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Yaylacioglu Tuncay F, Karaismailoglu E, Özdek Ş. Current clinical practice and needs assessment in inherited eye diseases from the perspective of ophthalmologists. Ophthalmic Genet 2024:1-8. [PMID: 38832414 DOI: 10.1080/13816810.2024.2358965] [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: 08/09/2023] [Accepted: 05/19/2024] [Indexed: 06/05/2024]
Abstract
BACKGROUND The clinical approach to inherited eye diseases has evolved due to advances in genetic testing methods and treatment opportunities. However, no data are available on the current practices of ophthalmologists in countries, such as Turkey, with higher rates of consanguinity and inherited eye diseases. The aim of this study was to evaluate the current practices, knowledge, and needs of ophthalmologists in Turkey regarding inherited eye diseases. METHODS A 29-item self-administered survey with a branching algorithm was developed through Google Forms. The survey link was sent to 2983 ophthalmologists in Turkey. The survey assessed respondents' occupational characteristics, current practices, knowledge about available diagnostic and therapeutic options, and opinions on improving continuing education and healthcare services. RESULTS Responses from 414 ophthalmologists (20.8%) were analyzed. The responses suggested that ophthalmologists mainly collaborate with medical geneticists in respect of inherited eye diseases. The majority of ophthalmologists reported a lack of knowledge about genetic diagnostic tests, and approximately 90% of the ophthalmologists thought training after residency was inadequate for inherited eye diseases. CONCLUSION This is the most extensive survey exploring ophthalmologists' practice patterns and needs in a setting without specialists or specialized centers in ophthalmic genetics. The results emphasize the need for continued education on updated approaches to inherited eye diseases.
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Affiliation(s)
- Fulya Yaylacioglu Tuncay
- Department of Medical Biology, Gülhane Medical Faculty, University of Health Sciences, Ankara, Turkey
| | - Eda Karaismailoglu
- Department of Medical Informatics, Gülhane Medical Faculty, University of Health Sciences, Ankara, Turkey
| | - Şengül Özdek
- Department of Ophthalmology, Medical Faculty, Gazi University, Ankara, Turkey
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2
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Kernohan KD, Boycott KM. The expanding diagnostic toolbox for rare genetic diseases. Nat Rev Genet 2024; 25:401-415. [PMID: 38238519 DOI: 10.1038/s41576-023-00683-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/22/2023] [Indexed: 05/23/2024]
Abstract
Genomic technologies, such as targeted, exome and short-read genome sequencing approaches, have revolutionized the care of patients with rare genetic diseases. However, more than half of patients remain without a diagnosis. Emerging approaches from research-based settings such as long-read genome sequencing and optical genome mapping hold promise for improving the identification of disease-causal genetic variants. In addition, new omic technologies that measure the transcriptome, epigenome, proteome or metabolome are showing great potential for variant interpretation. As genetic testing options rapidly expand, the clinical community needs to be mindful of their individual strengths and limitations, as well as remaining challenges, to select the appropriate diagnostic test, correctly interpret results and drive innovation to address insufficiencies. If used effectively - through truly integrative multi-omics approaches and data sharing - the resulting large quantities of data from these established and emerging technologies will greatly improve the interpretative power of genetic and genomic diagnostics for rare diseases.
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Affiliation(s)
- Kristin D Kernohan
- CHEO Research Institute, University of Ottawa, Ottawa, ON, Canada
- Newborn Screening Ontario, CHEO, Ottawa, ON, Canada
| | - Kym M Boycott
- CHEO Research Institute, University of Ottawa, Ottawa, ON, Canada.
- Department of Genetics, CHEO, Ottawa, ON, Canada.
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3
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Tesi B, Boileau C, Boycott KM, Canaud G, Caulfield M, Choukair D, Hill S, Spielmann M, Wedell A, Wirta V, Nordgren A, Lindstrand A. Precision medicine in rare diseases: What is next? J Intern Med 2023; 294:397-412. [PMID: 37211972 DOI: 10.1111/joim.13655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Molecular diagnostics is a cornerstone of modern precision medicine, broadly understood as tailoring an individual's treatment, follow-up, and care based on molecular data. In rare diseases (RDs), molecular diagnoses reveal valuable information about the cause of symptoms, disease progression, familial risk, and in certain cases, unlock access to targeted therapies. Due to decreasing DNA sequencing costs, genome sequencing (GS) is emerging as the primary method for precision diagnostics in RDs. Several ongoing European initiatives for precision medicine have chosen GS as their method of choice. Recent research supports the role for GS as first-line genetic investigation in individuals with suspected RD, due to its improved diagnostic yield compared to other methods. Moreover, GS can detect a broad range of genetic aberrations including those in noncoding regions, producing comprehensive data that can be periodically reanalyzed for years to come when further evidence emerges. Indeed, targeted drug development and repurposing of medicines can be accelerated as more individuals with RDs receive a molecular diagnosis. Multidisciplinary teams in which clinical specialists collaborate with geneticists, genomics education of professionals and the public, and dialogue with patient advocacy groups are essential elements for the integration of precision medicine into clinical practice worldwide. It is also paramount that large research projects share genetic data and leverage novel technologies to fully diagnose individuals with RDs. In conclusion, GS increases diagnostic yields and is a crucial step toward precision medicine for RDs. Its clinical implementation will enable better patient management, unlock targeted therapies, and guide the development of innovative treatments.
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Affiliation(s)
- Bianca Tesi
- Department of Molecular Medicine and Surgery and Centre of Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
- Center for Hematology and Regenerative Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Catherine Boileau
- Département de Génétique, APHP, Hôpital Bichat-Claude Bernard, Université Paris Cité, Paris, France
| | - Kym M Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Guillaume Canaud
- INSERM U1151, Unité de médecine translationnelle et thérapies ciblées, Hôpital Necker-Enfants Malades, Université Paris Cité, AP-HP, Paris, France
| | - Mark Caulfield
- William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Daniela Choukair
- Division of Pediatric Endocrinology and Diabetes, Center for Pediatrics and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany and Center for Rare Diseases, University Hospital Heidelberg, Heidelberg, Germany
| | - Sue Hill
- Chief Scientific Officer, NHS England, London, UK
| | - Malte Spielmann
- Institute of Human Genetics, University Hospitals Schleswig-Holstein, University of Lübeck and Kiel University, Lübeck, Kiel, Germany
| | - Anna Wedell
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Valtteri Wirta
- Science for Life Laboratory, Department of Microbiology, Tumour and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institutet of Technology, Stockholm, Sweden
| | - Ann Nordgren
- Department of Molecular Medicine and Surgery and Centre of Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
- Department of Laboratory Medicine, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Anna Lindstrand
- Department of Molecular Medicine and Surgery and Centre of Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
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Chen SC, Zhou XY, Li SY, Zhao MM, Huang HF, Jia J, Xu CM. Carrier burden of over 300 diseases in Han Chinese identified by expanded carrier testing of 300 couples using assisted reproductive technology. J Assist Reprod Genet 2023; 40:2157-2173. [PMID: 37450097 PMCID: PMC10440320 DOI: 10.1007/s10815-023-02876-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 06/22/2023] [Indexed: 07/18/2023] Open
Abstract
BACKGROUND Expanded carrier screening (ECS) has become a common practice for identifying carriers of monogenic diseases. However, existing large gene panels are not well-tailored to Chinese populations. In this study, ECS testing for pathogenic variants of both single-nucleotide variants (SNVs) and copy number variants (CNVs) in 330 genes implicated in 342 autosomal recessive (AR) or X-linked diseases was carried out. We assessed the differences in allele frequencies specific to the Chinese population who have used assisted reproductive technology (ART) and the important genes to screen for in this population. METHODOLOGY A total of 300 heterosexual couples were screened by our ECS panel using next-generation sequencing. A customed bioinformatic algorithm was used to analyze SNVs and CNVs. Guidelines from the American College of Medical Genetics and Genomics and the Association for Molecular Pathology were adapted for variant interpretation. Pathogenic or likely pathogenic (P/LP) SNVs located in high homology regions/deletions and duplications of one or more exons in length were independently verified with other methods. RESULTS 64.83% of the patients were identified to be carriers of at least one of 342 hereditary conditions. We identified 622 P/LP variants, 4.18% of which were flagged as CNVs. The rate of at-risk couples was 3%. A total of 149 AR diseases accounted for 64.05% of the cumulative carrier rate, and 48 diseases had a carrier rate above 1/200 in the test. CONCLUSION An expanded screening of inherited diseases by incorporating different variant types, especially CNVs, has the potential to reduce the occurrence of severe monogenic diseases in the offspring of patients using ART in China.
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Affiliation(s)
- Song-Chang Chen
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, 566 Fangxie Road, Huangpu District, Shanghai, 200001, China
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Xuan-You Zhou
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, 566 Fangxie Road, Huangpu District, Shanghai, 200001, China
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Shu-Yuan Li
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Ming-Min Zhao
- Fujungenetics Biotechnology Co., Ltd., No. 70 of Tongchuan Road, Putuo District, Shanghai, 200333, China
| | - He-Feng Huang
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, 566 Fangxie Road, Huangpu District, Shanghai, 200001, China
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200030, China
- Research Units of Embryo Original Diseases, Chinese Academy of Medical Sciences (No. 2019RU056), Shanghai, China
| | - Jia Jia
- Fujungenetics Biotechnology Co., Ltd., No. 70 of Tongchuan Road, Putuo District, Shanghai, 200333, China.
| | - Chen-Ming Xu
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, 566 Fangxie Road, Huangpu District, Shanghai, 200001, China.
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200030, China.
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5
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Callahan KP, Radack J, Wojcik MH, Jenkins SM, Nye RT, Skraban C, Wild KT, Feudtner C. Hospital-level variation in genetic testing in children's hospitals' neonatal intensive care units from 2016 to 2021. Genet Med 2023; 25:100357. [PMID: 36521640 PMCID: PMC9991964 DOI: 10.1016/j.gim.2022.12.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 12/07/2022] [Accepted: 12/08/2022] [Indexed: 12/14/2022] Open
Abstract
PURPOSE This study aimed to examine variation in genetic testing between neonatal intensive care units (NICUs) across hospitals over time. METHODS We performed a multicenter large-scale retrospective cohort study using NICU discharge data from the Pediatric Hospital Information System database between 2016 and 2021. We analyzed the variation in the percentage of NICU patients who had any genetic testing across hospitals and over time. We used a multivariable multilevel logistic regression model to investigate the potential association between patient characteristics and genetic testing. RESULTS The final analysis included 207,228 neonates from 38 hospitals. Overall, 13% of patients had at least 1 genetic test sent, although this varied from 4% to 50% across hospitals. Over the study period, the proportion of patients tested increased, with the increase disproportionately borne by hospitals already testing high proportions of patients. On average, patients who received genetic testing had higher illness severity. Controlling for severity, however, only minimally reduced the degree of hospital-level variation in genetic testing. CONCLUSION The percentage of NICU patients who undergo genetic testing varies among hospitals and increasingly so over time. Variation is largely unexplained by differences in severity between hospitals. The degree of variation suggests that clearer guidelines for NICU genetic testing are warranted.
