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Wang R, Ma XH, Qin ZZ, Hu XX, Mo ZY, Zhao YY, Zheng P, Lu QS, Li Q, Tang XY. Global, regional, and national burden of thalassemia during 1990-2019: A systematic analysis of the Global Burden of Disease Study 2019. Pediatr Blood Cancer 2024; 71:e31177. [PMID: 38967594 DOI: 10.1002/pbc.31177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 06/10/2024] [Accepted: 06/19/2024] [Indexed: 07/06/2024]
Abstract
INTRODUCTION Thalassemia represents a significant public health challenge globally. However, the global burden of thalassemia and the disparities associated with it remain poorly understood. Our study aims to uncover the long-term spatial and temporal trends in thalassemia at global, regional, and national levels, analyze the impacts of age, time periods, and birth cohorts, and pinpoint the global disparities in thalassemia burden. METHODS We extracted data on the thalassemia burden from the Global Burden of Disease Study (GBD) 2019. We employed a joinpoint regression model to assess temporal trends in thalassemia burden and an age-period-cohort model to evaluate the effects of age, period, and cohort on thalassemia mortality. RESULTS From 1990 to 2019, the number of thalassemia incident cases, prevalent cases, mortality cases, and disability-adjusted life years (DALYs) decreased by 20.9%, 3.1%, 38.6%, and 43.1%, respectively. Age-standardized rates of incidence, prevalence, mortality, and DALY declined across regions with high, high-middle, middle, and low-middle sociodemographic index (SDI), yet remained the highest in regions with low SDI and low-middle SDI as well as in Southeast Asia, peaking among children under five years of age. The global prevalence rate was higher in males than in females. The global mortality rate showed a consistent decrease with increasing age. CONCLUSION The global burden of thalassemia has significantly declined, yet notable disparities exist in terms of gender, age groups, periods, birth cohorts, SDI regions, and GBD regions. Systemic interventions that include early screening, genetic counseling, premarital health examinations, and prenatal diagnosis should be prioritized in regions with low, and low-middle SDI, particularly in Southeast Asia. Future population-based studies should focus specifically on thalassemia subtypes and transfusion requirements, and national registries should enhance data capture through newborn screening.
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Affiliation(s)
- Rui Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Guangxi Medical University, Nanning, People's Republic of China
| | - Xiao-Hong Ma
- Department of Epidemiology and Biostatistics, School of Public Health, Guangxi Medical University, Nanning, People's Republic of China
| | - Ze-Zhen Qin
- Department of Epidemiology and Biostatistics, School of Public Health, Guangxi Medical University, Nanning, People's Republic of China
| | - Xin-Xuan Hu
- Department of Epidemiology and Biostatistics, School of Public Health, Guangxi Medical University, Nanning, People's Republic of China
| | - Zhi-Yang Mo
- Department of Epidemiology and Biostatistics, School of Public Health, Guangxi Medical University, Nanning, People's Republic of China
| | - Ya-Ye Zhao
- Department of Epidemiology and Biostatistics, School of Public Health, Guangxi Medical University, Nanning, People's Republic of China
| | - Ping Zheng
- Department of Epidemiology and Biostatistics, School of Public Health, Guangxi Medical University, Nanning, People's Republic of China
| | - Qiao-Shan Lu
- Department of Epidemiology and Biostatistics, School of Public Health, Guangxi Medical University, Nanning, People's Republic of China
| | - Qiao Li
- Department of Epidemiology and Biostatistics, School of Public Health, Guangxi Medical University, Nanning, People's Republic of China
| | - Xian-Yan Tang
- Department of Epidemiology and Biostatistics, School of Public Health, Guangxi Medical University, Nanning, People's Republic of China
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Dholariya S, Parchwani DN, Sonagra A, Singh R, Motiani A, Kaliya M, Anandani G. Detection of HbD Punjab Trait in Saurashtra Region of Gujarat by HPLC Method. Indian J Clin Biochem 2024; 39:438-441. [PMID: 39005868 PMCID: PMC11239634 DOI: 10.1007/s12291-023-01160-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 10/14/2023] [Indexed: 07/16/2024]
Abstract
The HbD Punjab trait is a less common hemoglobin variant in the Saurashtra region of Gujarat. This patient presented to the General Medicine and Biochemistry Department at All India Institute of Medical Sciences, Rajkot, Hospital, for the HbA1c analysis by high-performance liquid chromatography (HPLC). The patient was 52 years old, a known case of type 2 diabetes mellitus and hypertension, and presented with complaints of generalized malaise and fatigability for the previous ten to twelve months. On physical examination, there was no evidence of pallor, lymphadenopathy, splenomegaly, or hepatomegaly. Peripheral blood smear revealed normocytic normochromic RBC, and platelets were adequate and normal in morphology. The HPLC analysis revealed heterozygous for hemoglobin D (HbD Punjab trait), and false high HbA1c corresponds to fasting plasma glucose (FPG) levels due to abnormal separation. However, genetic counseling is highly recommended to detect any potential reproductive risk factors.
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Affiliation(s)
- Sagar Dholariya
- All India Institute of Medical Sciences, Rajkot, Gujarat India
| | | | - Amit Sonagra
- All India Institute of Medical Sciences, Rajkot, Gujarat India
| | - Ragini Singh
- All India Institute of Medical Sciences, Rajkot, Gujarat India
| | - Anita Motiani
- All India Institute of Medical Sciences, Rajkot, Gujarat India
| | - Mehul Kaliya
- All India Institute of Medical Sciences, Rajkot, Gujarat India
| | - Garima Anandani
- All India Institute of Medical Sciences, Rajkot, Gujarat India
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Ciancia S, Madeo SF, Calabrese O, Iughetti L. The Approach to a Child with Dysmorphic Features: What the Pediatrician Should Know. CHILDREN (BASEL, SWITZERLAND) 2024; 11:578. [PMID: 38790573 PMCID: PMC11120268 DOI: 10.3390/children11050578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 05/01/2024] [Accepted: 05/06/2024] [Indexed: 05/26/2024]
Abstract
The advancement of genetic knowledge and the discovery of an increasing number of genetic disorders has made the role of the geneticist progressively more complex and fundamental. However, most genetic disorders present during childhood; thus, their early recognition is a challenge for the pediatrician, who will be also involved in the follow-up of these children, often establishing a close relationship with them and their families and becoming a referral figure. In this review, we aim to provide the pediatrician with a general knowledge of the approach to treating a child with a genetic syndrome associated with dysmorphic features. We will discuss the red flags, the most common manifestations, the analytic collection of the family and personal medical history, and the signs that should alert the pediatrician during the physical examination. We will offer an overview of the physical malformations most commonly associated with genetic defects and the way to describe dysmorphic facial features. We will provide hints about some tools that can support the pediatrician in clinical practice and that also represent a useful educational resource, either online or through apps downloaded on a smartphone. Eventually, we will offer an overview of genetic testing, the ethical considerations, the consequences of incidental findings, and the main indications and limitations of the principal technologies.
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Affiliation(s)
- Silvia Ciancia
- Pediatric Unit, Department of Medical and Surgical Sciences for Mothers, Children and Adults, University of Modena and Reggio Emilia, Largo del Pozzo 71, 41124 Modena, Italy
| | - Simona Filomena Madeo
- Pediatric Unit, Department of Medical and Surgical Sciences for Mothers, Children and Adults, University of Modena and Reggio Emilia, Largo del Pozzo 71, 41124 Modena, Italy
| | - Olga Calabrese
- Medical Genetics Unit, Department of Medical and Surgical Sciences for Mothers, Children and Adults, University of Modena and Reggio Emilia, 41124 Modena, Italy
| | - Lorenzo Iughetti
- Pediatric Unit, Department of Medical and Surgical Sciences for Mothers, Children and Adults, University of Modena and Reggio Emilia, Largo del Pozzo 71, 41124 Modena, Italy
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Johnson D, Del Fiol G, Kawamoto K, Romagnoli KM, Sanders N, Isaacson G, Jenkins E, Williams MS. Genetically guided precision medicine clinical decision support tools: a systematic review. J Am Med Inform Assoc 2024; 31:1183-1194. [PMID: 38558013 PMCID: PMC11031215 DOI: 10.1093/jamia/ocae033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 02/06/2024] [Accepted: 02/26/2024] [Indexed: 04/04/2024] Open
Abstract
OBJECTIVES Patient care using genetics presents complex challenges. Clinical decision support (CDS) tools are a potential solution because they provide patient-specific risk assessments and/or recommendations at the point of care. This systematic review evaluated the literature on CDS systems which have been implemented to support genetically guided precision medicine (GPM). MATERIALS AND METHODS A comprehensive search was conducted in MEDLINE and Embase, encompassing January 1, 2011-March 14, 2023. The review included primary English peer-reviewed research articles studying humans, focused on the use of computers to guide clinical decision-making and delivering genetically guided, patient-specific assessments, and/or recommendations to healthcare providers and/or patients. RESULTS The search yielded 3832 unique articles. After screening, 41 articles were identified that met the inclusion criteria. Alerts and reminders were the most common form of CDS used. About 27 systems were integrated with the electronic health record; 2 of those used standards-based approaches for genomic data transfer. Three studies used a framework to analyze the implementation strategy. DISCUSSION Findings include limited use of standards-based approaches for genomic data transfer, system evaluations that do not employ formal frameworks, and inconsistencies in the methodologies used to assess genetic CDS systems and their impact on patient outcomes. CONCLUSION We recommend that future research on CDS system implementation for genetically GPM should focus on implementing more CDS systems, utilization of standards-based approaches, user-centered design, exploration of alternative forms of CDS interventions, and use of formal frameworks to systematically evaluate genetic CDS systems and their effects on patient care.
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Affiliation(s)
- Darren Johnson
- Department of Genomic Health, Geisinger Health Systems, Danville, PA 17822, United States
| | - Guilherme Del Fiol
- Department of Biomedical Informatics, University of Utah, Salt Lake City, UT 84108, United States
| | - Kensaku Kawamoto
- Department of Biomedical Informatics, University of Utah, Salt Lake City, UT 84108, United States
| | - Katrina M Romagnoli
- Department of Genomic Health, Geisinger Health Systems, Danville, PA 17822, United States
| | - Nathan Sanders
- School of Medicine, Geisinger Health Systems, Danville, PA 17822, United States
| | - Grace Isaacson
- Family Medicine, Penn Highlands Healthcare, DuBois, PA 16830, United States
| | - Elden Jenkins
- School of Medicine, Noorda College of Osteopathic Medicine, Provo, UT 84606, United States
| | - Marc S Williams
- Department of Genomic Health, Geisinger Health Systems, Danville, PA 17822, United States
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Kingsmore SF, Nofsinger R, Ellsworth K. Rapid genomic sequencing for genetic disease diagnosis and therapy in intensive care units: a review. NPJ Genom Med 2024; 9:17. [PMID: 38413639 PMCID: PMC10899612 DOI: 10.1038/s41525-024-00404-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 02/15/2024] [Indexed: 02/29/2024] Open
Abstract
Single locus (Mendelian) diseases are a leading cause of childhood hospitalization, intensive care unit (ICU) admission, mortality, and healthcare cost. Rapid genome sequencing (RGS), ultra-rapid genome sequencing (URGS), and rapid exome sequencing (RES) are diagnostic tests for genetic diseases for ICU patients. In 44 studies of children in ICUs with diseases of unknown etiology, 37% received a genetic diagnosis, 26% had consequent changes in management, and net healthcare costs were reduced by $14,265 per child tested by URGS, RGS, or RES. URGS outperformed RGS and RES with faster time to diagnosis, and higher rate of diagnosis and clinical utility. Diagnostic and clinical outcomes will improve as methods evolve, costs decrease, and testing is implemented within precision medicine delivery systems attuned to ICU needs. URGS, RGS, and RES are currently performed in <5% of the ~200,000 children likely to benefit annually due to lack of payor coverage, inadequate reimbursement, hospital policies, hospitalist unfamiliarity, under-recognition of possible genetic diseases, and current formatting as tests rather than as a rapid precision medicine delivery system. The gap between actual and optimal outcomes in children in ICUs is currently increasing since expanded use of URGS, RGS, and RES lags growth in those likely to benefit through new therapies. There is sufficient evidence to conclude that URGS, RGS, or RES should be considered in all children with diseases of uncertain etiology at ICU admission. Minimally, diagnostic URGS, RGS, or RES should be ordered early during admissions of critically ill infants and children with suspected genetic diseases.
