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Bharathi SP, Ramaiyan V. Complexity in interpreting cardiac valve-associated thrombus from tumors in Li-Fraumeni syndrome. World J Clin Cases 2024; 12:6431-6435. [PMID: 39507123 PMCID: PMC11438693 DOI: 10.12998/wjcc.v12.i31.6431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 05/14/2024] [Accepted: 05/27/2024] [Indexed: 09/11/2024] Open
Abstract
Li-Fraumeni syndrome (LFS) is a well-defined autosomal dominant predisposition syndrome due to TP53 germline mutation that causes many cancer malignancies. This early-onset syndrome poses a state of widespread malignancy. Such an inherited condition possessing defective p53, guardian of the genome, in the germline has the potential to cause multiple cancers by predominantly affecting mesenchyme (connective tissues, blood cells), breast, brain, and adrenal cortex organs. The tumors initially identified in LFS can eventually propagate to cause secondary malignancies. LFS contributes to multiple cancers in individuals with defective p53 inheritance. When suspected to possess any mass, patients with other co-morbidities, in particular those with certain cardiovascular conditions, undergo screening using high-throughput techniques like transthoracic and transesophageal echocardiography or cardiothoracic magnetic resonance imaging to locate and interpret the size of the mass. In LFS cases, it is certain to presume these masses as cancers and plan their management employing invasive surgeries after performing all efficient diagnostic tools. There are only poor predictions to rule out the chances of any other pathology. This criterion emphasizes the necessity to speculate alternative precision diagnostic methods to affirm such new growth or masses encountered in LFS cases. Moreover, it has all the possibilities to ultimately influence surgical procedures that may be invasive or complicate operative prognosis. Hence, it is essential to strategize an ideal protocol to diagnose any new unexplored mass in the LFS community. In this editorial, we discuss the importance of diagnostic approaches on naïve pristine masses in LFS.
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Affiliation(s)
- Sainath Prasanna Bharathi
- Department of Pharmacology, Saveetha College of Pharmacy, Saveetha Institute of Medical and Technical Sciences, Chennai 602105, India
| | - Velmurugan Ramaiyan
- Department of Pharmacology, Saveetha College of Pharmacy, Saveetha Institute of Medical and Technical Sciences, Chennai 602105, India
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2
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Kingsmore SF, Nofsinger R, Ellsworth K. Rapid genomic sequencing for genetic disease diagnosis and therapy in intensive care units: a review. NPJ Genom Med 2024; 9:17. [PMID: 38413639 PMCID: PMC10899612 DOI: 10.1038/s41525-024-00404-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 02/15/2024] [Indexed: 02/29/2024] Open
Abstract
Single locus (Mendelian) diseases are a leading cause of childhood hospitalization, intensive care unit (ICU) admission, mortality, and healthcare cost. Rapid genome sequencing (RGS), ultra-rapid genome sequencing (URGS), and rapid exome sequencing (RES) are diagnostic tests for genetic diseases for ICU patients. In 44 studies of children in ICUs with diseases of unknown etiology, 37% received a genetic diagnosis, 26% had consequent changes in management, and net healthcare costs were reduced by $14,265 per child tested by URGS, RGS, or RES. URGS outperformed RGS and RES with faster time to diagnosis, and higher rate of diagnosis and clinical utility. Diagnostic and clinical outcomes will improve as methods evolve, costs decrease, and testing is implemented within precision medicine delivery systems attuned to ICU needs. URGS, RGS, and RES are currently performed in <5% of the ~200,000 children likely to benefit annually due to lack of payor coverage, inadequate reimbursement, hospital policies, hospitalist unfamiliarity, under-recognition of possible genetic diseases, and current formatting as tests rather than as a rapid precision medicine delivery system. The gap between actual and optimal outcomes in children in ICUs is currently increasing since expanded use of URGS, RGS, and RES lags growth in those likely to benefit through new therapies. There is sufficient evidence to conclude that URGS, RGS, or RES should be considered in all children with diseases of uncertain etiology at ICU admission. Minimally, diagnostic URGS, RGS, or RES should be ordered early during admissions of critically ill infants and children with suspected genetic diseases.
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Affiliation(s)
- Stephen F Kingsmore
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, CA, USA.
| | - Russell Nofsinger
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, CA, USA
| | - Kasia Ellsworth
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, CA, USA
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3
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Sack LM, Mertens L, Murphy E, Hutchinson L, Giersch ABS, Mason-Suares H. Leveraging Unique Chromosomal Microarray Probes to Accurately Detect Copy Number at the Highly Homologous 15q15.3 Deafness-Infertility Syndrome Locus. Clin Chem 2023; 69:583-594. [PMID: 37022747 DOI: 10.1093/clinchem/hvad032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 02/27/2023] [Indexed: 04/07/2023]
Abstract
BACKGROUND Biallelic deletions at 15q15.3, including STRC and CATSPER2, cause autosomal recessive deafness-infertility syndrome (DIS), while biallelic deletions of STRC alone cause nonsyndromic hearing loss. These deletions are among the leading genetic causes of mild-moderate hearing loss, but their detection using chromosomal microarray (CMA) is impeded by a tandem duplication containing highly homologous pseudogenes. We sought to assess copy number variant (CNV) detection in this region by a commonly-employed CMA platform. METHODS Twenty-two specimens with known 15q15.3 CNVs, determined by droplet digital PCR (ddPCR), were analyzed by CMA. To investigate the impact of pseudogene homology on CMA performance, a probe-level analysis of homology was performed, and log2 ratios of unique and pseudogene-homologous probes compared. RESULTS Assessment of 15q15.3 CNVs by CMA compared to ddPCR revealed 40.9% concordance, with frequent mis-assignment of zygosity by the CMA automated calling software. Probe-level analysis of pseudogene homology suggested that probes with high homology contributed to this discordance, with significant differences in log2 ratios between unique and pseudogene-homologous CMA probes. Two clusters containing several unique probes could reliably detect CNVs involving STRC and CATSPER2, despite the noise of surrounding probes, discriminating between homozygous vs heterozygous losses and complex rearrangements. CNV detection by these probe clusters showed 100% concordance with ddPCR. CONCLUSIONS Manual analysis of clusters containing unique CMA probes without significant pseudogene homology improves CNV detection and zygosity assignment in the highly homologous DIS region. Incorporation of this method into CMA analysis and reporting processes can improve DIS diagnosis and carrier detection.
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Affiliation(s)
- Laura M Sack
- Department of Pathology, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA
- Laboratory for Molecular Medicine, Mass General Brigham, Cambridge, MA, USA
| | - Lauren Mertens
- Department of Pathology, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA
| | - Elissa Murphy
- Laboratory for Molecular Medicine, Mass General Brigham, Cambridge, MA, USA
| | - Laura Hutchinson
- Laboratory for Molecular Medicine, Mass General Brigham, Cambridge, MA, USA
| | - Anne B S Giersch
- Department of Pathology, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA
| | - Heather Mason-Suares
- Department of Pathology, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA
- Laboratory for Molecular Medicine, Mass General Brigham, Cambridge, MA, USA
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4
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Carter MT, Srour M, Au PYB, Buhas D, Dyack S, Eaton A, Inbar-Feigenberg M, Howley H, Kawamura A, Lewis SME, McCready E, Nelson TN, Vallance H. Genetic and metabolic investigations for neurodevelopmental disorders: position statement of the Canadian College of Medical Geneticists (CCMG). J Med Genet 2023; 60:523-532. [PMID: 36822643 DOI: 10.1136/jmg-2022-108962] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 01/27/2023] [Indexed: 02/25/2023]
Abstract
PURPOSE AND SCOPE The aim of this position statement is to provide recommendations for clinicians regarding the use of genetic and metabolic investigations for patients with neurodevelopmental disorders (NDDs), specifically, patients with global developmental delay (GDD), intellectual disability (ID) and/or autism spectrum disorder (ASD). This document also provides guidance for primary care and non-genetics specialists caring for these patients while awaiting consultation with a clinical geneticist or metabolic specialist. METHODS OF STATEMENT DEVELOPMENT A multidisciplinary group reviewed existing literature and guidelines on the use of genetic and metabolic investigations for the diagnosis of NDDs and synthesised the evidence to make recommendations relevant to the Canadian context. The statement was circulated for comment to the Canadian College of Medical Geneticists (CCMG) membership-at-large and to the Canadian Pediatric Society (Mental Health and Developmental Disabilities Committee); following incorporation of feedback, it was approved by the CCMG Board of Directors on 1 September 2022. RESULTS AND CONCLUSIONS Chromosomal microarray is recommended as a first-tier test for patients with GDD, ID or ASD. Fragile X testing should also be done as a first-tier test when there are suggestive clinical features or family history. Metabolic investigations should be done if there are clinical features suggestive of an inherited metabolic disease, while the patient awaits consultation with a metabolic physician. Exome sequencing or a comprehensive gene panel is recommended as a second-tier test for patients with GDD or ID. Genetic testing is not recommended for patients with NDDs in the absence of GDD, ID or ASD, unless accompanied by clinical features suggestive of a syndromic aetiology or inherited metabolic disease.
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Affiliation(s)
| | - Myriam Srour
- Division of Neurology, McGill University Health Centre, Montreal, Québec, Canada
- Department of Pediatrics, McGill University, Montréal, QC, Canada
| | - Ping-Yee Billie Au
- Department of Medical Genetics, Alberta Children's Hospital, Calgary, Alberta, Canada
| | - Daniela Buhas
- Division of Medical Genetics, Department of Specialized Medicine, McGill University Health Centre, McGill University, Montreal, Québec, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Sarah Dyack
- Division of Medical Genetics, IWK Health Centre, Halifax, Nova Scotia, Canada
- Department of Pediatrics, Dalhousie University, Halifax, NS, Canada
| | - Alison Eaton
- Department of Medical Genetics, Stollery Children's Hospital, Edmonton, Alberta, Canada
- Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada
| | - Michal Inbar-Feigenberg
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Heather Howley
- Office of Research Services, CHEO Research Institute, Ottawa, Ontario, Canada
| | - Anne Kawamura
- Division of Developmental Pediatrics, Holland Bloorview Kids Rehabilitation Hospital, Toronto, Ontario, Canada
- Department of Paediatrics, University of Toronto, Toronto, ON, Canada
- Mental Health and Developmental Disability Committee, Canadian Pediatric Society, Ottawa, ON, Canada
- Canadian Paediatric Society, Toronto, Ontario, Canada
| | - Suzanne M E Lewis
- Department of Medical Genetics, BC Children's and Women's Hospital, Vancouver, British Columbia, Canada
| | - Elizabeth McCready
- Department of Pathology and Molecular Medicine, McMaster University, McMaster University, Hamilton, ON, Canada, Hamilton, Ontario, Canada
- Hamilton Regional Laboratory Medicine Program, Hamilton Health Sciences Centre, Hamilton, ON, Canada
| | - Tanya N Nelson
- Department of Pathology and Laboratory Medicine, BC Children's Hospital, University of British Columbia, Vancouver, British Columbia, Canada
| | - Hilary Vallance
- Department of Pathology and Laboratory Medicine, BC Children's Hospital, University of British Columbia, Vancouver, British Columbia, Canada
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Wojcik MH, Bresnahan M, del Rosario MC, Ojeda MM, Kritzer A, Fraiman YS. Rare diseases, common barriers: disparities in pediatric clinical genetics outcomes. Pediatr Res 2023; 93:110-117. [PMID: 35963884 PMCID: PMC9892172 DOI: 10.1038/s41390-022-02240-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 07/14/2022] [Accepted: 07/24/2022] [Indexed: 02/04/2023]
Abstract
BACKGROUND Identifying a precise genetic diagnosis can improve outcomes for individuals with rare disease, though the resources required to do so may impede access and exacerbate healthcare disparities leading to inequitable care. Our objective was therefore to determine the effect of multiple sociodemographic factors on the yield of the diagnostic evaluation for genetics outpatients. METHODS This is a retrospective cohort study from 2017 to 2019 of outpatient genetics referrals at a pediatric academic tertiary care center. Exposures included: primary language, insurance type, and neighborhood resources (via the Childhood Opportunity Index, COI). The primary outcome was identification of a genetic diagnosis within 2 years of the initial clinic visit. RESULTS COI quintile was not significantly associated with the odds of diagnosis but was significantly associated with clinic attendance, with lower neighborhood resources leading to incomplete referrals. Limited English proficiency was associated with a higher odds of diagnosis, though at an older age. Public insurance was associated with increased access to genetic testing. CONCLUSIONS Lower neighborhood resources are negatively associated with clinic attendance. Our findings further suggest delays in care and a referral bias for more severe phenotypes among families with limited English proficiency. Improved access to clinical genetics is needed to improve diagnostic equity. IMPACT The resources required to identify a genetic diagnosis may impede access and exacerbate healthcare disparities leading to inequitable care. In an analysis of pediatric outpatient genetics referrals, we observed a significant association between neighborhood resources and clinic attendance but not diagnostic yield for those attending, and a higher diagnostic yield for families with limited English proficiency, suggesting referral bias for more severe phenotypes. Thus, the primary barrier to finding a genetic diagnosis was initiation of care, not the ensuing diagnostic odyssey. Further research efforts should be directed at increasing access to clinical genetics evaluations for children with rare disease.
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Affiliation(s)
- Monica H Wojcik
- Division of Newborn Medicine, Department of Medicine, Boston Children's Hospital, Boston, MA, 02115, USA. .,Division of Genetics and Genomics, Department of Medicine, Boston Children's Hospital, Boston, MA, 02115, USA. .,Harvard Medical School, Boston, MA, USA.
| | - Mairead Bresnahan
- Genetics and Genomics, Department of Medicine, Boston Children’s Hospital, Boston, MA, 02115
| | - Maya C del Rosario
- Genetics and Genomics, Department of Medicine, Boston Children’s Hospital, Boston, MA, 02115
| | - Mayra Martinez Ojeda
- Genetics and Genomics, Department of Medicine, Boston Children’s Hospital, Boston, MA, 02115
| | - Amy Kritzer
- Genetics and Genomics, Department of Medicine, Boston Children’s Hospital, Boston, MA, 02115
| | - Yarden S. Fraiman
- Divisions of Newborn Medicine, Boston Children’s Hospital, Boston, MA, 02115.,Harvard Medical School, Boston, MA.,Department of Neonatology, Beth Israel Deaconess Medical Center, Boston, MA
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6
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Frueh JS, Press DZ, Sanders JS. Diagnosis and Workup of Intellectual Disability in Adults: Suggested Strategies for the Adult Neurologist. Neurol Clin Pract 2022; 11:534-540. [PMID: 34992961 DOI: 10.1212/cpj.0000000000001128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 06/24/2021] [Indexed: 11/15/2022]
Abstract
Purpose of Review Etiologic investigations for adults with intellectual disability (ID) pose a special challenge to many adult neurologists. The adaptability of pediatric guidelines for workup of ID to adult populations has not been clearly established. We review the current recommendations on etiologic workup of ID in children and adults and provide initial guidance for adult neurologists who care for individuals with ID of unknown etiology. Recent Findings Etiologic workup, including genetic testing, is recommended in individuals with ID of unknown origin. Workup should be guided by a thoughtful history and physical examination, which can help identify certain causes of ID. Summary Specific diagnoses may help guide management and surveillance of comorbid conditions in individuals with ID. Etiologic investigations of adults with ID include genetic and metabolic testing and brain imaging in the appropriate clinical setting.
