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Liu Y, Hu T, Qian Y, Wang J, Hu R, Xiao L, Liao N, Liu Z, Wang H, Liu S, Zhang Z. Prenatal diagnosis of chromosomal aberrations by chromosomal microarray analysis and pregnancy outcomes of fetuses with polyhydramnios. J Matern Fetal Neonatal Med 2024; 37:2344089. [PMID: 38710614 DOI: 10.1080/14767058.2024.2344089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 04/12/2024] [Indexed: 05/08/2024]
Abstract
OBJECTIVES To explore the prenatal clinical utility of chromosome microarray analysis (CMA) for polyhydramnios and evaluate the short and long-term prognosis of fetuses with polyhydramnios. METHODS A total of 600 singleton pregnancies with persistent polyhydramnios from 2014 to 2020 were retrospectively enrolled in this study. All cases received amniocentesis and were subjected to CMA results. All cases were categorized into two groups: isolated polyhydramnios and non-isolated polyhydramnios [with soft marker(s) or with sonographic structural anomalies]. All fetuses were followed up from 6 months to five years after amniocentesis to acquire short and long-term prognosis. RESULTS The detection rates of either aneuploidy or pathogenic copy number variants in fetuses with non-isolated polyhydramnios were significantly higher than those with isolated polyhydramnios (5.0 vs. 1.5%, p = 0.0243; 3.6 vs. 0.8%, p = 0.0288). The detection rate of total chromosomal abnormalities in the structural abnormality group was significantly higher than that in the isolated group (10.0 vs. 2.3%, p = 0.0003). In the CMA-negative cases, the incidence of termination of pregnancy, neonatal and childhood death, and non-neurodevelopmental disorders in fetuses combined with structural anomalies was significantly higher than that in fetuses with isolated polyhydramnios (p < 0.05). We did not observe any difference in the prognosis between the isolated group and the combined group of ultrasound soft markers. In addition, the risk of postnatal neurodevelopmental disorders was also consistent among the three groups (1.6 vs. 1.3 vs. 1.8%). CONCLUSION For low-risk pregnancies, invasive prenatal diagnosis of isolated polyhydramnios might be unnecessary. CMA should be considered for fetuses with structural anomalies. In CMA-negative cases, the prognosis of fetuses with isolated polyhydramnios was good, and polyhydramnios itself did not increase the risk of postnatal neurological development disorders. The worse prognosis mainly depends on the combination of polyhydramnios with structural abnormalities.
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Affiliation(s)
- Yanyan Liu
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan, China
| | - Ting Hu
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan, China
| | - Yanping Qian
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan, China
| | - Jiamin Wang
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan, China
| | - Rui Hu
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan, China
| | - Like Xiao
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan, China
| | - Na Liao
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan, China
| | - Zhushu Liu
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan, China
| | - He Wang
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan, China
| | - Shanling Liu
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan, China
| | - Zhu Zhang
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan, China
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Hamvas A, Chaudhari BP, Nogee LM. Genetic testing for diffuse lung diseases in children. Pediatr Pulmonol 2024; 59:2286-2297. [PMID: 37191361 DOI: 10.1002/ppul.26447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 04/04/2023] [Accepted: 04/23/2023] [Indexed: 05/17/2023]
Abstract
Newly developing genomic technologies are an increasingly important part of clinical care and thus, it is not only important to understand the technologies and their limitations, but to also interpret the findings in an actionable fashion. Clinical geneticists and genetic counselors are now an integral part of the clinical team and are able to bridge the complexities of this rapidly changing science between the bedside clinicians and patients. This manuscript reviews the terminology, the current technology, some of the known genetic disorders that result in lung disease, and indications for genetic testing with associated caveats. Because this field is evolving quickly, we also provide links to websites that provide continuously updated information important for integrating genomic technology results into clinical decision-making.
