set. GPrior selects an optimal composition of algorithms to tune the model for each specific phenotype. Altogether, GPrior fills an important niche of methods for GWAS data post-processing, significantly improving the ability to pinpoint disease genes compared to existing solutions.
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Affiliation(s)
- Nikita Kolosov
- ITMO University, St. Petersburg, Russia
- Almazov National Medical Research Center, St. Petersburg, Russia
- Broad Institute, Cambridge, MA, USA
| | - Mark J Daly
- Broad Institute, Cambridge, MA, USA.
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.
- Institute for Molecular Medicine Finland (FIMM), Helsinki, Finland.
| | - Mykyta Artomov
- ITMO University, St. Petersburg, Russia.
- Almazov National Medical Research Center, St. Petersburg, Russia.
- Broad Institute, Cambridge, MA, USA.
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.
- Institute for Molecular Medicine Finland (FIMM), Helsinki, Finland.
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25
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Danis D, Jacobsen JOB, Carmody LC, Gargano MA, McMurry JA, Hegde A, Haendel MA, Valentini G, Smedley D, Robinson PN. Interpretable prioritization of splice variants in diagnostic next-generation sequencing. Am J Hum Genet 2021; 108:1564-1577. [PMID: 34289339 DOI: 10.1016/j.ajhg.2021.06.014] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 06/18/2021] [Indexed: 12/11/2022] Open
Abstract
A critical challenge in genetic diagnostics is the computational assessment of candidate splice variants, specifically the interpretation of nucleotide changes located outside of the highly conserved dinucleotide sequences at the 5' and 3' ends of introns. To address this gap, we developed the Super Quick Information-content Random-forest Learning of Splice variants (SQUIRLS) algorithm. SQUIRLS generates a small set of interpretable features for machine learning by calculating the information-content of wild-type and variant sequences of canonical and cryptic splice sites, assessing changes in candidate splicing regulatory sequences, and incorporating characteristics of the sequence such as exon length, disruptions of the AG exclusion zone, and conservation. We curated a comprehensive collection of disease-associated splice-altering variants at positions outside of the highly conserved AG/GT dinucleotides at the termini of introns. SQUIRLS trains two random-forest classifiers for the donor and for the acceptor and combines their outputs by logistic regression to yield a final score. We show that SQUIRLS transcends previous state-of-the-art accuracy in classifying splice variants as assessed by rank analysis in simulated exomes, and is significantly faster than competing methods. SQUIRLS provides tabular output files for incorporation into diagnostic pipelines for exome and genome analysis, as well as visualizations that contextualize predicted effects of variants on splicing to make it easier to interpret splice variants in diagnostic settings.
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Affiliation(s)
- Daniel Danis
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT 06032, USA
| | - Julius O B Jacobsen
- William Harvey Research Institute, Charterhouse Square, Barts and the London School of Medicine and Dentistry Queen, Queen Mary University of London, EC1M 6BQ London, UK
| | - Leigh C Carmody
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT 06032, USA
| | - Michael A Gargano
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT 06032, USA
| | - Julie A McMurry
- University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Ayushi Hegde
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT 06032, USA
| | | | - Giorgio Valentini
- Anacleto Lab - Dipartimento di Informatica and DSRC, Università degli Studi di Milano, Via Celoria 18, 20133 Milan, Italy; CINI National Laboratory in Artificial Intelligence and Intelligent Systems-AIIS, Rome, Italy
| | - Damian Smedley
- William Harvey Research Institute, Charterhouse Square, Barts and the London School of Medicine and Dentistry Queen, Queen Mary University of London, EC1M 6BQ London, UK
| | - Peter N Robinson
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT 06032, USA; Institute for Systems Genomics, University of Connecticut, Farmington, CT 06032, USA.
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26
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Stark Z, Foulger RE, Williams E, Thompson BA, Patel C, Lunke S, Snow C, Leong IUS, Puzriakova A, Daugherty LC, Leigh S, Boustred C, Niblock O, Rueda-Martin A, Gerasimenko O, Savage K, Bellamy W, Lin VSK, Valls R, Gordon L, Brittain HK, Thomas ERA, Taylor Tavares AL, McEntagart M, White SM, Tan TY, Yeung A, Downie L, Macciocca I, Savva E, Lee C, Roesley A, De Fazio P, Deller J, Deans ZC, Hill SL, Caulfield MJ, North KN, Scott RH, Rendon A, Hofmann O, McDonagh EM. Scaling national and international improvement in virtual gene panel curation via a collaborative approach to discordance resolution. Am J Hum Genet 2021; 108:1551-1557. [PMID: 34329581 PMCID: PMC8456155 DOI: 10.1016/j.ajhg.2021.06.020] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 06/27/2021] [Indexed: 02/02/2023] Open
Abstract
Clinical validity assessments of gene-disease associations underpin analysis and reporting in diagnostic genomics, and yet wide variability exists in practice, particularly in use of these assessments for virtual gene panel design and maintenance. Harmonization efforts are hampered by the lack of agreed terminology, agreed gene curation standards, and platforms that can be used to identify and resolve discrepancies at scale. We undertook a systematic comparison of the content of 80 virtual gene panels used in two healthcare systems by multiple diagnostic providers in the United Kingdom and Australia. The process was enabled by a shared curation platform, PanelApp, and resulted in the identification and review of 2,144 discordant gene ratings, demonstrating the utility of sharing structured gene-disease validity assessments and collaborative discordance resolution in establishing national and international consensus.
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Affiliation(s)
- Zornitza Stark
- Australian Genomics Health Alliance, Melbourne, VIC 3052, Australia; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia; University of Melbourne, Melbourne, VIC 3010, Australia.
| | - Rebecca E Foulger
- Genomics England, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Eleanor Williams
- Genomics England, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Bryony A Thompson
- University of Melbourne, Melbourne, VIC 3010, Australia; Royal Melbourne Hospital, Melbourne, VIC 3050, Australia
| | - Chirag Patel
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Brisbane, QLD 4006, Australia
| | - Sebastian Lunke
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia; University of Melbourne, Melbourne, VIC 3010, Australia
| | - Catherine Snow
- Genomics England, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Ivone U S Leong
- Genomics England, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Arina Puzriakova
- Genomics England, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Louise C Daugherty
- Genomics England, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Sarah Leigh
- Genomics England, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Christopher Boustred
- Genomics England, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Olivia Niblock
- Genomics England, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Antonio Rueda-Martin
- Genomics England, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Oleg Gerasimenko
- Genomics England, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Kevin Savage
- Genomics England, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - William Bellamy
- Genomics England, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Victor San Kho Lin
- Centre for Cancer Research, University of Melbourne, Victorian Comprehensive Cancer Centre, Melbourne, VIC 3000, Australia
| | - Roman Valls
- Centre for Cancer Research, University of Melbourne, Victorian Comprehensive Cancer Centre, Melbourne, VIC 3000, Australia
| | - Lavinia Gordon
- Centre for Cancer Research, University of Melbourne, Victorian Comprehensive Cancer Centre, Melbourne, VIC 3000, Australia
| | - Helen K Brittain
- Genomics England, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Ellen R A Thomas
- Genomics England, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK; Guy's and St Thomas's NHS Trust, London SE1 9RS, UK
| | | | - Meriel McEntagart
- Genomics England, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK; St George's University Hospitals NHS Trust, London SW17 0QT, UK
| | - Susan M White
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia; University of Melbourne, Melbourne, VIC 3010, Australia
| | - Tiong Y Tan
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia; University of Melbourne, Melbourne, VIC 3010, Australia
| | - Alison Yeung
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia; University of Melbourne, Melbourne, VIC 3010, Australia
| | - Lilian Downie
- University of Melbourne, Melbourne, VIC 3010, Australia; Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia
| | - Ivan Macciocca
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia
| | - Elena Savva
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia
| | - Crystle Lee
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia
| | - Ain Roesley
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia
| | - Paul De Fazio
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia
| | - Jane Deller
- National Health Service England and National Health Service Improvement, London SE1 6LH, UK
| | - Zandra C Deans
- National Health Service England and National Health Service Improvement, London SE1 6LH, UK
| | - Sue L Hill
- National Health Service England and National Health Service Improvement, London SE1 6LH, UK
| | - Mark J Caulfield
- Genomics England, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Kathryn N North
- Australian Genomics Health Alliance, Melbourne, VIC 3052, Australia; University of Melbourne, Melbourne, VIC 3010, Australia; Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia
| | - Richard H Scott
- Genomics England, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Augusto Rendon
- Genomics England, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Oliver Hofmann
- Centre for Cancer Research, University of Melbourne, Victorian Comprehensive Cancer Centre, Melbourne, VIC 3000, Australia
| | - Ellen M McDonagh
- Genomics England, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK; Open Targets and European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK
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27
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Zurek B, Ellwanger K, Vissers LELM, Schüle R, Synofzik M, Töpf A, de Voer RM, Laurie S, Matalonga L, Gilissen C, Ossowski S, 't Hoen PAC, Vitobello A, Schulze-Hentrich JM, Riess O, Brunner HG, Brookes AJ, Rath A, Bonne G, Gumus G, Verloes A, Hoogerbrugge N, Evangelista T, Harmuth T, Swertz M, Spalding D, Hoischen A, Beltran S, Graessner H. Solve-RD: systematic pan-European data sharing and collaborative analysis to solve rare diseases. Eur J Hum Genet 2021; 29:1325-1331. [PMID: 34075208 PMCID: PMC8440542 DOI: 10.1038/s41431-021-00859-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 02/08/2021] [Accepted: 03/04/2021] [Indexed: 11/28/2022] Open
Abstract
For the first time in Europe hundreds of rare disease (RD) experts team up to actively share and jointly analyse existing patient's data. Solve-RD is a Horizon 2020-supported EU flagship project bringing together >300 clinicians, scientists, and patient representatives of 51 sites from 15 countries. Solve-RD is built upon a core group of four European Reference Networks (ERNs; ERN-ITHACA, ERN-RND, ERN-Euro NMD, ERN-GENTURIS) which annually see more than 270,000 RD patients with respective pathologies. The main ambition is to solve unsolved rare diseases for which a molecular cause is not yet known. This is achieved through an innovative clinical research environment that introduces novel ways to organise expertise and data. Two major approaches are being pursued (i) massive data re-analysis of >19,000 unsolved rare disease patients and (ii) novel combined -omics approaches. The minimum requirement to be eligible for the analysis activities is an inconclusive exome that can be shared with controlled access. The first preliminary data re-analysis has already diagnosed 255 cases form 8393 exomes/genome datasets. This unprecedented degree of collaboration focused on sharing of data and expertise shall identify many new disease genes and enable diagnosis of many so far undiagnosed patients from all over Europe.