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Affiliation(s)
- Julia Sophie Frueh
- Department of Neurology (JSF), Boston Children's Hospital, MA; Department of Neurology (JSF, DZP), Beth Israel Deaconess Medical Center, Boston, MA; and Department of Pediatrics (JSS), University of Colorado, Denver
| | - Daniel Zvi Press
- Department of Neurology (JSF), Boston Children's Hospital, MA; Department of Neurology (JSF, DZP), Beth Israel Deaconess Medical Center, Boston, MA; and Department of Pediatrics (JSS), University of Colorado, Denver
| | - Jessica Solomon Sanders
- Department of Neurology (JSF), Boston Children's Hospital, MA; Department of Neurology (JSF, DZP), Beth Israel Deaconess Medical Center, Boston, MA; and Department of Pediatrics (JSS), University of Colorado, Denver
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7
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Bajguz D, Danylchuk NR, Czarniecki M, Selig JP, Sutphen R, Kaylor J. Utilization of genetic testing: Analysis of 4,499 prior authorization requests for molecular genetic tests at four US regional health plans. J Genet Couns 2021; 31:771-780. [PMID: 34939253 DOI: 10.1002/jgc4.1543] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 11/29/2021] [Accepted: 12/05/2021] [Indexed: 11/11/2022]
Abstract
Continuous advances in genetic testing methodologies and an increased understanding of the genetic mechanisms of diseases have fueled genetic testing utilization across health care specialties. To our knowledge, national trends in the ordering of genetic testing have not been studied broadly across clinical indications, testing methodologies, and ordering provider specialties. We performed a retrospective analysis of 4,499 complete prior authorization requests for molecular genetic testing submitted to four regional health plans' commercial lines of business between May 1, 2019 and May 31, 2019. Ordering providers were characterized by their certification(s) and specialty of practice. Among 4,499 genetic testing requests, 92% were ordered by non-genetics providers. Obstetrician/gynecology (OBGYN) (63%), oncology (15%), and genetics (8%) providers ordered genetic testing most frequently. Reproductive, hereditary cancer, and tumor testing were the most frequently ordered genetic tests. Seventy-nine percent of all prior authorization requests were approved. When analyzing complex genetic testing requests, we found that testing ordered by genetics providers was more likely to be approved based on health plan policy than testing ordered by non-genetics providers. Our results suggest that health care providers across multiple medical specialties may benefit from involvement of genetics specialists in decision-making regarding molecular tests.
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Affiliation(s)
- Dominika Bajguz
- Genetic Counseling Department, College for Health Professions, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Noelle R Danylchuk
- Genetic Counseling Department, College for Health Professions, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | | | - James P Selig
- Biostatistics Department, College of Public Health, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | | | - Julie Kaylor
- Genetic Counseling Department, College for Health Professions, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA.,InformedDNA, Inc., St. Petersburg, Florida, USA
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8
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Strnadová I, Nevin SM, Scully JL, Palmer EE. The opinions and experiences of people with intellectual disability regarding genetic testing and genetic medicine: A systematic review. Genet Med 2021; 24:535-548. [PMID: 34906474 DOI: 10.1016/j.gim.2021.11.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 11/16/2021] [Indexed: 11/19/2022] Open
Abstract
PURPOSE Genetic testing is frequently conducted on people with intellectual disability. This systematic literature review sought to assess what research has been conducted with people with intellectual disability to investigate their opinions and experiences of genetic counselling and testing. METHODS A search of 5 online databases (from year of database creation to 2021) yielded 1162 articles. Seven articles met the inclusion criteria. We assessed the quality, accessibility, and inclusivity of each study and extracted the data. Deductive content analysis was performed. RESULTS Most study participants showed both the desire and the capability to learn more about genetic conditions and genetic tests. Participants expressed a wide variety of opinions about genetic tests, similar to the range of opinions of the general population. All studies were small and were from a limited number of countries, and analysis showed limited evidence of inclusivity or accessibility. CONCLUSION This review highlights major gaps in the understanding of the opinions, experiences, and preferences of people with intellectual disability regarding genetic counselling and testing. There is urgent need for research to codesign a more inclusive genomic model of care to address this failure in health care accessibility and equity.
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Affiliation(s)
- Iva Strnadová
- School of Education, UNSW Sydney, Sydney, New South Wales, Australia; Disability Innovation Institute, UNSW Sydney, Sydney, New South Wales, Australia
| | - Suzanne M Nevin
- School of Women's and Children's Health, UNSW Medicine, Randwick, New South Wales, Australia; Sydney Children's Hospitals Network, New South Wales, Australia
| | - Jackie Leach Scully
- Disability Innovation Institute, UNSW Sydney, Sydney, New South Wales, Australia
| | - Elizabeth E Palmer
- School of Women's and Children's Health, UNSW Medicine, Randwick, New South Wales, Australia; Sydney Children's Hospitals Network, New South Wales, Australia.
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9
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Su M, Page S, Haag M, Swisshelm K, Hennerich D, Graw S, LeRoux J, Brzeskiewicz P, Svihovec S, Bao L. Clinical utility and cost-effectiveness analysis of chromosome testing concomitant with chromosomal microarray of patients with constitutional disorders in a U.S. academic medical center. J Genet Couns 2021; 31:364-374. [PMID: 34397147 DOI: 10.1002/jgc4.1496] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 07/30/2021] [Accepted: 08/01/2021] [Indexed: 12/11/2022]
Abstract
Chromosomal microarray (CMA) is now widely used as first-tier testing for the detection of copy number variants (CNVs) and absence of heterozygosity (AOH) in patients with multiple congenital anomalies (MCA), autism spectrum disorder (ASD), developmental delay (DD), and/or intellectual disability (ID). Chromosome analysis is commonly used to complement CMA in the detection of balanced genomic aberrations. However, the cost-effectiveness and the impact on clinical management of chromosome analysis concomitant with CMA were not well studied, and there is no consensus on how to best utilize these two tests. To assess the clinical utility and cost-effectiveness of chromosome analysis concomitant with CMA in patients with MCA, ASD, DD, and/or ID, we retrospectively analyzed 3,360 postnatal cases for which CMA and concomitant chromosome analysis were performed in the Colorado Genetic Laboratory (CGL) at the University Of Colorado School Of Medicine. Chromosome analysis alone yielded a genetic diagnosis in two patients (0.06%) and contributed additional information to CMA results in 199 (5.92%) cases. The impact of abnormal chromosome results on patient management was primarily related to counseling for reproductive and recurrence risks assessment (101 cases, 3.01%) while a few (5 cases, 0.15%) led to changes in laboratory testing and specialist referral (25 cases, 0.74%). The incremental cost-effectiveness ratio (ICER) of combined testing demonstrated the cost of each informative chromosome finding was significantly higher for patients with clinically insignificant (CI) CMA findings versus clinically significant (CS) CMA results. Our results suggest that a stepwise approach with CMA testing with reflex to chromosome analysis on cases with CS CMA findings is a more cost-effective testing algorithm for patients with MCA, ASD, and/or DD/ID.
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Affiliation(s)
- Meng Su
- Colorado Genetics Laboratory, Department of Pathology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Stephanie Page
- Genetics Counseling Program, Department of Genetics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Mary Haag
- Colorado Genetics Laboratory, Department of Pathology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Karen Swisshelm
- Colorado Genetics Laboratory, Department of Pathology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Deborrah Hennerich
- Colorado Genetics Laboratory, Department of Pathology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Sharon Graw
- Colorado Genetics Laboratory, Department of Pathology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Jamie LeRoux
- Colorado Genetics Laboratory, Department of Pathology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Peter Brzeskiewicz
- Colorado Genetics Laboratory, Department of Pathology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Shayna Svihovec
- Clinical Genetics and Metabolism, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Liming Bao
- Colorado Genetics Laboratory, Department of Pathology, University of Colorado School of Medicine, Aurora, CO, USA
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10
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Comparison of the diagnostic yield of aCGH and genome-wide sequencing across different neurodevelopmental disorders. NPJ Genom Med 2021; 6:25. [PMID: 33767182 PMCID: PMC7994713 DOI: 10.1038/s41525-021-00188-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 02/26/2021] [Indexed: 02/07/2023] Open
Abstract
Most consensus recommendations for the genetic diagnosis of neurodevelopmental disorders (NDDs) do not include the use of next generation sequencing (NGS) and are still based on chromosomal microarrays, such as comparative genomic hybridization array (aCGH). This study compares the diagnostic yield obtained by aCGH and clinical exome sequencing in NDD globally and its spectrum of disorders. To that end, 1412 patients clinically diagnosed with NDDs and studied with aCGH were classified into phenotype categories: global developmental delay/intellectual disability (GDD/ID); autism spectrum disorder (ASD); and other NDDs. These categories were further subclassified based on the most frequent accompanying signs and symptoms into isolated forms, forms with epilepsy; forms with micro/macrocephaly and syndromic forms. Two hundred and forty-five patients of the 1412 were subjected to clinical exome sequencing. Diagnostic yield of aCGH and clinical exome sequencing, expressed as the number of solved cases, was compared for each phenotype category and subcategory. Clinical exome sequencing was superior than aCGH for all cases except for isolated ASD, with no additional cases solved by NGS. Globally, clinical exome sequencing solved 20% of cases (versus 5.7% by aCGH) and the diagnostic yield was highest for all forms of GDD/ID and lowest for Other NDDs (7.1% versus 1.4% by aCGH) and ASD (6.1% versus 3% by aCGH). In the majority of cases, diagnostic yield was higher in the phenotype subcategories than in the mother category. These results suggest that NGS could be used as a first-tier test in the diagnostic algorithm of all NDDs followed by aCGH when necessary.
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Abstract
Neurodevelopmental disorders are the most prevalent chronic medical conditions encountered in pediatric primary care. In addition to identifying appropriate descriptive diagnoses and guiding families to evidence-based treatments and supports, comprehensive care for individuals with neurodevelopmental disorders includes a search for an underlying etiologic diagnosis, primarily through a genetic evaluation. Identification of an underlying genetic etiology can inform prognosis, clarify recurrence risk, shape clinical management, and direct patients and families to condition-specific resources and supports. Here we review the utility of genetic testing in patients with neurodevelopmental disorders and describe the three major testing modalities and their yields - chromosomal microarray, exome sequencing (with/without copy number variant calling), and FMR1 CGG repeat analysis for fragile X syndrome. Given the diagnostic yield of genetic testing and the potential for clinical and personal utility, there is consensus that genetic testing should be offered to all patients with global developmental delay, intellectual disability, and/or autism spectrum disorder. Despite this recommendation, data suggest that a minority of children with autism spectrum disorder and intellectual disability have undergone genetic testing. To address this gap in care, we describe a structured but flexible approach to facilitate integration of genetic testing into clinical practice across pediatric specialties and discuss future considerations for genetic testing in neurodevelopmental disorders to prepare pediatric providers to care for patients with such diagnoses today and tomorrow.
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Affiliation(s)
- Juliann M. Savatt
- Autism & Developmental Medicine Institute, Geisinger, Danville, PA, United States
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12
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Langenfeld A, Schema L, Eckerle JK. Genetic developmental disability diagnosed in adulthood: a case report. J Med Case Rep 2021; 15:28. [PMID: 33494837 PMCID: PMC7831183 DOI: 10.1186/s13256-020-02590-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 11/17/2020] [Indexed: 11/17/2022] Open
Abstract
Background Developmental disabilities (DD) are an umbrella term for conditions associated with functional impairments in physical, learning, language, or behavior areas. Intellectual disability (ID) is a type of developmental disability that results in delays in cognitive or intellectual functioning, such as reasoning, learning, and problem-solving, and adaptive behaviors including social and practical life skills. DD can be due to a variety of factors, ranging from environmental exposures to genetic mutations, and studies suggest that up to 40% of DDs may be caused by genetic issues. Case presentation In this case study, we present an 18-year-old internationally adopted female Chinese American patient with a known history of developmental delay, intellectual disability, strabismus, and a congenital heart defect who had not been tested for genetic causes of her delay prior to presentation. When evaluated with chromosomal microarray, the patient demonstrated a deletion on the short arm of chromosome 5, an area associated with Cri-du-chat syndrome. This chromosomal deletion was a likely explanation for her history of developmental delays, intellectual disability, and congenital heart defect, in addition to her history of institutionalization and the trauma of multiple caregiver transitions in early childhood. The patient was referred for further evaluation by a geneticist and genetic counselor. Conclusions This case highlights that the underlying cause of developmental delay is often multifactorial, and underscores the importance of a full medical evaluation, including genetic testing, for children with intellectual disability. Using this approach, healthcare professionals can identify potential diagnoses and provide more targeted resources to families.