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Affiliation(s)
- Stephen F Kingsmore
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, CA, USA.
| | - Russell Nofsinger
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, CA, USA
| | - Kasia Ellsworth
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, CA, USA
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Akalin H, Sahin IO, Paskal SA, Tan B, Yalcinkaya E, Demir M, Yakubi M, Caliskan BO, Ekinci OG, Ercan M, Kucuk TY, Gokgoz G, Kiraz A, Per H, Ozgun MT, Baydilli N, Ozkul Y, Dundar M. Evaluation of chromosomal abnormalities in the postnatal cohort: A single-center study on 14,242 patients. J Clin Lab Anal 2024; 38:e24997. [PMID: 38115218 PMCID: PMC10829689 DOI: 10.1002/jcla.24997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 11/15/2023] [Accepted: 12/07/2023] [Indexed: 12/21/2023] Open
Abstract
BACKGROUND AND AIM Chromosomal analysis is a laboratory technique used to examine the chromosomes of an individual, offering insights into chromosome numbers, structures, and arrangements to diagnose and comprehend genetic diseases. This retrospective study provides a comprehensive understanding of the distribution by indications in a large cohort of 14,242 patients and the frequency of chromosomal abnormalities in different clinical populations. METHOD The study examined various indications for karyotype evaluation, with recurrent pregnancy loss being the most common indication, followed by intellectual disability, dysmorphic features, congenital anomalies, and developmental delay. RESULTS The overall chromosomal abnormality rate was found to be 5.4%, with numerical abnormalities accounting for the majority of cases (61.7%). Trisomies, particularly trisomy 21, were the most frequent numerical abnormalities. In terms of structural abnormalities, inversions and translocations were the most commonly identified. The rates of chromosomal anomalies varied in specific indications such as amenorrhea, disorders of sex development, and Turner syndrome. The study also highlighted significant differences between males and females in the presence of chromosomal abnormalities across certain indications. Males exhibited a higher incidence of chromosomal abnormalities in cases of Down syndrome and infertility, whereas females showed higher abnormalities in terms of recurrent pregnancy loss. CONCLUSION While this study provides valuable insights into the frequency and distribution of chromosomal abnormalities, it has limitations, including its retrospective design and reliance on data from a single medical genetics department. Nevertheless, the findings emphasize the importance of karyotype analysis in diagnosing chromosomal disorders and providing appropriate management, while also pointing to potential gender-related variations in chromosomal abnormalities that warrant further investigation.
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Affiliation(s)
- Hilal Akalin
- Department of Medical Genetics, Faculty of MedicineErciyes UniversityKayseriTürkiye
| | - Izem Olcay Sahin
- Department of Medical Genetics, Faculty of MedicineErciyes UniversityKayseriTürkiye
| | - Seyma Aktas Paskal
- Department of Medical Genetics, Faculty of MedicineErciyes UniversityKayseriTürkiye
| | - Busra Tan
- Department of Medical Genetics, Faculty of MedicineErciyes UniversityKayseriTürkiye
| | - Ezgi Yalcinkaya
- Department of Medical Genetics, Faculty of MedicineErciyes UniversityKayseriTürkiye
| | - Mikail Demir
- Department of Medical Genetics, Faculty of MedicineErciyes UniversityKayseriTürkiye
| | - Mustafa Yakubi
- Department of Medical Genetics, Faculty of MedicineErciyes UniversityKayseriTürkiye
| | - Busra Ozguc Caliskan
- Department of Medical Genetics, Faculty of MedicineErciyes UniversityKayseriTürkiye
| | - Ozlem Gokce Ekinci
- Department of Medical Genetics, Faculty of MedicineErciyes UniversityKayseriTürkiye
| | - Mehmet Ercan
- Department of Medical Genetics, Faculty of MedicineErciyes UniversityKayseriTürkiye
| | - Tugce Yasar Kucuk
- Department of Medical Genetics, Faculty of MedicineErciyes UniversityKayseriTürkiye
| | - Gizem Gokgoz
- Department of Medical Genetics, Faculty of MedicineErciyes UniversityKayseriTürkiye
| | - Aslihan Kiraz
- Department of Medical Genetics, Faculty of MedicineErciyes UniversityKayseriTürkiye
| | - Huseyin Per
- Department of Pediatric Neurology, Faculty of Medicine, Children's HospitalErciyes UniversityKayseriTürkiye
| | - Mahmut Tuncay Ozgun
- Department of Obstetrics and Gynecology, Faculty of MedicineErciyes UniversityKayseriTürkiye
| | - Numan Baydilli
- Department of Urology, Faculty of MedicineErciyes UniversityKayseriTürkiye
| | - Yusuf Ozkul
- Department of Medical Genetics, Faculty of MedicineErciyes UniversityKayseriTürkiye
| | - Munis Dundar
- Department of Medical Genetics, Faculty of MedicineErciyes UniversityKayseriTürkiye
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Huang D, Jiang J, Zhao T, Wu S, Li P, Lyu Y, Feng J, Wei M, Zhu Z, Gu J, Ren Y, Yu G, Lu H. diseaseGPS: auxiliary diagnostic system for genetic disorders based on genotype and phenotype. Bioinformatics 2023; 39:btad517. [PMID: 37647638 PMCID: PMC10500091 DOI: 10.1093/bioinformatics/btad517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 07/24/2023] [Accepted: 08/29/2023] [Indexed: 09/01/2023] Open
Abstract
SUMMARY The next-generation sequencing brought opportunities for the diagnosis of genetic disorders due to its high-throughput capabilities. However, the majority of existing methods were limited to only sequencing candidate variants, and the process of linking these variants to a diagnosis of genetic disorders still required medical professionals to consult databases. Therefore, we introduce diseaseGPS, an integrated platform for the diagnosis of genetic disorders that combines both phenotype and genotype data for analysis. It offers not only a user-friendly GUI web application for those without a programming background but also scripts that can be executed in batch mode for bioinformatics professionals. The genetic and phenotypic data are integrated using the ACMG-Bayes method and a novel phenotypic similarity method, to prioritize the results of genetic disorders. diseaseGPS was evaluated on 6085 cases from Deciphering Developmental Disorders project and 187 cases from Shanghai Children's hospital. The results demonstrated that diseaseGPS performed better than other commonly used methods. AVAILABILITY AND IMPLEMENTATION diseaseGPS is available to freely accessed at https://diseasegps.sjtu.edu.cn with source code at https://github.com/BioHuangDY/diseaseGPS.
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Affiliation(s)
- Daoyi Huang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- SJTU-Yale Joint Center for Biostatistics and Data Science, National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jianping Jiang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- SJTU-Yale Joint Center for Biostatistics and Data Science, National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Tingting Zhao
- Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Engineering Research Center for Big Data in Pediatric Precision Medicine, Shanghai, China
| | - Shengnan Wu
- Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Pin Li
- Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yongfen Lyu
- Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jincai Feng
- Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Mingyue Wei
- Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Zhixing Zhu
- Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Engineering Research Center for Big Data in Pediatric Precision Medicine, Shanghai, China
| | - Jianlei Gu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- SJTU-Yale Joint Center for Biostatistics and Data Science, National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yongyong Ren
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- SJTU-Yale Joint Center for Biostatistics and Data Science, National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Guangjun Yu
- Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Engineering Research Center for Big Data in Pediatric Precision Medicine, Shanghai, China
- School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong, China
| | - Hui Lu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- SJTU-Yale Joint Center for Biostatistics and Data Science, National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
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Gasteiger N, Vercell A, Khan N, Dowding D, Davies AC, Davies A. Digital interventions for genomics and genetics education, empowerment, and service engagement: A systematic review. J Community Genet 2023:10.1007/s12687-023-00648-w. [PMID: 37198378 DOI: 10.1007/s12687-023-00648-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 04/24/2023] [Indexed: 05/19/2023] Open
Abstract
BACKGROUND Patient-facing digital technologies may reduce barriers to and alleviate the burden on genetics services. However, no work has synthesised the evidence for patient-facing digital interventions for genomics/genetics education and empowerment, or to facilitate service engagement more broadly. It is also unclear which groups have been engaged by digital interventions. AIM This systematic review explores which existing patient-facing digital technologies have been used for genomics/genetics education and empowerment, or to facilitate service engagement, and for whom and for which purposes the interventions have been developed. METHODS The review adhered to the Preferred Reporting Items for Systematic reviews and Meta-Analyses guidelines. Eight databases were searched for literature. Information was extracted into an Excel sheet and analysed in a narrative manner. Quality assessments were conducted using the Mixed Methods Appraisal Tool. RESULTS Twenty-four studies were included, of which 21 were moderate or high quality. The majority (88%) were conducted in the United States of America or within a clinical setting (79%). More than half (63%) of the interventions were web-based tools, and almost all focussed on educating users (92%). There were promising results regarding educating patients and their families and facilitating engagement with genetics services. Few of the studies focussed on empowering patients or were community-based. CONCLUSION Digital interventions may be used to deliver information about genetics concepts and conditions, and positively impact service engagement. However, there is insufficient evidence related to empowering patients and engaging underserved communities or consanguineous couples. Future work should focus on co-developing content with end users and incorporating interactive features.
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Affiliation(s)
- Norina Gasteiger
- Division of Nursing, Midwifery and Social Work, School of Health Sciences, The University of Manchester, Manchester, UK
- Division of Informatics, Imaging and Data Sciences, School of Health Sciences, The University of Manchester, Manchester, UK
| | - Amy Vercell
- Division of Nursing, Midwifery and Social Work, School of Health Sciences, The University of Manchester, Manchester, UK
- The Christie NHS Foundation Trust, Wilmslow Road, Manchester, M20 4BX, UK
| | - Naz Khan
- Genomic Medicine, St. Mary's Hospital, Manchester Academic Health Science Centre, Central Manchester University Hospitals NHS Foundation Trust, Manchester, M13 9WL, UK
| | - Dawn Dowding
- Division of Nursing, Midwifery and Social Work, School of Health Sciences, The University of Manchester, Manchester, UK
| | - Angela C Davies
- Division of Informatics, Imaging and Data Sciences, School of Health Sciences, The University of Manchester, Manchester, UK
| | - Alan Davies
- Division of Informatics, Imaging and Data Sciences, School of Health Sciences, The University of Manchester, Manchester, UK.
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Núñez-Samudio V, Arcos-Burgos M, Landires I. Rare diseases: democratising genetic testing in LMICs. Lancet 2023; 401:1339-1340. [PMID: 37087169 DOI: 10.1016/s0140-6736(23)00343-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 02/09/2023] [Indexed: 04/24/2023]
Affiliation(s)
- Virginia Núñez-Samudio
- Unidad de Genética y Salud Pública, Instituto de Ciencias Médicas, Las Tablas 0710-00043, Panama; Sistema Nacional de Investigación, Secretaría Nacional de Ciencia, Tecnología e Innovación, Ciudad del Saber, Clayton, Panama
| | | | - Iván Landires
- Unidad de Genética y Salud Pública, Instituto de Ciencias Médicas, Las Tablas 0710-00043, Panama; Sistema Nacional de Investigación, Secretaría Nacional de Ciencia, Tecnología e Innovación, Ciudad del Saber, Clayton, Panama; Consulta de Genética Médica, Hospital Joaquín Pablo Franco Sayas, Ministry of Health, Las Tablas, Panama.
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Ciancia S, Goedegebuure WJ, Grootjen LN, Hokken-Koelega ACS, Kerkhof GF, van der Kaay DCM. Computer-aided facial analysis as a tool to identify patients with Silver-Russell syndrome and Prader-Willi syndrome. Eur J Pediatr 2023:10.1007/s00431-023-04937-x. [PMID: 36947243 PMCID: PMC10257592 DOI: 10.1007/s00431-023-04937-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 03/03/2023] [Accepted: 03/15/2023] [Indexed: 03/23/2023]
Abstract
Genetic syndromes often show facial features that provide clues for the diagnosis. However, memorizing these features is a challenging task for clinicians. In the last years, the app Face2Gene proved to be a helpful support for the diagnosis of genetic diseases by analyzing features detected in one or more facial images of affected individuals. Our aim was to evaluate the performance of the app in patients with Silver-Russell syndrome (SRS) and Prader-Willi syndrome (PWS). We enrolled 23 pediatric patients with clinically or genetically diagnosed SRS and 29 pediatric patients with genetically confirmed PWS. One frontal photo of each patient was acquired. Top 1, top 5, and top 10 sensitivities were analyzed. Correlation with the specific genetic diagnosis was investigated. When available, photos of the same patient at different ages were compared. In the SRS group, Face2Gene showed top 1, top 5, and top 10 sensitivities of 39%, 65%, and 91%, respectively. In 41% of patients with genetically confirmed SRS, SRS was the first syndrome suggested, while in clinically diagnosed patients, SRS was suggested as top 1 in 33% of cases (p = 0.74). Face2Gene performed better in younger patients with SRS: in all patients in whom a photo taken at a younger age than the age of enrollment was available, SRS was suggested as top 1, albeit with variable degree of probability. In the PWS group, the top 1, top 5, and top 10 sensitivities were 76%, 97%, and 100%, respectively. PWS was suggested as top 1 in 83% of patients genetically diagnosed with paternal deletion of chromosome 15q11-13 and in 60% of patients presenting with maternal uniparental disomy of chromosome 15 (p = 0.17). The performance was uniform throughout the investigated age range (1-15 years). CONCLUSION In addition to a thorough medical history and detailed clinical examination, the Face2Gene app can be a useful tool to support clinicians in identifying children with a potential diagnosis of SRS or PWS. WHAT IS KNOWN • Several genetic syndromes present typical facial features that may provide clues for the diagnosis. • Memorizing all syndromic facial characteristics is a challenging task for clinicians. WHAT IS NEW • Face2Gene may represent a useful support for pediatricians for the diagnosis of genetic syndromes. • Face2Gene app can be a useful tool to integrate in the diagnostic path of patients with SRS and PWS.