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Affiliation(s)
- Birte Zurek
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Kornelia Ellwanger
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Lisenka E L M Vissers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Rebecca Schüle
- Department of Neurodegeneration, Hertie Institute for Clinical Brain Research (HIH), University of Tübingen, Tübingen, Germany
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Matthis Synofzik
- Department of Neurodegeneration, Hertie Institute for Clinical Brain Research (HIH), University of Tübingen, Tübingen, Germany
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Ana Töpf
- John Walton Muscular Dystrophy Research Centre, Translational and Clinical Research Institute, Newcastle University and Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Richarda M de Voer
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Steven Laurie
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Leslie Matalonga
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Christian Gilissen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Stephan Ossowski
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Peter A C 't Hoen
- Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
- Center for Molecular and Biomolecular Informatics, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | | | - Olaf Riess
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- Centre for Rare Diseases, University of Tübingen, Tübingen, Germany
| | - Han G Brunner
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Clinical Genetics, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Anthony J Brookes
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Ana Rath
- INSERM, US14-Orphanet, Plateforme Maladies Rares, Paris, France
| | - Gisèle Bonne
- Sorbonne Université, INSERM UMRS 974, Center of Research in Myology, Paris, France
| | | | - Alain Verloes
- Genetics Department, APHP-Robert Debré University Hospital, Université de Paris, Paris, France
| | - Nicoline Hoogerbrugge
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | | | - Tina Harmuth
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Morris Swertz
- Department of Genetics, Genomics Coordination Center, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Dylan Spalding
- European Bioinformatics Institute, European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Alexander Hoischen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Sergi Beltran
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona (UB), Barcelona, Spain
| | - Holm Graessner
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany.
- Centre for Rare Diseases, University of Tübingen, Tübingen, Germany.
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28
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Landstrom AP, Kim JJ, Gelb BD, Helm BM, Kannankeril PJ, Semsarian C, Sturm AC, Tristani-Firouzi M, Ware SM. Genetic Testing for Heritable Cardiovascular Diseases in Pediatric Patients: A Scientific Statement From the American Heart Association. Circ Genom Precis Med 2021; 14:e000086. [PMID: 34412507 DOI: 10.1161/hcg.0000000000000086] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Genetic diseases that affect the cardiovascular system are relatively common and include cardiac channelopathies, cardiomyopathies, aortopathies, hypercholesterolemias, and structural diseases of the heart and great vessels. The rapidly expanding availability of clinical genetic testing leverages decades of research into the genetic origins of these diseases, helping inform diagnosis, clinical management, and prognosis. Although a number of guidelines and statements detail best practices for cardiovascular genetic testing, there is a paucity of pediatric-focused statements addressing the unique challenges in testing in this vulnerable population. In this scientific statement, we seek to coalesce the existing literature around the use of genetic testing for cardiovascular disease in infants, children, and adolescents.
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29
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Miller DE, Sulovari A, Wang T, Loucks H, Hoekzema K, Munson KM, Lewis AP, Fuerte EPA, Paschal CR, Walsh T, Thies J, Bennett JT, Glass I, Dipple KM, Patterson K, Bonkowski ES, Nelson Z, Squire A, Sikes M, Beckman E, Bennett RL, Earl D, Lee W, Allikmets R, Perlman SJ, Chow P, Hing AV, Wenger TL, Adam MP, Sun A, Lam C, Chang I, Zou X, Austin SL, Huggins E, Safi A, Iyengar AK, Reddy TE, Majoros WH, Allen AS, Crawford GE, Kishnani PS, King MC, Cherry T, Chong JX, Bamshad MJ, Nickerson DA, Mefford HC, Doherty D, Eichler EE. Targeted long-read sequencing identifies missing disease-causing variation. Am J Hum Genet 2021; 108:1436-1449. [PMID: 34216551 PMCID: PMC8387463 DOI: 10.1016/j.ajhg.2021.06.006] [Citation(s) in RCA: 87] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 06/07/2021] [Indexed: 12/28/2022] Open
Abstract
Despite widespread clinical genetic testing, many individuals with suspected genetic conditions lack a precise diagnosis, limiting their opportunity to take advantage of state-of-the-art treatments. In some cases, testing reveals difficult-to-evaluate structural differences, candidate variants that do not fully explain the phenotype, single pathogenic variants in recessive disorders, or no variants in genes of interest. Thus, there is a need for better tools to identify a precise genetic diagnosis in individuals when conventional testing approaches have been exhausted. We performed targeted long-read sequencing (T-LRS) using adaptive sampling on the Oxford Nanopore platform on 40 individuals, 10 of whom lacked a complete molecular diagnosis. We computationally targeted up to 151 Mbp of sequence per individual and searched for pathogenic substitutions, structural variants, and methylation differences using a single data source. We detected all genomic aberrations-including single-nucleotide variants, copy number changes, repeat expansions, and methylation differences-identified by prior clinical testing. In 8/8 individuals with complex structural rearrangements, T-LRS enabled more precise resolution of the mutation, leading to changes in clinical management in one case. In ten individuals with suspected Mendelian conditions lacking a precise genetic diagnosis, T-LRS identified pathogenic or likely pathogenic variants in six and variants of uncertain significance in two others. T-LRS accurately identifies pathogenic structural variants, resolves complex rearrangements, and identifies Mendelian variants not detected by other technologies. T-LRS represents an efficient and cost-effective strategy to evaluate high-priority genes and regions or complex clinical testing results.
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Affiliation(s)
- Danny E Miller
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA; Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA.
| | - Arvis Sulovari
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Tianyun Wang
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Hailey Loucks
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Kendra Hoekzema
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Katherine M Munson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Alexandra P Lewis
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Edith P Almanza Fuerte
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Catherine R Paschal
- Department of Laboratories, Seattle Children's Hospital, Seattle, WA 98105, USA; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Tom Walsh
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA; Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Jenny Thies
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - James T Bennett
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA; Department of Laboratories, Seattle Children's Hospital, Seattle, WA 98105, USA; Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98101, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
| | - Ian Glass
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Katrina M Dipple
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA; Center for Clinical and Translational Research, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Karynne Patterson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Emily S Bonkowski
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Zoe Nelson
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Audrey Squire
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Megan Sikes
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Erika Beckman
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Robin L Bennett
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Dawn Earl
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Winston Lee
- Department of Genetics and Development, Columbia University, New York, NY 10032, USA; Department of Ophthalmology, Columbia University, New York, NY 10032, USA
| | - Rando Allikmets
- Department of Ophthalmology, Columbia University, New York, NY 10032, USA; Department of Pathology and Cell Biology, Columbia University, New York, NY 10032, USA
| | - Seth J Perlman
- Department of Neurology, Seattle Children's Hospital, University of Washington, Seattle, WA 98105, USA
| | - Penny Chow
- Department of Pediatrics, Division of Craniofacial Medicine, University of Washington, Seattle, WA 98195, USA
| | - Anne V Hing
- Department of Pediatrics, Division of Craniofacial Medicine, University of Washington, Seattle, WA 98195, USA
| | - Tara L Wenger
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Margaret P Adam
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Angela Sun
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA; Center for Clinical and Translational Research, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Christina Lam
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA; Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Irene Chang
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Xue Zou
- Program in Computational Biology & Bioinformatics, Duke University, Durham, NC 27710, USA
| | - Stephanie L Austin
- Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, NC 27708, USA
| | - Erin Huggins
- Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, NC 27708, USA
| | - Alexias Safi
- Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, NC 27708, USA
| | - Apoorva K Iyengar
- Department of Biostatistics and Bioinformatics, Duke University; Durham, NC 27708, USA; University Program in Genetics and Genomics, Duke University; Durham, NC 27708, USA
| | - Timothy E Reddy
- Department of Biostatistics and Bioinformatics, Duke University; Durham, NC 27708, USA
| | - William H Majoros
- Department of Biostatistics and Bioinformatics, Duke University; Durham, NC 27708, USA
| | - Andrew S Allen
- Department of Biostatistics and Bioinformatics, Duke University; Durham, NC 27708, USA
| | - Gregory E Crawford
- Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, NC 27708, USA
| | - Priya S Kishnani
- Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, NC 27708, USA
| | - Mary-Claire King
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA; Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Tim Cherry
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Jessica X Chong
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
| | - Michael J Bamshad
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA; Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
| | - Heather C Mefford
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
| | - Dan Doherty
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA; Department of Pediatrics, Division of Developmental Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.