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Affiliation(s)
- Adam Langenfeld
- Division of Clinical Behavioral Neuroscience, Department of Pediatrics, University of Minnesota, 717 Delaware Street SE, Minneapolis, MN, 55414, USA.
| | - Lynn Schema
- Division of Pediatric Genetics and Metabolism, Department of Pediatrics, University of Minnesota, 606 24th Avenue S, Suite 500, Minneapolis, MN, 55454, USA
| | - Judith K Eckerle
- Division of General Pediatrics and Adolescent Health, Department of Pediatrics, University of Minnesota, 717 Delaware Street SE, Minneapolis, MN, 55414, USA
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Prenatal Testing or Screening? MATERNAL-FETAL MEDICINE 2020. [DOI: 10.1097/fm9.0000000000000061] [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] Open
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14
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Gürkan H, Atli Eİ, Atli E, Bozatli L, Altay MA, Yalçintepe S, Özen Y, Eker D, Akurut Ç, Demır S, Görker I. Chromosomal Microarray Analysis in Turkish Patients with Unexplained Developmental Delay and Intellectual Developmental Disorders. Noro Psikiyatr Ars 2020; 57:177-191. [PMID: 32952419 PMCID: PMC7481981 DOI: 10.29399/npa.24890] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 03/16/2020] [Indexed: 01/06/2023] Open
Abstract
INTRODUCTION Aneuploids, copy number variations (CNVs), and single nucleotide variants in specific genes are the main genetic causes of developmental delay (DD) and intellectual disability disorder (IDD). These genetic changes can be detected using chromosome analysis, chromosomal microarray (CMA), and next-generation DNA sequencing techniques. Therefore; In this study, we aimed to investigate the importance of CMA in determining the genomic etiology of unexplained DD and IDD in 123 patients. METHOD For 123 patients, chromosome analysis, DNA fragment analysis and microarray were performed. Conventional G-band karyotype analysis from peripheral blood was performed as part of the initial screening tests. FMR1 gene CGG repeat number and methylation analysis were carried out to exclude fragile X syndrome. RESULTS CMA analysis was performed in 123 unexplained IDD/DD patients with normal karyotypes and fragile X screening, which were evaluated by conventional cytogenetics. Forty-four CNVs were detected in 39 (39/123=31.7%) patients. Twelve CNV variant of unknown significance (VUS) (9.75%) patients and 7 CNV benign (5.69%) patients were reported. In 6 patients, one or more pathogenic CNVs were determined. Therefore, the diagnostic efficiency of CMA was found to be 31.7% (39/123). CONCLUSION Today, genetic analysis is still not part of the routine in the evaluation of IDD patients who present to psychiatry clinics. A genetic diagnosis from CMA can eliminate genetic question marks and thus alter the clinical management of patients. Approximately one-third of the positive CMA findings are clinically intervenable. However, the emergence of CNVs as important risk factors for multiple disorders increases the need for individuals with comorbid neurodevelopmental conditions to be the priority where the CMA test is recommended.
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Affiliation(s)
- Hakan Gürkan
- Faculty of Medicine, Department of Medical Genetics, Edirne, Trakya University, Edirne, Turkey
| | - Emine İkbal Atli
- Faculty of Medicine, Department of Medical Genetics, Edirne, Trakya University, Edirne, Turkey
| | - Engin Atli
- Faculty of Medicine, Department of Medical Genetics, Edirne, Trakya University, Edirne, Turkey
| | - Leyla Bozatli
- Faculty of Medicine, Department of Child and Adolescent Psychiatry, Trakya University, Edirne, Turkey
| | - Mengühan Araz Altay
- Faculty of Medicine, Department of Child and Adolescent Psychiatry, Trakya University, Edirne, Turkey
| | - Sinem Yalçintepe
- Faculty of Medicine, Department of Medical Genetics, Edirne, Trakya University, Edirne, Turkey
| | - Yasemin Özen
- Faculty of Medicine, Department of Medical Genetics, Edirne, Trakya University, Edirne, Turkey
| | - Damla Eker
- Faculty of Medicine, Department of Medical Genetics, Edirne, Trakya University, Edirne, Turkey
| | - Çisem Akurut
- Faculty of Medicine, Department of Medical Genetics, Edirne, Trakya University, Edirne, Turkey
| | - Selma Demır
- Faculty of Medicine, Department of Medical Genetics, Edirne, Trakya University, Edirne, Turkey
| | - Işık Görker
- Faculty of Medicine, Department of Child and Adolescent Psychiatry, Trakya University, Edirne, Turkey
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15
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Besterman AD, Sadik J, Enenbach MJ, Quintero-Rivera F, DeAntonio M, Martinez-Agosto JA. The Feasibility and Outcomes of Genetic Testing for Autism and Neurodevelopmental Disorders on an Inpatient Child and Adolescent Psychiatry Service. Autism Res 2020; 13:1450-1464. [PMID: 32662193 DOI: 10.1002/aur.2338] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 04/22/2020] [Accepted: 05/11/2020] [Indexed: 12/12/2022]
Abstract
Diagnostic genetic testing is recommended for children with autism spectrum disorder and other neurodevelopmental disorders. One approach to improve access to genetic testing is to offer it on the inpatient child and adolescent psychiatry (CAP) service. We provided medical genetics education to CAP fellows and retrospectively compared the genetic testing rates and diagnostic yield pre- and post-education. We compared demographics to similar patients who received testing on other clinical services and assessed rates of outpatient genetics follow-up post-discharge. The genetic testing rate on the inpatient CAP service was 1.6% before the educational intervention and 10.7% afterward. Genetic risk factors were identified in 4.3% of inpatients. However, 34.8% had variants of unknown significance. 39.1% of patients who received genetic testing while inpatients were underrepresented minorities, compared to 7.7% of inpatients who received genetic testing from other clinical services. 43.5% of patients were lost to outpatient genetics follow-up. We have demonstrated that it is feasible to provide medical genetics education to CAP fellows on an inpatient service, which may improve genetic testing rates. This preliminary evidence also suggests that genetic testing for inpatients may identify variants of unknown significance instead of well-known neurodevelopmental disorder risk variants. Genetic testing on an inpatient CAP service may also improve access to genetic services for underrepresented minorities, but assuring outpatient follow-up can be challenging. LAY SUMMARY: Genetic testing is recommended for children with autism and related developmental conditions. We provided genetic testing to a group of these children who were in a psychiatric hospital by teaching their doctors how it can be helpful. We identified a genetic risk factor in a small percentage of children and a possible genetic risk factor in a large percentage of children. However, many children did not end up receiving their genetic test results once they left the hospital. These results tell us that the psychiatric hospital may be a good place for children with autism and behavioral problems to get genetic testing, but that it is really important that doctors assure follow-up is feasible for all patients to receive their genetic test results once they leave the hospital. Autism Res 2020, 13: 1450-1464. © 2020 International Society for Autism Research, Wiley Periodicals, Inc.
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Affiliation(s)
- Aaron D Besterman
- Department of Psychiatry, UCLA Division of Child and Adolescent Psychiatry, Los Angeles, California, USA
- UCLA Semel Institute of Neuroscience and Human Behavior, Los Angeles, California, USA
- Department of Pediatrics, UCLA Division of Medical Genetics, Los Angeles, California, USA
- UCLA David Geffen School of Medicine, Los Angeles, California, USA
| | - Joshua Sadik
- UCLA David Geffen School of Medicine, Los Angeles, California, USA
| | - Michael J Enenbach
- Department of Psychiatry, UCLA Division of Child and Adolescent Psychiatry, Los Angeles, California, USA
- UCLA Semel Institute of Neuroscience and Human Behavior, Los Angeles, California, USA
- UCLA David Geffen School of Medicine, Los Angeles, California, USA
| | - Fabiola Quintero-Rivera
- UCLA David Geffen School of Medicine, Los Angeles, California, USA
- UCLA Department of Pathology and Laboratory Medicine, Los Angeles, California, USA
| | - Mark DeAntonio
- Department of Psychiatry, UCLA Division of Child and Adolescent Psychiatry, Los Angeles, California, USA
- UCLA Semel Institute of Neuroscience and Human Behavior, Los Angeles, California, USA
- UCLA David Geffen School of Medicine, Los Angeles, California, USA
| | - Julian A Martinez-Agosto
- UCLA Semel Institute of Neuroscience and Human Behavior, Los Angeles, California, USA
- Department of Pediatrics, UCLA Division of Medical Genetics, Los Angeles, California, USA
- UCLA David Geffen School of Medicine, Los Angeles, California, USA
- UCLA Department of Human Genetics, Los Angeles, California, USA
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16
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Lee H, Nelson SF. The frontiers of sequencing in undiagnosed neurodevelopmental diseases. Curr Opin Genet Dev 2020; 65:76-83. [PMID: 32599523 DOI: 10.1016/j.gde.2020.05.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 04/07/2020] [Accepted: 05/01/2020] [Indexed: 12/24/2022]
Abstract
Characterized by impairments in brain and central nervous system development, neurodevelopmental diseases causes are highly heterogeneous. Although many of these diseases are individually rare, collectively more than 3% of the children are reported to be affected with a type of neurodevelopmental diseases worldwide, and many remain undiagnosed even with current genomic tools. Identifying the genetic causes of these diseases allows better clinical management and expands our understanding of human neurodevelopment. Over the past decade, expansion of genomic sequencing and some methodologic improvements have improved molecular diagnostic yield as well as the discovery of novel genetic causes for wide spectrum of neurodevelopmental diseases. Here we review the current diagnostic workflow and propose ways of improving the diagnostic yield.
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Affiliation(s)
- Hane Lee
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
| | - Stanley F Nelson
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
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17
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Yusuf A, Peltekova I, Savion-Lemieux T, Frei J, Bruno R, Joober R, Howe J, Scherer SW, Elsabbagh M. Perceived utility of biological testing for autism spectrum disorder is associated with child and family functioning. RESEARCH IN DEVELOPMENTAL DISABILITIES 2020; 100:103605. [PMID: 32120048 DOI: 10.1016/j.ridd.2020.103605] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 01/28/2020] [Accepted: 02/04/2020] [Indexed: 06/10/2023]
Abstract
BACKGROUND The clinical integration of chromosomal microarray testing promises improvements in diagnostic yields in Autism Spectrum Disorder (ASD). While the impact on clinical management is promising for some families, the utility perceived by families, including the majority for whom results are negative, is unclear. With next generation genomic sequencing technologies poised for integration, along with promising ASD biomarkers being developed, there is a need to understand the extent to which genomic and other biological testing would have utility for the target recipients of these tests and their families. The purpose of the present cross-sectional study was to examine the predictors of perceived utility of biological testing among parents of a child with ASD. METHODS The Perceived Utility of Biotesting (PUB) Questionnaire was developed based on literature review and integrating family review. Following their child's diagnosis, families participating in an ongoing prospective study completed the PUB questionnaire along with self-reported measures of parent stress, child and family functioning, and family-centered care prior to undergoing genetic testing for both clinical and research purposes. RESULTS Based on n = 85 families, psychometric properties of the Perceived Utility of Biotesting questionnaire suggest a reliable and valid instrument. A stepwise regression analysis reveals that lower levels of child emotional and behavioural functioning and higher levels of family functioning correlated with higher perceived utility for biological testing. LIMITATIONS A main limitation in the study is the participation rate of 50 %, thus the possibility of self-selection bias cannot be ruled out. We also chose to assess perceived utility among parents rather than the individuals with ASD themselves: modifying the questionnaire to capture perceived utility from autistic individuals across the lifespan would prove essential in future studies. Finally, ongoing validation of the PUB by assessing the PUB's discriminant and convergent validity is still needed. CONCLUSIONS We conclude that the utility of biological testing perceived by families whose child is undergoing genetic testing around ASD diagnosis depends on their unique child and family characteristics. This signifies that engaging families in biomarker discovery for improving the impact of research and care requires systematic input from a representative sample of families.
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Affiliation(s)
- Afiqah Yusuf
- Azrieli Centre for Autism Research, Montreal Neurological Institute-Hospital, McGill University, Montreal, Canada; Research Institute of the McGill University Health Centre, Montreal, Canada
| | - Iskra Peltekova
- Azrieli Centre for Autism Research, Montreal Neurological Institute-Hospital, McGill University, Montreal, Canada; Research Institute of the McGill University Health Centre, Montreal, Canada
| | - Tal Savion-Lemieux
- Research Institute of the McGill University Health Centre, Montreal, Canada
| | - Jennifer Frei
- Research Institute of the McGill University Health Centre, Montreal, Canada
| | - Ruth Bruno
- Research Institute of the McGill University Health Centre, Montreal, Canada
| | - Ridha Joober
- Department of Psychiatry, McGill University, Montreal, Canada; Douglas Mental Health University Institute, Montreal, Canada
| | - Jennifer Howe
- The Centre for Applied Genomics, Hospital for Sick Children, Toronto, Canada
| | - Stephen W Scherer
- The Centre for Applied Genomics, Hospital for Sick Children, Toronto, Canada; McLaughlin Centre and Department of Molecular Genetics, University of Toronto, Canada
| | - Mayada Elsabbagh
- Azrieli Centre for Autism Research, Montreal Neurological Institute-Hospital, McGill University, Montreal, Canada; Research Institute of the McGill University Health Centre, Montreal, Canada.
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18
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Reuter CM, Kohler JN, Bonner D, Zastrow D, Fernandez L, Dries A, Marwaha S, Davidson J, Brokamp E, Herzog M, Hong J, Macnamara E, Rosenfeld JA, Schoch K, Spillmann R, The Undiagnosed Diseases Network, Loscalzo J, Krier J, Stoler J, Sweetser D, Palmer CG, Phillips JA, Shashi V, Adams DA, Yang Y, Ashley EA, Fisher PG, Mulvihill JJ, Bernstein JA, Wheeler MT. Yield of whole exome sequencing in undiagnosed patients facing insurance coverage barriers to genetic testing. J Genet Couns 2019; 28:1107-1118. [PMID: 31478310 PMCID: PMC6901723 DOI: 10.1002/jgc4.1161] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 07/12/2019] [Accepted: 07/27/2019] [Indexed: 01/02/2023]
Abstract
BACKGROUND Despite growing evidence of diagnostic yield and clinical utility of whole exome sequencing (WES) in patients with undiagnosed diseases, there remain significant cost and reimbursement barriers limiting access to such testing. The diagnostic yield and resulting clinical actions of WES for patients who previously faced insurance coverage barriers have not yet been explored. METHODS We performed a retrospective descriptive analysis of clinical WES outcomes for patients facing insurance coverage barriers prior to clinical WES and who subsequently enrolled in the Undiagnosed Diseases Network (UDN). Clinical WES was completed as a result of participation in the UDN. Payer type, molecular diagnostic yield, and resulting clinical actions were evaluated. RESULTS Sixty-six patients in the UDN faced insurance coverage barriers to WES at the time of enrollment (67% public payer, 26% private payer). Forty-two of 66 (64%) received insurance denial for clinician-ordered WES, 19/66 (29%) had health insurance through a payer known not to cover WES, and 5/66 (8%) had previous payer denial of other genetic tests. Clinical WES results yielded a molecular diagnosis in 23 of 66 patients (35% [78% pediatric, 65% neurologic indication]). Molecular diagnosis resulted in clinical actions in 14 of 23 patients (61%). CONCLUSIONS These data demonstrate that a substantial proportion of patients who encountered insurance coverage barriers to WES had a clinically actionable molecular diagnosis, supporting the notion that WES has value as a covered benefit for patients who remain undiagnosed despite objective clinical findings.