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Affiliation(s)
- Silvia Ciancia
- Department of Pediatrics, Subdivision of Endocrinology, Erasmus University Medical Center, Sophia Children's Hospital, Rotterdam, Netherlands
- Post-Graduate School of Pediatrics, Department of Medical and Surgical Sciences for Mothers, Children and Adults, University of Modena and Reggio Emilia, Modena, Italy
| | - Wesley J Goedegebuure
- Department of Pediatrics, Subdivision of Endocrinology, Erasmus University Medical Center, Sophia Children's Hospital, Rotterdam, Netherlands
| | - Lionne N Grootjen
- Department of Pediatrics, Subdivision of Endocrinology, Erasmus University Medical Center, Sophia Children's Hospital, Rotterdam, Netherlands
| | - Anita C S Hokken-Koelega
- Department of Pediatrics, Subdivision of Endocrinology, Erasmus University Medical Center, Sophia Children's Hospital, Rotterdam, Netherlands
| | - Gerthe F Kerkhof
- Department of Pediatrics, Subdivision of Endocrinology, Erasmus University Medical Center, Sophia Children's Hospital, Rotterdam, Netherlands
| | - Daniëlle C M van der Kaay
- Department of Pediatrics, Subdivision of Endocrinology, Erasmus University Medical Center, Sophia Children's Hospital, Rotterdam, Netherlands.
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11
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Park S, Jang SS, Lee S, Kim M, Sim H, Jeon H, Hong SE, Lee J, Lee J, Jeon EY, Lee J, Lee CR, Kim SY, Kim MJ, Yoon JG, Lim BC, Kim WJ, Kim KJ, Ko JM, Cho A, Lee JS, Choi M, Chae JH. Systematic analysis of inheritance pattern determination in genes that cause rare neurodevelopmental diseases. Front Genet 2022; 13:990015. [PMID: 36212160 PMCID: PMC9533195 DOI: 10.3389/fgene.2022.990015] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 08/23/2022] [Indexed: 01/09/2023] Open
Abstract
Despite recent advancements in our understanding of genetic etiology and its molecular and physiological consequences, it is not yet clear what genetic features determine the inheritance pattern of a disease. To address this issue, we conducted whole exome sequencing analysis to characterize genetic variants in 1,180 Korean patients with neurological symptoms. The diagnostic yield for definitive pathogenic variant findings was 50.8%, after including 33 cases (5.9%) additionally diagnosed by reanalysis. Of diagnosed patients, 33.4% carried inherited variants. At the genetic level, autosomal recessive-inherited genes were characterized by enrichments in metabolic process, muscle organization and metal ion homeostasis pathways. Transcriptome and interactome profiling analyses revealed less brain-centered expression and fewer protein-protein interactions for recessive genes. The majority of autosomal recessive genes were more tolerant of variation, and functional prediction scores of recessively-inherited variants tended to be lower than those of dominantly-inherited variants. Additionally, we were able to predict the rates of carriers for recessive variants. Our results showed that genes responsible for neurodevelopmental disorders harbor different molecular mechanisms and expression patterns according to their inheritance patterns. Also, calculated frequency rates for recessive variants could be utilized to pre-screen rare neurodevelopmental disorder carriers.
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Affiliation(s)
- Soojin Park
- Department of Pediatrics, Seoul National University College of Medicine, Seoul National University Children’s Hospital, Seoul, South Korea
| | - Se Song Jang
- Department of Pediatrics, Seoul National University College of Medicine, Seoul National University Children’s Hospital, Seoul, South Korea
| | - Seungbok Lee
- Department of Pediatrics, Seoul National University College of Medicine, Seoul National University Children’s Hospital, Seoul, South Korea,Department of Genomic Medicine, Seoul National University Hospital, Seoul, South Korea
| | - Minsoo Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
| | - Hyungtai Sim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
| | - Hyeongseok Jeon
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
| | - Sung Eun Hong
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
| | - Jean Lee
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
| | - Jeongeun Lee
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
| | - Eun Young Jeon
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
| | - Jeongha Lee
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
| | - Cho-Rong Lee
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
| | - Soo Yeon Kim
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, South Korea
| | - Man Jin Kim
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, South Korea,Rare Disease Center, Seoul National University Hospital, Seoul, South Korea
| | - Jihoon G. Yoon
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, South Korea
| | - Byung Chan Lim
- Department of Pediatrics, Seoul National University College of Medicine, Seoul National University Children’s Hospital, Seoul, South Korea
| | - Woo Joong Kim
- Department of Pediatrics, Seoul National University College of Medicine, Seoul National University Children’s Hospital, Seoul, South Korea
| | - Ki Joong Kim
- Department of Pediatrics, Seoul National University College of Medicine, Seoul National University Children’s Hospital, Seoul, South Korea
| | - Jung Min Ko
- Department of Pediatrics, Seoul National University College of Medicine, Seoul National University Children’s Hospital, Seoul, South Korea
| | - Anna Cho
- Department of Pediatrics, Seoul National University Bundang Hospital, Seongnam, South Korea
| | - Jin Sook Lee
- Department of Pediatrics, Seoul National University Hospital Child Cancer and Rare Disease Administration, Seoul National University Children’s Hospital, Seoul, South Korea
| | - Murim Choi
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea,*Correspondence: Murim Choi, ; Jong-Hee Chae,
| | - Jong-Hee Chae
- Department of Pediatrics, Seoul National University College of Medicine, Seoul National University Children’s Hospital, Seoul, South Korea,Department of Genomic Medicine, Seoul National University Hospital, Seoul, South Korea,*Correspondence: Murim Choi, ; Jong-Hee Chae,
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12
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Medical student acceptance on gene therapy to increase children's well-being with genetic diseases: a study in Indonesia. Future Sci OA 2022; 8:FSO800. [PMID: 35909997 PMCID: PMC9327639 DOI: 10.2144/fsoa-2021-0130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 05/04/2022] [Indexed: 11/23/2022] Open
Abstract
Aim: Gene therapy is expected to improve patients' quality of life. Medical students need to be aware about this technology as its application is becoming wider. Materials & methods: A web-based survey was conducted to measure the acceptance of Indonesian medical students regarding gene therapy. Results: Data from 621 valid responses showed that Indonesian medical students have little knowledge of this technology, with 34.4% of them ever heard of gene therapy. However, most of them support the approved gene therapy for health-related matters, but not on the non-health related matters. Their acceptance was determined by the sex, domicile and studentship status. Conclusion: Increasing medical students' knowledge of gene therapy is important to minimize the future conflict of gene therapy application.
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13
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Amor DJ, Savulescu J, Wilkins-Haug L. ISPD 2021 Debate - All IVF cycles should involve pre-implantation genetic testing to improve fetal health and pregnancy outcomes. Prenat Diagn 2022; 42:1015-1021. [PMID: 35470429 DOI: 10.1002/pd.6156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/19/2022] [Accepted: 04/21/2022] [Indexed: 11/09/2022]
Abstract
For three decades, couples at increased risk for a genetic disorder have been offered preimplantation genetic testing (PGT). Simultaneously, PGT for aneuploidy (PGT-A) to improve in vitro fertilization (IVF) outcomes was introduced, but evidence of value-added remains inconsistent. Recently, lower genetic testing costs and shorter turnaround time have reinvigorated PGT-A. Additionally, a shift from blastomere (day 3) to blastocyst (day 5) transfer and embryo freezing advances support PGT without the time constraints of immediate transfer. PGT-A transformed from a time-constrained analysis of 1-2 cells to an "add on" study for all IVF. But should it be offered to all IVF patients? And if not, under what conditions? Pre-debate polling found 64% opposed to PGT for all IVF cycles with concerns voiced about cost, informed consent, and a "slippery slope". Leaving aside the inconsistent evidence of IVF improvement whether measured as miscarriage or livebirths with PGT-A, the debaters grappled with patient and provider desires versus the ethical concerns for the unborn child. However, the audience was not swayed; two thirds remained opposed to PGT for all IVF cycles. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- David J Amor
- Alli Chair in Developmental Medicine; Padiatrics Royal Children's Hosptial, University of Melbourne
| | - Julian Savulescu
- Director of the Oxford Uehiro Centre for Practical Ethics, Uehiro Professor of Practical Ethics; Fellow of St Cross College, University of Oxford
| | - Louise Wilkins-Haug
- William Lambert Richardson Chair in Obstetrics, Brigham and Women's Hospital, Professor, Harvard Medical School, Department of Obstetrics, Gynecology and Reproductive Biology, 75 Francis Street, Boston, MA
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14
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He WB, Xiao WJ, Dai CL, Wang YR, Li XR, Gong F, Meng LL, Tan C, Zeng SC, Lu GX, Lin G, Tan YQ, Hu H, Du J. RNA splicing analysis contributes to reclassifying variants of uncertain significance and improves the diagnosis of monogenic disorders. J Med Genet 2022; 59:1010-1016. [PMID: 35121647 DOI: 10.1136/jmedgenet-2021-108013] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 01/06/2022] [Indexed: 11/04/2022]
Abstract
BACKGROUND Numerous variants of uncertain significance (VUSs) have been identified by whole exome sequencing in clinical practice. However, VUSs are not currently considered medically actionable. OBJECTIVE To assess the splicing patterns of 49 VUSs in 48 families identified clinically to improve genetic counselling and family planning. METHODS Forty-nine participants with 49 VUSs were recruited from the Reproductive and Genetic Hospital of CITIC-Xiangya. Bioinformatic analysis was performed to preliminarily predict the splicing effects of these VUSs. RT-PCR and minigene analysis were used to assess the splicing patterns of the VUSs. According to the results obtained, couples opted for different methods of reproductive interventions to conceive a child, including prenatal diagnosis and preimplantation genetic testing (PGT). RESULTS Eleven variants were found to alter pre-mRNA splicing and one variant caused nonsense-mediated mRNA decay, which resulted in the reclassification of these VUSs as likely pathogenic. One couple chose to undergo in vitro fertilisation with PGT treatment; a healthy embryo was transferred and the pregnancy is ongoing. Three couples opted for natural pregnancy with prenatal diagnosis. One couple terminated the pregnancy because the fetus was affected by short-rib thoracic dysplasia and harboured the related variant. The infants of the other two couples were born and were healthy at their last recorded follow-up. CONCLUSION RNA splicing analysis is an important method to assess the impact of sequence variants on splicing in clinical practice and can contribute to the reclassification of a significant proportion of VUSs. RNA splicing analysis should be considered for genetic disease diagnostics.