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Affiliation(s)
- Katharine Press Callahan
- Division of Neonatology, Children's Hospital of Philadelphia Philadelphia, PA; Department of Medical Ethics and Health Policy, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA.
| | - Joshua Radack
- Division of Neonatology, Children's Hospital of Philadelphia Philadelphia, PA
| | - Monica H Wojcik
- Divisions of Newborn Medicine and Genetics and Genomics, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Sabrina Malone Jenkins
- Division of Neonatology, Department of Pediatrics, School of Medicine, Health University of Utah, Salt Lake City, UT
| | - Russell T Nye
- Division of Neonatology, Children's Hospital of Philadelphia Philadelphia, PA
| | - Cara Skraban
- Division of Neonatology, Children's Hospital of Philadelphia Philadelphia, PA
| | | | - Chris Feudtner
- Division of Neonatology, Children's Hospital of Philadelphia Philadelphia, PA; Department of Medical Ethics and Health Policy, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
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6
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Abstract
Exome sequencing (ES) and genome sequencing (GS) have radically transformed the diagnostic approach to undiagnosed rare/ultrarare Mendelian diseases. Next-generation sequencing (NGS), the technology integral for ES, GS, and most large (100+) gene panels, has enabled previously unimaginable diagnoses, changes in medical management, new treatments, and accurate reproductive risk assessments for patients, as well as new disease gene discoveries. Yet, challenges remain, as most individuals remain undiagnosed with current NGS. Improved NGS technology has resulted in long-read sequencing, which may resolve diagnoses in some patients who do not obtain a diagnosis with current short-read ES and GS, but its effectiveness is unclear, and it is expensive. Other challenges that persist include the resolution of variants of uncertain significance, the urgent need for patients with ultrarare disorders to have access to therapeutics, the need for equity in patient access to NGS-based testing, and the study of ethical concerns. However, the outlook for undiagnosed disease resolution is bright, due to continual advancements in the field.
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Affiliation(s)
- Jennifer A Sullivan
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina, USA;
| | - Kelly Schoch
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina, USA;
| | - Rebecca C Spillmann
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina, USA;
| | - Vandana Shashi
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina, USA;
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7
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Chen G, Xiong S, Zou G, Wu F, Qu X, Alawbathani S, Sun L. A 6.3 Mb maternally derived microduplication of 20p13p12.2 in a fetus with Brachydactyly type D and related literature review. Mol Cytogenet 2022; 15:6. [PMID: 35227291 PMCID: PMC8887085 DOI: 10.1186/s13039-022-00584-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Accepted: 01/26/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
With the introduction of genetic tests such as chromosomal microarray analysis (CMA) and exome sequencing (ES) into fetal medical practices, genotype–phenotype correlations in intrauterine-onset disorders have substantially improved. The BMP2 gene, located on the long arm of chromosome 20 plays a role in bone and cartilage development and is associated with Brachydactyly type A2, an autosomal dominant disease characterized by malformations of the middle phalanx of the index finger and abnormalities of the second toe. However, the BMP2 gene has so far never been reported as a candidate gene for Brachydactyly type D (BDD) affecting only the thumbs.
Methods and
results
Here, we report one family possessing a maternally inherited 6.3 Mb microduplication of 20p13p12.2 including the BMP2 gene with discordant phenotypes between the mother and the fetus. The mother was affected with BDD alongside mild facial dysmorphism and learning difficulties, while the female fetus showed BDD, severe symmetric intrauterine growth restriction combined with oligohydramnios. The CMA and Trio ES tests were implemented. Trio ES ruled out other possible monogenic causes for the family. After reviewing cases and literature with duplications within this genomic region, we found that they are extremely rare and most of the cited cases were too small for comparison. The disturbance of the BMP2 gene could explain BDD, but the other clinical presentations in the mother and fetus are not yet fully understood.
Conclusion
This study provides important evidence for the current understanding of genotype–phenotype association of this 6.3 Mb size duplication in the 20p13p12.2 region. This duplication is a unique CNV occurring so far only in this family. Further cases and research are needed to understand the discordance in the phenotypes between the mother and fetus and establish the relationship between BMP2 gene and BDD.
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8
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Chow AJ, Iverson R, Lamoureux M, Tingley K, Jordan I, Pallone N, Smith M, Al-Baldawi Z, Chakraborty P, Brehaut J, Chan A, Cohen E, Dyack S, Gillis LJ, Goobie S, Graham ID, Greenberg CR, Grimshaw JM, Hayeems RZ, Jain-Ghai S, Jolly A, Khangura S, MacKenzie JJ, Major N, Mitchell JJ, Nicholls SG, Pender A, Potter M, Prasad C, Prosser LA, Schulze A, Siriwardena K, Sparkes R, Speechley K, Stockler S, Taljaard M, Teitelbaum M, Trakadis Y, van Karnebeek C, Walia JS, Wilson BJ, Wilson K, Potter BK. Families' healthcare experiences for children with inherited metabolic diseases: protocol for a mixed methods cohort study. BMJ Open 2022; 12:e055664. [PMID: 35193919 PMCID: PMC8867352 DOI: 10.1136/bmjopen-2021-055664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
INTRODUCTION Children with inherited metabolic diseases (IMDs) often have complex and intensive healthcare needs and their families face challenges in receiving high-quality, family centred health services. Improvement in care requires complex interventions involving multiple components and stakeholders, customised to specific care contexts. This study aims to comprehensively understand the healthcare experiences of children with IMDs and their families across Canada. METHODS AND ANALYSIS A two-stage explanatory sequential mixed methods design will be used. Stage 1: quantitative data on healthcare networks and encounter experiences will be collected from 100 parent/guardians through a care map, 2 baseline questionnaires and 17 weekly diaries over 5-7 months. Care networks will be analysed using social network analysis. Relationships between demographic or clinical variables and ratings of healthcare experiences across a range of family centred care dimensions will be analysed using generalised linear regression. Other quantitative data related to family experiences and healthcare experiences will be summarised descriptively. Ongoing analysis of quantitative data and purposive, maximum variation sampling will inform sample selection for stage 2: a subset of stage 1 participants will participate in one-on-one videoconference interviews to elaborate on the quantitative data regarding care networks and healthcare experiences. Interview data will be analysed thematically. Qualitative and quantitative data will be merged during analysis to arrive at an enhanced understanding of care experiences. Quantitative and qualitative data will be combined and presented narratively using a weaving approach (jointly on a theme-by-theme basis) and visually in a side-by-side joint display. ETHICS AND DISSEMINATION The study protocol and procedures were approved by the Children's Hospital of Eastern Ontario's Research Ethics Board, the University of Ottawa Research Ethics Board and the research ethics boards of each participating study centre. Findings will be published in peer-reviewed journals and presented at scientific conferences.
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Affiliation(s)
- Andrea J Chow
- School of Epidemiology and Public Health, University of Ottawa, Ottawa, Ontario, Canada
| | - Ryan Iverson
- Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | | | - Kylie Tingley
- School of Epidemiology and Public Health, University of Ottawa, Ottawa, Ontario, Canada
| | | | - Nicole Pallone
- Patient Partner, Canadian PKU & Allied Disorders Inc, Toronto, Ontario, Canada
| | - Maureen Smith
- Patient Partner, Canadian Organization for Rare Disorders, Toronto, Ontario, Canada
| | - Zobaida Al-Baldawi
- School of Epidemiology and Public Health, University of Ottawa, Ottawa, Ontario, Canada
| | - Pranesh Chakraborty
- Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
- Department of Pediatrics, University of Ottawa, Ottawa, Ontario, Canada
| | - Jamie Brehaut
- School of Epidemiology and Public Health, University of Ottawa, Ottawa, Ontario, Canada
- Clinical Epidemiology Program, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
| | - Alicia Chan
- Department of Medical Genetics, University of Alberta, Edmonton, Alberta, Canada
| | - Eyal Cohen
- Department of Pediatrics, University of Toronto, Toronto, Ontario, Canada
- Child Health Evaluative Sciences, The Hospital for Sick Children, Toronto, Ontario, Canada
- Division of Pediatric Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Sarah Dyack
- Division of Medical Genetics, Department of Pediatrics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Lisa Jane Gillis
- Department of Medicine, Johns Hopkins All Children's Hospital, St Petersburg, Florida, USA
| | - Sharan Goobie
- Division of Medical Genetics, Department of Pediatrics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Ian D Graham
- School of Epidemiology and Public Health, University of Ottawa, Ottawa, Ontario, Canada
- Clinical Epidemiology Program, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
| | - Cheryl R Greenberg
- Rady Faculty of Health Sciences, Max Rady College of Medicine, Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, Manitoba, Canada
- Children's Hospital Research Institute of Manitoba, Winnipeg, Manitoba, Canada
| | - Jeremy M Grimshaw
- Clinical Epidemiology Program, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
- Department of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Robin Z Hayeems
- Child Health Evaluative Sciences, The Hospital for Sick Children, Toronto, Ontario, Canada
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada
| | - Shailly Jain-Ghai
- Department of Medical Genetics, University of Alberta, Edmonton, Alberta, Canada
| | - Ann Jolly
- School of Epidemiology and Public Health, University of Ottawa, Ottawa, Ontario, Canada
- Contagion Consulting Group, Ottawa, Ontario, Canada
| | - Sara Khangura
- School of Epidemiology and Public Health, University of Ottawa, Ottawa, Ontario, Canada
| | - Jennifer J MacKenzie
- Hamilton Health Sciences, McMaster Children's Hospital, Hamilton, Ontario, Canada
| | - Nathalie Major
- Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
- Department of Pediatrics, University of Ottawa, Ottawa, Ontario, Canada
| | - John J Mitchell
- Division of Pediatric Endocrinology, Department of Pediatrics, Montreal Children's Hospital, Montreal, Quebec, Canada
| | - Stuart G Nicholls
- Clinical Epidemiology Program, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
- Ottawa Methods Centre, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
| | - Amy Pender
- Hamilton Health Sciences, McMaster Children's Hospital, Hamilton, Ontario, Canada
| | - Murray Potter
- Hamilton Health Sciences, McMaster Children's Hospital, Hamilton, Ontario, Canada
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Chitra Prasad
- Department of Pediatrics, Western University, London, Ontario, Canada
| | - Lisa A Prosser
- Department of Pediatrics, Susan B. Meister Child Health Evaluation and Research Center, University of Michigan, Ann Arbor, Michigan, USA
| | - Andreas Schulze
- Department of Pediatrics, University of Toronto, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
- Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Komudi Siriwardena
- Department of Medical Genetics, University of Alberta, Edmonton, Alberta, Canada
| | - Rebecca Sparkes
- Departments of Medical Genetics and Pediatrics, Alberta Children's Hospital, Calgary, Alberta, Canada
| | - Kathy Speechley
- Department of Pediatrics, Western University, London, Ontario, Canada
| | - Sylvia Stockler
- Department of Pediatrics, BC Children's Hospital, Vancouver, British Columbia, Canada
| | - Monica Taljaard
- School of Epidemiology and Public Health, University of Ottawa, Ottawa, Ontario, Canada
- Clinical Epidemiology Program, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
| | - Mari Teitelbaum
- Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Yannis Trakadis
- Department of Specialized Medicine, Division of Medical Genetics, McGill University Health Centre, Montreal, Quebec, Canada
| | - Clara van Karnebeek
- Department of Pediatrics, Radboud University Medical Center, Nijmegen, Gelderland, The Netherlands
- Department of Pediatrics, British Columbia Children's Hospital, Vancouver, British Columbia, Canada
| | - Jagdeep S Walia
- Medical Genetics, Department of Pediatrics, Kingston Health Sciences Centre, Kingston, Ontario, Canada
- Department of Pediatrics, Queen's University, Kingston, Ontario, Canada
| | - Brenda J Wilson
- Faculty of Medicine Division of Community Health and Humanities, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
| | - Kumanan Wilson
- School of Epidemiology and Public Health, University of Ottawa, Ottawa, Ontario, Canada
- Clinical Epidemiology Program, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
- Department of Medicine, University of Ottawa, Ottawa, Ontario, Canada
- Bruyere Research Institute, Ottawa, Ontario, Canada
| | - Beth K Potter
- School of Epidemiology and Public Health, University of Ottawa, Ottawa, Ontario, Canada
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Choudhury MC, Chaube P. Integrating rare disease management in public health programs in India: exploring the potential of National Health Mission. Orphanet J Rare Dis 2022; 17:43. [PMID: 35144652 PMCID: PMC8832777 DOI: 10.1186/s13023-022-02194-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 01/30/2022] [Indexed: 11/18/2022] Open
Abstract
Rare diseases (RD) are conditions that affect a small number of people and hence do not get the focus on government health priorities in a resource-constrained setting such as India. Therefore, it is essential to focus on strengthening and utilizing the existing public health framework for the optimal usage of healthcare resources. In this regard, National Health Mission (NHM) is one of the crucial programs initiated by the government of India to address the health needs of the under-served. As Phase 1 of the NHM moves towards completion, we explored the Reproductive, Maternal, Newborn, Child, and Adolescent Health (RMNCH + A) program under NHM to assess their potential and limitations to aid RD care. We found that some of the disease-prevention initiatives of NHM address certain RDs and can easily be expanded to manage many such preventable RDs. In addition, NHM programs can provide a unique epidemiological data repository to strengthen the National Rare Disease Registry. These programs can also play important role in providing a continuum of care for many RDs that need lifelong management. However, existing programs have a limited scope to provide specialized RD-related treatments, which is better served in a more focused system. Thus, considering RDs in the design of the existing programs may help RD management better through prevention, data collection, and providing a continuum of care.