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Affiliation(s)
- Chloe M. Reuter
- Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA
- Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA
| | - Jennefer N. Kohler
- Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA
- Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA
| | - Devon Bonner
- Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA
- Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA
| | - Diane Zastrow
- Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA
- Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA
| | - Liliana Fernandez
- Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA
- Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA
| | - Annika Dries
- Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA
- Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA
| | - Shruti Marwaha
- Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA
- Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA
| | - Jean Davidson
- Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA
- Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA
| | - Elly Brokamp
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN
| | - Matthew Herzog
- Department of Human Genetics, University of California Los Angeles, Los Angeles, CA
| | - Joyce Hong
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA
| | - Ellen Macnamara
- Undiagnosed Diseases Program, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Jill A. Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Kelly Schoch
- Department of Pediatrics, Duke University Medical Center, Durham, NC
| | - Rebecca Spillmann
- Department of Pediatrics, Duke University Medical Center, Durham, NC
| | | | - Joseph Loscalzo
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA
| | - Joel Krier
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA
| | - Joan Stoler
- Division of Genetics, Boston Children’s Hospital, Boston, MA
| | - David Sweetser
- Division of Medical Genetics and Metabolism, Department of Pediatrics, Massachusetts General Hospital, Boston, MA
| | - Christina G.S. Palmer
- Department of Human Genetics, University of California Los Angeles, Los Angeles, CA
- Psychiatry & Biobehavioral Sciences, University of California Los Angeles, Los Angeles, CA
- Institute for Society & Genetics, University of California Los Angeles, Los Angeles, CA
| | - John A Phillips
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN
| | - Vandana Shashi
- Department of Pediatrics, Duke University Medical Center, Durham, NC
| | - David A. Adams
- Undiagnosed Diseases Program, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Euan A. Ashley
- Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA
- Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA
| | - Paul G. Fisher
- Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA
| | - John J. Mulvihill
- Division of Genomic Medicine, National Human Genome Research Institute, Bethesda, MD
| | - Jonathan A. Bernstein
- Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA
| | - Matthew T. Wheeler
- Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA
- Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA
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Mazzola SE, O'Connor B, Yashar BM. Primary care physicians’ understanding and utilization of pediatric exome sequencing results. J Genet Couns 2019; 28:1130-1138. [DOI: 10.1002/jgc4.1163] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 06/21/2019] [Accepted: 08/12/2019] [Indexed: 11/11/2022]
Affiliation(s)
- Sarah E. Mazzola
- Genomic Medicine Institute Cleveland Clinic Foundation Cleveland Ohio
- Department of Human Genetics University of Michigan Ann Arbor Michigan
| | - Bridget O'Connor
- Division of Pediatric Genetics University of Michigan Ann Arbor Michigan
| | - Beverly M. Yashar
- Department of Human Genetics University of Michigan Ann Arbor Michigan
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Additive Diagnostic Yield of Homozygosity Regions Identified During Chromosomal microarray Testing in Children with Developmental Delay, Dysmorphic Features or Congenital Anomalies. Biochem Genet 2019; 58:74-101. [PMID: 31273557 DOI: 10.1007/s10528-019-09931-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Accepted: 06/27/2019] [Indexed: 11/26/2022]
Abstract
Chromosomal microarray (CMA) has emerged as a robust tool for identifying microdeletions and microduplications, termed copy number variants (CNVs). Nevertheless, data regarding its utility in different patient populations with developmental delay (DD), dysmorphic features (DF) and congenital anomalies (CA), is a matter of dense debate. Although regions of homozygosity (ROH) are not diagnostic of a specific condition, they may have pathogenic implications. Certain CNVs and ROH have ethnically specific occurrences and frequencies. We aimed to determine whether CMA testing offers additional diagnostic information over classical cytogenetics for identifying genomic imbalances in a pediatric cohort with idiopathic DD, DF, or CA. One hundred sixty-nine patients were offered cytogenetics and CMA simultaneously for etiological diagnosis of DD (n = 67), DF (n = 52) and CA (n = 50). CMA could identify additional, clinically significant anomalies as compared with cytogenetics. CMA detected 61 CNVs [21 (34.4%) pathogenic CNVs, 37 (60.7%) variants of uncertain clinical significance and 3 (4.9%) benign CNVs] in 44 patients. CMA identified one or more ROH in 116/169 (68.6%) patients. When considering pathogenic CNVs and aneuploidies as positive findings, 9/169 (5.3%) received a genetic diagnosis from cytogenetics, while 25/169 (14.8%) could have a genetic diagnosis from CMA. The identification of ROH was clinically significant in two cases (2/169), thereby, adding 1.2% to the diagnostic yield of CMA (16% vs. 5.3%, p < 0.001). CMA uncovers additional genetic diagnoses over cytogenetics, thereby, offering a much higher diagnostic yield. Our findings convincingly demonstrate the additive diagnostic value of clinically significant ROH identified during CMA testing, highlighting the need for careful clinical interpretation of these ROH.
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21
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Zhou W, Ma D, Sun AX, Tran HD, Ma DL, Singh BK, Zhou J, Zhang J, Wang D, Zhao Y, Yen PM, Goh E, Tan EK. PD-linked CHCHD2 mutations impair CHCHD10 and MICOS complex leading to mitochondria dysfunction. Hum Mol Genet 2019; 28:1100-1116. [PMID: 30496485 PMCID: PMC6423417 DOI: 10.1093/hmg/ddy413] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Revised: 10/31/2018] [Accepted: 11/22/2018] [Indexed: 12/13/2022] Open
Abstract
Coiled-coil-helix-coiled-coil-helix domain containing protein 2 (CHCHD2) mutations were linked with autosomal dominant Parkinson's disease (PD) and recently, Alzheimer's disease/frontotemporal dementia. In the current study, we generated isogenic human embryonic stem cell (hESC) lines harboring PD-associated CHCHD2 mutation R145Q or Q126X via clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9) method, aiming to unravel pathophysiologic mechanism and seek potential intervention strategy against CHCHD2 mutant-caused defects. By engaging super-resolution microscopy, we identified a physical proximity and similar distribution pattern of CHCHD2 along mitochondria with mitochondrial contact site and cristae organizing system (MICOS), a large protein complex maintaining mitochondria cristae. Isogenic hESCs and differentiated neural progenitor cells (NPCs) harboring CHCHD2 R145Q or Q126X mutation showed impaired mitochondria function, reduced CHCHD2 and MICOS components and exhibited nearly hollow mitochondria with reduced cristae. Furthermore, PD-linked CHCHD2 mutations lost their interaction with coiled-coil-helix-coiled-coil-helix domain containing protein 10 (CHCHD10), while transient knockdown of either CHCHD2 or CHCHD10 reduced MICOS and mitochondria cristae. Importantly, a specific mitochondria-targeted peptide, Elamipretide/MTP-131, now tested in phase 3 clinical trials for mitochondrial diseases, was found to enhance CHCHD2 with MICOS and mitochondria oxidative phosphorylation enzymes in isogenic NPCs harboring heterozygous R145Q, suggesting that Elamipretide is able to attenuate CHCHD2 R145Q-induced mitochondria dysfunction. Taken together, our results suggested CHCHD2-CHCHD10 complex may be a novel therapeutic target for PD and related neurodegenerative disorders, and Elamipretide may benefit CHCHD2 mutation-linked PD.
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Affiliation(s)
- Wei Zhou
- Neuroscience Research Laboratory, National Neuroscience Institute, Singapore
| | - Dongrui Ma
- Department of Neurology, Singapore General Hospital, Singapore
| | - Alfred Xuyang Sun
- Neuroscience Research Laboratory, National Neuroscience Institute, Singapore.,Stem Cell and Regenerative Biology Laboratory, Genome Institute of Singapore, Singapore
| | - Hoang-Dai Tran
- Neuroscience Research Laboratory, National Neuroscience Institute, Singapore.,Stem Cell and Regenerative Biology Laboratory, Genome Institute of Singapore, Singapore
| | - Dong-Liang Ma
- Neuroregeneration Laboratory, Singhealth Duke-NUS Neuroscience Academic Clinical Program, Singapore
| | - Brijesh K Singh
- Programs in Metabolic and Cardiovascular Disorders, Duke-NUS Graduate Medical School, Singapore
| | - Jin Zhou
- Programs in Metabolic and Cardiovascular Disorders, Duke-NUS Graduate Medical School, Singapore
| | - Jinyan Zhang
- Department of Neurology, Singapore General Hospital, Singapore
| | - Danlei Wang
- Stem Cell and Regenerative Biology Laboratory, Genome Institute of Singapore, Singapore
| | - Yi Zhao
- Department of Clinical Research, Singapore General Hospital, Singapore
| | - Paul M Yen
- Programs in Metabolic and Cardiovascular Disorders, Duke-NUS Graduate Medical School, Singapore
| | - Eyleen Goh
- Neuroregeneration Laboratory, Singhealth Duke-NUS Neuroscience Academic Clinical Program, Singapore.,Neuroregeneration Laboratory, National Neuroscience Institute, Singapore
| | - Eng-King Tan
- Neuroscience Research Laboratory, National Neuroscience Institute, Singapore.,Department of Neurology, Singapore General Hospital, Singapore
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22
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Srivastava S, Love-Nichols JA, Dies KA, Ledbetter DH, Martin CL, Chung WK, Firth HV, Frazier T, Hansen RL, Prock L, Brunner H, Hoang N, Scherer SW, Sahin M, Miller DT. Meta-analysis and multidisciplinary consensus statement: exome sequencing is a first-tier clinical diagnostic test for individuals with neurodevelopmental disorders. Genet Med 2019; 21:2413-2421. [PMID: 31182824 PMCID: PMC6831729 DOI: 10.1038/s41436-019-0554-6] [Citation(s) in RCA: 413] [Impact Index Per Article: 68.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 05/15/2019] [Indexed: 12/15/2022] Open
Abstract
Purpose For neurodevelopmental disorders (NDDs), etiological evaluation can
be a diagnostic odyssey involving numerous genetic tests, underscoring the need
to develop a streamlined algorithm maximizing molecular diagnostic yield for
this clinical indication. Our objective was to compare the yield of exome
sequencing (ES) with that of chromosomal microarray (CMA), the current
first-tier test for NDDs. Methods We performed a PubMed scoping review and meta-analysis investigating
the diagnostic yield of ES for NDDs as the basis of a consensus development
conference. We defined NDD as global developmental delay, intellectual
disability, and/or autism spectrum disorder. The consensus development
conference included input from genetics professionals, pediatric neurologists,
and developmental behavioral pediatricians. Results After applying strict inclusion/exclusion criteria, we identified 30
articles with data on molecular diagnostic yield in individuals with isolated
NDD, or NDD plus associated conditions (such as Rett-like features). Yield of ES
was 36% overall, 31% for isolated NDD, and 53% for the NDD plus associated
conditions. ES yield for NDDs is markedly greater than previous studies of CMA
(15–20%). Conclusion Our review demonstrates that ES consistently outperforms CMA for
evaluation of unexplained NDDs. We propose a diagnostic algorithm placing ES at
the beginning of the evaluation of unexplained NDDs.
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Affiliation(s)
- Siddharth Srivastava
- Translational Neuroscience Center, Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jamie A Love-Nichols
- Translational Neuroscience Center, Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Kira A Dies
- Translational Neuroscience Center, Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - David H Ledbetter
- Autism & Developmental Medicine Institute, Geisinger, Danville, PA, USA
| | - Christa L Martin
- Autism & Developmental Medicine Institute, Geisinger, Danville, PA, USA
| | - Wendy K Chung
- Departments of Pediatrics and Medicine, Columbia University, New York, NY, USA.,SFARI, Simons Foundation, New York, NY, USA
| | - Helen V Firth
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.,East Anglian Medical Genetics Service, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, UK
| | | | - Robin L Hansen
- MIND Institute, Department of Pediatrics, University of California Davis, Sacramento, CA, USA
| | - Lisa Prock
- Translational Neuroscience Center, Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.,Developmental Medicine Center, Boston Children's Hospital, Boston, MA, USA
| | - Han Brunner
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands.,The Netherlands; Department of Clinical Genetics and GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Ny Hoang
- Department of Genetic Counselling, The Hospital for Sick Children, Toronto, ON, Canada.,Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Stephen W Scherer
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada.,McLaughlin Centre and Department of Molecular Genetics, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Mustafa Sahin
- Translational Neuroscience Center, Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
| | - David T Miller
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
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Park KB, Nam KE, Cho AR, Jang W, Kim M, Park JH. Effects of Copy Number Variations on Developmental Aspects of Children With Delayed Development. Ann Rehabil Med 2019; 43:215-223. [PMID: 31072088 PMCID: PMC6509583 DOI: 10.5535/arm.2019.43.2.215] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 10/19/2018] [Indexed: 11/06/2022] Open
Abstract
Objective To determine effects of copy number variations (CNV) on developmental aspects of children suspected of having delayed development. Methods A retrospective chart review was done for 65 children who underwent array-comparative genomic hybridization after visiting physical medicine & rehabilitation department of outpatient clinic with delayed development as chief complaints. Children were evaluated with Denver Developmental Screening Test II (DDST-II), Sequenced Language Scale for Infants (SELSI), or Preschool Receptive-Expressive Language Scale (PRES). A Mann-Whitney U test was conducted to determine statistical differences of developmental quotient (DQ), receptive language quotient (RLQ), and expressive language quotient (ELQ) between children with CNV (CNV(+) group, n=16) and children without CNV (CNV(–) group, n=37). Results Of these subjects, the average age was 35.1 months (mean age, 35.1±24.2 months). Sixteen (30.2%) patients had copy number variations. In the CNV(+) group, 14 children underwent DDST-II. In the CNV(–) group, 29 children underwent DDST-II. Among variables, gross motor scale was significantly (p=0.038) lower in the CNV(+) group compared with the CNV(–) group. In the CNV(+) group, 5 children underwent either SELSI or PRES. In the CNV(–) group, 27 children underwent above language assessment examination. Both RLQ and ELQ were similar between the two groups. Conclusion The gross motor domain in DQ was significantly lower in children with CNV compared to that in children without CNV. This result suggests that additional genetic factors contribute to this variability. Active detection of genomic imbalance could play a vital role when prominent gross motor delay is presented in children with delayed development.