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Affiliation(s)
- Wen-Bin He
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, Hunan, China.,National Engineering and Research Center of Human Stem Cells, Changsha, Hunan, China.,Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, Hunan, China.,Clinical Research Center For Reproduction and Genetics In Hunan Province, Changsha, China
| | - Wen-Juan Xiao
- National Engineering and Research Center of Human Stem Cells, Changsha, Hunan, China.,Hunan Guangxiu Hospital, Medical College of Hunan Normal University, Changsha, Hunan, China
| | - Cong-Ling Dai
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, Hunan, China.,National Engineering and Research Center of Human Stem Cells, Changsha, Hunan, China.,Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, Hunan, China.,Clinical Research Center For Reproduction and Genetics In Hunan Province, Changsha, China
| | - Yu-Rong Wang
- Hunan Guangxiu Hospital, Medical College of Hunan Normal University, Changsha, Hunan, China
| | - Xiu-Rong Li
- Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, Hunan, China.,Clinical Research Center For Reproduction and Genetics In Hunan Province, Changsha, China
| | - Fei Gong
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, Hunan, China.,National Engineering and Research Center of Human Stem Cells, Changsha, Hunan, China.,Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, Hunan, China.,Clinical Research Center For Reproduction and Genetics In Hunan Province, Changsha, China
| | - Lan-Lan Meng
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, Hunan, China.,Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, Hunan, China
| | - Chen Tan
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, Hunan, China
| | - Si-Cong Zeng
- Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, Hunan, China.,Hunan Guangxiu Hospital, Medical College of Hunan Normal University, Changsha, Hunan, China
| | - Guang-Xiu Lu
- National Engineering and Research Center of Human Stem Cells, Changsha, Hunan, China.,Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, Hunan, China.,Clinical Research Center For Reproduction and Genetics In Hunan Province, Changsha, China.,Hunan Guangxiu Hospital, Medical College of Hunan Normal University, Changsha, Hunan, China
| | - Ge Lin
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, Hunan, China.,National Engineering and Research Center of Human Stem Cells, Changsha, Hunan, China.,Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, Hunan, China.,Clinical Research Center For Reproduction and Genetics In Hunan Province, Changsha, China
| | - Yue-Qiu Tan
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, Hunan, China.,National Engineering and Research Center of Human Stem Cells, Changsha, Hunan, China.,Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, Hunan, China.,Clinical Research Center For Reproduction and Genetics In Hunan Province, Changsha, China.,Hunan Guangxiu Hospital, Medical College of Hunan Normal University, Changsha, Hunan, China
| | - Hao Hu
- Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, Hunan, China .,Clinical Research Center For Reproduction and Genetics In Hunan Province, Changsha, China
| | - Juan Du
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, Hunan, China .,National Engineering and Research Center of Human Stem Cells, Changsha, Hunan, China.,Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, Hunan, China.,Clinical Research Center For Reproduction and Genetics In Hunan Province, Changsha, China
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15
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Riku S, Hedriana H, Carozza JA, Hoskovec J. Reflex single-gene non-invasive prenatal testing is associated with markedly better detection of fetuses affected with single-gene recessive disorders at lower cost. J Med Econ 2022; 25:403-411. [PMID: 35289246 DOI: 10.1080/13696998.2022.2053384] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
OBJECTIVE To evaluate the clinical benefits and achievable cost savings associated with the adoption of a carrier screen with reflex single-gene non-invasive prenatal test (sgNIPT) in prenatal care. METHOD A decision-analytic model was developed to compare carrier screen with reflex sgNIPT (maternal carrier status and fetal risk reported together) as first-line carrier screening to the traditional carrier screening workflow (positive maternal carrier screen followed by paternal screening to evaluate fetal risk). The model compared the clinical outcomes and healthcare costs associated with the two screening methods. These results were used to simulate appropriate pricing for reflex sgNIPT. RESULTS Reflex sgNIPT carrier screening-detected 108 of 110 affected pregnancies per 100,000 births (98.5% sensitivity), whereas traditional carrier screening-detected 46 of 110 affected pregnancies (41.5% sensitivity). The cost to identify one affected pregnancy was reduced by 62% in the reflex sgNIPT scenario compared to the traditional scenario. Adding together the testing cost savings and the savings from earlier clinical intervention made possible by reflex sgNIPT, the total cost savings was $37.6 million per 100,000 pregnancies. Based on these cost savings, we simulated appropriate reflex sgNIPT pricing range: if the cost to identify one affected pregnancy is the unit cost, carrier screening with reflex sgNIPT can be priced up to $1,859 per test (or $7,233 if sgNIPT is billed separately); if the cost per 100,000 pregnancies is the unit cost, carrier screening with sgNIPT can be priced up to $1,070 per test (or $2,336 if sgNIPT is billed separately). CONCLUSION Using the carrier screen with reflex sgNIPT as first-line screening improves the detection of affected fetuses by 2.4-fold and can save costs for the healthcare system. A real-life experience will be needed to assess the clinical utility and exact cost savings of carrier screen with reflex sgNIPT.
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Affiliation(s)
- Shan Riku
- BillionToOne, Inc., Menlo Park, CA, USA
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16
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Huang Y, Huang Z, Tang Z, Chen Y, Huang M, Liu H, Huang W, Ye Q, Jia B. Research Progress, Challenges, and Breakthroughs of Organoids as Disease Models. Front Cell Dev Biol 2021; 9:740574. [PMID: 34869324 PMCID: PMC8635113 DOI: 10.3389/fcell.2021.740574] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 10/28/2021] [Indexed: 01/14/2023] Open
Abstract
Traditional cell lines and xenograft models have been widely recognized and used in research. As a new research model, organoids have made significant progress and development in the past 10 years. Compared with traditional models, organoids have more advantages and have been applied in cancer research, genetic diseases, infectious diseases, and regenerative medicine. This review presented the advantages and disadvantages of organoids in physiological development, pathological mechanism, drug screening, and organ transplantation. Further, this review summarized the current situation of vascularization, immune microenvironment, and hydrogel, which are the main influencing factors of organoids, and pointed out the future directions of development.
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Affiliation(s)
- Yisheng Huang
- Department of Oral Surgery, Stomatological Hospital, Southern Medical University, Guangzhou, China
| | - Zhijie Huang
- Department of Oral Surgery, Stomatological Hospital, Southern Medical University, Guangzhou, China
| | - Zhengming Tang
- Department of Oral Surgery, Stomatological Hospital, Southern Medical University, Guangzhou, China
| | - Yuanxin Chen
- Department of Oral Surgery, Stomatological Hospital, Southern Medical University, Guangzhou, China
| | - Mingshu Huang
- Department of Oral Surgery, Stomatological Hospital, Southern Medical University, Guangzhou, China
| | - Hongyu Liu
- Department of Oral Surgery, Stomatological Hospital, Southern Medical University, Guangzhou, China
| | - Weibo Huang
- Department of stomatology, Guangdong Provincial Corps Hospital, Chinese People's Armed Police Force, Guangzhou, China
| | - Qingsong Ye
- Center of Regenerative Medicine, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, China.,School of Stomatology and Medicine, Foshan University, Foshan, China
| | - Bo Jia
- Department of Oral Surgery, Stomatological Hospital, Southern Medical University, Guangzhou, China
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17
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Mezzi N, Messaoud O, Mkaouar R, Zitouna N, Romdhane S, Abdessalem G, Charfeddine C, Maazoul F, Ouerteni I, Hamdi Y, Zaouak A, Mrad R, Abdelhak S, Romdhane L. Spectrum of Genetic Diseases in Tunisia: Current Situation and Main Milestones Achieved. Genes (Basel) 2021; 12:1820. [PMID: 34828426 PMCID: PMC8617973 DOI: 10.3390/genes12111820] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 10/30/2021] [Accepted: 11/03/2021] [Indexed: 02/06/2023] Open
Abstract
Genetic diseases in Tunisia are a real public health problem given their chronicity and the lack of knowledge concerning their prevalence and etiology, and the high rates of consanguinity. Hence, we performed systematic reviews of the literature in order to provide a more recent spectrum of these disorders and to expose the challenges that still exist to tackle these kinds of diseases. A manual textual data mining was conducted using MeSH and PubMed databases. Collected data were classified according to the CIM-10 classification and the transmission mode. The spectrum of these diseases is estimated to be 589 entities. This suggests remarkable progress through the development of biomedical health research activities and building capacities. Sixty percent of the reported disorders are autosomal recessive, which could be explained by the high prevalence of endogamous mating. Congenital malformations (29.54%) are the major disease group, followed by metabolic diseases (22%). Sixty percent of the genetic diseases have a known molecular etiology. We also reported additional cases of comorbidity that seem to be a common phenomenon in our population. We also noticed that epidemiological data are scarce. Newborn and carrier screening was only limited to pilot projects for a few genetic diseases. Collected data are being integrated into a database under construction that will be a valuable decision-making tool. This study provides the current situation of genetic diseases in Tunisia and highlights their particularities. Early detection of the disease is important to initiate critical intervention and to reduce morbidity and mortality.
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Affiliation(s)
- Nessrine Mezzi
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis 1002, Tunisia
- Department of Biology, Faculty of Sciences of Bizerte, Université Tunis Carthage, Jarzouna 7021, Tunisia
| | - Olfa Messaoud
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis 1002, Tunisia
| | - Rahma Mkaouar
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis 1002, Tunisia
| | - Nadia Zitouna
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis 1002, Tunisia
| | - Safa Romdhane
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis 1002, Tunisia
| | - Ghaith Abdessalem
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis 1002, Tunisia
| | - Cherine Charfeddine
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis 1002, Tunisia
- High Institute of Biotechnology of Sidi Thabet, Biotechpole of Sidi Thabet, University of Manouba, Ariana 2080, Tunisia
| | - Faouzi Maazoul
- Department of Congenital and Hereditary Diseases, Charles Nicolle Hospital, Tunis 1002, Tunisia
| | - Ines Ouerteni
- Department of Congenital and Hereditary Diseases, Charles Nicolle Hospital, Tunis 1002, Tunisia
| | - Yosr Hamdi
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis 1002, Tunisia
- Laboratory of Human and Experimental Pathology, Institut Pasteur de Tunis, Tunis 1002, Tunisia
| | - Anissa Zaouak
- Department of Dermatology, Research Unit Genodermatosis and Cancer LR12SP03, Habib Thameur Hospital, Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis 1002, Tunisia
| | - Ridha Mrad
- Department of Congenital and Hereditary Diseases, Charles Nicolle Hospital, Tunis 1002, Tunisia
| | - Sonia Abdelhak
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis 1002, Tunisia
| | - Lilia Romdhane
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis 1002, Tunisia
- Department of Biology, Faculty of Sciences of Bizerte, Université Tunis Carthage, Jarzouna 7021, Tunisia
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18
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Neumann A, Alcantara-Ortigoza MA, González-del Angel A, Zarate Díaz NA, Santana JS, Porchia LM, López-Bayghen E. Whole-genome amplification/preimplantation genetic testing for propionic acidemia of successful pregnancy in an obligate carrier Mexican couple: A case report. World J Clin Cases 2021; 9:8797-8803. [PMID: 34734058 PMCID: PMC8546821 DOI: 10.12998/wjcc.v9.i29.8797] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 07/28/2021] [Accepted: 09/08/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Identifying a potential single monogenetic disorder in healthy couples is costly due to the Assisted Reproduction facilities' current methodology for screening, which focuses on the detecting multiple genetic disorders at once. Here, we report the successful application of a low-cost and fast preimplantation genetic testing for monogenic/single gene defects (PGT-M) approach for detecting propionic acidemia (PA) in embryos obtained from a confirmed heterozygous propionyl-CoA carboxylase alpha subunit (PCCA) couple.
CASE SUMMARY A fertile 32-years old Mexican couple with denied consanguinity sought antenatal genetic counseling. They were suspected obligate PA carriers due to a previous deceased PA male newborn with an unknown PCCA/propionyl-CoA carboxylase beta subunit (PCCB) genotype. Next-Generation Sequencing revealed a heterozygous genotype for a pathogenic PCCA variant (c.2041-1G>T, ClinVar:RCV000802701.1; dbSNP:rs1367867218) in both parents. The couple requested in vitro fertilization (IVF) and PGT-M for PA. From IVF, 12 oocytes were collected and fertilized, of which two resulted in high-quality embryos. Trophectoderm biopsies and Whole Genome Amplification by a fragmentation/amplification-based method were performed and revealed that the two embryos were euploid. End-point polymerase chain reaction and further Sanger sequencing of the exon-intron borders revealed a wild-type PCCA male embryo and a heterozygous c.2041-1G>T female embryo. Both embryos were transferred, resulting in a clinical pregnancy and the delivery of a healthy male newborn (38 wk, weight: 4080 g, length: 49 cm, APGAR 9/9). The absence of PA was confirmed by expanded newborn screening.
CONCLUSION We show that using PGT-M with Whole Genome Amplification templates, coupled with IVF, can reduce the transmission of a pathogenic variant of the PCCA gene.