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30
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Toft CLF, Ingerslev HJ, Kesmodel US, Hatt L, Singh R, Ravn K, Nicolaisen BH, Christensen IB, Kølvraa M, Jeppesen LD, Schelde P, Vogel I, Uldbjerg N, Farlie R, Sommer S, Østergård MLV, Jensen AN, Mogensen H, Kjartansdóttir KR, Degn B, Okkels H, Ernst A, Pedersen IS. Cell-based non-invasive prenatal testing for monogenic disorders: confirmation of unaffected fetuses following preimplantation genetic testing. J Assist Reprod Genet 2021; 38:1959-1970. [PMID: 33677749 PMCID: PMC8417213 DOI: 10.1007/s10815-021-02104-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 02/04/2021] [Indexed: 11/23/2022] Open
Abstract
PURPOSE Proof of concept of the use of cell-based non-invasive prenatal testing (cbNIPT) as an alternative to chorionic villus sampling (CVS) following preimplantation genetic testing for monogenic disorders (PGT-M). METHOD PGT-M was performed by combined testing of short tandem repeat (STR) markers and direct mutation detection, followed by transfer of an unaffected embryo. Patients who opted for follow-up of PGT-M by CVS had blood sampled, from which potential fetal extravillous throphoblast cells were isolated. The cell origin and mutational status were determined by combined testing of STR markers and direct mutation detection using the same setup as during PGT. The cbNIPT results with respect to the mutational status were compared to those of genetic testing of the CVS. RESULTS Eight patients had blood collected between gestational weeks 10 and 13, from which 33 potential fetal cell samples were isolated. Twenty-seven out of 33 isolated cell samples were successfully tested (82%), of which 24 were of fetal origin (89%). This corresponds to a median of 2.5 successfully tested fetal cell samples per case (range 1-6). All fetal cell samples had a genetic profile identical to that of the transferred embryo confirming a pregnancy with an unaffected fetus, in accordance with the CVS results. CONCLUSION These findings show that although measures are needed to enhance the test success rate and the number of cells identified, cbNIPT is a promising alternative to CVS. TRIAL REGISTRATION NUMBER N-20180001.
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Affiliation(s)
- Christian Liebst Frisk Toft
- Department of Molecular Diagnostics, Aalborg University Hospital, Aalborg, Denmark.
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark.
| | | | - Ulrik Schiøler Kesmodel
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
- Fertility Unit, Aalborg University Hospital, Aalborg, Denmark
| | | | | | | | | | | | | | | | | | - Ida Vogel
- Department of Clinical Genetic, Aarhus University Hospital, Aarhus, Denmark
| | - Niels Uldbjerg
- Department of Obstetrics and Gynecology, Aarhus University Hospital, Aarhus, Denmark
| | - Richard Farlie
- Department of Obstetrics and Gynecology, Viborg Regional Hospital, Viborg, Denmark
| | - Steffen Sommer
- Department of Obstetrics and Gynecology, Horsens Regional Hospital, Horsens, Denmark
| | | | - Ann Nygaard Jensen
- Department of Obstetrics and Gynecology, Aalborg University Hospital, Aalborg, Denmark
| | - Helle Mogensen
- Department of Obstetrics and Gynecology, Kolding Regional Hospital, Kolding, Denmark
| | - Kristín Rós Kjartansdóttir
- Molecular Genetics Laboratory, Department of Clinical Genetics, University Hospital Copenhagen, Copenhagen, Denmark
| | - Birte Degn
- Department of Molecular Diagnostics, Aalborg University Hospital, Aalborg, Denmark
| | - Henrik Okkels
- Department of Molecular Diagnostics, Aalborg University Hospital, Aalborg, Denmark
| | - Anja Ernst
- Department of Molecular Diagnostics, Aalborg University Hospital, Aalborg, Denmark
| | - Inge Søkilde Pedersen
- Department of Molecular Diagnostics, Aalborg University Hospital, Aalborg, Denmark
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
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31
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Affiliation(s)
| | - Justin M. Zook
- Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, MD 20899
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32
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Abstract
Genetics evolved as a field of science after 1900 with new theories being derived from experiments obtained in fruit flies, bacteria, and viruses. This personal account suggests that the origins of human genetics can best be traced to the years 1949 to 1959. Several genetic scientific advances in genetics in 1949 yielded results directly relating to humans for the first time, except for a few earlier observations. In 1949 the first textbook of human genetics was published, the American Journal of Human Genetics was founded, and in the previous year the American Society of Human Genetics. In 1940 in Britain a textbook entitled Introduction to Medical Genetics served as a foundation for introducing genetic aspects into medicine. The introduction of new methods for analyzing chromosomes and new biochemical assays using cultured cells in 1959 and subsequent years revealed that many human diseases, including cancer, have genetic causes. It became possible to arrive at a precise cause-related genetic diagnosis. As a result the risk of occurrence or re-occurrence of a disease within a family could be assessed correctly. Genetic counseling as a new concept became a basis for improved patient care. Taken together the advances in medically orientated genetic research and patient care since 1949 have resulted in human genetics being both, a basic medical and a basic biological science. Prior to 1949 genetics was not generally viewed in a medical context. Although monogenic human diseases were recognized in 1902, their occurrence and distribution were considered mainly at the population level.
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Affiliation(s)
- Eberhard Passarge
- Institut für Humangenetik, Universitätsklinikum Essen, Essen, Germany.
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Zhang S, Lei C, Wu J, Xiao M, Zhou J, Zhu S, Fu J, Lu D, Sun X, Xu C. A comprehensive and universal approach for embryo testing in patients with different genetic disorders. Clin Transl Med 2021; 11:e490. [PMID: 34323405 PMCID: PMC8265165 DOI: 10.1002/ctm2.490] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 06/01/2021] [Accepted: 06/20/2021] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND In vitro fertilization (IVF) with preimplantation genetic testing (PGT) has markedly improved clinical pregnancy outcomes for carriers of gene mutations or chromosomal structural rearrangements by the selection of embryos free of disease-causing genes and chromosome abnormalities. However, for detecting whole or segmental chromosome aneuploidies, gene variants or balanced chromosome rearrangements in the same embryo require separate procedures, and none of the existing detection platforms is universal for all patients with different genetic disorders. METHODS Here, we report a cost-effective, family-based haplotype phasing approach that can simultaneously evaluate multiple genetic variants, including monogenic disorders, aneuploidy, and balanced chromosome rearrangements in the same embryo with a single test. A total of 12 monogenic diseases carrier couples and either of them carried chromosomal rearrangements were enrolled simultaneously in this present study. Genome-wide genotyping was performed with single-nucleotide polymorphism (SNP)-array, and aneuploidies were analyzed through SNP allele frequency and Log R ratio. Parental haplotypes were phased by an available genotype from a close relative, and the embryonic genome-wide haplotypes were determined through family haplotype linkage analysis (FHLA). Disease-causing genes and chromosomal rearrangements were detected by haplotypes located within the 2 Mb region covering the targeted genes or breakpoint regions. RESULTS Twelve blastocysts were thawed, and then transferred into the uterus of female patients. Nine pregnancies had reached the second trimester and five healthy babies have been born. Fetus validation results, performed with the amniotic fluid or umbilical cord blood samples, were consistent with those at the blastocyst stage diagnosed by PGT. CONCLUSIONS We demonstrate that SNP-based FHLA enables the accurate genetic detection of a wide spectrum of monogenic diseases and chromosome abnormalities in embryos, preventing the transfer of parental genetic abnormalities to the fetus. This method can be implemented as a universal platform for embryo testing in patients with different genetic disorders.