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Affiliation(s)
- Kee-Boem Park
- Department of Rehabilitation Medicine, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Kyung Eun Nam
- Department of Rehabilitation Medicine, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Ah-Ra Cho
- Department of Rehabilitation Medicine, St. Paul's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Woori Jang
- Department of Laboratory Medicine College of Medicine, The Catholic University of Korea, Seoul, Korea.,Department of Catholic Genetic Laboratory Center, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Myungshin Kim
- Department of Laboratory Medicine College of Medicine, The Catholic University of Korea, Seoul, Korea.,Department of Catholic Genetic Laboratory Center, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Joo Hyun Park
- Department of Rehabilitation Medicine, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
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24
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Jang W, Kim Y, Han E, Park J, Chae H, Kwon A, Choi H, Kim J, Son JO, Lee SJ, Hong BY, Jang DH, Han JY, Lee JH, Kim SY, Lee IG, Sung IK, Moon Y, Kim M, Park JH. Chromosomal Microarray Analysis as a First-Tier Clinical Diagnostic Test in Patients With Developmental Delay/Intellectual Disability, Autism Spectrum Disorders, and Multiple Congenital Anomalies: A Prospective Multicenter Study in Korea. Ann Lab Med 2019; 39:299-310. [PMID: 30623622 PMCID: PMC6340852 DOI: 10.3343/alm.2019.39.3.299] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2018] [Revised: 08/06/2018] [Accepted: 11/07/2018] [Indexed: 11/20/2022] Open
Abstract
Background To validate the clinical application of chromosomal microarray analysis (CMA) as a first-tier clinical diagnostic test and to determine the impact of CMA results on patient clinical management, we conducted a multicenter prospective study in Korean patients diagnosed as having developmental delay/intellectual disability (DD/ID), autism spectrum disorders (ASD), and multiple congenital anomalies (MCA). Methods We performed both CMA and G-banding cytogenetics as the first-tier tests in 617 patients. To determine whether the CMA results directly influenced treatment recommendations, the referring clinicians were asked to complete a 39-item questionnaire for each patient separately after receiving the CMA results. Results A total of 122 patients (19.8%) had abnormal CMA results, with either pathogenic variants (N=65) or variants of possible significance (VPS, N=57). Thirty-five well-known diseases were detected: 16p11.2 microdeletion syndrome was the most common, followed by Prader-Willi syndrome, 15q11-q13 duplication, Down syndrome, and Duchenne muscular dystrophy. Variants of unknown significance (VUS) were discovered in 51 patients (8.3%). VUS of genes putatively associated with developmental disorders were found in five patients: IMMP2L deletion, PTCH1 duplication, and ATRNL1 deletion. CMA results influenced clinical management, such as imaging studies, specialist referral, and laboratory testing in 71.4% of patients overall, and in 86.0%, 83.3%, 75.0%, and 67.3% of patients with VPS, pathogenic variants, VUS, and benign variants, respectively. Conclusions Clinical application of CMA as a first-tier test improves diagnostic yields and the quality of clinical management in patients with DD/ID, ASD, and MCA.
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Affiliation(s)
- Woori Jang
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea.,Catholic Genetic Laboratory Center, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Yonggoo Kim
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea.,Catholic Genetic Laboratory Center, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Eunhee Han
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea.,Catholic Genetic Laboratory Center, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Joonhong Park
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea.,Catholic Genetic Laboratory Center, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Hyojin Chae
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea.,Catholic Genetic Laboratory Center, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Ahlm Kwon
- Catholic Genetic Laboratory Center, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Hayoung Choi
- Catholic Genetic Laboratory Center, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Jiyeon Kim
- Catholic Genetic Laboratory Center, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Jung Ok Son
- Catholic Genetic Laboratory Center, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Sang Jee Lee
- Department of Rehabilitation Medicine, Daejeon St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Daejeon, Korea
| | - Bo Young Hong
- Department of Rehabilitation Medicine, St. Vincent's Hospital, College of Medicine, The Catholic University of Korea, Suwon, Korea
| | - Dae Hyun Jang
- Department of Rehabilitation Medicine, Incheon St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Incheon, Korea
| | - Ji Yoon Han
- Department of Pediatrics, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Jung Hyun Lee
- Department of Pediatrics, St. Vincent's Hospital, College of Medicine, The Catholic University of Korea, Suwon, Korea
| | - So Young Kim
- Department of Pediatrics, Yeouido St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - In Goo Lee
- Department of Pediatrics, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - In Kyung Sung
- Department of Pediatrics, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Yeonsook Moon
- Department of Laboratory Medicine, Inha University School of Medicine, Incheon, Korea
| | - Myungshin Kim
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea.,Catholic Genetic Laboratory Center, College of Medicine, The Catholic University of Korea, Seoul, Korea.
| | - Joo Hyun Park
- Department of Rehabilitation Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea
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25
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Bick D, Jones M, Taylor SL, Taft RJ, Belmont J. Case for genome sequencing in infants and children with rare, undiagnosed or genetic diseases. J Med Genet 2019; 56:783-791. [PMID: 31023718 PMCID: PMC6929710 DOI: 10.1136/jmedgenet-2019-106111] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 03/19/2019] [Indexed: 01/01/2023]
Abstract
Up to 350 million people worldwide suffer from a rare disease, and while the individual diseases are rare, in aggregate they represent a substantial challenge to global health systems. The majority of rare disorders are genetic in origin, with children under the age of five disproportionately affected. As these conditions are difficult to identify clinically, genetic and genomic testing have become the backbone of diagnostic testing in this population. In the last 10 years, next-generation sequencing technologies have enabled testing of multiple disease genes simultaneously, ranging from targeted gene panels to exome sequencing (ES) and genome sequencing (GS). GS is quickly becoming a practical first-tier test, as cost decreases and performance improves. A growing number of studies demonstrate that GS can detect an unparalleled range of pathogenic abnormalities in a single laboratory workflow. GS has the potential to deliver unbiased, rapid and accurate molecular diagnoses to patients across diverse clinical indications and complex presentations. In this paper, we discuss clinical indications for testing and historical testing paradigms. Evidence supporting GS as a diagnostic tool is supported by superior genomic coverage, types of pathogenic variants detected, simpler laboratory workflow enabling shorter turnaround times, diagnostic and reanalysis yield, and impact on healthcare.
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Affiliation(s)
- David Bick
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Marilyn Jones
- Rady Children's Hospital San Diego, San Diego, California, USA
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26
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Matias M, Wusik K, Neilson D, Zhang X, Valencia CA, Collins K. Comparison of medical management and genetic counseling options pre- and post-whole exome sequencing for patients with positive and negative results. J Genet Couns 2019; 28:182-193. [PMID: 30648779 DOI: 10.1002/jgc4.1054] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 10/16/2018] [Accepted: 10/20/2018] [Indexed: 12/14/2022]
Abstract
Whole exome sequencing (WES) is expected to impact patient management, but data surrounding the types of downstream effects and how frequently these effects are observed depending on the type of WES results received is limited. This study investigated changes to medical management and genetic counseling (GC) options following WES for individuals with positive and negative results. Electronic medical records of patients who had positive (n = 37) or negative (n = 41) WES results from Cincinnati Children's Hospital were retrospectively reviewed. Pre- and post-WES management and GC options were analyzed as were differences between positive and negative results. Almost all participants (97%) were observed to have at least one difference in medical management and/or GC options following WES. Comparing pre- and post-WES detected significant differences (p ≤ 0.05) in genetic testing, imaging, and metabolic testing regardless of WES results. Participants with positive results also had significant differences in recurrence risk, reproductive options, testing for family members, and support groups. Pre- to post-WES differences were significantly different between participants with positive and negative results in specialist referrals, lifestyle recommendations, recurrence risk, and all GC options (p ≤ 0.05); specifically, participants with positive results were more likely to have differences in these categories. Overall, differences in medical management and/or GC options were observed for participants with both types of WES results (positive and negative). Results from this study may contribute to the understanding of how WES impacts patients and their care and thus improve its utilization.
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Affiliation(s)
- Margret Matias
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio.,Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, Ohio.,UnityPoint-Health Meriter Hospital, Center for Perinatal Care, Madison, Wisconsin
| | - Katie Wusik
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio.,Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, Ohio
| | - Derek Neilson
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Xue Zhang
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - C Alexander Valencia
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Kathleen Collins
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio.,Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, Ohio
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27
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Tremblay I, Grondin S, Laberge AM, Cousineau D, Carmant L, Rowan A, Janvier A. Diagnostic and Therapeutic Misconception: Parental Expectations and Perspectives Regarding Genetic Testing for Developmental Disorders. J Autism Dev Disord 2018; 49:363-375. [DOI: 10.1007/s10803-018-3768-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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28
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Rutz A, Dent KM, Botto LD, Young PC, Carbone PS. Brief Report: Pediatrician Perspectives Regarding Genetic Evaluations of Children with Autism Spectrum Disorder. J Autism Dev Disord 2018; 49:794-808. [DOI: 10.1007/s10803-018-3738-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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29
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Clark MM, Stark Z, Farnaes L, Tan TY, White SM, Dimmock D, Kingsmore SF. Meta-analysis of the diagnostic and clinical utility of genome and exome sequencing and chromosomal microarray in children with suspected genetic diseases. NPJ Genom Med 2018; 3:16. [PMID: 30002876 PMCID: PMC6037748 DOI: 10.1038/s41525-018-0053-8] [Citation(s) in RCA: 402] [Impact Index Per Article: 57.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Revised: 04/30/2018] [Accepted: 05/10/2018] [Indexed: 12/14/2022] Open
Abstract
Genetic diseases are leading causes of childhood mortality. Whole-genome sequencing (WGS) and whole-exome sequencing (WES) are relatively new methods for diagnosing genetic diseases, whereas chromosomal microarray (CMA) is well established. Here we compared the diagnostic utility (rate of causative, pathogenic, or likely pathogenic genotypes in known disease genes) and clinical utility (proportion in whom medical or surgical management was changed by diagnosis) of WGS, WES, and CMA in children with suspected genetic diseases by systematic review of the literature (January 2011–August 2017) and meta-analysis, following MOOSE/PRISMA guidelines. In 37 studies, comprising 20,068 children, diagnostic utility of WGS (0.41, 95% CI 0.34–0.48, I2 = 44%) and WES (0.36, 95% CI 0.33–0.40, I2 = 83%) were qualitatively greater than CMA (0.10, 95% CI 0.08–0.12, I2 = 81%). Among studies published in 2017, the diagnostic utility of WGS was significantly greater than CMA (P < 0.0001, I2 = 13% and I2 = 40%, respectively). Among studies featuring within-cohort comparisons, the diagnostic utility of WES was significantly greater than CMA (P < 0.001, I2 = 36%). The diagnostic utility of WGS and WES were not significantly different. In studies featuring within-cohort comparisons of WGS/WES, the likelihood of diagnosis was significantly greater for trios than singletons (odds ratio 2.04, 95% CI 1.62–2.56, I2 = 12%; P < 0.0001). Diagnostic utility of WGS/WES with hospital-based interpretation (0.42, 95% CI 0.38–0.45, I2 = 48%) was qualitatively higher than that of reference laboratories (0.29, 95% CI 0.27–0.31, I2 = 49%); this difference was significant among studies published in 2017 (P < .0001, I2 = 22% and I2 = 26%, respectively). The clinical utility of WGS (0.27, 95% CI 0.17–0.40, I2 = 54%) and WES (0.17, 95% CI 0.12–0.24, I2 = 76%) were higher than CMA (0.06, 95% CI 0.05–0.07, I2 = 42%); this difference was significant for WGS vs CMA (P < 0.0001). In conclusion, in children with suspected genetic diseases, the diagnostic and clinical utility of WGS/WES were greater than CMA. Subgroups with higher WGS/WES diagnostic utility were trios and those receiving hospital-based interpretation. WGS/WES should be considered a first-line genomic test for children with suspected genetic diseases. Children with suspected genetic disease are more likely to receive a diagnosis when gene sequencing technologies are employed. At present, a microarray test for short pieces of missing or extra chromosomes (chromosomal microarray, CMA) is the recommended test for diagnosing genetic disease in children. The recent use of whole-genome sequencing (WGS) and whole-exome sequencing (WES) for diagnosing genetic disease prompted Stephen Kingsmore at Rady Children’s Institute for Genomic Medicine in San Diego, California, USA, and colleagues to examine the effectiveness of these methods compared with CMA. Analyses of studies comprising over 20,000 children showed that using WGS and WES increased the likelihood of diagnosis and led to a change in inpatient management to prevent or ameliorate adverse health outcomes. The authors advocate the use of WGS or WES as a first-line genomic test for genetic disease in children.