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Affiliation(s)
- Aaron Hamvas
- Department of Pediatrics, Division of Neonatology, Ann and Robert H. Lurie Children's Hospital of Chicago and Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Bimal P Chaudhari
- Divisions of Genetics and Genomic Medicine, Neonatology, Nationwide Children's Hospital, The Ohio State University College of Medicine, Columbus, Ohio, USA
| | - Lawrence M Nogee
- Department of Pediatrics, Eudowood Neonatal Pulmonary Division, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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Merner AR, Trotter PM, Ginn LA, Bach J, Freedberg KJ, Soda T, Storch EA, Pereira S, Lázaro-Muñoz G. Psychiatric polygenic risk scores: Experience, hope for utility, and concerns among child and adolescent psychiatrists. Psychiatry Res 2024; 339:116080. [PMID: 39002500 PMCID: PMC11321910 DOI: 10.1016/j.psychres.2024.116080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 06/26/2024] [Accepted: 07/05/2024] [Indexed: 07/15/2024]
Abstract
Recent advances in psychiatric genetics have enabled the use of polygenic risk scores (PRS) to estimate genetic risk for psychiatric disorders. However, the potential use of PRS in child and adolescent psychiatry has raised concerns. This study provides an in-depth examination of attitudes among child and adolescent psychiatrists (CAP) regarding the use of PRS in psychiatry. We conducted semi-structured interviews with U.S.-based CAP (n = 29) who possess expertise in genetics. The majority of CAP indicated that PRS have limited clinical utility in their current form and are not ready for clinical implementation. Most clinicians stated that nothing would motivate them to generate PRS at present; however, some exceptions were noted (e.g., parent/family request). Clinicians spoke to challenges related to ordering, interpreting, and explaining PRS to patients and families. CAP raised concerns regarding the potential for this information to be misinterpreted or misused by patients, families, clinicians, and outside entities such as insurance companies. Finally, some CAP noted that PRS may lead to increased stigmatization of psychiatric disorders, and at the extreme, could be used to support eugenics. As PRS testing increases, it will be critical to examine CAP and other stakeholders' views to ensure responsible implementation of this technology.
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Affiliation(s)
- Amanda R Merner
- Center for Bioethics, Harvard Medical School, Boston, MA 02115, United States
| | - Page M Trotter
- Center for Medical Ethics & Health Policy at Baylor College of Medicine, United States
| | - Lauren A Ginn
- Center for Medical Ethics & Health Policy at Baylor College of Medicine, United States; Department of Biosciences, Rice University, Houston, Texas, United States
| | - Jason Bach
- University of Pennsylvania Law School, Philadelphia, Pennsylvania, United States
| | | | - Takahiro Soda
- Department of Psychiatry, University of Florida, Gainesville, Florida, United States; Center for Autism and Neurodevelopment, University of Florida, Gainesville, Florida, United States
| | - Eric A Storch
- Department of Psychiatry & Behavioral Sciences, Baylor College of Medicine, Houston, Texas, United States
| | - Stacey Pereira
- Center for Medical Ethics & Health Policy at Baylor College of Medicine, United States
| | - Gabriel Lázaro-Muñoz
- Center for Bioethics, Harvard Medical School, Boston, MA 02115, United States; Department of Psychiatry, Massachusetts General Hospital, Boston, Massachusetts, United States.
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4
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Bibi A, Ji W, Jeffries L, Zerillo C, Konstantino M, Mis EK, Khursheed F, Khokha MK, Lakhani SA, Malik S. Exome sequencing reveals genetic heterogeneity in consanguineous Pakistani families with neurodevelopmental and neuromuscular disorders. AMERICAN JOURNAL OF MEDICAL GENETICS. PART C, SEMINARS IN MEDICAL GENETICS 2024:e32103. [PMID: 39152716 DOI: 10.1002/ajmg.c.32103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Revised: 07/15/2024] [Accepted: 07/26/2024] [Indexed: 08/19/2024]
Abstract
There remains a crucial need to address inequalities in genomic research and include populations from low- and middle-income countries (LMIC). Here we present eight consanguineous families from Pakistan, five with neurodevelopmental disorders (NDDs) and three with neuromuscular disorders (NMDs). Affected individuals were clinically characterized, and genetic variants were identified through exome sequencing (ES), followed by family segregation analysis. Affected individuals in six out of eight families (75%) carried homozygous variants that met ACMG criteria for being pathogenic (in the genes ADGRG1, METTL23, SPG11) or likely pathogenic (in the genes GPAA1, MFN2, SGSH). The remaining two families had homozygous candidate variants in the genes (AP4M1 and FAM126A) associated with phenotypes consistent with their clinical presentations, but the variants did not meet the criteria for pathogenicity and were hence classified as variants of unknown significance. Notably, the variants in ADGRG1, AP4M1, FAM126A, and SGSH did not have prior reports in the literature, demonstrating the importance of including diverse populations in genomic studies. We provide clinical phenotyping along with analyses of ES data that support the utility of ES in making accurate molecular diagnoses in these patients, as well as in unearthing novel variants in known disease-causing genes in underrepresented populations from LMIC.