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Affiliation(s)
- Shuo Zhang
- Shanghai Ji Ai Genetics & IVF Institute, Obstetrics and Gynecology HospitalFudan UniversityShanghaiChina
| | - Caixia Lei
- Shanghai Ji Ai Genetics & IVF Institute, Obstetrics and Gynecology HospitalFudan UniversityShanghaiChina
| | - Junping Wu
- Shanghai Ji Ai Genetics & IVF Institute, Obstetrics and Gynecology HospitalFudan UniversityShanghaiChina
| | - Min Xiao
- Shanghai Ji Ai Genetics & IVF Institute, Obstetrics and Gynecology HospitalFudan UniversityShanghaiChina
| | - Jing Zhou
- Shanghai Ji Ai Genetics & IVF Institute, Obstetrics and Gynecology HospitalFudan UniversityShanghaiChina
| | - Saijuan Zhu
- Shanghai Ji Ai Genetics & IVF Institute, Obstetrics and Gynecology HospitalFudan UniversityShanghaiChina
| | - Jing Fu
- Shanghai Ji Ai Genetics & IVF Institute, Obstetrics and Gynecology HospitalFudan UniversityShanghaiChina
| | - Daru Lu
- State Key Laboratory of Genetic Engineering, School of Life ScienceFudan UniversityShanghaiChina
- NHC Key Laboratory of Birth Defects and Reproductive Health, Chongqing Key Laboratory of Birth Defects and Reproductive Health, Chongqing Population and Family PlanningScience and Technology Research InstituteChongqingChina
| | - Xiaoxi Sun
- Shanghai Ji Ai Genetics & IVF Institute, Obstetrics and Gynecology HospitalFudan UniversityShanghaiChina
- Key Laboratory of Female Reproductive Endocrine Related Diseases, Obstetrics and Gynecology HospitalFudan UniversityShanghaiChina
| | - Congjian Xu
- Shanghai Ji Ai Genetics & IVF Institute, Obstetrics and Gynecology HospitalFudan UniversityShanghaiChina
- Key Laboratory of Female Reproductive Endocrine Related Diseases, Obstetrics and Gynecology HospitalFudan UniversityShanghaiChina
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Anderson JL, Kruisselbrink TM, Lisi EC, Hughes TM, Steyermark JM, Winkler EM, Berg CM, Vierkant RA, Gupta R, Ali AH, Faubion SS, Aoudia SL, McAllister TM, Farrugia G, Stewart AK, Lazaridis KN. Clinically Actionable Findings Derived From Predictive Genomic Testing Offered in a Medical Practice Setting. Mayo Clin Proc 2021; 96:1407-1417. [PMID: 33890576 DOI: 10.1016/j.mayocp.2020.08.051] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 08/28/2020] [Accepted: 08/31/2020] [Indexed: 02/07/2023]
Abstract
OBJECTIVE To assess the presence of clinically actionable results and other genetic findings in an otherwise healthy population of adults seen in a medical practice setting and offered "predictive" genomic testing. PATIENTS AND METHODS In 2014, a predictive genomics clinic for generally healthy adults was launched through the Mayo Clinic Executive Health Program. Self-identified interested patients met with a genomic nurse and genetic counselor for pretest advice and education. Two genome sequencing platforms and one gene panel-based health screen were offered. Posttest genetic counseling was available for patients who elected testing. From March 1, 2014, through June 1, 2019, 1281 patients were seen and 301 (23.5%) chose testing. Uptake rates increased to 36.3% [70 of 193]) in 2019 from 11.8% [2 of 17] in 2014. Clinically actionable results and genetic findings were analyzed using descriptive statistics. RESULTS Clinically actionable results were detected in 11.6% of patients (35 of 301), and of those, 51.7% (15 of 29) with a cancer or cardiovascular result = did not have a personal or family history concerning for a hereditary disorder. The most common actionable results were in the BCHE, BRCA2, CHEK2, LDLR, MUTYH, and MYH7 genes. A carrier of at least one recessive condition was found in 53.8% of patients (162 of 301). At least one variant associated with multifactorial disease was found in 44.5% (134 of 301) (eg, 25 patients were heterozygous for the F5 factor V Leiden variant associated with thrombophilia risk). CONCLUSION Our predictive screening revealed that 11.6% of individuals will test positive for a clinically actionable, likely pathogenic/pathogenic variant. This finding suggests that wider knowledge and adoption of predictive genomic services could be beneficial in medical practice, although additional studies are needed.
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Affiliation(s)
| | | | - Emily C Lisi
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN
| | | | | | - Erin M Winkler
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN
| | - Corinne M Berg
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN
| | - Robert A Vierkant
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN
| | - Ruchi Gupta
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN
| | - Ahmad H Ali
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN
| | | | - Stacy L Aoudia
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN
| | | | - Gianrico Farrugia
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN
| | - A Keith Stewart
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN
| | - Konstantinos N Lazaridis
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN; Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN.
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Dodge DL, Cherian SV, Ali YD, Murzabdillaeva A, Hu Z, Estrada-Y-Martin RM. A 35-Year-Old Woman With Progressive Dyspnea and Cough. Chest 2021; 158:e103-e106. [PMID: 32892884 DOI: 10.1016/j.chest.2020.02.068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 02/16/2020] [Accepted: 02/29/2020] [Indexed: 11/18/2022] Open
Abstract
CASE PRESENTATION A 35-year-old woman with no known medical history presented to the ED with complaints of progressive dyspnea for several months. The patient also reported episodic cough with yellow to green sputum production. She denied fever, chills, weight loss, or hemoptysis. She also denied any history of previous lung diseases in her family. She denied any history of tobacco or recreational drug use or any exposures. She was originally from El Salvador and immigrated to the United States approximately 3 years earlier. She was evaluated in El Salvador at age 15 for "lung issues" but had never received a formal diagnosis.
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Affiliation(s)
- Daniel L Dodge
- Divisions of Pulmonary, Critical Care and Sleep Medicine, University of Texas Health, McGovern Medical School, Houston, TX
| | - Sujith V Cherian
- Divisions of Pulmonary, Critical Care and Sleep Medicine, University of Texas Health, McGovern Medical School, Houston, TX.
| | - Yasir D Ali
- Department of Pathology and Laboratory Medicine, University of Texas Health, McGovern Medical School, Houston, TX
| | - Albina Murzabdillaeva
- Department of Pathology and Laboratory Medicine, University of Texas Health, McGovern Medical School, Houston, TX
| | - Zhihong Hu
- Department of Pathology and Laboratory Medicine, University of Texas Health, McGovern Medical School, Houston, TX
| | - Rosa M Estrada-Y-Martin
- Divisions of Pulmonary, Critical Care and Sleep Medicine, University of Texas Health, McGovern Medical School, Houston, TX
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Lee I, Alur-Gupta S, Gallop R, Dokras A. Utilization of preimplantation genetic testing for monogenic disorders. Fertil Steril 2021; 114:854-860. [PMID: 33040985 DOI: 10.1016/j.fertnstert.2020.05.045] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 05/06/2020] [Accepted: 05/11/2020] [Indexed: 11/20/2022]
Abstract
OBJECTIVE To determine the rate of utilization, factors influencing the decision-making process, and patient satisfaction with preimplantation genetic diagnosis for monogenic disorders (PGT-M). DESIGN Survey study. SETTING Academic center. PATIENT(S) Genetically at-risk patients seen for PGT-M consultation between January 2010 and 2018. INTERVENTION(S) Electronic survey including demographics, genetic history, consultation experience, decision-making process, and satisfaction with PGT-M process. MAIN OUTCOME MEASURE(S) Rate of utilization of PGT-M, importance of decision-making factors, and satisfaction with PGT-M process. RESULT(S) Among survey respondents (n = 49), the rate of utilization of PGT-M after consultation was 89.8%. Ninety-three percent of participants decided whether to pursue PGT-M within 3 months of consultation. Factors that were considered most important to this decision-making process included information provided at consultation, accuracy of test results after PGT-M, avoidance of suffering of an affected child, and ability to avoid termination of an affected pregnancy. Key barriers to utilization included financial burden and overall complexity of the in vitro fertilization (IVF)/PGT-M process. Of those utilizing PGT-M (n = 44), 72.1% had at least one live birth or were pregnant during the study period. Satisfaction with PGT-M was high, and most couples would use IVF/PGT-M for a future pregnancy (84.1%). Participants with a live birth were more satisfied with the PGT-M process than those who had no live birth. CONCLUSION(S) Most patients seeking consultation for PGT-M were likely to pursue this technology despite financial burden and complexity of the process. Exploring factors that influence patient decision-making regarding PGT-M is important for tailoring the consultation and optimizing the overall experience.
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Affiliation(s)
- Iris Lee
- Department of Obstetrics and Gynecology, Perelman School of Medicine, University of Pennsylvania Hospital, Philadelphia, Pennsylvania
| | - Snigdha Alur-Gupta
- Department of Obstetrics and Gynecology, Perelman School of Medicine, University of Pennsylvania Hospital, Philadelphia, Pennsylvania
| | - Robert Gallop
- Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Anuja Dokras
- Department of Obstetrics and Gynecology, Perelman School of Medicine, University of Pennsylvania Hospital, Philadelphia, Pennsylvania.