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Affiliation(s)
- Michelle M Clark
- Rady Children's Institute for Genomic Medicine, San Diego, CA USA
| | - Zornitza Stark
- 2Murdoch Children's Research Institute, Melbourne, Australia
| | - Lauge Farnaes
- Rady Children's Institute for Genomic Medicine, San Diego, CA USA.,3Department of Pediatrics, University of California San Diego, San Diego, CA USA
| | - Tiong Y Tan
- 2Murdoch Children's Research Institute, Melbourne, Australia.,4Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Susan M White
- 2Murdoch Children's Research Institute, Melbourne, Australia.,4Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - David Dimmock
- Rady Children's Institute for Genomic Medicine, San Diego, CA USA
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30
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Xu M, Ji Y, Zhang T, Jiang X, Fan Y, Geng J, Li F. Clinical Application of Chromosome Microarray Analysis in Han Chinese Children with Neurodevelopmental Disorders. Neurosci Bull 2018; 34:981-991. [PMID: 29948840 DOI: 10.1007/s12264-018-0238-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 04/05/2018] [Indexed: 02/04/2023] Open
Abstract
Chromosome microarray analysis (CMA) is a cost-effective molecular cytogenetic technique that has been used as a first-line diagnostic test in neurodevelopmental disorders in the USA since 2011. The impact of CMA results on clinical practice in China is not yet well studied, so we aimed to better evaluate this phenomenon. We analyzed the CMA results from 434 patients in our clinic, and characterized their molecular diagnoses, clinical features, and follow-up clinical actions based on these results. The overall diagnostic yield for our patients was 13.6% (59 out of 434). This gave a detection rate of 14.7% for developmental delay/intellectual disability (DD/ID, 38/259) and 12% for autism spectrum disorders (ASDs, 21/175). Thirty-three recurrent (n ≥ 2) variants were found, distributed at six chromosomal loci involving known chromosome syndromes (such as DiGeorge, Williams Beuren, and Angelman/Prader-Willi syndromes). The spectrum of positive copy number variants in our study was comparable to that reported in Caucasian populations, but with specific characteristics. Parental origin tests indicated an effect involving a significant maternal transmission bias to sons. The majority of patients with positive results (94.9%) had benefits, allowing earlier diagnosis (36/59), prioritized full clinical management (28/59), medication changes (7/59), a changed prognosis (30/59), and prenatal genetic counseling (15/59). Our results provide information on de novo mutations in Chinese children with DD/ID and/or ASDs. Our data showed that microarray testing provides immediate clinical utility for patients. It is expected that the personalized medical care of children with developmental disabilities will lead to improved outcomes in long-term developmental potential. We advocate using the diagnostic yield of clinically actionable results to evaluate CMA as it provides information of both clinical validity and clinical utility.
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Affiliation(s)
- Mingyu Xu
- Developmental and Behavioral Pediatric & Child Primary Care Department, Ministry of Education-Shanghai Key Laboratory of Children's Environmental Health, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China
| | - Yiting Ji
- Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Ting Zhang
- Developmental and Behavioral Pediatric & Child Primary Care Department, Ministry of Education-Shanghai Key Laboratory of Children's Environmental Health, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China
| | - Xiaodong Jiang
- Developmental and Behavioral Pediatric & Child Primary Care Department, Ministry of Education-Shanghai Key Laboratory of Children's Environmental Health, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China.,Wuhan Children's Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430016, China
| | - Yun Fan
- Developmental and Behavioral Pediatric & Child Primary Care Department, Ministry of Education-Shanghai Key Laboratory of Children's Environmental Health, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China
| | - Juan Geng
- Hangzhou Joingenome Diagnostics, Hangzhou, 311188, China.
| | - Fei Li
- Developmental and Behavioral Pediatric & Child Primary Care Department, Ministry of Education-Shanghai Key Laboratory of Children's Environmental Health, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China. .,Shanghai Institute of Pediatric Research, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China.
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31
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Kim HJ, Park CI, Lim JW, Lee GM, Cho E, Kim HJ. Phenotypic Analysis of Korean Patients with Abnormal Chromosomal Microarray in Patients with Unexplained Developmental Delay/Intellectual Disability. Yonsei Med J 2018; 59:431-437. [PMID: 29611406 PMCID: PMC5889996 DOI: 10.3349/ymj.2018.59.3.431] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 12/13/2017] [Accepted: 01/19/2018] [Indexed: 01/18/2023] Open
Abstract
PURPOSE The present study aimed to investigate chromosomal microarray (CMA) and clinical data in patients with unexplained developmental delay/intellectual disability (DD/ID) accompanying dysmorphism, congenital anomalies, or epilepsy. We also aimed to evaluate phenotypic clues in patients with pathogenic copy number variants (CNVs). MATERIALS AND METHODS We collected clinical and CMA data from patients at Konyang University Hospital between September 2013 and October 2014. We included patients who had taken the CMA test to evaluate the etiology of unexplained DD/ID. RESULTS All of the 50 patients identified had DD/ID. Thirty-nine patients had dysmorphism, 19 patients suffered from epilepsy, and 12 patients had congenital anomalies. Twenty-nine of the 50 patients (58%) showed abnormal results. Eighteen (36%) were considered to have pathogenic CNVs. Dysmorphism (p=0.028) was significantly higher in patients with pathogenic CNVs than in those with normal CMA. Two or more clinical features were presented by 61.9% (13/21) of the patients with normal CMA and by 83.3% (15/18) of the patients with pathogenic CMA. CONCLUSION Dysmorphism can be a phenotypic clue to pathogenic CNVs. Furthermore, pathogenic CNV might be more frequently found if patients have two or more clinical features in addition to DD/ID.
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Affiliation(s)
- Hyo Jeong Kim
- Department of Pediatrics, Gachon University Gil Medical Center, Incheon, Korea
| | - Chang Il Park
- Department of Rehabilitation Medicine, Konyang University College of Medicine, Daejeon, Korea
| | - Jae Woo Lim
- Department of Pediatrics, Konyang University College of Medicine, Daejeon, Korea
| | - Gyung Min Lee
- Department of Pediatrics, Konyang University College of Medicine, Daejeon, Korea
| | | | - Hyon J Kim
- Department of Medical Genetics, Konyang University College of Medicine, Daejeon, Korea.
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32
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Tremblay I, Laberge AM, Cousineau D, Carmant L, Rowan A, Janvier A. Paediatricians' expectations and perspectives regarding genetic testing for children with developmental disorders. Acta Paediatr 2018; 107:838-844. [PMID: 29280190 DOI: 10.1111/apa.14203] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 12/18/2017] [Accepted: 12/20/2017] [Indexed: 12/27/2022]
Abstract
AIM To investigate paediatricians' expectations and perspectives of genetic testing for children with developmental disorders. METHODS Paediatricians working in a developmental clinic were surveyed each time they ordered a chromosomal microarray (CMA) for a child with developmental disorders. Clinical charts were reviewed. Results were analysed using mixed methodology. RESULTS Ninety-seven % (73/76) of surveys were completed. Paediatricians reported that 36% of parents had difficulties understanding genetic testing and that 40% seemed anxious. The majority expected testing to have positive impacts on children/families. The themes raised were (i) clarifying the diagnosis (56%), (ii) understanding the aetiology of the condition (55%), (iii) enabling prenatal diagnosis/counselling (43%), (iv) improving medical care for the child (15%) and (v) decreasing parental guilt/anxiety (8%). Less than half anticipated negative impacts; 74% expected that the most helpful result for their patient would be an abnormal result explaining the disorder. Among the 73 children for whom CMA was ordered, 81% got tested: 66% of the results were normal, 19% were abnormal and contributed to explain the condition and 12% were abnormal but of unknown significance. CONCLUSION Paediatricians generally expect many positive and less negative impacts of genetic testing for children with developmental disorders. Parental perspectives are needed.
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Affiliation(s)
- Isabelle Tremblay
- CHU Sainte-Justine Research Center; Montréal QC Canada
- Department of Psychology; CHU Sainte-Justine; Montréal QC Canada
- Department of Medical Genetics; CHU Sainte-Justine; Montréal QC Canada
- Centre Intégré du Réseau en Neuro-Développement de l'enfant (CIRENE); CHU Sainte-Justine; Montréal QC Canada
- Unité d’éthique Clinique; CHU Sainte-Justine; Montréal QC Canada
| | - Anne-Marie Laberge
- CHU Sainte-Justine Research Center; Montréal QC Canada
- Department of Medical Genetics; CHU Sainte-Justine; Montréal QC Canada
| | - Dominique Cousineau
- Centre Intégré du Réseau en Neuro-Développement de l'enfant (CIRENE); CHU Sainte-Justine; Montréal QC Canada
- Department of Pediatrics; CHU Sainte-Justine; Montréal QC Canada
- Department of Pediatrics; Université de Montréal; Montréal QC Canada
| | - Lionel Carmant
- CHU Sainte-Justine Research Center; Montréal QC Canada
- Centre Intégré du Réseau en Neuro-Développement de l'enfant (CIRENE); CHU Sainte-Justine; Montréal QC Canada
- Department of Neurology; CHU Sainte-Justine; Montréal QC Canada
| | | | - Annie Janvier
- CHU Sainte-Justine Research Center; Montréal QC Canada
- Unité d’éthique Clinique; CHU Sainte-Justine; Montréal QC Canada
- Department of Pediatrics; Université de Montréal; Montréal QC Canada
- Division of Neonatology; CHU Sainte-Justine; Montréal QC Canada
- Bureau de l’éthique clinique; Université de Montréal; Montréal QC Canada. Palliative Care Unit; CHU Sainte-Justine; Montréal QC Canada. Unité de recherche en éthique clinique et partenariat famille (UREPAF); Montréal QC Canada
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Genetic disorders and mortality in infancy and early childhood: delayed diagnoses and missed opportunities. Genet Med 2018; 20:1396-1404. [PMID: 29790870 PMCID: PMC6185816 DOI: 10.1038/gim.2018.17] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 01/17/2018] [Indexed: 12/11/2022] Open
Abstract
PURPOSE Infants admitted to a level IV neonatal intensive care unit (NICU) who do not survive early childhood are a population that is probably enriched for rare genetic disease; we therefore characterized their genetic diagnostic evaluation. METHODS This is a retrospective analysis of infants admitted to our NICU between 1 January 2011 and 31 December 2015 who were deceased at the time of records review, with age at death less than 5 years. RESULTS A total of 2,670 infants were admitted; 170 later died. One hundred six of 170 (62%) had an evaluation for a genetic or metabolic disorder. Forty-seven of 170 (28%) had laboratory-confirmed genetic diagnoses, although 14/47 (30%) diagnoses were made postmortem. Infants evaluated for a genetic disorder spent more time in the NICU (median 13.5 vs. 5.0 days; p = 0.003), were older at death (median 92.0 vs. 17.5 days; p < 0.001), and had similarly high rates of redirection of care (86% vs. 79%; p = 0.28). CONCLUSION Genetic disorders were suspected in many infants but found in a minority. Approximately one-third of diagnosed infants died before a laboratory-confirmed genetic diagnosis was made. This highlights the need to improve genetic diagnostic evaluation in the NICU, particularly to support end-of-life decision making.
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Maini I, Ivanovski I, Djuric O, Caraffi SG, Errichiello E, Marinelli M, Franchi F, Bizzarri V, Rosato S, Pollazzon M, Gelmini C, Malacarne M, Fusco C, Gargano G, Bernasconi S, Zuffardi O, Garavelli L. Prematurity, ventricular septal defect and dysmorphisms are independent predictors of pathogenic copy number variants: a retrospective study on array-CGH results and phenotypical features of 293 children with neurodevelopmental disorders and/or multiple congenital anomalies. Ital J Pediatr 2018; 44:34. [PMID: 29523172 PMCID: PMC5845186 DOI: 10.1186/s13052-018-0467-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 02/21/2018] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND Since 2010, array-CGH (aCGH) has been the first-tier test in the diagnostic approach of children with neurodevelopmental disorders (NDD) or multiple congenital anomalies (MCA) of unknown origin. Its broad application led to the detection of numerous variants of uncertain clinical significance (VOUS). How to appropriately interpret aCGH results represents a challenge for the clinician. METHOD We present a retrospective study on 293 patients with age range 1 month - 29 years (median 7 years) with NDD and/or MCA and/or dysmorphisms, investigated through aCGH between 2005 and 2016. The aim of the study was to analyze clinical and molecular cytogenetic data in order to identify what elements could be useful to interpret unknown or poorly described aberrations. Comparison of phenotype and cytogenetic characteristics through univariate analysis and multivariate logistic regression was performed. RESULTS Copy number variations (CNVs) with a frequency < 1% were detected in 225 patients of the total sample, while 68 patients presented only variants with higher frequency (heterozygous deletions or amplification) and were considered to have negative aCGH. Proved pathogenic CNVs were detected in 70 patients (20.6%). Delayed psychomotor development, intellectual disability, intrauterine growth retardation (IUGR), prematurity, congenital heart disease, cerebral malformations and dysmorphisms correlated to reported pathogenic CNVs. Prematurity, ventricular septal defect and dysmorphisms remained significant predictors of pathogenic CNVs in the multivariate logistic model whereas abnormal EEG and limb dysmorphisms were mainly detected in the group with likely pathogenic VOUS. A flow-chart regarding the care for patients with NDD and/or MCA and/or dysmorphisms and the interpretation of aCGH has been made on the basis of the data inferred from this study and literature. CONCLUSION Our work contributes to make the investigative process of CNVs more informative and suggests possible directions in aCGH interpretation and phenotype correlation.