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Affiliation(s)
| | - Pragya Chaube
- DST Center for Policy Research, Indian Institute of Science, Bengaluru, India
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Propionic acidemia identified in twin siblings conceived by in vitro fertilization (IVF) with parents who were unknown carriers of a PCCA mutation. BMC Pregnancy Childbirth 2020; 20:689. [PMID: 33183246 PMCID: PMC7659086 DOI: 10.1186/s12884-020-03391-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Accepted: 10/30/2020] [Indexed: 11/15/2022] Open
Abstract
Background Propionic acidemia (PA) is a severe monogenic disorder characterized by a deficiency of the mitochondrial protein propionyl-CoA carboxylase (PCC) enzyme, which is caused by mutations in the PCCA or PCCB gene. Preconception carrier screening could provide couples with meaningful information for their reproductive options; however, it is not widely performed in China. Case presentation This report describes a case of dizygotic twin siblings conceived by in vitro fertilization (IVF) and diagnosed with propionic acidemia (PA). Their parents had no history of PA. Tandem mass spectrometry and urine gas chromatography/mass spectrometry (GC/MS) of the twin siblings revealed markedly elevated propionyl carnitine (C3), C3/C2, and 3-hydroxypropionate in the plasma and urine. Whole-exome sequencing was performed for the twin siblings. A homozygous missense mutation, c.2002G > A (p.Gly668Arg) in PCCA, was identified in the twin siblings. Sanger sequencing confirmed the homozygous mutation in the twin siblings and identified their parents as heterozygous carriers of the c.2002G > A mutation in PCCA. Both neonates in this case died. This is an emotionally and financially devastating outcome that could have been avoided with genetic carrier screening before conception. If couples are screened before IVF and found to be silent carriers, then reproductive options (such as preimplantation genetic diagnosis or prenatal diagnosis) can be offered to achieve a healthy newborn. Conclusion This case is a reminder to infertile couples seeking IVF that it is beneficial to clarify whether they are silent carriers before undergoing IVF. Supplementary Information The online version contains supplementary material available at 10.1186/s12884-020-03391-z.
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11
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Hartley T, Lemire G, Kernohan KD, Howley HE, Adams DR, Boycott KM. New Diagnostic Approaches for Undiagnosed Rare Genetic Diseases. Annu Rev Genomics Hum Genet 2020; 21:351-372. [DOI: 10.1146/annurev-genom-083118-015345] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Accurate diagnosis is the cornerstone of medicine; it is essential for informed care and promoting patient and family well-being. However, families with a rare genetic disease (RGD) often spend more than five years on a diagnostic odyssey of specialist visits and invasive testing that is lengthy, costly, and often futile, as 50% of patients do not receive a molecular diagnosis. The current diagnostic paradigm is not well designed for RGDs, especially for patients who remain undiagnosed after the initial set of investigations, and thus requires an expansion of approaches in the clinic. Leveraging opportunities to participate in research programs that utilize new technologies to understand RGDs is an important path forward for patients seeking a diagnosis. Given recent advancements in such technologies and international initiatives, the prospect of identifying a molecular diagnosis for all patients with RGDs has never been so attainable, but achieving this goal will require global cooperation at an unprecedented scale.
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Affiliation(s)
- Taila Hartley
- CHEO Research Institute, University of Ottawa, Ottawa, Ontario K1H 8L1, Canada;, , , ,
| | - Gabrielle Lemire
- CHEO Research Institute, University of Ottawa, Ottawa, Ontario K1H 8L1, Canada;, , , ,
- Department of Genetics, CHEO, Ottawa, Ontario K1H 8L1, Canada
| | - Kristin D. Kernohan
- CHEO Research Institute, University of Ottawa, Ottawa, Ontario K1H 8L1, Canada;, , , ,
- Newborn Screening Ontario, CHEO, Ottawa, Ontario K1H 9M8, Canada
| | - Heather E. Howley
- CHEO Research Institute, University of Ottawa, Ottawa, Ontario K1H 8L1, Canada;, , , ,
| | - David R. Adams
- Office of the Clinical Director, National Human Genome Research Institute and Undiagnosed Diseases Program, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Kym M. Boycott
- CHEO Research Institute, University of Ottawa, Ottawa, Ontario K1H 8L1, Canada;, , , ,
- Department of Genetics, CHEO, Ottawa, Ontario K1H 8L1, Canada
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12
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Issa MY, Chechlacz Z, Stanley V, George RD, McEvoy-Venneri J, Belandres D, Elbendary HM, Gaber KR, Nabil A, Abdel-Hamid MS, Zaki MS, Gleeson JG. Molecular diagnosis in recessive pediatric neurogenetic disease can help reduce disease recurrence in families. BMC Med Genomics 2020; 13:68. [PMID: 32404165 PMCID: PMC7218834 DOI: 10.1186/s12920-020-0714-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 04/23/2020] [Indexed: 12/13/2022] Open
Abstract
Background The causes for thousands of individually rare recessive diseases have been discovered since the adoption of next generation sequencing (NGS). Following the molecular diagnosis in older children in a family, parents could use this information to opt for fetal genotyping in subsequent pregnancies, which could inform decisions about elective termination of pregnancy. The use of NGS diagnostic sequencing in families has not been demonstrated to yield benefit in subsequent pregnancies to reduce recurrence. Here we evaluated whether genetic diagnosis in older children in families supports reduction in recurrence of recessive neurogenetic disease. Methods Retrospective study involving families with a child with a recessive pediatric brain disease (rPBD) that underwent NGS-based molecular diagnosis. Prenatal molecular testing was offered to couples in which a molecular diagnosis was made, to help couples seeking to prevent recurrence. With this information, families made decisions about elective termination. Pregnancies that were carried to term were assessed for the health of child and mother, and compared with historic recurrence risk of recessive disease. Results Between 2010 and 2016, 1172 families presented with a child a likely rPBD, 526 families received a molecular diagnosis, 91 families returned to the clinic with 101 subsequent pregnancies, and 84 opted for fetal genotyping. Sixty tested negative for recurrence for the biallelic mutation in the fetus, and all, except for one spontaneous abortion, carried to term, and were unaffected at follow-up. Of 24 that genotyped positive for the biallelic mutation, 16 were electively terminated, and 8 were carried to term and showed features of disease similar to that of the older affected sibling(s). Among the 101 pregnancies, disease recurrence in living offspring deviated from the expected 25% to the observed 12% ([95% CI 0·04 to 0·20], p = 0·011). Conclusions Molecular diagnosis in an older child, coupled with prenatal fetal genotyping in subsequent pregnancies and genetic counselling, allows families to make informed decisions to reduce recessive neurogenetic disease recurrence.
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Affiliation(s)
- Mahmoud Y Issa
- Clinical Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo, 12311, Egypt
| | - Zinayida Chechlacz
- Departments of Neurosciences and Pediatrics, Rady Children's Institute for Genomic Medicine, Howard Hughes Medical Institute, University of California San Diego, La Jolla, CA, 92093, USA
| | - Valentina Stanley
- Departments of Neurosciences and Pediatrics, Rady Children's Institute for Genomic Medicine, Howard Hughes Medical Institute, University of California San Diego, La Jolla, CA, 92093, USA
| | - Renee D George
- Departments of Neurosciences and Pediatrics, Rady Children's Institute for Genomic Medicine, Howard Hughes Medical Institute, University of California San Diego, La Jolla, CA, 92093, USA
| | - Jennifer McEvoy-Venneri
- Departments of Neurosciences and Pediatrics, Rady Children's Institute for Genomic Medicine, Howard Hughes Medical Institute, University of California San Diego, La Jolla, CA, 92093, USA
| | - Denice Belandres
- Departments of Neurosciences and Pediatrics, Rady Children's Institute for Genomic Medicine, Howard Hughes Medical Institute, University of California San Diego, La Jolla, CA, 92093, USA
| | - Hasnaa M Elbendary
- Clinical Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo, 12311, Egypt
| | - Khaled R Gaber
- Prenatal Diagnosis and Fetal Medicine Department, Human Genetics and Genome Research Division, National Research Centre, Cairo, 12311, Egypt
| | - Ahmed Nabil
- Prenatal Diagnosis and Fetal Medicine Department, Human Genetics and Genome Research Division, National Research Centre, Cairo, 12311, Egypt
| | - Mohamed S Abdel-Hamid
- Medical Molecular Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Maha S Zaki
- Clinical Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo, 12311, Egypt.
| | - Joseph G Gleeson
- Departments of Neurosciences and Pediatrics, Rady Children's Institute for Genomic Medicine, Howard Hughes Medical Institute, University of California San Diego, La Jolla, CA, 92093, USA.
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13
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Doble B, Schofield D, Evans CA, Groza T, Mattick JS, Field M, Roscioli T. Impacts of genomics on the health and social costs of intellectual disability. J Med Genet 2020; 57:479-486. [PMID: 31980565 DOI: 10.1136/jmedgenet-2019-106445] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 12/17/2019] [Accepted: 01/03/2020] [Indexed: 11/03/2022]
Abstract
BACKGROUND This study provides an integrated assessment of the economic and social impacts of genomic sequencing for the detection of monogenic disorders resulting in intellectual disability (ID). METHODS Multiple knowledge bases were cross-referenced and analysed to compile a reference list of monogenic disorders associated with ID. Multiple literature searches were used to quantify the health and social costs for the care of people with ID. Health and social expenditures and the current cost of whole-exome sequencing and whole-genome sequencing were quantified in relation to the more common causes of ID and their impact on lifespan. RESULTS On average, individuals with ID incur annual costs in terms of health costs, disability support, lost income and other social costs of US$172 000, accumulating to many millions of dollars over a lifetime. CONCLUSION The diagnosis of monogenic disorders through genomic testing provides the opportunity to improve the diagnosis and management, and to reduce the costs of ID through informed reproductive decisions, reductions in unproductive diagnostic tests and increasingly targeted therapies.
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Affiliation(s)
- Brett Doble
- Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia .,Programme in Health Services and Systems Research, Duke-NUS Medical School, Singapore
| | - Deborah Schofield
- Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia.,GenImpact, School of Economics, Faculty of Business and Economics, Macquarie University, Sydney, New South Wales, Australia
| | - Carey-Anne Evans
- Neuroscience Research Australia, Prince of Wales Clinical School, University of New South Wales, Randwick, New South Wales, Australia
| | - Tudor Groza
- Pryzm Health, Gold Coast, Queensland, Australia
| | - John S Mattick
- Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia.,St Vincent's Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Mike Field
- The Genetics of Learning Disability Service, Waratah, New South Wales, Australia
| | - Tony Roscioli
- Neuroscience Research Australia, Prince of Wales Clinical School, University of New South Wales, Randwick, New South Wales, Australia.,NSW Health Pathology East Laboratory, Prince of Wales Private Hospital, Randwick, New South Wales, Australia
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14
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Rowe CA, Wright CF. Expanded universal carrier screening and its implementation within a publicly funded healthcare service. J Community Genet 2019; 11:21-38. [PMID: 31828606 PMCID: PMC6962405 DOI: 10.1007/s12687-019-00443-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 10/28/2019] [Indexed: 11/25/2022] Open
Abstract
Carrier screening, a well-established clinical initiative, has been slow to take advantage of the new possibilities offered by high-throughput next generation sequencing technologies. There is evidence of significant benefit in expanding carrier screening to include multiple autosomal recessive conditions and offering a ‘universal’ carrier screen that could be used for a pan-ethnic population. However, the challenges of implementing such a programme and the difficulties of demonstrating efficacy worthy of public health investment are significant barriers. In order for such a programme to be successful, it would need to be applicable and acceptable to the population, which may be ethnically and culturally diverse. There are significant practical and ethical implications associated with determining which variants, genes and conditions to include whilst maintaining adequate sensitivity and accuracy. Although preconception screening would maximise the potential benefits from universal carrier screening, the resource implications of different modes of delivery need to be carefully evaluated and balanced against maximising reproductive autonomy and ensuring equity of access. Currently, although a number of existing initiatives are increasing access to carrier screening, there is insufficient evidence to inform the development of a publicly funded, expanded, universal carrier screening programme that would justify investment over other healthcare interventions.