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Affiliation(s)
- Adina Neumann
- Laboratorio de Investigación y Diagnóstico Molecular, Ingenes, Mexico City 05320, Mexico
| | - Miguel Angel Alcantara-Ortigoza
- Laboratorio de Biología Molecular, Subdirección de Investigación Médica, Instituto Nacional de Pediatría, Mexico City 04530, Mexico
- DNA-GEN S.C. Centro de Alta Especialidad en Genética Humana, Mexico City 14070, Mexico
| | - Ariadna González-del Angel
- Laboratorio de Biología Molecular, Subdirección de Investigación Médica, Instituto Nacional de Pediatría, Mexico City 04530, Mexico
- DNA-GEN S.C. Centro de Alta Especialidad en Genética Humana, Mexico City 14070, Mexico
| | | | | | - Leonardo M Porchia
- Departamento de Toxicología, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mexico City 07360, Mexico
| | - Esther López-Bayghen
- Departamento de Toxicología, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mexico City 07360, Mexico
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Karyotype analysis of amniotic fluid cells and report of chromosomal abnormalities in 15,401 cases of Iranian women. Sci Rep 2021; 11:19402. [PMID: 34593920 PMCID: PMC8484541 DOI: 10.1038/s41598-021-98928-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 09/01/2021] [Indexed: 12/02/2022] Open
Abstract
The aim of present study was to assess the karyotypes of amniotic fluid cells and find the frequency of chromosomal abnormalities and their significance in clinical setting. A total of 15,401 pregnant women were assessed from March 2016 to May 2019, and 14,968 amniotic fluid samples were successfully cultured. These fetuses were grouped according to different indications including advanced maternal age, abnormal nuchal translucency (NT) values, positive first/second trimester screening results, high risk NIPT results, very low PAPP-A and free β-hCG multiples of the normal median (MoM) results, abnormal ultrasound findings or previous history of chromosomal abnormalities. Results indicated the presence of normal karyotype in 90.2% (13,497/14,968) of fetuses. Totally, 46.4% (6945/14,968) of fetuses were 46,XX and 43.8% (6552/14,968) had 46,XY chromosome pattern. A total of 1077 abnormal karyotypes were found among 14,968 fetuses, thus the rate of abnormal fetuses was calculated to be 7.2% (1072/14,968). Meanwhile, a total of 394 cases (2.8%) had a normal polymorphism in their karyotype. In other words, abnormal karyotypes were detected in one of 13.9 cases of patients underwent amniocentesis. Down syndrome, Edward’s syndrome, abnormal mosaicisms and Patau’s syndrome were detected in 4.4% (659/14,968), 0.57% (85/14,968), 0.49% (74/14,968) and 0.24% (36/14,968) of cases, respectively. Sex chromosomal abnormalities including Klinefelter syndrome, Turner syndrome and 47,XXX karyotype were detected in 64 cases (0.43%). In this article, the rates of chromosomal abnormalities are compared between different groups of patients based on the advanced maternal age, abnormal NT values, very low PAPP-A and free β-hCG MoMs results, and positive FTS results. The current investigation provides insight into the most appropriate indications for amniocentesis in Iran.
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Zhong A, Xia K, Hadjis Z, Lifman G, Njambi L, Dimaras H. Opportunities and barriers for genetic service delivery in Kenya from a health personnel perspective. J Community Genet 2021; 12:525-538. [PMID: 34228349 PMCID: PMC8257851 DOI: 10.1007/s12687-021-00532-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 05/04/2021] [Indexed: 11/25/2022] Open
Abstract
Genetic counselling and testing are essential health services for the management of heritable diseases. However, in low-and-middle income countries like Kenya, genetic counsellors are not yet a licenced profession, and there is limited availability of and access to genetic testing. This study aimed to uncover opportunities and barriers for genetic service delivery in the Kenyan healthcare system from the perspectives of those who provide genetic testing and/or genetic counselling. Participants included Kenyan health personnel who deliver genetic services. This was a qualitative study that collected data via semi-structured one-on-one interviews and analyzed it using inductive thematic analysis. Participant demographics and characteristics of clinical genetic service provision were collected using a survey and results summarized using descriptive statistics. Themes revealed during analysis were compared to the clinical characteristics of genetic service provision to inform the opportunities and barriers. Fifteen interviews were conducted in total. Thematic analysis indicated that participants believed that the barriers facing genetic service delivery were linked to three themes: (1) education and training, (2) costs, and (3) counselling challenges. The opportunities for genetic service delivery were linked to four themes: (1) demand, (2) education and training, (3) encouraging a multidisciplinary approach to care, and (4) enhancing laboratory infrastructure. These findings are crucial for the development of a national evidence-informed and culturally appropriate model for genetic service delivery.
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Affiliation(s)
- Adrina Zhong
- Department of Social and Behavioural Health Sciences, Dalla Lana School of Public Health, The University of Toronto, Toronto, ON, Canada
- Schulich School of Medicine & Dentistry, Western University, London, ON, Canada
| | - Kaiwen Xia
- Department of Molecular Genetics, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Zissis Hadjis
- The Munk School of Global Affairs and Public Policy, University of Toronto, Toronto, ON, Canada
| | - Gavin Lifman
- Centre for Global Child Health, SickKids Research Institute, Toronto, ON, Canada
| | - Lucy Njambi
- Department of Ophthalmology, Kenyatta National Hospital, University of Nairobi, Nairobi, Kenya
| | - Helen Dimaras
- Centre for Global Child Health, SickKids Research Institute, Toronto, ON, Canada.
- Division Clinical Public Health, Dalla Lana School of Public Health, The University of Toronto, Toronto, ON, Canada.
- Department of Ophthalmology & Vision Sciences, Faculty of Medicine, University of Toronto, Toronto, ON, Canada.
- Child Health Evaluative Sciences Program, SickKids Research Institute, Toronto, ON, Canada.
- Department of Ophthalmology & Vision Sciences, The Hospital for Sick Children, Toronto, ON, Canada.
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21
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DGK and DZHK position paper on genome editing: basic science applications and future perspective. Basic Res Cardiol 2021; 116:2. [PMID: 33449167 PMCID: PMC7810637 DOI: 10.1007/s00395-020-00839-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 12/09/2020] [Indexed: 12/18/2022]
Abstract
For a long time, gene editing had been a scientific concept, which was limited to a few applications. With recent developments, following the discovery of TALEN zinc-finger endonucleases and in particular the CRISPR/Cas system, gene editing has become a technique applicable in most laboratories. The current gain- and loss-of function models in basic science are revolutionary as they allow unbiased screens of unprecedented depth and complexity and rapid development of transgenic animals. Modifications of CRISPR/Cas have been developed to precisely interrogate epigenetic regulation or to visualize DNA complexes. Moreover, gene editing as a clinical treatment option is rapidly developing with first trials on the way. This article reviews the most recent progress in the field, covering expert opinions gathered during joint conferences on genome editing of the German Cardiac Society (DGK) and the German Center for Cardiovascular Research (DZHK). Particularly focusing on the translational aspect and the combination of cellular and animal applications, the authors aim to provide direction for the development of the field and the most frequent applications with their problems.
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Singh K, Bijarnia-Mahay S, Ramprasad VL, Puri RD, Nair S, Sharda S, Saxena R, Kohli S, Kulshreshtha S, Ganguli I, Gujral K, Verma IC. NGS-based expanded carrier screening for genetic disorders in North Indian population reveals unexpected results - a pilot study. BMC MEDICAL GENETICS 2020; 21:216. [PMID: 33138774 PMCID: PMC7607710 DOI: 10.1186/s12881-020-01153-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 10/20/2020] [Indexed: 12/25/2022]
Abstract
Background To determine the carrier frequency and pathogenic variants of common genetic disorders in the north Indian population by using next generation sequencing (NGS). Methods After pre-test counselling, 200 unrelated individuals (including 88 couples) were screened for pathogenic variants in 88 genes by NGS technology. The variants were classified as per American College of Medical Genetics criteria. Pathogenic and likely pathogenic variants were subjected to thorough literature-based curation in addition to the regular filters. Variants of unknown significance were not reported. Individuals were counselled explaining the implications of the results, and cascade screening was advised when necessary. Results Of the 200 participants, 52 (26%) were found to be carrier of one or more disorders. Twelve individuals were identified to be carriers for congenital deafness, giving a carrier frequency of one in 17 for one of the four genes tested (SLC26A4, GJB2, TMPRSS3 and TMC1 in decreasing order). Nine individuals were observed to be carriers for cystic fibrosis, with a frequency of one in 22. Three individuals were detected to be carriers for Pompe disease (frequency one in 67). None of the 88 couples screened were found to be carriers for the same disorder. The pathogenic variants observed in many disorders (such as deafness, cystic fibrosis, Pompe disease, Canavan disease, primary hyperoxaluria, junctional epidermolysis bullosa, galactosemia, medium chain acyl CoA deficiency etc.) were different from those commonly observed in the West. Conclusion A higher carrier frequency for genetic deafness, cystic fibrosis and Pompe disease was unexpected, and contrary to the generally held view about their prevalence in Asian Indians. In spite of the small sample size, this study would suggest that population-based carrier screening panels for India would differ from those in the West, and need to be selected with due care. Testing should comprise the study of all the coding exons with its boundaries in the genes through NGS, as all the variants are not well characterized. Only study of entire coding regions in the genes will detect carriers with adequate efficiency, in order to reduce the burden of genetic disorders in India and other resource poor countries. Supplementary Information The online version contains supplementary material available at 10.1186/s12881-020-01153-4.
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Affiliation(s)
- Kanika Singh
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Sunita Bijarnia-Mahay
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India.
| | | | - Ratna Dua Puri
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Sandhya Nair
- Medgenome Laboratories Pvt Ltd., Bangalore, India
| | | | - Renu Saxena
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Sudha Kohli
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Samarth Kulshreshtha
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Indrani Ganguli
- Institute of Obstetrics and Gynaecology, Sir Ganga Ram Hospital, New Delhi, India
| | - Kanwal Gujral
- Institute of Obstetrics and Gynaecology, Sir Ganga Ram Hospital, New Delhi, India
| | - Ishwar C Verma
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India.
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Nilakantam SR, Bhat D, Ravi M, Dayananda (CM, Basavanagowdappa H, Kumar K J. Comprehensive Rare Disease Care model for screening and diagnosis of rare genetic diseases - an experience of private medical college and hospital, South India. Intractable Rare Dis Res 2020; 9:179-183. [PMID: 32844078 PMCID: PMC7441030 DOI: 10.5582/irdr.2020.03039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Rare diseases (RD) of genetic origin are raising public health concern contributing to a massive economic burden in India. Establishing Specialty Centers to bridge the RD community with apex centers is felt as a need in developing countries. Hence a Comprehensive Rare Disease Care (CRDC) model was set up at the department of pediatrics under Center for Human Genomics and Counseling at a medical college hospital in South India. The patients suspected to have genetic disease were evaluated as per the work flow of the designed model. The utilization statistics depict the outcome of this model. In the face of limited resources, it was possible to establish a functional RD unit with meticulous planning, supportive administration and trained interdisciplinary staff. A scalable prototype that could be replicated in other Medical colleges and Hospitals of India is described.
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Affiliation(s)
- Sathish Raju Nilakantam
- Department of Hospital Administration, JSS Medical College & Hospital, JSS Academy of Higher Education and Research, Mysuru, Karnataka, India
| | - Deepa Bhat
- Centre for Medical Genomics & Counseling, Department of Medical Genetics, JSS Medical College & Hospital, JSS Academy of Higher Education and Research, Mysuru, Karnataka, India
- Department of Anatomy, JSS Medical College & Hospital, JSS Academy of Higher Education and Research, Mysuru, Karnataka, India
- Address correspondence to:Deepa Bhat, Department of Medical Genetics and Department of Anatomy, JSS Medical College & Hospital, JSS Academy of Higher Education and Research, Mysuru - 570004, Karnataka, India. E-mail:
| | - M.D. Ravi
- Department of Paediatrics, JSS Medical College & Hospital, JSS Academy of Higher Education and Research, Mysuru, Karnataka, India
| | - (Col) M Dayananda
- Department of Hospital Administration, JSS Medical College & Hospital, JSS Academy of Higher Education and Research, Mysuru, Karnataka, India
| | - H. Basavanagowdappa
- Department of General Medicine, JSS Medical College & Hospital, JSS Academy of Higher Education and Research, Mysuru, Karnataka, India
| | - Jagadish Kumar K
- Department of Paediatrics, JSS Medical College & Hospital, JSS Academy of Higher Education and Research, Mysuru, Karnataka, India
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Beresford C, Hall S, Smedley A, Mathad N, Waters R, Chakraborty A, Sparrow OC, Tsitouras V. Prenatal diagnosis of arachnoid cysts: a case series and systematic review. Childs Nerv Syst 2020; 36:729-741. [PMID: 31897633 DOI: 10.1007/s00381-019-04477-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 12/17/2019] [Indexed: 12/01/2022]
Abstract
INTRODUCTION Primary cysts are believed to arise from the splitting of the arachnoid membrane during prenatal development and can be diagnosed in utero. Prenatal diagnosis is uncommon; therefore, the evidence base for counselling expectant mothers is limited. The purpose of this article is to present a case series and review the current literature on prenatally diagnosed arachnoid cysts. METHOD A keyword search of hospital electronic records was performed for all patients with a prenatally diagnosed arachnoid cyst at a tertiary neurosurgical centre. Case notes were reviewed for all patients diagnosed between 2005 and 2017. The Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines were used to structure a systematic review of all English language articles published up to May 2018. RESULTS A total of eight eligible patients were identified from our own records and 123 from the literature. Sixty-eight per cent of patients had a normal outcome. Sixty-three per cent of patients underwent surgical intervention which was not associated with abnormal outcome. The diagnosis of syndromic/genetic diagnosis (p < 0.001) and the presence of other intra-cranial anatomical abnormalities (p = 0.05) were significant predictors of abnormal outcome. CONCLUSION The pathogenesis and prognosis of a prenatal arachnoid cyst diagnosis remain unclear. These results suggest favourable outcomes from simple cysts without associated abnormalities and expectant mothers should be counselled accordingly. A wider prospective review is required to better established evidence-based practice.