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MESH Headings
- Abnormalities, Multiple/diagnosis
- Abnormalities, Multiple/genetics
- Adolescent
- Adult
- Child
- Child, Preschool
- Comparative Genomic Hybridization/methods
- DNA Copy Number Variations
- Facies
- Female
- Genetic Testing
- Heart Septal Defects, Ventricular/diagnosis
- Heart Septal Defects, Ventricular/genetics
- Humans
- Infant
- Infant, Newborn
- Infant, Premature, Diseases/diagnosis
- Infant, Premature, Diseases/genetics
- Male
- Muscular Atrophy/diagnosis
- Muscular Atrophy/genetics
- Neurodevelopmental Disorders/diagnosis
- Neurodevelopmental Disorders/genetics
- Phenotype
- Retrospective Studies
- Young Adult
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Affiliation(s)
- I. Maini
- Clinical Genetics Unit, Maternal and Child Health Department, AUSL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
- Child Neuropsychiatry Unit, Maternal and Child Health Department, AUSL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
| | - I. Ivanovski
- Clinical Genetics Unit, Maternal and Child Health Department, AUSL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
- Department of Surgical, Medical, Dental and Morphological Sciences with Interest in Transplant, Oncology and Regenerative Medicine, University of Modena and Reggio Emilia, Modena, Italy
| | - O. Djuric
- Institute of Epidemiology, School of Medicine, University of Belgrade, Belgrade, Serbia
| | - S. G. Caraffi
- Clinical Genetics Unit, Maternal and Child Health Department, AUSL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
| | - E. Errichiello
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - M. Marinelli
- Laboratory of Genetics, Maternal and Child Health Department, AUSL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
| | - F. Franchi
- Laboratory of Genetics, Maternal and Child Health Department, AUSL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
| | - V. Bizzarri
- Laboratory of Genetics, Maternal and Child Health Department, AUSL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
| | - S. Rosato
- Clinical Genetics Unit, Maternal and Child Health Department, AUSL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
| | - M. Pollazzon
- Clinical Genetics Unit, Maternal and Child Health Department, AUSL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
| | - C. Gelmini
- Clinical Genetics Unit, Maternal and Child Health Department, AUSL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
| | - M. Malacarne
- Division of Medical Genetics, Galliera Hospital, Genoa, Italy
| | - C. Fusco
- Child Neuropsychiatry Unit, Maternal and Child Health Department, AUSL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
| | - G. Gargano
- Neonatal Intensive Care Unit (NICU), Maternal and Child Health Department, AUSL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
| | - S. Bernasconi
- Former Director Pediatric Department, University of Parma, Parma, Italy
| | - O. Zuffardi
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - L. Garavelli
- Clinical Genetics Unit, Maternal and Child Health Department, AUSL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
- Santa Maria Nuova Hospital, viale Risorgimento 80, 42123 Reggio Emilia, Italy
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Evans MI, Evans SM, Bennett TA, Wapner RJ. The price of abandoning diagnostic testing for cell-free fetal DNA screening. Prenat Diagn 2018; 38:243-245. [DOI: 10.1002/pd.5226] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Accepted: 12/27/2017] [Indexed: 01/13/2023]
Affiliation(s)
- Mark I. Evans
- Department of Obstetrics and Gynecology; Mt Sinai School of Medicine; New York NY USA
- Fetal Medicine Foundation of America; New York NY USA
- Comprehensive Genetics; New York NY USA
| | - Shara M. Evans
- Fetal Medicine Foundation of America; New York NY USA
- Comprehensive Genetics; New York NY USA
| | - Terry Ann Bennett
- Department of Obstetrics and Gynecology, Tisch Medical School; New York University; New York NY USA
| | - Ronald J. Wapner
- Department of Obstetrics and Gynecology; Columbia University College of Physicians and Surgeons; New York NY USA
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36
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Clark MM, Stark Z, Farnaes L, Tan TY, White SM, Dimmock D, Kingsmore SF. Meta-analysis of the diagnostic and clinical utility of genome and exome sequencing and chromosomal microarray in children with suspected genetic diseases. NPJ Genom Med 2018; 3:16. [PMID: 30002876 DOI: 10.1101/255299] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Revised: 04/30/2018] [Accepted: 05/10/2018] [Indexed: 05/22/2023] Open
Abstract
Genetic diseases are leading causes of childhood mortality. Whole-genome sequencing (WGS) and whole-exome sequencing (WES) are relatively new methods for diagnosing genetic diseases, whereas chromosomal microarray (CMA) is well established. Here we compared the diagnostic utility (rate of causative, pathogenic, or likely pathogenic genotypes in known disease genes) and clinical utility (proportion in whom medical or surgical management was changed by diagnosis) of WGS, WES, and CMA in children with suspected genetic diseases by systematic review of the literature (January 2011-August 2017) and meta-analysis, following MOOSE/PRISMA guidelines. In 37 studies, comprising 20,068 children, diagnostic utility of WGS (0.41, 95% CI 0.34-0.48, I2 = 44%) and WES (0.36, 95% CI 0.33-0.40, I2 = 83%) were qualitatively greater than CMA (0.10, 95% CI 0.08-0.12, I2 = 81%). Among studies published in 2017, the diagnostic utility of WGS was significantly greater than CMA (P < 0.0001, I2 = 13% and I2 = 40%, respectively). Among studies featuring within-cohort comparisons, the diagnostic utility of WES was significantly greater than CMA (P < 0.001, I2 = 36%). The diagnostic utility of WGS and WES were not significantly different. In studies featuring within-cohort comparisons of WGS/WES, the likelihood of diagnosis was significantly greater for trios than singletons (odds ratio 2.04, 95% CI 1.62-2.56, I2 = 12%; P < 0.0001). Diagnostic utility of WGS/WES with hospital-based interpretation (0.42, 95% CI 0.38-0.45, I2 = 48%) was qualitatively higher than that of reference laboratories (0.29, 95% CI 0.27-0.31, I2 = 49%); this difference was significant among studies published in 2017 (P < .0001, I2 = 22% and I2 = 26%, respectively). The clinical utility of WGS (0.27, 95% CI 0.17-0.40, I2 = 54%) and WES (0.17, 95% CI 0.12-0.24, I2 = 76%) were higher than CMA (0.06, 95% CI 0.05-0.07, I2 = 42%); this difference was significant for WGS vs CMA (P < 0.0001). In conclusion, in children with suspected genetic diseases, the diagnostic and clinical utility of WGS/WES were greater than CMA. Subgroups with higher WGS/WES diagnostic utility were trios and those receiving hospital-based interpretation. WGS/WES should be considered a first-line genomic test for children with suspected genetic diseases.
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Affiliation(s)
- Michelle M Clark
- Rady Children's Institute for Genomic Medicine, San Diego, CA USA
| | - Zornitza Stark
- 2Murdoch Children's Research Institute, Melbourne, Australia
| | - Lauge Farnaes
- Rady Children's Institute for Genomic Medicine, San Diego, CA USA
- 3Department of Pediatrics, University of California San Diego, San Diego, CA USA
| | - Tiong Y Tan
- 2Murdoch Children's Research Institute, Melbourne, Australia
- 4Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Susan M White
- 2Murdoch Children's Research Institute, Melbourne, Australia
- 4Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - David Dimmock
- Rady Children's Institute for Genomic Medicine, San Diego, CA USA
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Disruptive Behavior, Global Developmental Delay, and Obesity in a 5-Year-Old Boy with a Chromosome Microduplication. J Dev Behav Pediatr 2018; 39:81-84. [PMID: 29293472 DOI: 10.1097/dbp.0000000000000528] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Ryan is a 5-year-old boy who was seen in a Developmental Behavioral Pediatrics clinic for disruptive behavior and developmental delay. His medical history was notable for a tethered spinal cord repaired at age 4 months, alternating exotropia with multiple surgeries, and obesity (body mass index at 99%). Ryan's development was globally delayed. He sat at age 10 months and walked at 24 months. An Autism Diagnostic Observation Schedule-Toddler module (ADOS-T) was completed at age 19 months and demonstrated little-to-no concern for autism spectrum disorder.Ryan's parents described behavioral challenges including hyperactivity, impulsivity, aggression toward him self and others, severe tantrums, a short attention span, and difficulty sleeping. They also endorsed repetitive behaviors including head rocking, walking in circles, and perseverative speech. Expressive language was significantly limited. There was no family history of autism or intellectual disability.Ryan's physical examination was notable for alternating exotropia, hypertelorism, upslanting palpebral fissures, and obesity. His speech was limited to 1-word utterances. Neurological and general examinations were normal.He was referred for repeat psychological testing at age 5 years. The ADOS-2 (Module 2) was consistent with a classification of autism with a high level of autism-related symptoms. A fragile X test was negative, and microarray demonstrated a microduplication in the region of 2p25.3 including the myelin transcription factor 1-like gene.
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38
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Ko JM. Chromosomal Microarray: Application for Congenital Heart Diseases. Korean Circ J 2018; 48:233-235. [PMID: 29557111 PMCID: PMC5861317 DOI: 10.4070/kcj.2018.0032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 01/29/2018] [Indexed: 11/16/2022] Open
Affiliation(s)
- Jung Min Ko
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul National University College of Medicine, Seoul, Korea.
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39
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Cost Effectiveness of Karyotyping, Chromosomal Microarray Analysis, and Targeted Next-Generation Sequencing of Patients with Unexplained Global Developmental Delay or Intellectual Disability. Mol Diagn Ther 2017; 22:129-138. [DOI: 10.1007/s40291-017-0309-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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40
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Hayeems RZ, Bhawra J, Tsiplova K, Meyn MS, Monfared N, Bowdin S, Stavropoulos DJ, Marshall CR, Basran R, Shuman C, Ito S, Cohn I, Hum C, Girdea M, Brudno M, Cohn RD, Scherer SW, Ungar WJ. Care and cost consequences of pediatric whole genome sequencing compared to chromosome microarray. Eur J Hum Genet 2017; 25:1303-1312. [PMID: 29158552 PMCID: PMC5865210 DOI: 10.1038/s41431-017-0020-3] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 08/10/2017] [Accepted: 09/09/2017] [Indexed: 01/14/2023] Open
Abstract
The clinical use of whole-genome sequencing (WGS) is expected to alter pediatric medical management. The study aimed to describe the type and cost of healthcare activities following pediatric WGS compared to chromosome microarray (CMA). Healthcare activities prompted by WGS and CMA were ascertained for 101 children with developmental delay over 1 year. Activities following receipt of non-diagnostic CMA were compared to WGS diagnostic and non-diagnostic results. Activities were costed in 2016 Canadian dollars (CDN). Ongoing care accounted for 88.6% of post-test activities. The mean number of lab tests was greater following CMA than WGS (0.55 vs. 0.09; p = 0.007). The mean number of specialist visits was greater following WGS than CMA (0.41 vs. 0; p = 0.016). WGS results (diagnostic vs. non-diagnostic) modified the effect of test type on mean number of activities (p < 0.001). The cost of activities prompted by diagnostic WGS exceeded $557CDN for 10% of cases. In complex pediatric care, CMA prompted additional diagnostic investigations while WGS prompted tailored care guided by genotypic variants. Costs for prompted activities were low for the majority and constitute a small proportion of total test costs. Optimal use of WGS depends on robust evaluation of downstream care and cost consequences.
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Affiliation(s)
- Robin Z Hayeems
- Child Health Evaluative Sciences, The Hospital for Sick Children, Toronto, Canada.
- Institute of Health Policy Management and Evaluation, University of Toronto, Toronto, Canada.
| | - Jasmin Bhawra
- School of Public Health and Health Systems, University of Waterloo, Waterloo, Canada
| | - Kate Tsiplova
- Child Health Evaluative Sciences, The Hospital for Sick Children, Toronto, Canada
| | - M Stephen Meyn
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
- Department of Pediatrics, University of Toronto, Toronto, Canada
| | - Nasim Monfared
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Canada
- Department of Genetic Counselling, The Hospital for Sick Children, Toronto, Canada
| | - Sarah Bowdin
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Canada
- Department of Pediatrics, University of Toronto, Toronto, Canada
| | - D James Stavropoulos
- Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Christian R Marshall
- Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Canada
| | - Raveen Basran
- Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Canada
| | - Cheryl Shuman
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
- Department of Genetic Counselling, The Hospital for Sick Children, Toronto, Canada
| | - Shinya Ito
- Division of Clinical Pharmacology and Toxicology, The Hospital for Sick Children, Toronto, Canada
| | - Iris Cohn
- Division of Clinical Pharmacology and Toxicology, The Hospital for Sick Children, Toronto, Canada
| | - Courtney Hum
- Prenatal Diagnosis and Medical Genetics Program, Sinai Health System, Toronto, Canada
| | - Marta Girdea
- Centre for Computational Medicine, The Hospital for Sick Children, Toronto, Canada
| | - Michael Brudno
- Centre for Computational Medicine, The Hospital for Sick Children, Toronto, Canada
- Department of Computer Science, University of Toronto, Toronto, Canada
- Program in Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Canada
| | - Ronald D Cohn
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
- Department of Pediatrics, University of Toronto, Toronto, Canada
- Program in Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Canada
- Division of Pediatric Medicine, The Hospital for Sick Children, Toronto, Canada
| | - Stephen W Scherer
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Canada
- Program in Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Canada
- McLaughlin Centre, University of Toronto, Toronto, Canada
| | - Wendy J Ungar
- Child Health Evaluative Sciences, The Hospital for Sick Children, Toronto, Canada
- Institute of Health Policy Management and Evaluation, University of Toronto, Toronto, Canada
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Caballero Pérez V, López Pisón F, Miramar Gallart M, González Álvarez A, García Jiménez M, García Iñiguez J, Orden Rueda C, Gil Hernández I, Fuertes Rodrigo C, Fernando Martínez R, Rodríguez Valle A, Alcaine Villarroya M. Phenotype in patients with intellectual disability and pathological results in array CGH. NEUROLOGÍA (ENGLISH EDITION) 2017. [DOI: 10.1016/j.nrleng.2016.03.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Hnoonual A, Thammachote W, Tim-Aroon T, Rojnueangnit K, Hansakunachai T, Sombuntham T, Roongpraiwan R, Worachotekamjorn J, Chuthapisith J, Fucharoen S, Wattanasirichaigoon D, Ruangdaraganon N, Limprasert P, Jinawath N. Chromosomal microarray analysis in a cohort of underrepresented population identifies SERINC2 as a novel candidate gene for autism spectrum disorder. Sci Rep 2017; 7:12096. [PMID: 28935972 PMCID: PMC5608768 DOI: 10.1038/s41598-017-12317-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 09/07/2017] [Indexed: 01/11/2023] Open
Abstract
Chromosomal microarray (CMA) is now recognized as the first-tier genetic test for detection of copy number variations (CNVs) in patients with autism spectrum disorder (ASD). The aims of this study were to identify known and novel ASD associated-CNVs and to evaluate the diagnostic yield of CMA in Thai patients with ASD. The Infinium CytoSNP-850K BeadChip was used to detect CNVs in 114 Thai patients comprised of 68 retrospective ASD patients (group 1) with the use of CMA as a second line test and 46 prospective ASD and developmental delay patients (group 2) with the use of CMA as the first-tier test. We identified 7 (6.1%) pathogenic CNVs and 22 (19.3%) variants of uncertain clinical significance (VOUS). A total of 29 patients with pathogenic CNVs and VOUS were found in 22% (15/68) and 30.4% (14/46) of the patients in groups 1 and 2, respectively. The difference in detected CNV frequencies between the 2 groups was not statistically significant (Chi square = 1.02, df = 1, P = 0.31). In addition, we propose one novel ASD candidate gene, SERINC2, which warrants further investigation. Our findings provide supportive evidence that CMA studies using population-specific reference databases in underrepresented populations are useful for identification of novel candidate genes.