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Affiliation(s)
- Charlotte A Rowe
- University of Exeter, St Luke's Campus, 79 Heavitree Rd, Exeter, EX1 1TX, UK. .,Post Graduate Centre, Royal Cornwall Hospitals NHS Trust, Treliske, Truro, Cornwall, TR1 3LQ, UK.
| | - Caroline F Wright
- Institute of Biomedical and Clinical Science, College of Medicine and Health, University of Exeter, RILD Building, RD&E, Barrack Road, Exeter, EX2 5DW, UK.
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15
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Ferreira CR. The burden of rare diseases. Am J Med Genet A 2019; 179:885-892. [PMID: 30883013 DOI: 10.1002/ajmg.a.61124] [Citation(s) in RCA: 197] [Impact Index Per Article: 39.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 02/27/2019] [Accepted: 03/05/2019] [Indexed: 01/06/2023]
Abstract
The subject of rare disease numbers is rife with misconceptions, not just in websites and other layman's literature, but also in the medical literature. Various websites mention numbers that are not validated by any solid data, while in turn the medical literature cites the aforementioned websites as sources, thus perpetuating a number of myths about rare diseases and their burden. We review the existing literature on rare disease numbers, in an attempt to demystify the subject. Specifically, we summarize data pertaining to: (a) known number and cumulative prevalence of rare diseases; (b) rare disease-associated mortality; (c) rare disease-associated morbidity, including numbers on health care services related to rare diseases; and (d) orphan drug numbers.
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Affiliation(s)
- Carlos R Ferreira
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
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16
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Capalbo A, Chokoshvili D, Dugoff L, Franasiak J, Gleicher N, Pennings G, Simon C. Should the reproductive risk of a couple aiming to conceive be tested in the contemporary clinical context? Fertil Steril 2019; 111:229-238. [PMID: 30642571 DOI: 10.1016/j.fertnstert.2018.11.045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 11/30/2018] [Indexed: 11/27/2022]
Affiliation(s)
| | - Davit Chokoshvili
- Centre for Biomedical Ethics and Law, Department of Public Health and Primary Care, University of Leuven, Leuven, Belgium
| | - Lorraine Dugoff
- Maternal Fetal Medicine and Reproductive Genetics, Department of Obstetrics and Gynecology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania
| | - Jason Franasiak
- IVI-RMA America, Reproductive Medicine Associates of New Jersey, Basking Ridge, New Jersey; Department of Obstetrics and Gynecology, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Norbert Gleicher
- Center for Human Reproduction, New York, New York; Foundation for Reproductive Medicine, New York, New York; Stem Cell Biology and Molecular Embryology Laboratory, Rockefeller University, New York, New York; Department of Obstetrics and Gynecology, Vienna University of Medicine, Vienna, Austria
| | - Guido Pennings
- Bioethics Institute Ghent (BIG), Department of Philosophy and Moral Science, Ghent University, Ghent, Belgium
| | - Carlos Simon
- Department of Obstetrics and Gynecology, Valencia University, and INCLIVA, Valencia, Spain; Department of Obstetrics and Gynecology, Stanford University, Stanford, California; Igenomix, Valencia, Spain.
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17
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Hogan GJ, Vysotskaia VS, Beauchamp KA, Seisenberger S, Grauman PV, Haas KR, Hong SH, Jeon D, Kash S, Lai HH, Melroy LM, Theilmann MR, Chu CS, Iori K, Maguire JR, Evans EA, Haque IS, Mar-Heyming R, Kang HP, Muzzey D. Validation of an Expanded Carrier Screen that Optimizes Sensitivity via Full-Exon Sequencing and Panel-wide Copy Number Variant Identification. Clin Chem 2018; 64:1063-1073. [PMID: 29760218 DOI: 10.1373/clinchem.2018.286823] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 03/26/2018] [Indexed: 11/06/2022]
Abstract
BACKGROUND By identifying pathogenic variants across hundreds of genes, expanded carrier screening (ECS) enables prospective parents to assess the risk of transmitting an autosomal recessive or X-linked condition. Detection of at-risk couples depends on the number of conditions tested, the prevalence of the respective diseases, and the screen's analytical sensitivity for identifying disease-causing variants. Disease-level analytical sensitivity is often <100% in ECS tests because copy number variants (CNVs) are typically not interrogated because of their technical complexity. METHODS We present an analytical validation and preliminary clinical characterization of a 235-gene sequencing-based ECS with full coverage across coding regions, targeted assessment of pathogenic noncoding variants, panel-wide CNV calling, and specialized assays for technically challenging genes. Next-generation sequencing, customized bioinformatics, and expert manual call review were used to identify single-nucleotide variants, short insertions and deletions, and CNVs for all genes except FMR1 and those whose low disease incidence or high technical complexity precluded novel variant identification or interpretation. RESULTS Screening of 36859 patients' blood or saliva samples revealed the substantial impact on fetal disease-risk detection attributable to novel CNVs (9.19% of risk) and technically challenging conditions (20.2% of risk), such as congenital adrenal hyperplasia. Of the 7498 couples screened, 335 were identified as at risk for an affected pregnancy, underscoring the clinical importance of the test. Validation of our ECS demonstrated >99% analytical sensitivity and >99% analytical specificity. CONCLUSIONS Validated high-fidelity identification of different variant types-especially for diseases with complicated molecular genetics-maximizes at-risk couple detection.
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18
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Moorthie S, Blencowe H, W Darlison M, Lawn JE, Mastroiacovo P, Morris JK, Modell B. An overview of concepts and approaches used in estimating the burden of congenital disorders globally. J Community Genet 2017; 9:347-362. [PMID: 29022220 PMCID: PMC6167265 DOI: 10.1007/s12687-017-0335-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 06/30/2017] [Indexed: 01/15/2023] Open
Abstract
Congenital disorders are an important cause of pregnancy loss, premature death and life-long disability. A range of interventions can greatly reduce their burden, but the absence of local epidemiological data on their prevalence and the impact of interventions impede policy and service development in many countries. In an attempt to overcome these deficiencies, we have developed a tool—The Modell Global Database of Congenital Disorders (MGDb) that combines general biological principles and available observational data with demographic data, to generate estimates of the birth prevalence and effects of interventions on mortality and disability due to congenital disorders. MGDb aims to support policy development by generating country, regional and global epidemiological estimates. Here we provide an overview of the concepts and methodological approach used to develop MGDb.
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Affiliation(s)
| | - Hannah Blencowe
- Centre for Maternal, Adolescent, Reproductive, and Child Health, London School of Hygiene and Tropical Medicine, London, UK
| | - Matthew W Darlison
- WHO Collaborating Centre for Community Genetics, Centre for Health Informatics and Multiprofessional Education (CHIME), University College London, London, UK.
| | - Joy E Lawn
- Centre for Maternal, Adolescent, Reproductive, and Child Health, London School of Hygiene and Tropical Medicine, London, UK
| | - Pierpaolo Mastroiacovo
- Coordinating Centre of the International Clearinghouse for Birth Defects Surveillance and Research, Rome, Italy
| | - Joan K Morris
- Centre for Environmental and Preventive Medicine, Wolfson Institute of Preventive Medicine, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Bernadette Modell
- WHO Collaborating Centre for Community Genetics, Centre for Health Informatics and Multiprofessional Education (CHIME), University College London, London, UK
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19
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Chevalier RL. Evolutionary Nephrology. Kidney Int Rep 2017; 2:302-317. [PMID: 28845468 PMCID: PMC5568830 DOI: 10.1016/j.ekir.2017.01.012] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 01/11/2017] [Accepted: 01/25/2017] [Indexed: 01/05/2023] Open
Abstract
Progressive kidney disease follows nephron loss, hyperfiltration, and incomplete repair, a process described as "maladaptive." In the past 20 years, a new discipline has emerged that expands research horizons: evolutionary medicine. In contrast to physiologic (homeostatic) adaptation, evolutionary adaptation is the result of reproductive success that reflects natural selection. Evolutionary explanations for physiologically maladaptive responses can emerge from mismatch of the phenotype with environment or evolutionary tradeoffs. Evolutionary adaptation to a terrestrial environment resulted in a vulnerable energy-consuming renal tubule and a hypoxic, hyperosmolar microenvironment. Natural selection favors successful energy investment strategy: energy is allocated to maintenance of nephron integrity through reproductive years, but this declines with increasing senescence after ~40 years of age. Risk factors for chronic kidney disease include restricted fetal growth or preterm birth (life history tradeoff resulting in fewer nephrons), evolutionary selection for APOL1 mutations (that provide resistance to trypanosome infection, a tradeoff), and modern life experience (Western diet mismatch leading to diabetes and hypertension). Current advances in genomics, epigenetics, and developmental biology have revealed proximate causes of kidney disease, but attempts to slow kidney disease remain elusive. Evolutionary medicine provides a complementary approach by addressing ultimate causes of kidney disease. Marked variation in nephron number at birth, nephron heterogeneity, and changing susceptibility to kidney injury throughout life history are the result of evolutionary processes. Combined application of molecular genetics, evolutionary developmental biology (evo-devo), developmental programming and life history theory may yield new strategies for prevention and treatment of chronic kidney disease.
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Affiliation(s)
- Robert L. Chevalier
- Department of Pediatrics, The University of Virginia, Charlottesville, Virginia, USA
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20
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Spillmann RC, McConkie-Rosell A, Pena L, Jiang YH, Schoch K, Walley N, Sanders C, Sullivan J, Hooper SR, Shashi V. A window into living with an undiagnosed disease: illness narratives from the Undiagnosed Diseases Network. Orphanet J Rare Dis 2017; 12:71. [PMID: 28416019 PMCID: PMC5392939 DOI: 10.1186/s13023-017-0623-3] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 04/04/2017] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Patients' stories of their illnesses help bridge the divide between patients and providers, facilitating more humane medical care. Illness narratives have been classified into three types: restitution (expectation of recovery), chaos (suffering and loss), and quest (unexpected positive effect from illness). Undiagnosed patients have unique illness experiences and obtaining their narratives would provide insights into the medical and emotional impact of living with an undiagnosed illness. Adults and children with undiagnosed diseases apply to be evaluated by the Undiagnosed Diseases Network (UDN). Written illness narratives from 40 UDN applicants, including 20 adult probands who applied for themselves and 20 parents who applied for their children, were analyzed for: 1) narrative content and 2) narrative type. RESULTS Narrative content: could be grouped into three themes: 1) Expectations of the UDN: the majority felt they had no further healthcare options and hoped the UDN would provide them with a diagnosis, with the adults expecting to return to their previously healthy life and the parents wanting information to manage their child's healthcare. 2) Personal medical information: the narratives reported worsening of symptoms and some offered opinions regarding the cause of their illness. The proband narratives had few objective findings, while parental narratives had detailed objective information. 3) Experiences related to living with their undiagnosed illness: frustration at being undiagnosed was expressed. The adults felt they had to provide validation of their symptoms to providers, given the lack of objective findings. The parents worried that something relevant to their child's management was being overlooked. Narrative type: All the narratives were of the chaos type, but for different reasons, with the probands describing loss and suffering and the parents expressing fear for their child's future. The parental narratives also had elements of restitution and quest, with acceptance of "a new normal", and an emphasis on the positive aspects of their child's illness which was absent from the probands. CONCLUSIONS These narratives illustrate the chaos that coexists with being undiagnosed. The differences between the proband and parental narratives suggest that these two groups have different needs that need to be considered during their evaluation and management.