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Affiliation(s)
- Charles Beresford
- Faculty of Medicine, University of Southampton, Southampton General Hospital, Tremona Road, Southampton, SO16 6YD, UK
| | - Samuel Hall
- Department of Neurosurgery, Wessex Neurological Centre, Southampton General Hospital, Tremona Road, Southampton, SO16 6YD, UK.
| | - Alexander Smedley
- Department of Neurosurgery, Wessex Neurological Centre, Southampton General Hospital, Tremona Road, Southampton, SO16 6YD, UK
| | - Nijaguna Mathad
- Department of Neurosurgery, Wessex Neurological Centre, Southampton General Hospital, Tremona Road, Southampton, SO16 6YD, UK
| | - Ryan Waters
- Department of Neurosurgery, Wessex Neurological Centre, Southampton General Hospital, Tremona Road, Southampton, SO16 6YD, UK
| | - Aabir Chakraborty
- Department of Neurosurgery, Wessex Neurological Centre, Southampton General Hospital, Tremona Road, Southampton, SO16 6YD, UK
| | - Owen C Sparrow
- Department of Neurosurgery, Wessex Neurological Centre, Southampton General Hospital, Tremona Road, Southampton, SO16 6YD, UK
| | - Vassilios Tsitouras
- Department of Neurosurgery, Wessex Neurological Centre, Southampton General Hospital, Tremona Road, Southampton, SO16 6YD, UK
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Murphy NM, Samarasekera TS, Macaskill L, Mullen J, Rombauts LJF. Genome sequencing of human in vitro fertilisation embryos for pathogenic variation screening. Sci Rep 2020; 10:3795. [PMID: 32123222 PMCID: PMC7052235 DOI: 10.1038/s41598-020-60704-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 02/13/2020] [Indexed: 12/22/2022] Open
Abstract
Whole-genome sequencing of preimplantation human embryos to detect and screen for genetic diseases is a technically challenging extension to preconception screening. Combining preconception genetic screening with preimplantation testing of human embryos facilitates the detection of de novo mutations and self-validates transmitted variant detection in both the reproductive couple and the embryo’s samples. Here we describe a trio testing workflow that involves whole-genome sequencing of amplified DNA from biopsied embryo trophectoderm cells and genomic DNA from both parents. Variant prediction software and annotation databases were used to assess variants of unknown significance and previously not described de novo variants in five single-gene preimplantation genetic testing couples and eleven of their embryos. Pathogenic variation, tandem repeat, copy number and structural variations were examined against variant calls for compound heterozygosity and predicted disease status was ascertained. Multiple trio testing showed complete concordance with known variants ascertained by single-nucleotide polymorphism array and uncovered de novo and transmitted pathogenic variants. This pilot study describes a method of whole-genome sequencing and analysis for embryo selection in high-risk couples to prevent early life fatal genetic conditions that adversely affect the quality of life of the individual and families.
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Affiliation(s)
- Nicholas M Murphy
- Genetic Technologies Ltd., Victoria, Australia. .,Monash IVF, Clayton, Victoria, Australia. .,GenEmbryomics Pty. Ltd., Victoria, Australia. .,Drug Delivery Disposition and Dynamics, Faculty of Pharmacy and Pharmaceutical Sciences, Parkville, Melbourne, Victoria, Australia.
| | | | | | | | - Luk J F Rombauts
- Monash IVF, Clayton, Victoria, Australia.,Centre for Reproductive Health, Hudson Institute of Medical Research, Clayton, Victoria, Australia.,Department of Obstetrics and Gynaecology, Monash University, Clayton, Victoria, Australia.,Monash Women's & Newborn Program, Monash Health, Victoria, Australia
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26
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Selič P, Klemenc-Ketiš Z, Zelko E, Kravos A, Rifel J, Makivić I, Poplas Susič A, Tevžič Š, Cerovič M, Peterlin B, Kopčavar Guček N. Development of an Algorithm for Determining of Genetic Risk at the Primary Healthcare Level - A New Tool for Primary Prevention: A Study Protocol. Zdr Varst 2020; 59:27-32. [PMID: 32952700 PMCID: PMC7478082 DOI: 10.2478/sjph-2020-0004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 10/21/2019] [Indexed: 01/05/2023] Open
Abstract
INTRODUCTION Family history (FH) is an important part of the patients' medical history during preventive management at model family medicine practices (MFMP). It currently includes a one (or two) generational inquiry, predominately in terms of cardiovascular diseases, arterial hypertension, and diabetes, but not of other diseases with a probable genetic aetiology. Beside family history, no application-based algorithm is available to determine the risk level for specific chronic diseases in Slovenia. METHODS A web application-based algorithm aimed at determining the risk level for selected monogenic and polygenic diseases will be developed. The data will be collected in MFMP; approximately 40 overall with a sample including healthy preventive examination attendees (approximately 1,000). Demographic data, a three-generational FH, a medical history of acquired and congenital risk factors for the selected diseases, and other important clinical factors will be documented. RESULTS The results will be validated by a clinical genetic approach based on family pedigrees and the next-generation genetic sequencing method. After the risk of genetic diseases in the Slovenian population has been determined, clinical pathways for acting according to the assessed risk level will be prepared. CONCLUSION By means of a public health tool providing an assessment of family predisposition, a contribution to the effective identification of people at increased risk of the selected monogenic and polygenic diseases is expected, lessening a significant public health burden.
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Affiliation(s)
- Polona Selič
- University of Ljubljana, Faculty of Medicine, Department of Family Medicine, Poljanski nasip 58, 1000Ljubljana, Slovenia
| | - Zalika Klemenc-Ketiš
- University of Ljubljana, Faculty of Medicine, Department of Family Medicine, Poljanski nasip 58, 1000Ljubljana, Slovenia
- Community Health Centre Ljubljana, Metelkova 9, 1000Ljubljana, Slovenia
- University of Maribor, Faculty of Medicine, Department of Family Medicine, Taborska 8, 2000Maribor, Slovenia
| | - Erika Zelko
- Community Health Centre Ljubljana, Metelkova 9, 1000Ljubljana, Slovenia
- University of Maribor, Faculty of Medicine, Department of Family Medicine, Taborska 8, 2000Maribor, Slovenia
| | - Andrej Kravos
- University of Maribor, Faculty of Medicine, Department of Family Medicine, Taborska 8, 2000Maribor, Slovenia
| | - Janez Rifel
- University of Ljubljana, Faculty of Medicine, Department of Family Medicine, Poljanski nasip 58, 1000Ljubljana, Slovenia
| | - Irena Makivić
- Community Health Centre Ljubljana, Metelkova 9, 1000Ljubljana, Slovenia
| | | | - Špela Tevžič
- Community Health Centre Ljubljana, Metelkova 9, 1000Ljubljana, Slovenia
| | - Metka Cerovič
- Community Health Centre dr. Adolfa Drolca Maribor, Ulica talcev 9, 2000Maribor, Slovenia
| | - Borut Peterlin
- University Medical Centre Ljubljana, Clinical Institute of Medical Genetics, Šlajmerjeva 4, 1000Ljubljana, Slovenia
| | - Nena Kopčavar Guček
- University of Ljubljana, Faculty of Medicine, Department of Family Medicine, Poljanski nasip 58, 1000Ljubljana, Slovenia
- Community Health Centre Ljubljana, Metelkova 9, 1000Ljubljana, Slovenia
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Abstract
Immigrant and refugee children are at increased risk for physical, developmental, and behavioral health challenges. This article provides an overview of physical, developmental, and behavioral health considerations for immigrant and refugee children within an ecological framework that highlights family, community, and sociocultural influences. Experiences and exposures relevant to immigrant and refugee children are discussed. Clinical pearls are provided for topics of chronic disease, nutrition, infectious disease, developmental screening, and mental health assessment. Interdisciplinary and community partnerships are emphasized as a means to decrease barriers to care and facilitate family navigation of complex social, educational, and health care systems.
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Affiliation(s)
- Abigail L H Kroening
- Division of Developmental and Behavioral Pediatrics, Golisano Children's Hospital, University of Rochester, 601 Elmwood Avenue Box #671, Rochester, NY 14623, USA.
| | - Elizabeth Dawson-Hahn
- Division of General Pediatrics, University of Washington, 6200 Northeast 74th Street Suite 110, Seattle, WA 98115-81860, USA
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Kaur M, Hadley DW, Muenke M, Hart PS. An International Summit in Human Genetics and Genomics: Empowering clinical practice and research in developing countries. Mol Genet Genomic Med 2019; 7:e00599. [PMID: 30786327 PMCID: PMC6382448 DOI: 10.1002/mgg3.599] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 01/16/2019] [Accepted: 01/16/2019] [Indexed: 12/30/2022] Open
Abstract
To help fill the knowledge gap in human genetics and genomics, an International Summit (IS) in Human Genetics and Genomics was conceived and organized by the National Human Genome Research Institute (NHGRI) of the National Institutes of Health (NIH) as a 5‐year initiative, from 2016 to 2020. In its first 3 years, 71 professionals from 34 countries received training.![]()
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Affiliation(s)
- Manjit Kaur
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Donald W Hadley
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Maximilian Muenke
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - P Suzanne Hart
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
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Clinical whole genome sequencing as a first-tier test at a resource-limited dysmorphology clinic in Mexico. NPJ Genom Med 2019; 4:5. [PMID: 30792901 PMCID: PMC6375919 DOI: 10.1038/s41525-018-0076-1] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 12/19/2018] [Indexed: 11/14/2022] Open
Abstract
Patients with rare, undiagnosed, or genetic disease (RUGD) often undergo years of serial testing, commonly referred to as the “diagnostic odyssey”. Patients in resource-limited areas face even greater challenges—a definitive diagnosis may never be reached due to difficulties in gaining access to clinicians, appropriate specialists, and diagnostic testing. Here, we report on a collaboration of the Illumina iHope Program with the Foundation for the Children of the Californias and Hospital Infantil de Las Californias, to enable deployment of clinical whole genome sequencing (cWGS) as first-tier test in a resource-limited dysmorphology clinic in northern Mexico. A total of 60 probands who were followed for a suspected genetic diagnosis and clinically unresolved after expert examination were tested with cWGS, and the ordering clinicians completed a semi-structured survey to investigate change in clinical management resulting from cWGS findings. Clinically significant genomic findings were identified in 68.3% (n = 41) of probands. No recurrent molecular diagnoses were observed. Copy number variants or gross chromosomal abnormalities accounted for 48.8% (n = 20) of the diagnosed cases, including a mosaic trisomy and suspected derivative chromosomes. A qualitative assessment of clinical management revealed 48.8% (n = 20) of those diagnosed had a change in clinical course based on their cWGS results, despite resource limitations. These data suggest that a cWGS first-tier testing approach can benefit patients with suspected genetic disorders. Whole-genome sequencing (WGS) provides a valuable first-tier diagnostic test at pediatric clinics in resource-limited
parts of the world, according to a study of children with suspected genetic disease treated in northern Mexico. A team led by Marilyn Jones from the Rady Children’s Hospital and Ryan Taft from Illumina Inc., both in San Diego, California, USA, describe a collaboration with a volunteer-led clinic in Tijuana, Mexico, where they offered genome sequencing for children with suspected genetic conditions—philanthropically through the iHope Program. Among the 60 families that participated, the clinical laboratory team identified genomic variants with diagnostic relevance in 41 (68%) cases. The genomic information contributed to changes in clinical management for 20 of these children, demonstrating the impact of WGS in places where patients generally don’t have access to medical specialists or other sophisticated molecular tests.