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Putscher E, Hecker M, Fitzner B, Lorenz P, Zettl UK. Principles and Practical Considerations for the Analysis of Disease-Associated Alternative Splicing Events Using the Gateway Cloning-Based Minigene Vectors pDESTsplice and pSpliceExpress. Int J Mol Sci 2021; 22:5154. [PMID: 34068052 PMCID: PMC8152502 DOI: 10.3390/ijms22105154] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/11/2021] [Accepted: 05/12/2021] [Indexed: 12/23/2022] Open
Abstract
Splicing is an important RNA processing step. Genetic variations can alter the splicing process and thereby contribute to the development of various diseases. Alterations of the splicing pattern can be examined by gene expression analyses, by computational tools for predicting the effects of genetic variants on splicing, and by splicing reporter minigene assays for studying alternative splicing events under defined conditions. The minigene assay is based on transient transfection of cells with a vector containing a genomic region of interest cloned between two constitutive exons. Cloning can be accomplished by the use of restriction enzymes or by site-specific recombination using Gateway cloning. The vectors pDESTsplice and pSpliceExpress represent two minigene systems based on Gateway cloning, which are available through the Addgene plasmid repository. In this review, we describe the features of these two splicing reporter minigene systems. Moreover, we provide an overview of studies in which determinants of alternative splicing were investigated by using pDESTsplice or pSpliceExpress. The studies were reviewed with regard to the investigated splicing regulatory events and the experimental strategy to construct and perform a splicing reporter minigene assay. We further elaborate on how analyses on the regulation of RNA splicing offer promising prospects for gaining important insights into disease mechanisms.
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Affiliation(s)
- Elena Putscher
- Division of Neuroimmunology, Department of Neurology, Rostock University Medical Center, Gehlsheimer Street 20, 18147 Rostock, Germany; (E.P.); (B.F.); (U.K.Z.)
| | - Michael Hecker
- Division of Neuroimmunology, Department of Neurology, Rostock University Medical Center, Gehlsheimer Street 20, 18147 Rostock, Germany; (E.P.); (B.F.); (U.K.Z.)
| | - Brit Fitzner
- Division of Neuroimmunology, Department of Neurology, Rostock University Medical Center, Gehlsheimer Street 20, 18147 Rostock, Germany; (E.P.); (B.F.); (U.K.Z.)
| | - Peter Lorenz
- Rostock University Medical Center, Institute of Immunology, Schillingallee 70, 18057 Rostock, Germany;
| | - Uwe Klaus Zettl
- Division of Neuroimmunology, Department of Neurology, Rostock University Medical Center, Gehlsheimer Street 20, 18147 Rostock, Germany; (E.P.); (B.F.); (U.K.Z.)
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Anys S, Billon C, Mazzella JM, Karam N, Pechmajou L, Youssfi Y, Bellenfant F, Jost D, Jabre P, Soulat G, Bruneval P, Weizman O, Varlet E, Baudinaud P, Dumas F, Bougouin W, Cariou A, Lavergne T, Wahbi K, Jouven X, Marijon E. [Fighting against unexplained sudden death]. Ann Cardiol Angeiol (Paris) 2021; 70:129-135. [PMID: 33972104 DOI: 10.1016/j.ancard.2021.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 03/25/2021] [Indexed: 11/18/2022]
Abstract
Sudden cardiac death, mostly related to ventricular arrhythmia, is a major public health issue, with still very poor survival at hospital discharge. Although coronary artery disease remains the leading cause, other etiologies should be systematically investigated. Exhaustive and standardized exploration is required to eventually offer specific therapeutics and management to the patient as well as his/her family members in case of inherited cardiac disease. Identification and establishing direct causality of the detected cardiac anomaly may remain challenging, underlying the need for a multidisciplinary and experimented team.
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MESH Headings
- Adult
- Age Factors
- Algorithms
- Arrhythmias, Cardiac/complications
- Arrhythmias, Cardiac/diagnosis
- Autopsy
- Cardiomyopathies/complications
- Coronary Artery Disease/complications
- Death, Sudden, Cardiac/epidemiology
- Death, Sudden, Cardiac/etiology
- Death, Sudden, Cardiac/prevention & control
- Female
- France/epidemiology
- Genetic Diseases, Inborn/complications
- Genetic Diseases, Inborn/diagnosis
- Heart Defects, Congenital/complications
- Heart Defects, Congenital/diagnosis
- Humans
- Male
- Middle Aged
- Myocardial Infarction/complications
- Registries
- Risk Factors
- Sex Factors
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Affiliation(s)
- S Anys
- Centre d'Expertise Mort Subite de Paris (Paris-CEMS), Inserm U970, 56, rue Leblanc, 75015 Paris, France; Université de Paris, 85, boulevard Saint Germain, 75006 Paris, France; Service de cardiologie, Unité de rythmologie, Hôpital européen Georges-Pompidou, 20, rue Leblanc, 75015 Paris, France
| | - C Billon
- Université de Paris, 85, boulevard Saint Germain, 75006 Paris, France; Service de génétique, Hôpital européen Georges-Pompidou, 20, rue Leblanc, 75015 Paris, France
| | - J-M Mazzella
- Service de génétique, Hôpital européen Georges-Pompidou, 20, rue Leblanc, 75015 Paris, France
| | - N Karam
- Centre d'Expertise Mort Subite de Paris (Paris-CEMS), Inserm U970, 56, rue Leblanc, 75015 Paris, France; Université de Paris, 85, boulevard Saint Germain, 75006 Paris, France; Service de cardiologie, Unité de cardiologie interventionnelle, Hôpital européen Georges-Pompidou, 20, rue Leblanc, 75015 Paris, France
| | - L Pechmajou
- Centre d'Expertise Mort Subite de Paris (Paris-CEMS), Inserm U970, 56, rue Leblanc, 75015 Paris, France; Université de Paris, 85, boulevard Saint Germain, 75006 Paris, France; Service de cardiologie, Unité de cardiologie interventionnelle, Hôpital européen Georges-Pompidou, 20, rue Leblanc, 75015 Paris, France
| | - Y Youssfi
- Centre d'Expertise Mort Subite de Paris (Paris-CEMS), Inserm U970, 56, rue Leblanc, 75015 Paris, France; École Polytechnique, route de Saclay, 91120 Palaiseau, France
| | - F Bellenfant
- Centre d'Expertise Mort Subite de Paris (Paris-CEMS), Inserm U970, 56, rue Leblanc, 75015 Paris, France; Unité de soins intensifs, Hôpital européen Georges-Pompidou, 20, rue Leblanc, 75015 Paris, France
| | - D Jost
- Centre d'Expertise Mort Subite de Paris (Paris-CEMS), Inserm U970, 56, rue Leblanc, 75015 Paris, France; Brigade de Sapeurs-Pompiers de Paris (BSPP), 1, place Jules-Renard, 75017 Paris, France
| | - P Jabre
- Centre d'Expertise Mort Subite de Paris (Paris-CEMS), Inserm U970, 56, rue Leblanc, 75015 Paris, France; Service d'aide médicale d'urgence (Samu) de Paris, Paris, France
| | - G Soulat
- Université de Paris, 85, boulevard Saint Germain, 75006 Paris, France; Service de radiologie, Hôpital européen Georges-Pompidou, 20, rue Leblanc, 75015 Paris, France
| | - P Bruneval
- Université de Paris, 85, boulevard Saint Germain, 75006 Paris, France; Service anatomie pathologie, Hôpital européen Georges-Pompidou, 20, rue Leblanc, 75015 Paris, France
| | - O Weizman
- Centre hospitalier régional universitaire de Nancy, 54511 Vandœuvre-Lès-Nancy, France
| | - E Varlet
- Centre d'Expertise Mort Subite de Paris (Paris-CEMS), Inserm U970, 56, rue Leblanc, 75015 Paris, France; Service de cardiologie, Unité de rythmologie, Hôpital européen Georges-Pompidou, 20, rue Leblanc, 75015 Paris, France
| | - P Baudinaud
- Centre d'Expertise Mort Subite de Paris (Paris-CEMS), Inserm U970, 56, rue Leblanc, 75015 Paris, France; Université de Paris, 85, boulevard Saint Germain, 75006 Paris, France; Service de cardiologie, Unité de rythmologie, Hôpital européen Georges-Pompidou, 20, rue Leblanc, 75015 Paris, France
| | - F Dumas
- Centre d'Expertise Mort Subite de Paris (Paris-CEMS), Inserm U970, 56, rue Leblanc, 75015 Paris, France; Université de Paris, 85, boulevard Saint Germain, 75006 Paris, France; Département de médecine d'urgence, Hôpital Cochin, 27, rue du Faubourg-Saint-Jacques, 75014 Paris, France
| | - W Bougouin
- Centre d'Expertise Mort Subite de Paris (Paris-CEMS), Inserm U970, 56, rue Leblanc, 75015 Paris, France; Université de Paris, 85, boulevard Saint Germain, 75006 Paris, France; Unité de soins intensifs, Hôpital privé Jacques-Cartier, Ramsay Santé, 6, avenue du Noyer-Lambert, 91300 Massy, France
| | - A Cariou
- Centre d'Expertise Mort Subite de Paris (Paris-CEMS), Inserm U970, 56, rue Leblanc, 75015 Paris, France; Université de Paris, 85, boulevard Saint Germain, 75006 Paris, France; Unité de soins intensifs, Hôpital Cochin, 27, rue du Faubourg-Saint-Jacques, 75014 Paris, France
| | - T Lavergne
- Centre d'Expertise Mort Subite de Paris (Paris-CEMS), Inserm U970, 56, rue Leblanc, 75015 Paris, France; Université de Paris, 85, boulevard Saint Germain, 75006 Paris, France; Service de cardiologie, Unité de rythmologie, Hôpital européen Georges-Pompidou, 20, rue Leblanc, 75015 Paris, France
| | - K Wahbi
- Centre d'Expertise Mort Subite de Paris (Paris-CEMS), Inserm U970, 56, rue Leblanc, 75015 Paris, France; Université de Paris, 85, boulevard Saint Germain, 75006 Paris, France; Service de cardiologie, hôpital Cochin, 27, rue du Faubourg-Saint-Jacques, 75014 Paris, France
| | - X Jouven
- Centre d'Expertise Mort Subite de Paris (Paris-CEMS), Inserm U970, 56, rue Leblanc, 75015 Paris, France; Université de Paris, 85, boulevard Saint Germain, 75006 Paris, France; Service de cardiologie, Unité de rythmologie, Hôpital européen Georges-Pompidou, 20, rue Leblanc, 75015 Paris, France
| | - E Marijon
- Centre d'Expertise Mort Subite de Paris (Paris-CEMS), Inserm U970, 56, rue Leblanc, 75015 Paris, France; Université de Paris, 85, boulevard Saint Germain, 75006 Paris, France; Service de cardiologie, Unité de rythmologie, Hôpital européen Georges-Pompidou, 20, rue Leblanc, 75015 Paris, France.