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Affiliation(s)
- Rebecca C. Spillmann
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC USA
| | - Allyn McConkie-Rosell
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC USA
| | - Loren Pena
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC USA
| | - Yong-Hui Jiang
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC USA
| | - Kelly Schoch
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC USA
| | - Nicole Walley
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC USA
| | - Camilla Sanders
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC USA
| | - Jennifer Sullivan
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC USA
| | - Stephen R. Hooper
- Department of Allied Health Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina USA
| | - Vandana Shashi
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC USA
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Abou Tayoun AN, Krock B, Spinner NB. Sequencing-based diagnostics for pediatric genetic diseases: progress and potential. Expert Rev Mol Diagn 2016; 16:987-99. [PMID: 27388938 DOI: 10.1080/14737159.2016.1209411] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
INTRODUCTION The last two decades have witnessed revolutionary changes in clinical diagnostics, fueled by the Human Genome Project and advances in high throughput, Next Generation Sequencing (NGS). We review the current state of sequencing-based pediatric diagnostics, associated challenges, and future prospects. AREAS COVERED We present an overview of genetic disease in children, review the technical aspects of Next Generation Sequencing and the strategies to make molecular diagnoses for children with genetic disease. We discuss the challenges of genomic sequencing including incomplete current knowledge of variants, lack of data about certain genomic regions, mosaicism, and the presence of regions with high homology. Expert commentary: NGS has been a transformative technology and the gap between the research and clinical communities has never been so narrow. Therapeutic interventions are emerging based on genomic findings and the applications of NGS are progressing to prenatal genetics, epigenomics and transcriptomics.
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Affiliation(s)
- Ahmad N Abou Tayoun
- a Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine , The Children's Hospital of Philadelphia , Philadelphia , PA , USA.,b The Perelman School of Medicine , The University of Pennsylvania , Philadelphia , PA , USA
| | - Bryan Krock
- a Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine , The Children's Hospital of Philadelphia , Philadelphia , PA , USA.,b The Perelman School of Medicine , The University of Pennsylvania , Philadelphia , PA , USA
| | - Nancy B Spinner
- a Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine , The Children's Hospital of Philadelphia , Philadelphia , PA , USA.,b The Perelman School of Medicine , The University of Pennsylvania , Philadelphia , PA , USA
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Farwell Hagman KD, Shinde DN, Mroske C, Smith E, Radtke K, Shahmirzadi L, El-Khechen D, Powis Z, Chao EC, Alcaraz WA, Helbig KL, Sajan SA, Rossi M, Lu HM, Huether R, Li S, Wu S, Nuñes ME, Tang S. Candidate-gene criteria for clinical reporting: diagnostic exome sequencing identifies altered candidate genes among 8% of patients with undiagnosed diseases. Genet Med 2016; 19:224-235. [PMID: 27513193 PMCID: PMC5303763 DOI: 10.1038/gim.2016.95] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 05/25/2016] [Indexed: 02/07/2023] Open
Abstract
Purpose: Diagnostic exome sequencing (DES) is now a commonly ordered test for individuals with undiagnosed genetic disorders. In addition to providing a diagnosis for characterized diseases, exome sequencing has the capacity to uncover novel candidate genes for disease. Methods: Family-based DES included analysis of both characterized and novel genetic etiologies. To evaluate candidate genes for disease in the clinical setting, we developed a systematic, rule-based classification schema. Results: Testing identified a candidate gene among 7.7% (72/934) of patients referred for DES; 37 (4.0%) and 35 (3.7%) of the genes received evidence scores of “candidate” and “suspected candidate,” respectively. A total of 71 independent candidate genes were reported among the 72 patients, and 38% (27/71) were subsequently corroborated in the peer-reviewed literature. This rate of corroboration increased to 51.9% (27/52) among patients whose gene was reported at least 12 months previously. Conclusions: Herein, we provide transparent, comprehensive, and standardized scoring criteria for the clinical reporting of candidate genes. These results demonstrate that DES is an integral tool for genetic diagnosis, especially for elucidating the molecular basis for both characterized and novel candidate genetic etiologies. Gene discoveries also advance the understanding of normal human biology and more common diseases. Genet Med19 2, 224–235.
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Affiliation(s)
| | - Deepali N Shinde
- Department of Clinical Genomics, Ambry Genetics, Aliso Viejo, California, USA
| | - Cameron Mroske
- Department of Clinical Genomics, Ambry Genetics, Aliso Viejo, California, USA
| | - Erica Smith
- Department of Clinical Genomics, Ambry Genetics, Aliso Viejo, California, USA
| | - Kelly Radtke
- Department of Clinical Genomics, Ambry Genetics, Aliso Viejo, California, USA
| | - Layla Shahmirzadi
- Department of Clinical Genomics, Ambry Genetics, Aliso Viejo, California, USA
| | - Dima El-Khechen
- Department of Clinical Genomics, Ambry Genetics, Aliso Viejo, California, USA
| | - Zöe Powis
- Department of Clinical Genomics, Ambry Genetics, Aliso Viejo, California, USA
| | - Elizabeth C Chao
- Department of Clinical Genomics, Ambry Genetics, Aliso Viejo, California, USA.,Division of Genetics and Genomics, Department of Pediatrics, University of California, Irvine, Irvine, California, USA
| | - Wendy A Alcaraz
- Department of Clinical Genomics, Ambry Genetics, Aliso Viejo, California, USA
| | - Katherine L Helbig
- Department of Clinical Genomics, Ambry Genetics, Aliso Viejo, California, USA
| | - Samin A Sajan
- Department of Clinical Genomics, Ambry Genetics, Aliso Viejo, California, USA
| | - Mari Rossi
- Department of Clinical Genomics, Ambry Genetics, Aliso Viejo, California, USA
| | - Hsiao-Mei Lu
- Department of Clinical Genomics, Ambry Genetics, Aliso Viejo, California, USA
| | - Robert Huether
- Department of Clinical Genomics, Ambry Genetics, Aliso Viejo, California, USA
| | - Shuwei Li
- Department of Clinical Genomics, Ambry Genetics, Aliso Viejo, California, USA
| | - Sitao Wu
- Department of Clinical Genomics, Ambry Genetics, Aliso Viejo, California, USA
| | - Mark E Nuñes
- Department of Genetics, Kaiser Permanente, San Diego, California, USA
| | - Sha Tang
- Department of Clinical Genomics, Ambry Genetics, Aliso Viejo, California, USA
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Padmanabhan VT, Sugunan AP, Brahmaputhran CK, Nandini K, Pavithran K. Heritable Anomalies among the Inhabitants of Regions of Normal and High Background Radiation in Kerala: Results of a Cohort Study, 1988–1994. INTERNATIONAL JOURNAL OF HEALTH SERVICES 2016; 34:483-515. [PMID: 15346682 DOI: 10.2190/3xye-qjpu-01bf-8yke] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In a genetic epidemiological and fertility survey among 70,000 inhabitants in a high-background radiation region (HBRR) and normal radiation region (NRR) in Kerala, India, 985 persons were found to have heritable anomalies. Suggested etiologies for the anomalies were chromosomal and Mendelian, 15 percent; multifactorial, 60 percent; and congenital, 25 percent. There was a statistically significant increase of Down syndrome, autosomal dominant anomalies, and multifactorial diseases and an insignificant increase of autosomal recessive and X-linked recessive anomalies in the HBRR. The total fertility rate was 3.85 per couple; 9 percent of live-born children were reported dead. The rate of untoward pregnancy outcome—death of the offspring or presence of an anomaly in a living child—was 6.4 percent among the unrelated couples in the NRR, with one spouse born outside the area of current residence (“migrant”). Considering this as the base, the excess relative risks in the other groups are: “NRR-nonmigrant,” 35 percent; “HBRR-nonmigrant,” 69 percent; “NRR-consanguineous,” 76 percent; and “NBRR-consanguineous,” 157 percent. Ionizing radiation, consanguinity, and nearness of birthplace of the spouse are risk factors for the death of offspring and for anomalies. The higher risk among the “nonmigrant” couples may be due to geographic inbreeding. The findings are suggestive of an autosomal recessive etiology for the majority of the multifactorial anomalies.
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24
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Correction of Pathological Morphofunctional Changes in the Mammalian Retina. NEUROPHYSIOLOGY+ 2016. [DOI: 10.1007/s11062-016-9549-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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25
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Martin J, Asan, Yi Y, Alberola T, Rodríguez-Iglesias B, Jiménez-Almazán J, Li Q, Du H, Alama P, Ruiz A, Bosch E, Garrido N, Simon C. Comprehensive carrier genetic test using next-generation deoxyribonucleic acid sequencing in infertile couples wishing to conceive through assisted reproductive technology. Fertil Steril 2015; 104:1286-93. [PMID: 26354092 DOI: 10.1016/j.fertnstert.2015.07.1166] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 07/29/2015] [Accepted: 07/29/2015] [Indexed: 02/08/2023]
Abstract
OBJECTIVE To develop an expanded pan-ethnic preconception carrier genetic screening test for use in assisted reproductive technology (ART) patients and donors. DESIGN Retrospective analysis of results obtained from 2,570 analyses. SETTING Reproductive genetic laboratory. PATIENT(S) The 2,570 samples comprised 1,170 individuals from the gamete donor programs; 1,124 individuals corresponding to the partner of the patient receiving the donated gamete; and 276 individuals from 138 couples seeking ART using their own gametes. INTERVENTION(S) None. MAIN OUTCOME MEASURE(S) Next-generation sequencing of 549 recessive and X-linked genes involved in severe childhood phenotypes reinforced with five complementary tests covering high prevalent mutations not detected by next-generation sequencing. RESULT(S) Preclinical validation included 48 DNA samples carrying known mutations for 27 genes, resulting in a sensitivity of 99%. In the clinical dataset, 2,161 samples (84%) tested positive, with an average carrier burden of 2.3 per sample. Five percent of the couples using their own gametes were found to have pathogenic variants conferring high risk for six different diseases. These high-risk couples and patients received genetic counseling and recommendations for preimplantation genetic diagnosis. For patients receiving gamete donation, we applied a genetic testing and blinded matching system to avoid high-risk combinations regardless of their carrier burden. For female donors, 1.94% were positive for X-linked conditions; they received genetic counselling and were discarded. CONCLUSION(S) We have developed a comprehensive carrier genetic screening test that, combined with our matching system and genetic counseling, constitutes a powerful tool to avoid more than 600 mendelian diseases in the offspring of patients undergoing ART.