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Affiliation(s)
- Anisa Bibi
- Human Genetics Program, Department of Zoology, Quaid-i-Azam University, Islamabad, Pakistan
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Weizhen Ji
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Lauren Jeffries
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Cynthia Zerillo
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Monica Konstantino
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Emily K Mis
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Filza Khursheed
- Human Genetics Program, Department of Zoology, Quaid-i-Azam University, Islamabad, Pakistan
| | - Mustafa K Khokha
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Saquib A Lakhani
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Sajid Malik
- Human Genetics Program, Department of Zoology, Quaid-i-Azam University, Islamabad, Pakistan
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5
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Jacobsmeyer AT, Carter LB, Buitrago-Mogollon TL, White B, Charles JR, Clarke-Pounder JP, Amador J. Improving genetic testing utilization in a tertiary care neonatal intensive care unit through quality improvement. Am J Med Genet A 2024:e63834. [PMID: 39132941 DOI: 10.1002/ajmg.a.63834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 07/12/2024] [Accepted: 07/24/2024] [Indexed: 08/13/2024]
Abstract
There is an increasing recognition of the importance of diagnosing genetic conditions with an ever-growing list of genetic testing options. However, most providers do not have formal genetics training, which makes choosing the most appropriate test to order challenging. Our project sought to improve cytogenetic testing utilization in a tertiary care neonatal intensive care unit (NICU) through utilizing quality improvement techniques, specifically the Model for Improvement framework with rapid Plan-Do-Study-Act cycles. Our project utilized various interventions including the implementation of a NICU genetic testing algorithm. Interventions demonstrated improvement in all areas, specifically a 92% reduction in unnecessary cytogenetic testing with improvement in the diagnostic rate. Our work also resulted in a 59% decrease in charges with an estimated projected savings of $21,000 per year. Quality improvement can minimize redundancies and inefficiencies in genetic testing in a Level IV NICU in a large tertiary care children's hospital and result in substantial cost-savings.
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Affiliation(s)
- Andrew T Jacobsmeyer
- Division of Pediatric Hospital Medicine, Department of Pediatrics, Atrium Health Levine Children's Hospital, Charlotte, North Carolina, USA
| | - Lauren B Carter
- Division of Medical Genetics, Department of Pediatrics, Atrium Health Levine Children's Hospital, Charlotte, North Carolina, USA
| | - Talia L Buitrago-Mogollon
- Center for Advancing Pediatric Excellence, Atrium Health Levine Children's Hospital, Charlotte, North Carolina, USA
| | - Blanche White
- Center for Advancing Pediatric Excellence, Atrium Health Levine Children's Hospital, Charlotte, North Carolina, USA
| | - Jasmyne-Rian Charles
- Center for Advancing Pediatric Excellence, Atrium Health Levine Children's Hospital, Charlotte, North Carolina, USA
| | - Jessica P Clarke-Pounder
- Division of Neonatology, Department of Pediatrics, Atrium Health Levine Children's Hospital, Charlotte, North Carolina, USA
| | - Jodi Amador
- Division of Neonatology, Department of Pediatrics, Atrium Health Levine Children's Hospital, Charlotte, North Carolina, USA
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6
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Pereira SSS, Pinto IP, Santos VCDP, Silva RC, Costa EOA, da Cruz AS, da Cruz AD, da Silva CC, Minasi LB. Analysis of parental origin of de novo pathogenic CNVs in patients with intellectual disability. Genet Mol Biol 2024; 47:e20230313. [PMID: 39136576 PMCID: PMC11320663 DOI: 10.1590/1678-4685-gmb-2023-0313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 06/25/2024] [Indexed: 08/16/2024] Open
Abstract
Chromosomal Microarray Analysis (CMA) has increased the comprehension of the mechanisms of copy number variation (CNV) formation, classification of these rearrangements, type of recurrence, and its origin, and has also been a powerful approach to identifying CNVs in individuals with intellectual disability. The aim of this study was to establish the parental origin of de novo pathogenic CNV in a cohort of patients with intellectual disability from the public health system of Goiás-Brazil. CMA was done in 76 trios and we identified 15 de novo pathogenic CNVs in 12 patients with intellectual disability. In a total of 15 de novo pathogenic CNV, 60% were derived from the maternal germline and 40% from the paternal germline. CNV flanked by low copy repeats (LCR) were identified in 46.7% and most of them were of maternal origin. No significant association was observed between paternal age and the mutation rate of de novo CNVs. The presence of high-identity LCRs increases the occurrence of CNV formation mediated by non-allelic homologous recombination and the majority of paternal CNVs are non-recurrent. The mechanism of formation of these CNV may have been by microhomology-mediated break-induced replication or non-homologous end joining.