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Wang W, Yang J, Xue J, Mu W, Zhang X, Wu W, Xu M, Gong Y, Liu Y, Zhang Y, Xie X, Gu W, Bai J, Cram DS. A comprehensive multiplex PCR based exome-sequencing assay for rapid bloodspot confirmation of inborn errors of metabolism. BMC MEDICAL GENETICS 2019; 20:3. [PMID: 30612563 PMCID: PMC6322297 DOI: 10.1186/s12881-018-0731-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 11/28/2018] [Indexed: 01/22/2023]
Abstract
BACKGROUND Tandem mass spectrometry (MS MS) and simple fluorometric assays are currently used in newborn screening programs to detect inborn errors of metabolism (IEM). The aim of the study was to evaluate the clinical utility of exome sequencing as a second tier screening method to assist clinical diagnosis of the newborn. METHODS A novel PCR-exome amplification and re-sequencing (PEARS) assay was designed and used to detect mutations in 122 genes associated with 101 IEM. Newborn bloodspots positive by biochemical testing were analysed by PEARS assay to detect pathogenic mutations relevant to the IEM. RESULTS In initial validation studies of genomic DNA samples, PEARS assay correctly detected 25 known mutations associated with 17 different IEM. Retrospective gene analysis of newborns with clinical phenylketonuria (PKU), identified compound heterozygote phenylalanine hydroxylase (PAH) gene mutations in eight of nine samples (89%). Prospective analysis of 211 bloodspots correctly identified the two true PKU samples, yielding positive and negative predictive values of 100%. Testing of 8 true positive MS MS samples correctly identified potentially pathogenic compound heterozygote genotypes in 2 cases of citrullinemia type 1 and one case each of methylmalonic acidemia, isobutyryl-CoA dehydrogenase deficiency, short chain acyl-CoA dehydrogenase deficiency and glutaric acid type II and heterozygous genotypes in 2 cases of autosomal dominant methioninemia. Analysis of 11 of 12 false positive MS MS samples for other IEM identified heterozygous carriers in 8 cases for the relevant genes associated with the suspected IEM. In the remaining 3 cases, the test revealed compound heterozygote mutations in other metabolic genes not associated with the suspected IEM, indicating a misinterpretation of the original MS MS data. CONCLUSIONS The PEARS assay has clinical utility as a rapid and cost effective second-tier test to assist the clinician to accurately diagnose newborns with a suspected IEM.
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Affiliation(s)
- Wenjie Wang
- Children and Women's Hospital of Shanxi, Women Health Center of Shanxi, Taiyuan, Shanxi, China
| | - Jianping Yang
- Children and Women's Hospital of Shanxi, Newborn Disease Screening Center of Shanxi Province, Taiyuan, Shanxi, China
| | - Jinjie Xue
- Children and Women's Hospital of Shanxi, Women Health Center of Shanxi, Taiyuan, Shanxi, China
| | - Wenjuan Mu
- Children and Women's Hospital of Shanxi, Newborn Disease Screening Center of Shanxi Province, Taiyuan, Shanxi, China
| | - Xiaogang Zhang
- Children and Women's Hospital of Shanxi, Newborn Disease Screening Center of Shanxi Province, Taiyuan, Shanxi, China
| | - Wang Wu
- Beijing Berry Genomics Corporation, Building 5, Courtyard 4, Yiliaoyuan Road, ZGC Life Science Park, Beijing, 102206, Changping District, China
| | - Mengnan Xu
- Beijing Berry Genomics Corporation, Building 5, Courtyard 4, Yiliaoyuan Road, ZGC Life Science Park, Beijing, 102206, Changping District, China
| | - Yuyan Gong
- Beijing Berry Genomics Corporation, Building 5, Courtyard 4, Yiliaoyuan Road, ZGC Life Science Park, Beijing, 102206, Changping District, China
| | - Yiqian Liu
- Beijing Berry Genomics Corporation, Building 5, Courtyard 4, Yiliaoyuan Road, ZGC Life Science Park, Beijing, 102206, Changping District, China
| | - Yu Zhang
- Beijing Berry Genomics Corporation, Building 5, Courtyard 4, Yiliaoyuan Road, ZGC Life Science Park, Beijing, 102206, Changping District, China
| | - Xiaobing Xie
- Beijing Chigene Translational Medicial Research Center Co., Beijing, 101111, China
| | - Weiyue Gu
- Beijing Chigene Translational Medicial Research Center Co., Beijing, 101111, China
| | - Jigeng Bai
- Children and Women's Hospital of Shanxi, Women Health Center of Shanxi, Taiyuan, Shanxi, China
| | - David S Cram
- Children and Women's Hospital of Shanxi, Women Health Center of Shanxi, Taiyuan, Shanxi, China. .,Beijing Berry Genomics Corporation, Building 5, Courtyard 4, Yiliaoyuan Road, ZGC Life Science Park, Beijing, 102206, Changping District, China.
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Medizinische Maßnahmen bei immigrierenden Kindern und Jugendlichen – Aktualisierung vom 28.02.2018. Monatsschr Kinderheilkd 2018. [DOI: 10.1007/s00112-018-0497-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Blencowe H, Moorthie S, Darlison MW, Gibbons S, Modell B. Methods to estimate access to care and the effect of interventions on the outcomes of congenital disorders. J Community Genet 2018; 9:363-376. [PMID: 29549604 PMCID: PMC6167260 DOI: 10.1007/s12687-018-0359-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 02/15/2018] [Indexed: 12/11/2022] Open
Abstract
In the absence of intervention, early-onset congenital disorders lead to pregnancy loss, early death, or disability. Currently, lack of epidemiological data from many settings limits the understanding of the burden of these conditions, thus impeding health planning, policy-making, and commensurate resource allocation. The Modell Global Database of Congenital Disorders (MGDb) seeks to meet this need by combining general biological principles with observational and demographic data, to generate estimates of the burden of congenital disorders. A range of interventions along the life course can modify adverse outcomes associated with congenital disorders. Hence, access to and quality of services available for the prevention and care of congenital disorders affects both their birth prevalence and the outcomes for affected individuals. Information on this is therefore important to enable burden estimates for settings with limited observational data, but is lacking from many settings. This paper, the third in this special issue on methods used in the MGDb for estimating the global burden of congenital disorders, describes key interventions that impact on outcomes of congenital disorders and methods used to estimate their coverage where empirical data are not available.
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Affiliation(s)
- Hannah Blencowe
- Centre for Maternal, Adolescent, Reproductive, and Child Health, London School of Hygiene & Tropical Medicine, London, UK
| | | | - Matthew W Darlison
- Centre for Health Informatics and Multiprofessional Education (CHIME), University College London, London, UK.
| | - Stephen Gibbons
- Department of Geography and Environment, London School of Economics, London, UK
| | - Bernadette Modell
- Centre for Health Informatics and Multiprofessional Education (CHIME), University College London, London, UK
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Phadke SR, Puri RD, Ranganath P. Prenatal screening for genetic disorders: Suggested guidelines for the Indian Scenario. Indian J Med Res 2018; 146:689-699. [PMID: 29664026 PMCID: PMC5926339 DOI: 10.4103/ijmr.ijmr_1788_15] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Prenatal testing is the best strategy for reducing the burden of genetic disorders and congenital disabilities that cause significant postnatal functional impairment. Universal prenatal screening is advisable for common genetic disorders and congenital anomalies such as Down syndrome, beta-thalassaemia and neural tube defects. Several prenatal-screening tests are now available for Down syndrome, but knowledge about the appropriate timing of the test and the need for pre- and post-test counselling may not be updated among the primary care physicians. There is also a considerable degree of confusion regarding the prenatal screening test to be chosen in each case, due to the availability of a number of new and advanced screening techniques. At present, there is no nation-wide consensus regarding the nature and timing of these prenatal-screening protocols. Due to the absence of any definite guidelines and the additional lacunae in the awareness regarding the appropriate prenatal screening in the country, the optimum benefits of these screening protocols are not reaching the population. This review focuses on the various prenatal screening and diagnostic tests that are available for common genetic conditions and congenital disabilities and attempts to outline the most cost-effective and gestational age-appropriate strategies for prenatal screening for the Indian healthcare set-up. The recommendations suggested would serve as a source guide for formulating prenatal-screening guidelines for reducing the incidence of common genetic disorders and congenital disabilities in India.
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Affiliation(s)
- Shubha R Phadke
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
| | - Ratna D Puri
- Institute of Medical Genetics & Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Prajnya Ranganath
- Department of Medical Genetics, Nizam's Institute of Medical Sciences, Hyderabad, India
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Wilson RD. Woman's Pre-Conception Evaluation: Genetic and Fetal Risk Considerations for Counselling and Informed Choice. JOURNAL OF OBSTETRICS AND GYNAECOLOGY CANADA 2018; 40:935-949. [DOI: 10.1016/j.jogc.2017.07.024] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Revised: 07/26/2017] [Accepted: 07/26/2017] [Indexed: 12/30/2022]
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Clinical validity of phenotype-driven analysis software PhenoVar as a diagnostic aid for clinical geneticists in the interpretation of whole-exome sequencing data. Genet Med 2018; 20:942-949. [PMID: 29388948 DOI: 10.1038/gim.2017.239] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 11/20/2017] [Indexed: 12/12/2022] Open
Abstract
PURPOSE We sought to determine the diagnostic yield of whole-exome sequencing (WES) combined with phenotype-driven analysis of variants in patients with suspected genetic disorders. METHODS WES was performed on a cohort of 51 patients presenting dysmorphisms with or without neurodevelopmental disorders of undetermined etiology. For each patient, a clinical geneticist reviewed the phenotypes and used the phenotype-driven analysis software PhenoVar (http://phenovar.med.usherbrooke.ca/) to analyze WES variants. The prioritized list of potential diagnoses returned was reviewed by the clinical geneticist, who selected candidate variants to be confirmed by segregation analysis. Conventional analysis of the individual variants was performed in parallel. The resulting candidate variants were subsequently reviewed by the same geneticist, to identify any additional potential diagnoses. RESULTS A molecular diagnosis was identified in 35% of the patients using the conventional analysis, and 17 of these 18 diagnoses were independently identified using PhenoVar. The only diagnosis initially missed by PhenoVar was rescued when the optional "minimal phenotypic cutoff" filter was omitted. PhenoVar reduced by half the number of potential diagnoses per patient compared with the conventional analysis. CONCLUSION Phenotype-driven software prioritizes WES variants, provides an efficient diagnostic aid to clinical geneticists and laboratories, and should be incorporated in clinical practice.
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Expanded carrier screening and preimplantation genetic diagnosis in a couple who delivered a baby affected with congenital factor VII deficiency. BMC MEDICAL GENETICS 2018; 19:15. [PMID: 29368589 PMCID: PMC5784596 DOI: 10.1186/s12881-018-0525-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 01/09/2018] [Indexed: 12/24/2022]
Abstract
Background Preimplantation genetic diagnosis (PGD) is a powerful tool for preventing the transmission of Mendelian disorders from generation to generation. However, PGD only can identify monogenically inherited diseases, but not other potential monogenic pathologies. We aimed to use PGD to deliver a healthy baby without congenital FVII deficiency or other common Mendelian diseases in a couple in which both individuals carried a deleterious mutation in the F7 gene. Methods After both members of the couple were confirmed to be carriers of the F7 gene mutation by Sanger sequencing, expanded carrier screening (ECS) for 623 recessive inheritance diseases was performed to detect pathological mutations in other genes. PGD and preimplantational genetic screening (PGS) were employed to exclude monogenic disorders and aneuploidy for their embryos. Results ECS using targeted capture sequencing technology revealed that the couple carried the heterozygous disease-causative mutations c.3659C > T (p.Thr1220Ile) and c.3209G > A (p.Arg1070Gln) in the CFTR gene. After PGD and PGS, one of their embryos that was free of congenital FVII deficiency, cystic fibrosis (CF) and aneuploidy was transferred, resulting in the birth of a healthy 3200 g male infant. Conclusion We successfully implemented PGD for congenital FVII deficiency and PGD after ECS to exclude CF for the first time to the best of our knowledge. Our work significantly improved the reproductive outcome for the couple and provides a clear example of the use of ECS combined with PGD to avoid the delivery of offspring affected not only by identified monogenically inherited diseases but also by other potential monogenic pathologies and aneuploidy.