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Affiliation(s)
- Julio Martin
- IGenomix, Parc Cientific Univeristat Valencia, Valencia, Spain.
| | - Asan
- Binhai Genomics Institute and Tianjin Translational Genomics Center, BGI-Tianjin, Tianjin, People's Republic of China
| | - Yuting Yi
- Binhai Genomics Institute and Tianjin Translational Genomics Center, BGI-Tianjin, Tianjin, People's Republic of China
| | | | | | | | - Qin Li
- BGI-Shenzen, Shenzhen, People's Republic of China
| | - Huiqian Du
- Binhai Genomics Institute and Tianjin Translational Genomics Center, BGI-Tianjin, Tianjin, People's Republic of China
| | - Pilar Alama
- Instituto Valenciano de Infertilidad Valencia and Fundación Instituto Valenciano de Infertilidad, Valencia, Spain
| | - Amparo Ruiz
- Instituto Valenciano de Infertilidad Valencia and Fundación Instituto Valenciano de Infertilidad, Valencia, Spain
| | - Ernesto Bosch
- Instituto Valenciano de Infertilidad Valencia and Fundación Instituto Valenciano de Infertilidad, Valencia, Spain
| | | | - Carlos Simon
- IGenomix, Parc Cientific Univeristat Valencia, Valencia, Spain; Instituto Valenciano de Infertilidad Valencia and Fundación Instituto Valenciano de Infertilidad, Valencia, Spain; Department of Obstetrics and Gynecology, Valencia University, Instituto Universitario IVI/INCLIVA, Valencia, Spain
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26
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Rivera-Garcia C, Bristow SL, Yarnall S, Kumar N, Rodriguez S, De Veaux N, Bisignano A, Chu B, Prates R, Munne S. Retracted: Validation of a multiplex genotyping platform using a novel genomic database approach. Genet Med 2015. [DOI: 10.1038/gim.2015.101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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27
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"Is It Worth Knowing?" Focus Group Participants' Perceived Utility of Genomic Preconception Carrier Screening. J Genet Couns 2015; 25:135-45. [PMID: 26093606 PMCID: PMC4726717 DOI: 10.1007/s10897-015-9851-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 06/02/2015] [Indexed: 12/22/2022]
Abstract
As genome sequencing technology advances, research is needed to guide decision-making about what results can or should be offered to patients in different clinical settings. We conducted three focus groups with individuals who had prior preconception genetic testing experience to explore perceived advantages and disadvantages of genome sequencing for preconception carrier screening, compared to usual care. Using a discussion guide, a trained qualitative moderator facilitated the audio-recorded focus groups. Sixteen individuals participated. Thematic analysis of transcripts started with a grounded approach and subsequently focused on participants’ perceptions of the value of genetic information. Analysis uncovered two orientations toward genomic preconception carrier screening: “certain” individuals desiring all possible screening information; and “hesitant” individuals who were more cautious about its value. Participants revealed valuable information about barriers to screening: fear/anxiety about results; concerns about the method of returning results; concerns about screening necessity; and concerns about partner participation. All participants recommended offering choice to patients to enhance the value of screening and reduce barriers. Overall, two groups of likely users of genome sequencing for preconception carrier screening demonstrated different perceptions of the advantages or disadvantages of screening, suggesting tailored approaches to education, consent, and counseling may be warranted with each group.
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28
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Bhattacharjee A, Sokolsky T, Wyman SK, Reese MG, Puffenberger E, Strauss K, Morton H, Parad RB, Naylor EW. Development of DNA confirmatory and high-risk diagnostic testing for newborns using targeted next-generation DNA sequencing. Genet Med 2015; 17:337-47. [PMID: 25255367 DOI: 10.1038/gim.2014.117] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Accepted: 07/31/2014] [Indexed: 12/30/2022] Open
Abstract
PURPOSE Genetic testing is routinely used for second-tier confirmation of newborn sequencing results to rule out false positives and to confirm diagnoses in newborns undergoing inpatient and outpatient care. We developed a targeted next-generation sequencing panel coupled with a variant processing pipeline and demonstrated utility and performance benchmarks across multiple newborn disease presentations in a retrospective clinical study. METHODS The test utilizes an in silico gene filter that focuses directly on 126 genes related to newborn screening diseases and is applied to the exome or a next-generation sequencing panel called NBDx. NBDx targets the 126 genes and additional newborn-specific disorders. It integrates DNA isolation from minimally invasive biological specimens, targeted next-generation screening, and rapid characterization of genetic variation. RESULTS We report a rapid parallel processing of 8 to 20 cases within 105 hours with high coverage on our NBDx panel. Analytical sensitivity of 99.8% was observed across known mutation hotspots. Concordance calls with or without clinical summaries were 94% and 75%, respectively. CONCLUSION Rapid, automated targeted next-generation sequencing and analysis are practical in newborns for second-tier confirmation and neonatal intensive care unit diagnoses, laying a foundation for future primary DNA-based molecular screening of additional disorders and improving existing molecular testing options for newborns.
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Affiliation(s)
| | | | | | | | | | - Kevin Strauss
- Clinic for Special Children, Strasburg, Pennsylvania, USA
| | - Holmes Morton
- Clinic for Special Children, Strasburg, Pennsylvania, USA
| | - Richard B Parad
- Department of Pediatric Newborn Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Edwin W Naylor
- 1] Parabase Genomics, Boston, Massachusetts, USA [2] Division of Genetics, Department of Pediatrics, Medical University of South Carolina, Charleston, South Carolina, USA
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29
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Vattulainen S, Aho J, Salmenperä P, Bruce S, Tallila J, Gentile M, Sankelo M, Laitinen T, Koskenvuo JW, Alastalo TP, Myllykangas S. Accurate genetic diagnosis of Finnish pulmonary arterial hypertension patients using oligonucleotide-selective sequencing. Mol Genet Genomic Med 2015; 3:354-62. [PMID: 26247051 PMCID: PMC4521970 DOI: 10.1002/mgg3.147] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 03/24/2015] [Indexed: 01/09/2023] Open
Abstract
The genetic basis of pulmonary arterial hypertension (PAH) among Finnish PAH patients is poorly understood. We adopted a novel-targeted next-generation sequencing (NGS) approach called Oligonucleotide-Selective Sequencing (OS-Seq) and developed a custom data analysis and interpretation pipeline to identify pathogenic base substitutions, insertions, and deletions in seven genes associated with PAH (BMPR2, BMPR1B, ACVRL1, ENG, SMAD9, CAV1, and KCNK3) from Finnish PAH patients. This study represents the first clinical study with OS-Seq technology on patients suffering from a rare genetic disorder. We analyzed DNA samples from 21 Finnish PAH patients, whose BMPR2 and ACVRL1 mutation status had been previously studied using Sanger sequencing. Our sequencing panel covered 100% of the targeted base pairs with >15× sequencing depth. Pathogenic base substitutions were identified in the BMPR2 gene in 29% of the Finnish PAH cases. Two of the pathogenic variant-positive patients had been previously tested negative using Sanger sequencing. No clinically significant variants were identified in the six other PAH genes. Our study validates the use of targeted OS-Seq for genetic diagnostics of PAH and revealed pathogenic variants that had been previously missed using Sanger sequencing.
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Affiliation(s)
- Sanna Vattulainen
- Pediatric Cardiology, Children's Hospital Helsinki, University of Helsinki and Helsinki University Central Hospital Helsinki, Finland
| | - Joonas Aho
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku Turku, Finland
| | | | | | | | | | - Marja Sankelo
- Department of Internal Medicine, Tampere University Hospital Tampere, Finland
| | - Tarja Laitinen
- Department of Pulmonary Diseases and Allergology, Turku University Hospital and University of Turku Turku, Finland
| | - Juha W Koskenvuo
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku Turku, Finland ; Blueprint Genetics Helsinki, Finland ; Department of Clinical Physiology and Nuclear Medicine, HUS Medical Imaging Center, Helsinki University of Central Hospital and University of Helsinki Helsinki, Finland
| | - Tero-Pekka Alastalo
- Pediatric Cardiology, Children's Hospital Helsinki, University of Helsinki and Helsinki University Central Hospital Helsinki, Finland ; Blueprint Genetics Helsinki, Finland
| | - Samuel Myllykangas
- Blueprint Genetics Helsinki, Finland ; Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki Helsinki, Finland
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30
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Abstract
Rapid progress in genomic medicine in recent years has made it possible to diagnose subtle genetic abnormalities in a clinical setting on routine basis. This has allowed for detailed genotype-phenotype correlations and the identification of the genetic basis of many congenital anomalies. In addition to the availability of chromosomal microarray analysis, exome and whole-genome sequencing on pre- and postnatal samples of cell-free DNA has revolutionized the field of prenatal diagnosis. Incorporation of these technologies in perinatal pathology is bound to play a major role in coming years. In this communication, we briefly present the current experience with use of classical chromosome analysis, fluorescence in situ hybridization, and microarray testing, development of whole-genome analysis by next-generation sequencing technology, offer a detailed review of the history and current status of non-invasive prenatal testing using cell-free DNA, and discuss the advents of these new genomic technologies in perinatal medicine.
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Affiliation(s)
- David G. Peters
- Department of Obstetrics, Gynecology, and Reproductive Sciences,
University of Pittsburgh, Pittsburgh, PA 15213,Magee-Womens Research Institute, University of Pittsburgh,
Pittsburgh, PA 15213
| | - Svetlana A. Yatsenko
- Department of Obstetrics, Gynecology, and Reproductive Sciences,
University of Pittsburgh, Pittsburgh, PA 15213,Department of Pathology, University of Pittsburgh, Pittsburgh, PA
15213
| | - Urvashi Surti
- Department of Obstetrics, Gynecology, and Reproductive Sciences,
University of Pittsburgh, Pittsburgh, PA 15213,Department of Pathology, University of Pittsburgh, Pittsburgh, PA
15213,Magee-Womens Research Institute, University of Pittsburgh,
Pittsburgh, PA 15213,Department of Human Genetics, University of Pittsburgh, Pittsburgh,
PA 15213
| | - Aleksandar Rajkovic
- Department of Obstetrics, Gynecology, and Reproductive Sciences,
University of Pittsburgh, Pittsburgh, PA 15213,Department of Pathology, University of Pittsburgh, Pittsburgh, PA
15213,Magee-Womens Research Institute, University of Pittsburgh,
Pittsburgh, PA 15213,Department of Human Genetics, University of Pittsburgh, Pittsburgh,
PA 15213
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31
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Farwell KD, Shahmirzadi L, El-Khechen D, Powis Z, Chao EC, Tippin Davis B, Baxter RM, Zeng W, Mroske C, Parra MC, Gandomi SK, Lu I, Li X, Lu H, Lu HM, Salvador D, Ruble D, Lao M, Fischbach S, Wen J, Lee S, Elliott A, Dunlop CL, Tang S. Enhanced utility of family-centered diagnostic exome sequencing with inheritance model–based analysis: results from 500 unselected families with undiagnosed genetic conditions. Genet Med 2014; 17:578-86. [DOI: 10.1038/gim.2014.154] [Citation(s) in RCA: 345] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Accepted: 09/24/2014] [Indexed: 12/21/2022] Open
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32
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Itin PH. Etiology and pathogenesis of ectodermal dysplasias. Am J Med Genet A 2014; 164A:2472-7. [PMID: 24715647 DOI: 10.1002/ajmg.a.36550] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Accepted: 02/28/2014] [Indexed: 02/04/2023]
Abstract
Ectodermal dysplasias are a large group of heterogeneous heritable conditions characterized by congenital defects of one or more ectodermal structures and their appendages. The skin and its appendages are mainly composed by ectodermal components but development initiation of appendages is orchestrated by signals of the mesoderm with the help of placodes. A complex network of signaling pathways coordinates the formation and function of ectodermal structures. In recent years much has been discovered regarding the molecular mechanisms of ectodermal embryogenesis and this facilitates a rational basis for classification of ectodermal dysplasia. Interestingly, not only complex ectodermal syndromes but also mono- or oligosymptomatic ectodermal malformations may result from a mutation in a gene that is critical for ectodermal development. Mesodermal, and occasionally endodermal malformations may coexist. Embryogenesis occurs in distinct tissue organizational fields and specific interactions among the germ layers exist that may lead to a wide range of ectodermal dysplasias. Of the approximately 200 different ectodermal dysplasias, about 80 have been characterized at the molecular level with identification of the genes that are mutated in these disorders. Modern molecular genetics will increasingly elucidate the basic defects of these distinct syndromes and shed more light into the regulatory mechanisms of embryology. The upcoming classification of ectodermal dysplasias will combine detailed clinical and molecular knowledge.
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Affiliation(s)
- Peter H Itin
- Department of Dermatology, University Hospital Basel, Basel, Switzerland; Research Group of Dermatology, Department of Biomedicine, University Hospital Basel, Basel, Switzerland
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33
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Xu L, Shi R. Noninvasive prenatal diagnosis using next-generation sequencing. Gynecol Obstet Invest 2013; 77:73-7. [PMID: 24192219 DOI: 10.1159/000355693] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Accepted: 09/17/2013] [Indexed: 11/19/2022]
Abstract
Nowadays, prenatal diagnosis is necessary for pregnant women. For the parents who are expecting a child, the genetic test may provide the information whether they are carrying rare gene mutations and whether they are at risk of passing them onto their offspring. However, the ultimate determination of genetic diseases often requires invasive procedures such as amniocentesis and chorionic villus sampling, which may cause fetal miscarriage. A noninvasive type of prenatal diagnosis needs to be developed in clinical practice to dispel safety concerns. In this paper, we will review the technical advancement of using maternal circulating nucleic acids as the sample in noninvasive studies, and highlight the utilization of next-generation sequencing in the screening of genetic diseases.