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Li HY, You ZH, Wang L, Yan X, Li ZW. DF-MDA: An effective diffusion-based computational model for predicting miRNA-disease association. Mol Ther 2021; 29:1501-1511. [PMID: 33429082 DOI: 10.1016/j.ymthe.2021.01.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 12/21/2020] [Accepted: 01/01/2021] [Indexed: 12/28/2022] Open
Abstract
It is reported that microRNAs (miRNAs) play an important role in various human diseases. However, the mechanisms of miRNA in these diseases have not been fully understood. Therefore, detecting potential miRNA-disease associations has far-reaching significance for pathological development and the diagnosis and treatment of complex diseases. In this study, we propose a novel diffusion-based computational method, DF-MDA, for predicting miRNA-disease association based on the assumption that molecules are related to each other in human physiological processes. Specifically, we first construct a heterogeneous network by integrating various known associations among miRNAs, diseases, proteins, long non-coding RNAs (lncRNAs), and drugs. Then, more representative features are extracted through a diffusion-based machine-learning method. Finally, the Random Forest classifier is adopted to classify miRNA-disease associations. In the 5-fold cross-validation experiment, the proposed model obtained the average area under the curve (AUC) of 0.9321 on the HMDD v3.0 dataset. To further verify the prediction performance of the proposed model, DF-MDA was applied in three significant human diseases, including lymphoma, lung neoplasms, and colon neoplasms. As a result, 47, 46, and 47 out of top 50 predictions were validated by independent databases. These experimental results demonstrated that DF-MDA is a reliable and efficient method for predicting potential miRNA-disease associations.
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Affiliation(s)
- Hao-Yuan Li
- School of Computer Science and Technology, China University of Mining and Technology, Xuzhou 221116, China
| | - Zhu-Hong You
- Xinjiang Technical Institutes of Physics and Chemistry, Chinese Academy of Sciences, Urumqi 830011, China.
| | - Lei Wang
- Xinjiang Technical Institutes of Physics and Chemistry, Chinese Academy of Sciences, Urumqi 830011, China; College of Information Science and Engineering, Zaozhuang University, Zaozhuang 277100, China.
| | - Xin Yan
- School of Computer Science and Technology, China University of Mining and Technology, Xuzhou 221116, China; School of Foreign Languages, Zaozhuang University, Zaozhuang, Shandong 277100, China.
| | - Zheng-Wei Li
- School of Computer Science and Technology, China University of Mining and Technology, Xuzhou 221116, China
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Lin CH, Chou IC, Hong SY. Genetic factors and the risk of drug-resistant epilepsy in young children with epilepsy and neurodevelopment disability: A prospective study and updated meta-analysis. Medicine (Baltimore) 2021; 100:e25277. [PMID: 33761731 PMCID: PMC8049163 DOI: 10.1097/md.0000000000025277] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 03/03/2021] [Indexed: 11/26/2022] Open
Abstract
Drug-resistant epilepsy (DRE) affects 7% to 20% of children with epilepsy. Although some risk factors for DRE have been identified, the results have not been consistent. Moreover, data regarding the risk factors for epilepsy and its seizure outcome in the first 2 years of life are limited.We analyzed data for children aged 0 to 2 years with epilepsy and neurodevelopmental disability from January, 2013, through December, 2017. These patients were followed up to compare the risk of DRE in patients with genetic defect (genetic group) with that without genetic defect (nongenetic group). Additionally, we conducted a meta-analysis to identify the pooled prevalence of genetic factors in children with DRE.A total of 96 patients were enrolled. A total of 68 patients were enrolled in the nongenetic group, whereas 28 patients were enrolled in the genetic group. The overall DRE risk in the genetic group was 6.5 times (95% confidence interval [CI], 2.15-19.6; p = 0.03) higher than that in the nongenetic group. Separately, a total of 1308 DRE patients were participated in the meta-analysis. The pooled prevalence of these patients with genetic factors was 22.8% (95% CI 17.4-29.3).The genetic defect plays a crucial role in the development of DRE in younger children with epilepsy and neurodevelopmental disability. The results can serve as a reference for further studies of epilepsy panel design and may also assist in the development of improved treatments and prevention strategies for DRE.
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Affiliation(s)
- Chien-Heng Lin
- Division of Pediatrics Pulmonology, China Medical University, Children's Hospital, Taichung, Taiwan
- Department of Biomedical Imaging and Radiological Science, College of Medicine, China Medical University
| | - I-Ching Chou
- Division of Pediatrics Neurology, China Medical University, Children's Hospital
- Graduate Institute of Integrated Medicine, College of Chinese Medicine, China Medical University, Taichung, Taiwan
| | - Syuan-Yu Hong
- Division of Pediatrics Neurology, China Medical University, Children's Hospital
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Abstract
An increasing number of countries are investing efforts to exploit the human genome, in order to improve genetic diagnostics and to pave the way for the integration of precision medicine into health systems. The expected benefits include improved understanding of normal and pathological genomic variation, shorter time-to-diagnosis, cost-effective diagnostics, targeted prevention and treatment, and research advances.We review the 41 currently active individual national projects concerning their aims and scope, the number and age structure of included subjects, funding, data sharing goals and methods, and linkage with biobanks, medical data, and non-medical data (exposome). The main aims of ongoing projects were to determine normal genomic variation (90%), determine pathological genomic variation (rare disease, complex diseases, cancer, etc.) (71%), improve infrastructure (59%), and enable personalized medicine (37%). Numbers of subjects to be sequenced ranges substantially, from a hundred to over a million, representing in some cases a significant portion of the population. Approximately half of the projects report public funding, with the rest having various mixed or private funding arrangements. 90% of projects report data sharing (public, academic, and/or commercial with various levels of access) and plan on linking genomic data and medical data (78%), existing biobanks (44%), and/or non-medical data (24%) as the basis for enabling personal/precision medicine in the future.Our results show substantial diversity in the analysed categories of 41 ongoing national projects. The overview of current designs will hopefully inform national initiatives in designing new genomic projects and contribute to standardisation and international collaboration.
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Affiliation(s)
- Anja Kovanda
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Slajmerjeva 4, Ljubljana, Slovenia
| | - Ana Nyasha Zimani
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Slajmerjeva 4, Ljubljana, Slovenia
| | - Borut Peterlin
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Slajmerjeva 4, Ljubljana, Slovenia.
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Abstract
There have been two major eras in the history of gene discovery. The first was the era of linkage analysis, with approximately 1,300 disease-related genes identified by positional cloning by the turn of the millennium. The second era has been powered by two major breakthroughs: the publication of the human genome and the development of massively parallel sequencing (MPS). MPS has greatly accelerated disease gene identification, such that disease genes that would have taken years to map previously can now be determined in a matter of weeks. Additionally, the number of affected families needed to map a causative gene and the size of such families have fallen: de novo mutations, previously intractable by linkage analysis, can be identified through sequencing of the parent-child trio, and genes for recessive disease can be identified through MPS even of a single affected individual. MPS technologies include whole exome sequencing (WES), whole genome sequencing (WGS), and panel sequencing, each with their strengths. While WES has been responsible for most gene discoveries through MPS, WGS is superior in detecting copy number variants, chromosomal rearrangements, and repeat-rich regions. Panels are commonly used for diagnostic purposes as they are extremely cost-effective and generate manageable quantities of data, with no risk of unexpected findings. However, in instances of diagnostic uncertainty, it can be challenging to choose the right panel, and in these circumstances WES has a higher diagnostic yield. MPS has ethical, social, and legal implications, many of which are common to genetic testing generally but amplified due to the magnitude of data (e.g., relationship misattribution, identification of variants of uncertain significance, and genetic discrimination); others are unique to WES and WGS technologies (e.g., incidental or secondary findings). Nonetheless, MPS is rapidly translating into clinical practice as an extremely useful part of the clinical armamentarium.