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Kranendonk EJ, Hennekam RC, Ploem MC. Paediatric biobanking: Dutch experts reflecting on appropriate legal standards for practice. Eur J Pediatr 2017; 176:75-82. [PMID: 27866271 PMCID: PMC5219008 DOI: 10.1007/s00431-016-2810-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 11/04/2016] [Accepted: 11/08/2016] [Indexed: 12/01/2022]
Abstract
Large sets of data and human specimens, such as blood, tumour tissue and DNA, are deposited in biobanks for research purposes, preferably for long periods of time and with broadly defined research aims. Our research focuses on the retention of data and biological materials obtained from children. However important such paediatric biobanks may be, the privacy interests of the children involved and the related risks may not be ignored. The privacy issues arising from paediatric biobanks are the central focus of this article. We first review the international regulations that apply to biobanks and then summarise viewpoints expressed by experts in a round-table discussion. We confine ourselves here to two normative questions: (1) How much control should children's parents or legal representatives, and later the children themselves, have over the stored materials and data? (2) What should be done if research findings emerge that have serious implications for a child's health? CONCLUSION On the basis of international legal standards and the views of experts, involved in paediatric biobanking, we argue that biological material of children may only be stored in a biobank for scientific purposes if parents provide their explicit consent, the child is re-contacted at 16 or 18 years of age to reconsider storage and use of its material, and the biobank maintains a limited policy in disclosure of individual research findings to the child's parents. What is Known: • Increasingly, biological material of children is stored in biobanks for research purposes. • Clear standards on the conditions under which children's cells or tissues may be stored and used are lacking. What is New: • According to experts, storage and use of children's materials should only be allowed if performed in accordance with appropriate consent procedures and feedback policies.
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Affiliation(s)
- Elcke J. Kranendonk
- Department of Public Health, Academic Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
- Department of Public Health AMC, Room J2-210, P.O. Box 22660, 1100 DD Amsterdam, The Netherlands
| | - Raoul C. Hennekam
- Department of Pediatrics, Academic Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - M. Corrette Ploem
- Department of Public Health, Academic Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
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Aleksandrova N, Shubina E, Ekimov A, Kodyleva T, Mukosey I, Makarova N, Kulakova E, Levkov L, Trofimov D, Sukhikh G. Comparison of the results of preimplantation genetic screening obtained by a-CGH and NGS methods from the same embryos. Gynecol Endocrinol 2016; 32:1-4. [PMID: 27759447 DOI: 10.1080/09513590.2016.1232892] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Chromosomal aneuploidies are known for being the main cause of abnormal development of embryos with normal morphology, their implantation failure and early reproductive losses in IVF treatments. Preimplantation genetic screening (PGS) allows selecting embryos with normal chromosomal content and increases IVF treatment efficiency due to higher implantation rates and less frequent early pregnancy losses. New technologies used for PGS allow making genome-wide analysis of the presence of all chromosomes in embryos. This article presents our study of evaluation of two techniques used for PGS: previously developed and used in our laboratory a-CGH assay based on Agilent technology and newly tested semi-conductive NGS technique (Torrent technology).
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Affiliation(s)
- N Aleksandrova
- a Federal State Budget Institution "Research Center for Obstetrics, Gynecology and Perinatology" Ministry of Healthcare of the Russian Federation , Russia
| | - E Shubina
- a Federal State Budget Institution "Research Center for Obstetrics, Gynecology and Perinatology" Ministry of Healthcare of the Russian Federation , Russia
| | - A Ekimov
- a Federal State Budget Institution "Research Center for Obstetrics, Gynecology and Perinatology" Ministry of Healthcare of the Russian Federation , Russia
| | - T Kodyleva
- a Federal State Budget Institution "Research Center for Obstetrics, Gynecology and Perinatology" Ministry of Healthcare of the Russian Federation , Russia
| | - I Mukosey
- a Federal State Budget Institution "Research Center for Obstetrics, Gynecology and Perinatology" Ministry of Healthcare of the Russian Federation , Russia
| | - N Makarova
- a Federal State Budget Institution "Research Center for Obstetrics, Gynecology and Perinatology" Ministry of Healthcare of the Russian Federation , Russia
| | - E Kulakova
- a Federal State Budget Institution "Research Center for Obstetrics, Gynecology and Perinatology" Ministry of Healthcare of the Russian Federation , Russia
| | - L Levkov
- a Federal State Budget Institution "Research Center for Obstetrics, Gynecology and Perinatology" Ministry of Healthcare of the Russian Federation , Russia
| | - D Trofimov
- a Federal State Budget Institution "Research Center for Obstetrics, Gynecology and Perinatology" Ministry of Healthcare of the Russian Federation , Russia
| | - G Sukhikh
- a Federal State Budget Institution "Research Center for Obstetrics, Gynecology and Perinatology" Ministry of Healthcare of the Russian Federation , Russia
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Pietropolli A, Capogna MV, Cascella R, Germani C, Bruno V, Strafella C, Sarta S, Ticconi C, Marmo G, Gallaro S, Longo G, Marsella LT, Novelli A, Novelli G, Piccione E, Giardina E. Three-hour analysis of non-invasive foetal sex determination: application of Plexor chemistry. Hum Genomics 2016; 10:9. [PMID: 27044517 PMCID: PMC4820952 DOI: 10.1186/s40246-016-0066-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 03/28/2016] [Indexed: 11/26/2022] Open
Abstract
Background The knowledge of the individual genetic “status” in the prenatal era is particularly relevant in the case of positive family history for genetic diseases, in advanced maternal age and in the general screening for foetal abnormalities. In this context, here, we report an innovative molecular assay which utilizes the cell-free foetal DNA (cffDNA) as a source for the early and fast detection of the foetal sex. The study involved 132 pregnant women in their first 3 months of pregnancy, who agreed to give a blood sample. All the collected samples were immediately subjected to the separation of the plasma, which was utilized for the extraction of the cffDNA. Successively, the extracted cffDNA was analysed by a quantitative PCR (qPCR) method based on Plexor-HY chemistry, which is able to simultaneously identify, quantify and discriminate the autosomal DNA from the sex-linked DNA. Results Overall, the Plexor-HY assay demonstrated to be sensitive and specific for the determination of low-template DNA, such as the cffDNA. In fact, the Plexor-HY assay has been successfully performed in all the samples, identifying 70 males and 62 females. As the foetal sex can be provided in 120 min just by utilizing a maternal blood sample as cffDNA source, the assay represents a very fast, safe and non-invasive prenatal method. Conclusions The possibility of determining the foetal sex in the early prenatal life consents the application of our assay as a helpful screening test for subjects and families at risk of sex-linked disorders. Moreover, the early knowledge of the foetal sex may be of great help even for the specialist, who might promptly advise the patients concerning the foetal risk of inheriting sex-linked disorders and the clinical utility of performing an invasive prenatal diagnosis. Electronic supplementary material The online version of this article (doi:10.1186/s40246-016-0066-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Adalgisa Pietropolli
- Section of Gynecology and Obstetrics, Academic Department of Biomedicine and Prevention, "Tor Vergata" University Hospital, Oxford Street, 81, 00133, Rome, Italy.,Clinical Department of Surgery, "Tor Vergata" University Hospital, Oxford Street, 81, 00133, Rome, Italy
| | - Maria Vittoria Capogna
- Section of Gynecology and Obstetrics, Academic Department of Biomedicine and Prevention, "Tor Vergata" University Hospital, Oxford Street, 81, 00133, Rome, Italy.,Clinical Department of Surgery, "Tor Vergata" University Hospital, Oxford Street, 81, 00133, Rome, Italy
| | - Raffaella Cascella
- Department of Biomedicine and Prevention, School of Medicine, University of Rome "Tor Vergata", Montpelier Street, 1, 00133, Rome, Italy. .,Emotest Laboratory, M. Licola Patria Street, 60, 80078, Pozzuoli, NA, Italy.
| | - Chiara Germani
- Molecular Genetics Laboratory UILDM, Santa Lucia Foundation, Ardeatina Street, 306, 00142, Rome, Italy
| | - Valentina Bruno
- Section of Gynecology and Obstetrics, Academic Department of Biomedicine and Prevention, "Tor Vergata" University Hospital, Oxford Street, 81, 00133, Rome, Italy.,Clinical Department of Surgery, "Tor Vergata" University Hospital, Oxford Street, 81, 00133, Rome, Italy
| | - Claudia Strafella
- Department of Biomedicine and Prevention, School of Medicine, University of Rome "Tor Vergata", Montpelier Street, 1, 00133, Rome, Italy
| | - Simona Sarta
- Section of Gynecology and Obstetrics, Academic Department of Biomedicine and Prevention, "Tor Vergata" University Hospital, Oxford Street, 81, 00133, Rome, Italy.,Clinical Department of Surgery, "Tor Vergata" University Hospital, Oxford Street, 81, 00133, Rome, Italy
| | - Carlo Ticconi
- Section of Gynecology and Obstetrics, Academic Department of Biomedicine and Prevention, "Tor Vergata" University Hospital, Oxford Street, 81, 00133, Rome, Italy.,Clinical Department of Surgery, "Tor Vergata" University Hospital, Oxford Street, 81, 00133, Rome, Italy
| | - Giusy Marmo
- Department of Biomedicine and Prevention, School of Medicine, University of Rome "Tor Vergata", Montpelier Street, 1, 00133, Rome, Italy
| | - Sara Gallaro
- Department of Biomedicine and Prevention, School of Medicine, University of Rome "Tor Vergata", Montpelier Street, 1, 00133, Rome, Italy
| | - Giuliana Longo
- Department of Biomedicine and Prevention, School of Medicine, University of Rome "Tor Vergata", Montpelier Street, 1, 00133, Rome, Italy
| | - Luigi Tonino Marsella
- Department of Biomedicine and Prevention, School of Medicine, University of Rome "Tor Vergata", Montpelier Street, 1, 00133, Rome, Italy
| | - Antonio Novelli
- Bambino Gesù Children's Hospital, IRCCS, Sant'Onofrio Square, 4, Rome, Italy
| | - Giuseppe Novelli
- Department of Biomedicine and Prevention, School of Medicine, University of Rome "Tor Vergata", Montpelier Street, 1, 00133, Rome, Italy
| | - Emilio Piccione
- Section of Gynecology and Obstetrics, Academic Department of Biomedicine and Prevention, "Tor Vergata" University Hospital, Oxford Street, 81, 00133, Rome, Italy.,Clinical Department of Surgery, "Tor Vergata" University Hospital, Oxford Street, 81, 00133, Rome, Italy
| | - Emiliano Giardina
- Department of Biomedicine and Prevention, School of Medicine, University of Rome "Tor Vergata", Montpelier Street, 1, 00133, Rome, Italy.,Molecular Genetics Laboratory UILDM, Santa Lucia Foundation, Ardeatina Street, 306, 00142, Rome, Italy
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Chakrabarty S, Kabekkodu SP, Brand A, Satyamoorthy K. Perspectives on Translational Genomics and Public Health in India. Public Health Genomics 2015; 19:61-8. [PMID: 26683060 DOI: 10.1159/000442518] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 11/18/2015] [Indexed: 11/19/2022] Open
Abstract
It is now recognized worldwide that anticipation and prevention of diseases have significant advantages for the health and healthy ageing of the population. Early recognition of the disease in a vulnerable population such as in children aged <5 years and adults aged >60 years enhances our preparedness for any eventualities and future burden of the diseases to society. It is also recognized that current public health practices alone cannot bring about the desired outcome. When tackling public health-related issues, such problems must be recognized and state-of-the-art principles and innovations from genomic sciences, information technologies, and medical specialties must be encompassed and embraced. These will enhance strategies for preparedness and provide us with a better understanding of how to identify, manage, and control disease burdens. The ever expanding landscape of genomics research also includes experimental and computational approaches for effectively utilizing DNA sequence information. From these perspectives, the intricacies of Mendelian single gene disorders are the least challenging compared to intricacies of multi-dimensional host factors for infectious diseases or complex disorders such as cancer. The concepts of public health in India are on firm footing; however, integration of contemporary advances to implement public health principles into practice has neither been attempted nor impacted on disease burden or our preparedness to prevent eventualities. At the same time, translational genomics is gradually paving the way for personalized medicine. Principles of personalized medicine remain to be fully understood and practiced despite the pharmacogenomics-based future of drug development, and treatment has not been as exciting as the advances in genomics we are witnessing today. The relevance, importance, and translational impediments of these advances will be discussed.
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