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Affiliation(s)
- Liang Xu
- Department of Obstetrics and Gynecology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
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Shashi V, McConkie-Rosell A, Rosell B, Schoch K, Vellore K, McDonald M, Jiang YH, Xie P, Need A, Goldstein DB, Goldstein DG. The utility of the traditional medical genetics diagnostic evaluation in the context of next-generation sequencing for undiagnosed genetic disorders. Genet Med 2013; 16:176-82. [PMID: 23928913 DOI: 10.1038/gim.2013.99] [Citation(s) in RCA: 200] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Accepted: 06/11/2013] [Indexed: 12/16/2022] Open
Abstract
PURPOSE The purpose of this study was to assess the diagnostic yield of the traditional, comprehensive clinical evaluation and targeted genetic testing, within a general genetics clinic. These data are critically needed to develop clinically and economically grounded diagnostic algorithms that consider presenting phenotype, traditional genetics testing, and the emerging role of next-generation sequencing (whole-exome/genome sequencing). METHODS We retrospectively analyzed a cohort of 500 unselected consecutive patients who received traditional genetic diagnostic evaluations at a tertiary medical center. We calculated the diagnosis rate, number of visits to diagnosis, genetic tests, and the cost of testing. RESULTS Thirty-nine patients were determined to not have a genetic disorder; 212 of the remaining 461 (46%) received a genetic diagnosis, and 72% of these were diagnosed on the first visit. The cost per subsequent successful genetic diagnosis was estimated at $25,000. CONCLUSION Almost half of the patients were diagnosed using the traditional approach, most at the initial visit. For those remaining undiagnosed, next-generation sequencing may be clinically and economically beneficial. Estimating a 50% success rate for next-generation sequencing in undiagnosed genetic disorders, its application after the first clinical visit could result in a higher rate of genetic diagnosis at a considerable cost savings per successful diagnosis.
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Affiliation(s)
- Vandana Shashi
- Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, Durham, North Carolina, USA
| | - Allyn McConkie-Rosell
- Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, Durham, North Carolina, USA
| | - Bruce Rosell
- Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, Durham, North Carolina, USA
| | - Kelly Schoch
- Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, Durham, North Carolina, USA
| | - Kasturi Vellore
- Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, Durham, North Carolina, USA
| | - Marie McDonald
- Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, Durham, North Carolina, USA
| | - Yong-Hui Jiang
- Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, Durham, North Carolina, USA
| | - Pingxing Xie
- Center for Human Genome Variation, Duke University Medical Center, Durham, North Carolina, USA
| | - Anna Need
- Center for Human Genome Variation, Duke University Medical Center, Durham, North Carolina, USA
| | | | - David G Goldstein
- Center for Human Genome Variation, Duke University Medical Center, Durham, North Carolina, USA
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35
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Kingsmore S. Comprehensive carrier screening and molecular diagnostic testing for recessive childhood diseases. PLOS CURRENTS 2012; 4:e4f9877ab8ffa9. [PMID: 22872815 PMCID: PMC3392137 DOI: 10.1371/4f9877ab8ffa9] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Of 7,028 disorders with suspected Mendelian inheritance, 1,139 are recessive and have an established molecular basis. Although individually uncommon, Mendelian diseases collectively account for ~20% of infant mortality and ~18% of pediatric hospitalizations. Molecular diagnostic testing is currently available for only ~300 recessive disorders. Preconception screening, together with genetic counseling of carriers, has resulted in remarkable declines in the incidence of several severe recessive diseases including Tay-Sachs disease and cystic fibrosis. However, extension of preconception screening and molecular diagnostic testing to most recessive disease genes has hitherto been impractical. Recently, we reported a preconception carrier screen / molecular diagnostic test for 448 recessive childhood diseases. The current status of this test is reviewed here. Currently, this reports analytical validity of the comprehensive carrier test. As the clinical validity and clinical utility in the contexts described is ascertained, this article will be updated.
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36
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Kingsmore SF, Dinwiddie DL, Miller NA, Soden SE, Saunders CJ. Adopting orphans: comprehensive genetic testing of Mendelian diseases of childhood by next-generation sequencing. Expert Rev Mol Diagn 2012; 11:855-68. [PMID: 22022947 DOI: 10.1586/erm.11.70] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Orphan diseases are individually uncommon but collectively contribute significantly to pediatric morbidity, mortality and healthcare costs. Current molecular testing for rare genetic disorders is often a lengthy and costly endeavor, and in many cases a molecular diagnosis is never achieved despite extensive testing. Diseases with locus heterogeneity or overlapping signs and symptoms are especially challenging owing to the number of potential targets. Consequently, there is immense need for scalable, economical, rapid, multiplexed diagnostic testing for rare Mendelian diseases. Recent advances in next-generation sequencing and bioinformatic technologies have the potential to change the standard of care for the diagnosis of rare genetic disorders. These advances will be reviewed in the setting of a recently developed test for 592 autosomal recessive and X-linked diseases.
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Affiliation(s)
- Stephen F Kingsmore
- Children's Mercy Hospital & Clinics, 2401 Gillham Road, Kansas City, MO 64108, USA.
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37
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Application of Next Generation Sequencing to Molecular Diagnosis of Inherited Diseases. CHEMICAL DIAGNOSTICS 2012; 336:19-45. [DOI: 10.1007/128_2012_325] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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38
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Kingsmore SF, Saunders CJ. Deep sequencing of patient genomes for disease diagnosis: when will it become routine? Sci Transl Med 2011; 3:87ps23. [PMID: 21677196 DOI: 10.1126/scitranslmed.3002695] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Next-generation sequencing technologies have greatly lowered the cost of whole-genome sequencing (WGS) and related approaches. Thus, comprehensive sequencing for diagnostic purposes may clear this financial hurdle in the near future. The report by Bainbridge and colleagues in this issue of Science Translational Medicine illustrates the diagnostic power of WGS. In this Perspective, we discuss whether and how genome sequencing might become routine for clinical diagnosis.
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Bell CJ, Dinwiddie DL, Miller NA, Hateley SL, Ganusova EE, Mudge J, Langley RJ, Zhang L, Lee CC, Schilkey FD, Sheth V, Woodward JE, Peckham HE, Schroth GP, Kim RW, Kingsmore SF. Carrier testing for severe childhood recessive diseases by next-generation sequencing. Sci Transl Med 2011; 3:65ra4. [PMID: 21228398 PMCID: PMC3740116 DOI: 10.1126/scitranslmed.3001756] [Citation(s) in RCA: 482] [Impact Index Per Article: 37.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Of 7028 disorders with suspected Mendelian inheritance, 1139 are recessive and have an established molecular basis. Although individually uncommon, Mendelian diseases collectively account for ~20% of infant mortality and ~10% of pediatric hospitalizations. Preconception screening, together with genetic counseling of carriers, has resulted in remarkable declines in the incidence of several severe recessive diseases including Tay-Sachs disease and cystic fibrosis. However, extension of preconception screening to most severe disease genes has hitherto been impractical. Here, we report a preconception carrier screen for 448 severe recessive childhood diseases. Rather than costly, complete sequencing of the human genome, 7717 regions from 437 target genes were enriched by hybrid capture or microdroplet polymerase chain reaction, sequenced by next-generation sequencing (NGS) to a depth of up to 2.7 gigabases, and assessed with stringent bioinformatic filters. At a resultant 160x average target coverage, 93% of nucleotides had at least 20x coverage, and mutation detection/genotyping had ~95% sensitivity and ~100% specificity for substitution, insertion/deletion, splicing, and gross deletion mutations and single-nucleotide polymorphisms. In 104 unrelated DNA samples, the average genomic carrier burden for severe pediatric recessive mutations was 2.8 and ranged from 0 to 7. The distribution of mutations among sequenced samples appeared random. Twenty-seven percent of mutations cited in the literature were found to be common polymorphisms or misannotated, underscoring the need for better mutation databases as part of a comprehensive carrier testing strategy. Given the magnitude of carrier burden and the lower cost of testing compared to treating these conditions, carrier screening by NGS made available to the general population may be an economical way to reduce the incidence of and ameliorate suffering associated with severe recessive childhood disorders.
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Affiliation(s)
- Callum J. Bell
- National Center for Genome Resources, Santa Fe, NM 87505, USA
| | - Darrell L. Dinwiddie
- National Center for Genome Resources, Santa Fe, NM 87505, USA
- Children’s Mercy Hospital, Kansas City, MO 64108, USA
| | - Neil A. Miller
- National Center for Genome Resources, Santa Fe, NM 87505, USA
- Children’s Mercy Hospital, Kansas City, MO 64108, USA
| | | | | | - Joann Mudge
- National Center for Genome Resources, Santa Fe, NM 87505, USA
| | - Ray J. Langley
- National Center for Genome Resources, Santa Fe, NM 87505, USA
| | - Lu Zhang
- Illumina Inc., Hayward, CA 94545, USA
| | | | | | | | | | | | | | - Ryan W. Kim
- National Center for Genome Resources, Santa Fe, NM 87505, USA
| | - Stephen F. Kingsmore
- National Center for Genome Resources, Santa Fe, NM 87505, USA
- Children’s Mercy Hospital, Kansas City, MO 64108, USA
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Srinivasan BS, Evans EA, Flannick J, Patterson AS, Chang CC, Pham T, Young S, Kaushal A, Lee J, Jacobson JL, Patrizio P. A universal carrier test for the long tail of Mendelian disease. Reprod Biomed Online 2010; 21:537-51. [PMID: 20729146 DOI: 10.1016/j.rbmo.2010.05.012] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2010] [Revised: 05/22/2010] [Accepted: 05/24/2010] [Indexed: 01/03/2023]
Abstract
Mendelian disorders are individually rare but collectively common, forming a 'long tail' of genetic disease. A single highly accurate assay for this long tail would allow the scaling up of the Jewish community's successful campaign of population screening for Tay-Sachs disease to the general population, thereby improving millions of lives, greatly benefiting minority health and saving billions of dollars. This need has been addressed by designing a universal carrier test: a non-invasive, saliva-based assay for more than 100 Mendelian diseases across all major population groups. The test has been exhaustively validated with a median of 147 positive and 525 negative samples per variant, demonstrating a multiplex assay whose performance compares favourably with the previous standard of care, namely blood-based single-gene carrier tests. Because the test represents a dramatic reduction in the cost and complexity of large-scale population screening, an end to many preventable genetic diseases is now in sight. Moreover, given that the assay is inexpensive and requires only a saliva sample, it is now increasingly feasible to make carrier testing a routine part of preconception care.
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Inherited metabolic disorders involving the eye: a clinico-biochemical perspective. Eye (Lond) 2009; 24:507-18. [PMID: 19798114 DOI: 10.1038/eye.2009.229] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The diagnosis of inborn errors of metabolism is challenging for most physicians. Improvements in medical technology and greater knowledge of the human genome are resulting in significant changes in the diagnosis, classification, and treatment of inherited metabolic disorders (IMDs). Many known inborn errors of metabolism will be recognised earlier or treated differently because of these changes. It is important that physicians recognise the clinical signs of IMDs and know when to propose advanced laboratory testing or referral to a higher centre for better patient management. Ocular manifestations occur in various metabolic disorders. Although there is an extensive understanding of many inborn errors of metabolism at the biochemical, molecular, and metabolic levels, little is known about their pathogenesis. In particular, how systemic metabolic disease contributes to ocular defects remains to be elucidated in IMDs. The occurrence of eye abnormalities could be due to direct toxic mechanisms of abnormal metabolic products or accumulation of normal metabolites by errors of synthetic pathways or by deficient energy metabolism. A detailed ophthalmological assessment is essential. Definitive diagnosis and management of patients with IMDs is ideally carried out by a combination of specialists, including an ophthalmologist, paediatrician, biochemist, and medical geneticist. Recent advances in the diagnosis and treatment of IMDs have substantially improved the prognosis for many of these conditions.