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Affiliation(s)
- Aideen M. McInerney-Leo
- Dermatology Research Centre, University of Queensland Diamantina Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Emma L. Duncan
- Department of Twin Research & Genetic Epidemiology, Faculty of Life Sciences and Medicine, School of Life Course Sciences, King’s College London, London, United Kingdom
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43
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Albertini DF. How genetics human ART style is making dreams come true: the stairway to eugenics. J Assist Reprod Genet 2021; 38:261-263. [PMID: 33564934 DOI: 10.1007/s10815-021-02096-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 01/28/2021] [Indexed: 11/26/2022] Open
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Shapiro AJ, Kroener L, Quinn MM. Expanded carrier screening for recessively inherited disorders: economic burden and factors in decision-making when one individual in a couple is identified as a carrier. J Assist Reprod Genet 2021; 38:957-963. [PMID: 33501564 DOI: 10.1007/s10815-021-02084-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 01/20/2021] [Indexed: 11/27/2022] Open
Abstract
PURPOSE When undergoing expanded carrier screening (ECS), couples are often screened sequentially to reduce need for a second individual's test. It is unknown how often partners of individuals found to be carriers complete the recommended testing with a sequential approach and what factors contribute to decision-making regarding partner testing. Additionally, the economic burden placed on individuals by ECS testing and its effect on partner testing has not been evaluated. METHODS In part 1, all individuals at a university-affiliated reproductive endocrinology and infertility practice identified to be carriers of a recessively inherited mutation using the Counsyl/Foresight ECS were included. Conditions were categorized by severity according to a previously described classification system. In part 2, all individuals who underwent ECS with a single test provider between September 1, 2013 and February 1, 2020 were contacted via email to complete a confidential and anonymized online survey. RESULTS In part 1, a total of 2061 patients were screened. 36.9% were carriers of one or more recessively inherited disorders. Twenty-seven percent of positively screened individuals did not have their partner screened. Carriers of a moderate condition had a trend towards a reduced odds for having their partner screened compared to a profound condition (OR 0.36, 95% CI 0.12-1.05, p = 0.06). Number of conditions was not predictive of subsequent partner screening (OR 0.95, 95% CI 0.72-1.25, p = 0.72). In part 2, the cost of ECS was not covered by insurance for 54.5% (103/189) and most paid over $300 out-of-pocket for testing (47.6%). The most common reason for not completing partner testing was that the results would not alter their course when seeking conception (33.3%). 73.5% of patients knew that the largest benefit of ECS comes from knowing a partner's results as well as their own. CONCLUSIONS Not all carriers of recessively inherited disorders choose to undergo partner screening. Patients found to be carrier of more debilitating genetic disorders may be more likely to screen their reproductive partners. For many, ECS testing is not covered by insurance, and this test may impose a significant economic burden. For some patients, the results of ECS would not change what they would do when seeking conception. Providers should evaluate whether a patient's ECS result would change their treatment course prior to testing.
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Affiliation(s)
- Alice J Shapiro
- Department of Obstetrics and Gynecology, University of California, Los Angeles, Los Angeles, CA, USA.
| | - Lindsay Kroener
- Department of Obstetrics and Gynecology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Molly M Quinn
- Department of Obstetrics and Gynecology, University of California, Los Angeles, Los Angeles, CA, USA
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Lee JY, Kwon JY, Na S, Choe SA, Seol HJ, Kim M, Kim MA, Park CW, Kim K, Ryu HM, Hwang HS, Shim JY. Clinical Practice Guidelines for Prenatal Aneuploidy Screening and Diagnostic Testing from Korean Society of Maternal-Fetal Medicine: (2) Invasive Diagnostic Testing for Fetal Chromosomal Abnormalities. J Korean Med Sci 2021; 36:e26. [PMID: 33496085 PMCID: PMC7834898 DOI: 10.3346/jkms.2021.36.e26] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 11/06/2020] [Indexed: 11/20/2022] Open
Abstract
The Korean Society of Maternal Fetal Medicine proposed the first Korean guideline on prenatal aneuploidy screening and diagnostic testing, in April 2019. The clinical practice guideline (CPG) was developed for Korean women using an adaptation process based on good-quality practice guidelines, previously developed in other countries, on prenatal screening and invasive diagnostic testing for fetal chromosome abnormalities. We reviewed current guidelines and developed a Korean CPG on invasive diagnostic testing for fetal chromosome abnormalities according to the adaptation process. Recommendations for selected 11 key questions are: 1) Considering the increased risk of fetal loss in invasive prenatal diagnostic testing for fetal genetic disorders, it is not recommended for all pregnant women aged over 35 years. 2) Because early amniocentesis performed before 14 weeks of pregnancy increases the risk of fetal loss and malformation, chorionic villus sampling (CVS) is recommended for pregnant women who will undergo invasive prenatal diagnostic testing for fetal genetic disorders in the first trimester of pregnancy. However, CVS before 9 weeks of pregnancy also increases the risk of fetal loss and deformity. Thus, CVS is recommended after 9 weeks of pregnancy. 3) Amniocentesis is recommended to distinguish true fetal mosaicism from confined placental mosaicism. 4) Anti-immunoglobulin should be administered within 72 hours after the invasive diagnostic testing. 5) Since there is a high risk of vertical transmission, an invasive prenatal diagnostic testing is recommended according to the clinician's discretion with consideration of the condition of the pregnant woman. 6) The use of antibiotics is not recommended before or after an invasive diagnostic testing. 7) The chromosomal microarray test as an alternative to the conventional cytogenetic test is not recommended for all pregnant women who will undergo an invasive diagnostic testing. 8) Amniocentesis before 14 weeks of gestation is not recommended because it increases the risk of fetal loss and malformation. 9) CVS before 9 weeks of gestation is not recommended because it increases the risk of fetal loss and malformation. 10) Although the risk of fetal loss associated with invasive prenatal diagnostic testing (amniocentesis and CVS) may vary based on the proficiency of the operator, the risk of fetal loss due to invasive prenatal diagnostic testing is higher in twin pregnancies than in singleton pregnancies. 11) When a monochorionic twin is identified in early pregnancy and the growth and structure of both fetuses are consistent, an invasive prenatal diagnostic testing can be performed on one fetus alone. However, an invasive prenatal diagnostic testing is recommended for each fetus in cases of pregnancy conceived via in vitro fertilization, or in cases in which the growth of both fetuses differs, or in those in which at least one fetus has a structural abnormality. The guidelines were established and approved by the Korean Academy of Medical Sciences. This guideline is revised and presented every 5 years.
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Affiliation(s)
- Ji Yeon Lee
- Department of Obstetrics and Gynecology, CHA Bundang Medical Center, CHA University School of Medicine, Seongnam, Korea
| | - Ji Young Kwon
- Department of Obstetrics and Gynecology, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Sunghun Na
- Department of Obstetrics and Gynecology, Kangwon National University Hospital, Kangwon National University School of Medicine, Chuncheon, Korea
| | - Seung Ah Choe
- Department of Preventive Medicine, Korea University College of Medicine, Seoul, Korea
| | - Hyun Joo Seol
- Department of Obstetrics and Gynecology, Kyung Hee University Hospital at Gangdong, College of Medicine, Kyung Hee University, Seoul, Korea
| | - Minhyoung Kim
- Department of Obstetrics and Gynecology, MizMedi Hospital, Seoul, Korea
| | - Min A Kim
- Department of Obstetrics and Gynecology, Gangnam Severance Hospital, Institute of Women's Life Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - Chan Wook Park
- Department of Obstetrics and Gynecology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | | | - Hyun Mee Ryu
- Department of Obstetrics and Gynecology, CHA Bundang Medical Center, CHA University School of Medicine, Seongnam, Korea
| | - Han Sung Hwang
- Department of Obstetrics and Gynecology, Research Institute of Medical Science, Konkuk University Medical Center, Konkuk University School of Medicine, Seoul, Korea.
| | - Jae Yoon Shim
- Mirae & Heemang Obstetrics and Gynecology Clinic, Seoul, Korea.
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46
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Affiliation(s)
- Francis S Collins
- From the National Institutes of Health, Bethesda, MD (F.S.C., C.N.R.); the Department of Molecular and Cell Biology and the Department of Chemistry, University of California, Berkeley, Berkeley (J.A.D.); and the Broad Institute of the Massachusetts Institute of Technology and Harvard, Cambridge, MA (E.S.L.)
| | - Jennifer A Doudna
- From the National Institutes of Health, Bethesda, MD (F.S.C., C.N.R.); the Department of Molecular and Cell Biology and the Department of Chemistry, University of California, Berkeley, Berkeley (J.A.D.); and the Broad Institute of the Massachusetts Institute of Technology and Harvard, Cambridge, MA (E.S.L.)
| | - Eric S Lander
- From the National Institutes of Health, Bethesda, MD (F.S.C., C.N.R.); the Department of Molecular and Cell Biology and the Department of Chemistry, University of California, Berkeley, Berkeley (J.A.D.); and the Broad Institute of the Massachusetts Institute of Technology and Harvard, Cambridge, MA (E.S.L.)
| | - Charles N Rotimi
- From the National Institutes of Health, Bethesda, MD (F.S.C., C.N.R.); the Department of Molecular and Cell Biology and the Department of Chemistry, University of California, Berkeley, Berkeley (J.A.D.); and the Broad Institute of the Massachusetts Institute of Technology and Harvard, Cambridge, MA (E.S.L.)