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Affiliation(s)
- Areerat Hnoonual
- Graduate Program in Biomedical Sciences, Prince of Songkla University, Songkhla, Thailand
| | - Weerin Thammachote
- Program in Translational Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Thipwimol Tim-Aroon
- Division of Medical Genetics, Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Kitiwan Rojnueangnit
- Division of Medical Genetics, Department of Pediatrics, Faculty of Medicine, Thammasart University, Pathumthani, Thailand
| | - Tippawan Hansakunachai
- Division of Child Development, Department of Pediatrics, Faculty of Medicine, Thammasart University, Pathumthani, Thailand
| | - Tasanawat Sombuntham
- Division of Developmental-Behavioral Pediatrics, Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Rawiwan Roongpraiwan
- Division of Developmental-Behavioral Pediatrics, Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Juthamas Worachotekamjorn
- Division of Child Development, Department of Pediatrics, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand
| | - Jariya Chuthapisith
- Division of Developmental-Behavioral Pediatrics, Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Suthat Fucharoen
- Thalassemia Research Center, Institute of Molecular Biosciences, Mahidol University, Salaya, Nakhon Pathom, Thailand
| | - Duangrurdee Wattanasirichaigoon
- Division of Medical Genetics, Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Nichara Ruangdaraganon
- Division of Developmental-Behavioral Pediatrics, Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Pornprot Limprasert
- Division of Human Genetics, Department of Pathology, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand.
| | - Natini Jinawath
- Program in Translational Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand. .,Integrative Computational Bioscience Center, Mahidol University, Salaya, Nakhon Pathom, Thailand.
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43
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McKay V, Efron D, Palmer EE, White SM, Pearson C, Danchin M. Current use of chromosomal microarray by Australian paediatricians and implications for the implementation of next generation sequencing. J Paediatr Child Health 2017; 53:650-656. [PMID: 28449382 DOI: 10.1111/jpc.13523] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 12/10/2016] [Accepted: 12/21/2016] [Indexed: 11/30/2022]
Abstract
AIM Chromosomal microarray (CMA) is an important diagnostic test for children with multiple congenital anomalies or certain developmental behavioural problems suggestive of an underlying genetic diagnosis. However, there are medical and ethical complexities to its use and few Australian policies to guide practice. We aimed to describe the current practice of Australian paediatricians in relation to CMA testing. We hypothesised that there are knowledge gaps in their use of CMA. METHODS Online survey completed between September 2015 and January 2016 by paediatricians in secondary care settings. Participants were members of the Australian Paediatric Research Network. One hundred and sixty five (43%) of 383 active members responded. Our main outcome measures comprised: (i) the indications for which paediatricians request CMA; (ii) their approach to consent; (iii) their interpretation of results; and (iv) their understanding of the impact on patient management. RESULTS A significant proportion of paediatricians (21-52%) did not regularly use CMA for conditions with established evidence of diagnostic yield. Paediatricians under-estimated the potential for CMA findings to alter patient management. There was wide variability in paediatricians' approach to consent, and low use of consent forms and fact sheets. Paediatricians reported difficulties interpreting CMA results, with high rates of referral to clinical genetics services. CONCLUSIONS The reported practice of Australian paediatricians is not consistent with international standards on CMA. Australian practice could be improved by a standardised approach to ordering CMA, consenting patients and interpreting results. We provide resources for CMA ordering and make recommendations about preparation for next generation sequencing.
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Affiliation(s)
- Victoria McKay
- Department of General Medicine, Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Daryl Efron
- Department of General Medicine, Royal Children's Hospital, Melbourne, Victoria, Australia.,Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - Elizabeth E Palmer
- Sydney Children's Hospital, Sydney, New South Wales, Australia.,Department of Women and Children's Health, Randwick Campus, University of New South Wales, Sydney, New South Wales, Australia.,Genetics of Learning Disability Service, Newcastle, New South Wales, Australia
| | - Susan M White
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia.,Victorian Clinical Genetics Service, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Chris Pearson
- Department of General Medicine, Women's and Children's Hospital, Adelaide, South Australia, Australia
| | - Margie Danchin
- Department of General Medicine, Royal Children's Hospital, Melbourne, Victoria, Australia.,Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
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Hensel C, Vanzo R, Martin M, Dixon S, Lambert C, Levy B, Nelson L, Peiffer A, Ho KS, Rushton P, Serrano M, South S, Ward K, Wassman E. Analytical and Clinical Validity Study of FirstStepDx PLUS: A Chromosomal Microarray Optimized for Patients with Neurodevelopmental Conditions. PLOS CURRENTS 2017; 9. [PMID: 28357155 PMCID: PMC5346028 DOI: 10.1371/currents.eogt.7d92ce775800ef3fbc72e3840fb1bc22] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Introduction: Chromosomal microarray analysis (CMA) is recognized as the first-tier test in the genetic evaluation of children with developmental delays, intellectual disabilities, congenital anomalies and autism spectrum disorders of unknown etiology. Array Design: To optimize detection of clinically relevant copy number variants associated with these conditions, we designed a whole-genome microarray, FirstStepDx PLUS (FSDX). A set of 88,435 custom probes was added to the Affymetrix CytoScanHD platform targeting genomic regions strongly associated with these conditions. This combination of 2,784,985 total probes results in the highest probe coverage and clinical yield for these disorders. Results and Discussion: Clinical testing of this patient population is validated on DNA from either non-invasive buccal swabs or traditional blood samples. In this report we provide data demonstrating the analytic and clinical validity of FSDX and provide an overview of results from the first 7,570 consecutive patients tested clinically. We further demonstrate that buccal sampling is an effective method of obtaining DNA samples, which may provide improved results compared to traditional blood sampling for patients with neurodevelopmental disorders who exhibit somatic mosaicism.
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Affiliation(s)
| | - Rena Vanzo
- Clinical Genetic Services, Lineagen, Inc., Salt Lake City, Utah, USA
| | | | - Sean Dixon
- Operations, Lineagen, Inc., Salt Lake City, Utah, USA
| | - Christophe Lambert
- Department of Internal Medicine, Center for Global Health, Division of Translational Informatics, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, USA
| | - Brynn Levy
- Department of Pathology & Cell Biology, Columbia University Medical Center, New York, New York, USA
| | - Lesa Nelson
- Affiliated Genetics Laboratory, Inc., Salt Lake City, Utah, USA
| | - Andy Peiffer
- Department of Pediatrics, University of Utah, Salt Lake City, Utah, USA; Lineagen, Inc., Salt Lake City, Utah, USA
| | - Karen S Ho
- Department of Pediatrics, University of Utah, Salt Lake City, Utah, USA; Lineagen, Inc., Salt Lake City, Utah, USA
| | | | | | - Sarah South
- ARUP Laboratories, Salt Lake City, Utah, USA; 23andMe, Inc., Mountain View, California, USA
| | - Kenneth Ward
- Affiliated Genetics Laboratory, Inc., Salt Lake City, Utah, USA
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Peabody J, Martin M, DeMaria L, Florentino J, Paculdo D, Paul M, Vanzo R, Wassman ER, Burgon T. Clinical Utility of a Comprehensive, Whole Genome CMA Testing Platform in Pediatrics: A Prospective Randomized Controlled Trial of Simulated Patients in Physician Practices. PLoS One 2016; 11:e0169064. [PMID: 28036350 PMCID: PMC5201278 DOI: 10.1371/journal.pone.0169064] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 12/12/2016] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Developmental disorders (DD), including autism spectrum disorder (ASD) and intellectual disability (ID), are a common group of clinical manifestations caused by a variety of genetic abnormalities. Genetic testing, including chromosomal microarray (CMA), plays an important role in diagnosing these conditions, but CMA can be limited by incomplete coverage of genetic abnormalities and lack of guidance for conditions rarely seen by treating physicians. METHODS We conducted a longitudinal, randomized controlled trial investigating the impact of a higher resolution 2.8 million (MM) probe-CMA test on the quality of care delivered by practicing general pediatricians and specialists. To overcome the twin problems of finding an adequate sample size of multiple rare conditions and under/incorrect diagnoses, we used standardized simulated patients known as CPVs. Physicians, randomized into control and intervention groups, cared for the CPV pediatric patients with DD/ASD/ID. Care responses were scored against evidence-based criteria. In round one, participants could order diagnostic tests including existing CMA tests. In round two, intervention physicians could order the 2.8MM probe-CMA test. Outcome measures included overall quality of care and quality of the diagnosis and treatment plan. RESULTS Physicians ordering CMA testing had 5.43% (p<0.001) higher overall quality scores than those who did not. Intervention physicians ordering the 2.8MM probe-CMA test had 7.20% (p<0.001) higher overall quality scores. Use of the 2.8MM probe-CMA test led to a 10.9% (p<0.001) improvement in the diagnosis and treatment score. Introduction of the 2.8MM probe-CMA test led to significant improvements in condition-specific interventions including an 8.3% (p = 0.04) improvement in evaluation and therapy for gross motor delays caused by Hunter syndrome, a 27.5% (p = 0.03) increase in early cognitive intervention for FOXG1-related disorder, and an 18.2% (p<0.001) improvement in referrals to child neurology for Dravet syndrome. CONCLUSION Physician use of the 2.8MM probe-CMA test significantly improves overall quality as well as diagnosis and treatment quality for simulated cases of pediatric DD/ASD/ID patients, and delivers additional clinical utility over existing CMA tests.
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Affiliation(s)
- John Peabody
- University of California, San Francisco, CA, United States of America
- University of California, Los Angeles, CA, United States of America
- QURE Healthcare, San Francisco, CA, United States of America
| | - Megan Martin
- Lineagen, Salt Lake City, UT, United States of America
| | - Lisa DeMaria
- QURE Healthcare, San Francisco, CA, United States of America
| | | | - David Paculdo
- QURE Healthcare, San Francisco, CA, United States of America
| | - Michael Paul
- Lineagen, Salt Lake City, UT, United States of America
| | - Rena Vanzo
- Lineagen, Salt Lake City, UT, United States of America
| | | | - Trever Burgon
- QURE Healthcare, San Francisco, CA, United States of America
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Chromosomal Microarray Analysis of Consecutive Individuals with Autism Spectrum Disorders Using an Ultra-High Resolution Chromosomal Microarray Optimized for Neurodevelopmental Disorders. Int J Mol Sci 2016; 17:ijms17122070. [PMID: 27941670 PMCID: PMC5187870 DOI: 10.3390/ijms17122070] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Revised: 11/29/2016] [Accepted: 12/04/2016] [Indexed: 02/07/2023] Open
Abstract
Copy number variants (CNVs) detected by chromosomal microarray analysis (CMA) significantly contribute to understanding the etiology of autism spectrum disorder (ASD) and other related conditions. In recognition of the value of CMA testing and its impact on medical management, CMA is in medical guidelines as a first-tier test in the evaluation of children with these disorders. As CMA becomes adopted into routine care for these patients, it becomes increasingly important to report these clinical findings. This study summarizes the results of over 4 years of CMA testing by a CLIA-certified clinical testing laboratory. Using a 2.8 million probe microarray optimized for the detection of CNVs associated with neurodevelopmental disorders, we report an overall CNV detection rate of 28.1% in 10,351 consecutive patients, which rises to nearly 33% in cases without ASD, with only developmental delay/intellectual disability (DD/ID) and/or multiple congenital anomalies (MCA). The overall detection rate for individuals with ASD is also significant at 24.4%. The detection rate and pathogenic yield of CMA vary significantly with the indications for testing, age, and gender, as well as the specialty of the ordering doctor. We note discrete differences in the most common recurrent CNVs found in individuals with or without a diagnosis of ASD.
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Clinical Performance of an Ultrahigh Resolution Chromosomal Microarray Optimized for Neurodevelopmental Disorders. BIOMED RESEARCH INTERNATIONAL 2016; 2016:3284534. [PMID: 27975050 PMCID: PMC5128689 DOI: 10.1155/2016/3284534] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 09/27/2016] [Accepted: 10/20/2016] [Indexed: 11/21/2022]
Abstract
Copy number variants (CNVs) as detected by chromosomal microarray analysis (CMA) significantly contribute to the etiology of neurodevelopmental disorders, such as developmental delay (DD), intellectual disability (ID), and autism spectrum disorder (ASD). This study summarizes the results of 3.5 years of CMA testing by a CLIA-certified clinical testing laboratory 5487 patients with neurodevelopmental conditions were clinically evaluated for rare copy number variants using a 2.8-million probe custom CMA optimized for the detection of CNVs associated with neurodevelopmental disorders. We report an overall detection rate of 29.4% in our neurodevelopmental cohort, which rises to nearly 33% when cases with DD/ID and/or MCA only are considered. The detection rate for the ASD cohort is also significant, at 25%. Additionally, we find that detection rate and pathogenic yield of CMA vary significantly depending on the primary indications for testing, the age of the individuals tested, and the specialty of the ordering doctor. We also report a significant difference between the detection rate on the ultrahigh resolution optimized array in comparison to the array from which it originated. This increase in detection can significantly contribute to the efficient and effective medical management of neurodevelopmental conditions in the clinic.
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DICER1 deletion and 14q32 microdeletion syndrome: an additional case and a review of the literature. Clin Dysmorphol 2016; 25:37-40. [PMID: 26513514 DOI: 10.1097/mcd.0000000000000105] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Zhang LN, Meng Z, He ZW, Li DF, Luo XY, Liang LY. [Clinical phenotypes and copy number variations in children with microdeletion and microduplication syndromes: an analysis of 50 cases]. ZHONGGUO DANG DAI ER KE ZA ZHI = CHINESE JOURNAL OF CONTEMPORARY PEDIATRICS 2016; 18:840-845. [PMID: 27655541 PMCID: PMC7389961 DOI: 10.7499/j.issn.1008-8830.2016.09.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 06/14/2016] [Indexed: 06/06/2023]
Abstract
OBJECTIVE To investigate the association between genotype and phenotype of microdeletion and microduplication syndromes (MMSs) and the pathogenesis of pathogenic copy number variations (CNVs). METHODS A total of 50 children with MMSs diagnosed by chromosomal microarray analysis (CMA) from June 2013 to September 2015 were enrolled, and the clinical manifestations and features of pathogenic CNVs were analyzed. RESULTS The main clinical manifestations of children with MMSs included mental retardation, developmental delay, short stature, and unusual facies, with the presence of abnormalities in multiple systems. There were 54 pathogenic CNVs in total, consisting of 36 microdeletion segments and 18 microduplication segments, with sizes ranging from 28 kb to 48.5 Mb (mean 13.86 Mb). Pathogenic CNVs often occurred in chromosomes X, 15, and 1. CONCLUSIONS The clinical manifestations of MMSs are not specific, and a genotype-first approach can be used for diagnosis. Mode of inheritance, type of recombination (deletion or duplication), size of segment, and functional genes included helps with the interpretation of CNVs of de novo mutations, and in-depth research on rare pathogenesis may become breakthrough points for the identification of new MMSs.
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Affiliation(s)
- Li-Na Zhang
- Department of Pediatric Endocrinology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510260, China.
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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: 2.0] [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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