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Affiliation(s)
- Samara Socorro Silva Pereira
- Pontifícia Universidade Católica de Goiás, Escola de Ciências Médicas e da Vida, Programa de Pós-Graduação em Genética, Núcleo de Pesquisa Replicon, Goiânia, GO, Brazil
- Universidade Federal de Goiás, Programa de Pós-Graduação em Genética e Biologia Molecular, Goiânia, GO, Brazil
| | - Irene Plaza Pinto
- Pontifícia Universidade Católica de Goiás, Escola de Ciências Médicas e da Vida, Programa de Pós-Graduação em Genética, Núcleo de Pesquisa Replicon, Goiânia, GO, Brazil
| | - Victor Cortázio do Prado Santos
- Pontifícia Universidade Católica de Goiás, Escola de Ciências Médicas e da Vida, Programa de Pós-Graduação em Genética, Núcleo de Pesquisa Replicon, Goiânia, GO, Brazil
- Universidade Federal de Goiás, Programa de Pós-Graduação em Genética e Biologia Molecular, Goiânia, GO, Brazil
| | - Rafael Carneiro Silva
- Pontifícia Universidade Católica de Goiás, Escola de Ciências Médicas e da Vida, Programa de Pós-Graduação em Genética, Núcleo de Pesquisa Replicon, Goiânia, GO, Brazil
| | - Emília Oliveira Alves Costa
- Pontifícia Universidade Católica de Goiás, Escola de Ciências Médicas e da Vida, Programa de Pós-Graduação em Genética, Núcleo de Pesquisa Replicon, Goiânia, GO, Brazil
| | - Alex Silva da Cruz
- Pontifícia Universidade Católica de Goiás, Escola de Ciências Médicas e da Vida, Programa de Pós-Graduação em Genética, Núcleo de Pesquisa Replicon, Goiânia, GO, Brazil
| | - Aparecido Divino da Cruz
- Pontifícia Universidade Católica de Goiás, Escola de Ciências Médicas e da Vida, Programa de Pós-Graduação em Genética, Núcleo de Pesquisa Replicon, Goiânia, GO, Brazil
- Secretaria Estadual de Saúde de Goiás, Centro Estadual de Reabilitação e Readaptação Dr. Henrique Santillo, Goiânia, GO, Brazil
- Universidade Federal de Goiás, Programa de Pós-Graduação em Genética e Biologia Molecular, Goiânia, GO, Brazil
| | - Cláudio Carlos da Silva
- Pontifícia Universidade Católica de Goiás, Escola de Ciências Médicas e da Vida, Programa de Pós-Graduação em Genética, Núcleo de Pesquisa Replicon, Goiânia, GO, Brazil
- Secretaria Estadual de Saúde de Goiás, Centro Estadual de Reabilitação e Readaptação Dr. Henrique Santillo, Goiânia, GO, Brazil
| | - Lysa Bernardes Minasi
- Pontifícia Universidade Católica de Goiás, Escola de Ciências Médicas e da Vida, Programa de Pós-Graduação em Genética, Núcleo de Pesquisa Replicon, Goiânia, GO, Brazil
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Boughalem A, Ciorna-Monferrato V, Sloboda N, Guegan A, Page F, Zimmer S, Benazra M, Kleinfinger P, Lohmann L, Valduga M, Receveur A, Martin F, Trost D. Optical genome mapping identifies a homozygous deletion in the non-coding region of the SCN9A gene in individuals from the same family with congenital insensitivity to pain. Front Genet 2024; 15:1375770. [PMID: 39156962 PMCID: PMC11327051 DOI: 10.3389/fgene.2024.1375770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 07/18/2024] [Indexed: 08/20/2024] Open
Abstract
We report an index patient with complete insensitivity to pain and a history of painless fractures, joint hypermobility, and behavioral problems. The index patient descends from a family with notable cases among his maternal relatives, including his aunt and his mother's first cousin, both of whom suffer from congenital insensitivity to pain. The patient had normal results for prior genetic testing: fragile-X syndrome testing, chromosomal microarray analysis, and exome sequencing. Optical genome mapping detected a homozygous deletion affecting the noncoding 5' untranslated region (UTR) and the first non-coding exon of the SCN9A gene in all affected family members, compatible with recessive disease transmission. Pathogenic homozygous loss-of-function variants in the SCN9A gene are associated with impaired pain sensation in humans. Optical genome mapping can thus detect pathogenic structural variants in patients without molecular etiology by standard diagnostic procedures and is a more accessible diagnostic tool than short-read or long-read whole-genome sequencing.