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47
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Fujita Y, Bando H, Iguchi G, Iida K, Nishizawa H, Kanie K, Yoshida K, Matsumoto R, Suda K, Fukuoka H, Ogawa W, Takahashi Y. Clinical Heterogeneity of Acquired Idiopathic Isolated Adrenocorticotropic Hormone Deficiency. Front Endocrinol (Lausanne) 2021; 12:578802. [PMID: 33679614 PMCID: PMC7933588 DOI: 10.3389/fendo.2021.578802] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 01/04/2021] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVE Heterogeneous clinical characteristics are observed in acquired isolated adrenocorticotropic hormone (ACTH) deficiency (IAD); however, its classification remains to be established because of its largely unknown pathophysiology. In IAD, anti-pituitary antibodies have been detected in some patients, although their significance remains unclear. Therefore, this study aimed to classify patients with IAD and to clarify the significance of anti-pituitary antibodies. DESIGN AND METHODS We analyzed 46 consecutive patients with IAD. Serum anti-pituitary antibodies were analyzed via immunofluorescence staining using a mouse pituitary tissue. Principal component and cluster analyses were performed to classify IAD patients based on clinical characteristics and autoantibodies. RESULTS Immunofluorescence analysis using the sera revealed that 58% of patients showed anti-corticotroph antibodies and 6% of patients showed anti-follicular stellate cell (FSC) antibodies. Principal component analysis demonstrated that three parameters could explain 70% of the patients. Hierarchical cluster analysis showed three clusters: Groups A and B comprised patients who were positive for anti-corticotroph antibodies, and plasma ACTH levels were extremely low. Groups A and B comprised middle-aged or elderly men and middle-aged women, respectively. Group C comprised patients who were positive for the anti-FSC antibody and elderly men; plasma ACTH levels were relatively high. CONCLUSIONS Patients with IAD were classified into three groups based on clinical characteristics and autoantibodies. The presence of anti-corticotroph antibody suggested severe injury to corticotrophs. This new classification clearly demonstrated the heterogeneity in the pathogenesis of IAD.
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Affiliation(s)
- Yasunori Fujita
- Division of Diabetes and Endocrinology, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Hironori Bando
- Division of Diabetes and Endocrinology, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Genzo Iguchi
- Division of Diabetes and Endocrinology, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe, Japan
- Medical Center for Student Health, Kobe University, Kobe, Japan
- Division of Biosignal Pathophysiology, Kobe University, Kobe, Japan
| | - Keiji Iida
- Division of Diabetes and Endocrinology, Hyogo Prefectural Kakogawa Medical Center, Kakogawa, Japan
| | - Hitoshi Nishizawa
- Division of Diabetes and Endocrinology, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Keitaro Kanie
- Division of Diabetes and Endocrinology, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Kenichi Yoshida
- Division of Diabetes and Endocrinology, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Ryusaku Matsumoto
- Division of Diabetes and Endocrinology, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Kentaro Suda
- Division of Diabetes and Endocrinology, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Hidenori Fukuoka
- Division of Diabetes and Endocrinology, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Wataru Ogawa
- Division of Diabetes and Endocrinology, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Yutaka Takahashi
- Division of Diabetes and Endocrinology, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe, Japan
- Department of Diabetes and Endocrinology, Nara Medical University, Kashihara, Japan
- *Correspondence: Yutaka Takahashi,
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Haghshenas S, Bhai P, Aref-Eshghi E, Sadikovic B. Diagnostic Utility of Genome-Wide DNA Methylation Analysis in Mendelian Neurodevelopmental Disorders. Int J Mol Sci 2020; 21:ijms21239303. [PMID: 33291301 PMCID: PMC7730976 DOI: 10.3390/ijms21239303] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 12/03/2020] [Accepted: 12/04/2020] [Indexed: 12/14/2022] Open
Abstract
Mendelian neurodevelopmental disorders customarily present with complex and overlapping symptoms, complicating the clinical diagnosis. Individuals with a growing number of the so-called rare disorders exhibit unique, disorder-specific DNA methylation patterns, consequent to the underlying gene defects. Besides providing insights to the pathophysiology and molecular biology of these disorders, we can use these epigenetic patterns as functional biomarkers for the screening and diagnosis of these conditions. This review summarizes our current understanding of DNA methylation episignatures in rare disorders and describes the underlying technology and analytical approaches. We discuss the computational parameters, including statistical and machine learning methods, used for the screening and classification of genetic variants of uncertain clinical significance. Describing the rationale and principles applied to the specific computational models that are used to develop and adapt the DNA methylation episignatures for the diagnosis of rare disorders, we highlight the opportunities and challenges in this emerging branch of diagnostic medicine.
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Affiliation(s)
- Sadegheh Haghshenas
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada;
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON N6A 5W9, Canada;
| | - Pratibha Bhai
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON N6A 5W9, Canada;
| | - Erfan Aref-Eshghi
- Division of Genomic Diagnostics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA;
| | - Bekim Sadikovic
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada;
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON N6A 5W9, Canada;
- Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5C1, Canada
- Correspondence:
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Abraham RS. How to evaluate for immunodeficiency in patients with autoimmune cytopenias: laboratory evaluation for the diagnosis of inborn errors of immunity associated with immune dysregulation. Hematology Am Soc Hematol Educ Program 2020; 2020:661-672. [PMID: 33275711 PMCID: PMC7727558 DOI: 10.1182/hematology.2020000173] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The identification of genetic disorders associated with dysregulated immunity has upended the notion that germline pathogenic variants in immune genes universally result in susceptibility to infection. Immune dysregulation (autoimmunity, autoinflammation, lymphoproliferation, and malignancy) and immunodeficiency (susceptibility to infection) represent 2 sides of the same coin and are not mutually exclusive. Also, although autoimmunity implies dysregulation within the adaptive immune system and autoinflammation indicates disordered innate immunity, these lines may be blurred, depending on the genetic defect and diversity in clinical and immunological phenotypes. Patients with immune dysregulatory disorders may present to a variety of clinical specialties, depending on the dominant clinical features. Therefore, awareness of these disorders, which may manifest at any age, is essential to avoid a protracted diagnostic evaluation and associated complications. Availability of and access to expanded immunological testing has altered the diagnostic landscape for immunological diseases. Nonetheless, there are constraints in using these resources due to a lack of awareness, challenges in systematic and logical evaluation, interpretation of results, and using results to justify additional advanced testing, when needed. The ability to molecularly characterize immune defects and develop "bespoke" therapy and management mandates a new paradigm for diagnostic evaluation of these patients. The immunological tests run the gamut from triage to confirmation and can be used for both diagnosis and refinement of treatment or management strategies. However, the complexity of testing and interpretation of results often necessitates dialogue between laboratory immunologists and specialty physicians to ensure timely and appropriate use of testing and delivery of care.
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Affiliation(s)
- Roshini S Abraham
- Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Columbus, OH
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Lambert MP. Improving interpretation of genetic testing for hereditary hemorrhagic, thrombotic, and platelet disorders. Hematology Am Soc Hematol Educ Program 2020; 2020:76-81. [PMID: 33275718 PMCID: PMC7727548 DOI: 10.1182/hematology.2020000091] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The last 10 years have seen an explosion in the amount of data available through next-generation sequencing. These data are advancing quickly, and this pace makes it difficult for most practitioners to easily keep up with all of the new information. Complicating this understanding is sometimes conflicting information about variant pathogenicity or even about the role of some genes in the pathogenesis of disease. The more widespread clinical use of sequencing has expanded phenotypes, including the identification of mild phenotypes associated with previously serious disease, such as with some variants in RUNX1, MYH9, ITG2A, and others. Several organizations have taken up the task of cataloging and systematically evaluating genes and variants using a standardized approach and making the data publicly available so that others can benefit from their gene/variant curation. The efforts in testing for hereditary hemorrhagic, thrombotic, and platelet disorders have been led by the International Society on Thrombosis and Haemostasis Scientific Standardization Committee on Genomics in Thrombosis and Hemostasis, the American Society of Hematology, and the National Institutes of Health National Human Genome Research Institute Clinical Genome Resource. This article outlines current efforts to improve the interpretation of genetic testing and the role of standardizing and disseminating information. By assessing the strength of gene-disease associations, standardizing variant curation guidelines, sharing genomic data among expert members, and incorporating data from existing disease databases, the number of variants of uncertain significance will decrease, thereby improving the value of genetic testing as a diagnostic tool.
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Affiliation(s)
- Michele P Lambert
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA; and Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
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