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Cotton RGH, Auerbach AD, Axton M, Barash CI, Berkovic SF, Brookes AJ, Burn J, Cutting G, den Dunnen JT, Flicek P, Freimer N, Greenblatt MS, Howard HJ, Katz M, Macrae FA, Maglott D, Möslein G, Povey S, Ramesar RS, Richards CS, Seminara D, Smith TD, Sobrido MJ, Solbakk JH, Tanzi RE, Tavtigian SV, Taylor GR, Utsunomiya J, Watson M. GENETICS. The Human Variome Project. Science 2008; 322:861-2. [PMID: 18988827 PMCID: PMC2810956 DOI: 10.1126/science.1167363] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
An ambitious plan to collect, curate, and make accessible information on genetic variations affecting human health is beginning to be realized.
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Affiliation(s)
- Richard G H Cotton
- Genomic Disorders Research Centre, Howard Florey Institute, Melbourne, Australia.
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Campeau PM, Scriver CR, Mitchell JJ. A 25-year longitudinal analysis of treatment efficacy in inborn errors of metabolism. Mol Genet Metab 2008; 95:11-6. [PMID: 18701331 DOI: 10.1016/j.ymgme.2008.07.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/26/2008] [Revised: 07/01/2008] [Accepted: 07/01/2008] [Indexed: 12/30/2022]
Abstract
We report here the results of treatment in a panel of 65 inborn errors of metabolism, obtained in the 25th year of a longitudinal project, first reported in 1983. The phenotypic impact of these 65 diseases was scored before and after treatment using a consistent set of parameters, which we have retained to measure change in clinical phenotype throughout the project. We observed significant improvements in the response to treatment for the disease set as a whole. The number of conditions for which there is no response to treatment has progressively decreased; from 31 in 1983, to 20 in 1993, to 17 in 2008. Concomitantly, there has been an increase in the number of conditions that fully respond to treatment (from 8 in 1983 and 1993, to 20 in 2008), and in those for which there is a partial response. Reasons for improved treatment responses include new small molecules, new enzyme replacement therapies, more conditions that can be treated by organ and cell transplantation, and new experimental approaches to substrate reduction and chaperone assisted therapy. However, the most important and new development was not found in one or other particular therapeutic modality but in the access to new knowledge surrounding the individual diseases via the Internet and related resources. Our longitudinal analysis of treatment efficacy for this subset of inborn errors of metabolism continues to constitute a robust and representative assessment of our ability to restore more normal homeostasis in the inborn errors of metabolism.
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Affiliation(s)
- Philippe M Campeau
- Division of Medical Genetics, Department of Pediatrics, A-608, Montreal Children's Hospital, McGill University Health Center, Montreal, Quebec, Canada.
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Genetik in der Pädiatrie als Interaktion zwischen Klinik und Labor. Monatsschr Kinderheilkd 2008. [DOI: 10.1007/s00112-008-1681-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Abstract
"Inborn errors of metabolism," first recognized 100 years ago by Garrod, were seen as transforming evidence for chemical and biological individuality. Phenylketonuria (PKU), a Mendelian autosomal recessive phenotype, was identified in 1934 by Asbjörn Fölling. It is a disease with impaired postnatal cognitive development resulting from a neurotoxic effect of hyperphenylalaninemia (HPA). Its metabolic phenotype is accountable to multifactorial origins both in nurture, where the normal nutritional experience introduces L-phenylalanine, and in nature, where mutations (>500 alleles) occur in the phenylalanine hydroxylase gene (PAH) on chromosome 12q23.2 encoding the L-phenylalanine hydroxylase enzyme (EC 1.14.16.1). The PAH enzyme converts phenylalanine to tyrosine in the presence of molecular oxygen and catalytic amounts of tetrahydrobiopterin (BH4), its nonprotein cofactor. PKU is among the first of the human genetic diseases to enter, through newborn screening, the domain of public health, and to show a treatment effect. This effect caused a paradigm shift in attitudes about genetic disease. The PKU story contains many messages, including: a framework on which to appreciate the complexity of PKU in which phenotype reflects both locus-specific and genomic components; what the human PAH gene tells us about human population genetics and evolution of modern humans; and how our interest in PKU is served by a locus-specific mutation database (http://www.pahdb.mcgill.ca; last accessed 20 March 2007). The individual Mendelian PKU phenotype has no "simple" or single explanation; every patient has her/his own complex PKU phenotype and will be treated accordingly. Knowledge about PKU reveals genomic components of both disease and health.
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Affiliation(s)
- Charles R Scriver
- Department of Human Genetics, Faculty of Medicine, McGill University, Montreal, Quebec, Canada.
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Thompson PN, Heesterbeek JAP, van Arendonk JAM. Changes in disease gene frequency over time with differential genotypic fitness and various control strategies. J Anim Sci 2006; 84:2629-35. [PMID: 16971563 DOI: 10.2527/jas.2005-774] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A spreadsheet model was constructed to describe the change in allelic frequency over time for a lethal recessive mutation in an animal population. The model allowed relative fitness to differ between genotypes, between sexes, and over time. Whereas a lethal recessive allele is naturally eliminated very slowly from a population, a small selective disadvantage of the heterozygote results in a large increase in the rate of elimination. With selective advantage of the heterozygote through linkage with a production trait or pleiotropy, the allele is never naturally eliminated but tends toward a stable equilibrium frequency. The model was used to investigate various alternative control programs based on the detection of heterozygotes by genotyping and their exclusion from breeding. The programs (genotyping males only, genotyping males and 50% of females, and genotyping all breeding animals) were modeled for various initial heterozygote frequencies, and the results were described in terms of the number of generations, number of tests, and number of culls required to reduce the heterozygote frequency to a predefined level. The model can be used to compare the feasibility and cost of various control strategies and to illustrate clearly to breeders the expected outcomes, as well as the danger of prematurely terminating a control program when there is a selective advantage of the heterozygote.
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Affiliation(s)
- P N Thompson
- Department of Production Animal Studies, Faculty of Veterinary Science, University of Pretoria, Onderstepoort, 0110, South Africa.
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Hinkson DAR, Atenafu E, Kennedy SJ, Vohra S, Garg D, Levin AV. Cornelia de Lange syndrome: Parental preferences regarding the provision of medical information. Am J Med Genet A 2006; 140:2170-9. [PMID: 16906566 DOI: 10.1002/ajmg.a.31404] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
We surveyed 57 caregivers of children with Cornelia de Lange syndrome (CdLS) using a self-report questionnaire designed to elicit their experiences with receiving information regarding health complications associated with this multisystem disorder. Their most frequent sources of information at the time of diagnosis were a health care provider (86%) and the CdLS Foundation (72%). Although most caregivers (82%) indicated a desire to receive information about all possible CdLS related health complications, on average they recalled receiving information on only 64% of their child's current or future health complications. For two of the top three complications (as ranked by caregivers), information was available to fewer than half of the caregivers at diagnosis. Only 40% of caregivers were satisfied with the amount of information received at diagnosis, while only 45% felt that the information they received was useful. Caregivers indicated a preference for receiving information in written format (59%) or verbally (39%). Our results indicate that caregivers of children with CdLS report a high need for information at diagnosis, regarding their child's actual or potential health complications. Dissatisfaction may result both from a deficiency in information provided, as well as a mismatch between issues mentioned and those that caregivers deem most important. Caregivers may benefit maximally from receiving information in person at the time of diagnosis as well as having an additional written source of information. These findings highlight the importance of complementary sources of information for caregivers and are likely to be relevant for other multisystem disorders.
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Affiliation(s)
- Deborah A R Hinkson
- Division of Clinical & Metabolic Genetics, The Hospital for Sick Children, Toronto, Canada
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Huizing M, Brooks BP, Anikster Y. Optic atrophies in metabolic disorders. Mol Genet Metab 2005; 86:51-60. [PMID: 16194617 PMCID: PMC8336112 DOI: 10.1016/j.ymgme.2005.07.034] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2005] [Revised: 07/24/2005] [Accepted: 07/26/2005] [Indexed: 02/01/2023]
Abstract
Optic nerve involvement in metabolic disorders often results from apoptosis of cells that form or support the optic nerve, the retinal ganglion cell (RGC) axons, the myelin-forming oligodendrocytes, or the supporting vascular system. Given their high energy demands and the long course of their axons, RGCs are particularly sensitive to intracellular metabolic defects. Defects in energy metabolism, formation of reactive oxygen species, and storage of metabolites can all cause apoptosis of RGCs, decreased myelin formation of oligodendrocytes and increased pressure on the optic nerve. Clinically, the loss of RGC axons manifests as pale optic nerves. In general, the ophthalmologist can identify the underlying cause of an optic atrophy by careful examination, neuro-imaging, and family history. In some cases, however, the diagnosis proves elusive. In these instances, and especially when optic atrophy is accompanied by other systemic involvement, a metabolic disorder should be considered. Here, we review the underlying mechanisms of optic atrophy and its significance in metabolic disorders. Early identification of optic atrophy aids the diagnosis and subsequent management of the underlying condition, including anticipation of symptoms, genetic counseling, and possible therapeutic interventions. For many metabolic disorders, molecular testing is available.
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Affiliation(s)
- Marjan Huizing
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
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Poll-The BT, Maillette de Buy Wenniger-Prick LJ, Barth PG, Duran M. The eye as a window to inborn errors of metabolism. J Inherit Metab Dis 2003; 26:229-44. [PMID: 12889663 DOI: 10.1023/a:1024493318913] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Ocular manifestations in inborn errors of metabolism occur in many diseases and may be associated with any part of all eye components. In a minority of diseases it is possible to attribute the eye symptoms to a single hereditary pathogenetic mechanism. More often the aetiological relationship of the ocular defects to the metabolic disease is unknown. Diverse pathogenetic mechanisms may act via a common pathological pathway inducing ocular damage. The occurrence of eye abnormalities in metabolic disorders suggests that they are associated with direct toxic actions, errors of synthetic pathways or deficient energy metabolism. In this review, metabolic disorders with major abnormalities in the cornea, lens, retina and optic nerve are presented. In all cases, an appropriate combined approach by the ophthalmologist, paediatrician/neurologist, geneticist and clinical biochemist is the only way to diagnostic success.
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Affiliation(s)
- B T Poll-The
- Department of Pediatrics/Emma Children's Hospital and Laboratory of Genetic Metabolic Diseases, Amsterdam, The Netherlands.
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Abstract
Hereditary metabolic diseases in the context of evolutionary biology elicit interesting questions about ageing and senescence: Will persons successfully treated for inborn errors of metabolism, age and die prematurely because of compromised longevity? Because some unhealthy longevity has its origins in germline and somatic mutational processes, and in an inability to withstand metabolic stress, are there lessons to be learned about senescence from hereditary metabolic disease? Why are ageing, senescence and death necessary for Homo sapiens and how do they happen? These questions form the theme upon which several variations are played during the course of this essay. The theory of the disposable soma recognizes genomic and environmental events, well-seasoned by Chance, as determinants of ageing and senescence. Together, they cause the somatic damage that results in death. Genomics will reveal genes involved in longevity, both healthy and unhealthy. There will be schedules of gene expression behind our life-history traits. As in the field of hereditary metabolic disease, analogous genetic enquiries about ageing can be formulated. For example, how will heterozygotes age? Will association studies in centenarians reveal 'longevity genes'? Will disparate longevity in sib pairs reveal genetic factors? If there are 'ageing' mutations, of what types and with what effects? Will these initiatives lead to healthier longevity? A deeper question yet remains: why has human biology invested so greatly in grandparenthood?
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Affiliation(s)
- C R Scriver
- Department of Human Genetics, McGill University and McGill University Health Centre, Montreal, Quebec, Canada.
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