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Affiliation(s)
- Aïcha Boughalem
- Department of Human Genetics, Laboratoire CERBA SA, Saint Ouen L’aumône, France
| | - Viorica Ciorna-Monferrato
- Génétique Médicale et Oncogénétique, Hôpital Femme Mère Enfant, CHR Metz-Thionville, site de Mercy, 1, Allée du Château, Metz Cedex, France
| | - Natacha Sloboda
- Génétique Médicale et Oncogénétique, Hôpital Femme Mère Enfant, CHR Metz-Thionville, site de Mercy, 1, Allée du Château, Metz Cedex, France
| | - Amélie Guegan
- Department of Human Genetics, Laboratoire CERBA SA, Saint Ouen L’aumône, France
| | - François Page
- Department of Human Genetics, Laboratoire CERBA SA, Saint Ouen L’aumône, France
| | - Sophie Zimmer
- Department of Human Genetics, Laboratoire CERBA SA, Saint Ouen L’aumône, France
| | - Marion Benazra
- Department of Human Genetics, Laboratoire CERBA SA, Saint Ouen L’aumône, France
| | - Pascale Kleinfinger
- Department of Human Genetics, Laboratoire CERBA SA, Saint Ouen L’aumône, France
| | - Laurence Lohmann
- Department of Human Genetics, Laboratoire CERBA SA, Saint Ouen L’aumône, France
| | - Mylène Valduga
- Department of Human Genetics, Laboratoire CERBA SA, Saint Ouen L’aumône, France
| | - Aline Receveur
- Department of Human Genetics, Laboratoire CERBA SA, Saint Ouen L’aumône, France
| | - Fernando Martin
- Department of Human Genetics, Laboratoire CERBA SA, Saint Ouen L’aumône, France
| | - Detlef Trost
- Department of Human Genetics, Laboratoire CERBA SA, Saint Ouen L’aumône, France
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Kim J, Lee J, Kim M, Jang DH. Diagnostic Yield of Trio Whole-Genome Sequencing in Children with Undiagnosed Developmental Delay or Congenital Anomaly: A Prospective Cohort Study. Diagnostics (Basel) 2024; 14:1680. [PMID: 39125556 PMCID: PMC11312062 DOI: 10.3390/diagnostics14151680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2024] [Revised: 07/24/2024] [Accepted: 07/29/2024] [Indexed: 08/12/2024] Open
Abstract
Developmental delays (DD) and congenital anomalies (CA) are prevalent yet often remain undiagnosed despite comprehensive genetic testing. This study aims to investigate the diagnostic yield of trio whole-genome sequencing (WGS) in children presenting with DD or CA who remained undiagnosed after previous genetic testing. A prospective cohort study was conducted on children with undiagnosed DD or CA at a single tertiary hospital. All participants suspected of genetic conditions had undergone chromosome analysis, chromosome microarray analysis (CMA), and clinical exome sequencing (CES); however, a subset remained undiagnosed. The WGS test was administered to both the affected children and their parents. A total of 52 children were included, and 10 (19.2%) had undergone a genetic diagnosis through WGS. Eight of these cases were associated with autosomal dominant and de novo variants. WGS led to successful diagnosis due to several factors, including small structural variants, genes not covered in the CES panel, the discovery of newly implicated genes, issues related to coverage depth, low variant allele frequency, challenges in variant interpretation, and differences in the interpretation of variants of unknown significance among clinicians. This study highlights the clinical value of trio WGS testing in undiagnosed children with DD or CA. Notably, an additional 19.2% of affected children were diagnosed through this method.
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Affiliation(s)
- Jaewon Kim
- Department of Physical Medicine and Rehabilitation, Incheon St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Jaewoong Lee
- Department of Laboratory Medicine, Incheon St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea;
| | - Myungshin Kim
- Department of Laboratory Medicine, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Dae-Hyun Jang
- Department of Physical Medicine and Rehabilitation, Incheon St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
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Karlin A, Ruggiero S, Fitzgerald M. Genetic testing for unexplained epilepsy: A review of diagnostic approach, benefits, and referral algorithm. Curr Probl Pediatr Adolesc Health Care 2024; 54:101579. [PMID: 38480044 DOI: 10.1016/j.cppeds.2024.101579] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 08/03/2024]
Abstract
In the last several decades, advances in genetic testing have transformed the diagnostic and therapeutic approach to pediatric epilepsy. However, the interpretation of these genetic tests often requires expert analysis and counseling. For this reason, as our molecular understanding of the linkages between abnormal cerebral physiology and genetics has grown, so too has the field of clinical epilepsy genetics. Here we explore recent advances in genetic testing, describe the benefits of genetic testing in epilepsy, and provide a practice guideline for testing and referrals to specialized epilepsy genetics centers, highlighting the Epilepsy NeuroGenetics Initiative (ENGIN) Clinic and the Center for Epilepsy and Neurodevelopmental Disorders (ENDD) at the Children's Hospital of Philadelphia as an illustration of such a specialized center.
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Affiliation(s)
- Alexis Karlin
- Division of Child Neurology, Department of Neurology and Pediatrics, Buerger Center for Advanced Pediatric Care, Children's Hospital of Philadelphia, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Sarah Ruggiero
- Division of Child Neurology, Department of Neurology and Pediatrics, Buerger Center for Advanced Pediatric Care, Children's Hospital of Philadelphia, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Mark Fitzgerald
- Division of Child Neurology, Department of Neurology and Pediatrics, Buerger Center for Advanced Pediatric Care, Children's Hospital of Philadelphia, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, United States; Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States.
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10
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Smith HS, Rubanovich CK, Robinson JO, Levchenko AN, Classen SA, Malek J, Biesecker B, Brothers KB, Wilfond BS, Rini C, Knight SJ, McGuire AL, Bloss CS. Measuring perceived utility of genomic sequencing: Development and validation of the GENEtic Utility (GENE-U) scale for pediatric diagnostic testing. Genet Med 2024; 26:101146. [PMID: 38676451 PMCID: PMC11298290 DOI: 10.1016/j.gim.2024.101146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 04/16/2024] [Accepted: 04/17/2024] [Indexed: 04/28/2024] Open
Abstract
PURPOSE Measuring the effects of genomic sequencing (GS) on patients and families is critical for translational research. We aimed to develop and validate an instrument to assess parents' perceived utility of pediatric diagnostic GS. METHODS Informed by a 5-domain conceptual model, the study comprised 5 steps: (1) item writing, (2) cognitive testing, (3) pilot testing and item reduction, (4) psychometric testing, and (5) evaluation of construct validity. Parents of pediatric patients who had received results of clinically indicated GS participated in structured cognitive interviews and 2 rounds of surveys. After eliminating items based on theory and quantitative performance, we conducted an exploratory factor analysis and calculated Pearson correlations with related instruments. RESULTS We derived the 21-item Pediatric Diagnostic version of the GENEtic Utility (GENE-U) scale, which has a 2-factor structure that includes an Informational Utility subscale (16 items, α = 0.91) and an Emotional Utility subscale (5 items, α = 0.71). Scores can be summed to calculate a Total scale score (α = 0.87). The Informational Utility subscale was strongly associated with empowerment and personal utility of GS, and the Emotional Utility subscale was moderately associated with psychosocial impact and depression and anxiety. CONCLUSION The pediatric diagnostic GENE-U scale demonstrated good psychometric performance in this initial evaluation and could be a useful tool for translational genomics researchers, warranting additional validation.
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Affiliation(s)
- Hadley Stevens Smith
- PRecisiOn Medicine Translational Research (PROMoTeR) Center, Department of Population Medicine, Harvard Medical School, Boston, MA; Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX.
| | - Caryn Kseniya Rubanovich
- San Diego State University/University of California San Diego Joint Doctoral Program in Clinical Psychology, San Diego, CA
| | - Jill Oliver Robinson
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX
| | - Ariel N Levchenko
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX
| | - Sarah A Classen
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX
| | - Janet Malek
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX
| | | | - Kyle B Brothers
- Norton Children's Research Institute affiliated with the University of Louisville School of Medicine, Louisville, KY
| | - Benjamin S Wilfond
- Treuman Katz Center for Pediatric Bioethics and Palliative Care, Seattle Children's Research Institute and Hospital, Seattle, WA; Division of Bioethics and Palliative Care, Department of Pediatrics, University of Washington School of Medicine, Seattle, WA
| | - Christine Rini
- Department of Medical Social Sciences, Northwestern University Feinberg School of Medicine, Chicago, IL; Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL
| | - Sara J Knight
- Division of Epidemiology, Department of Internal Medicine, University of Utah, Salt Lake City, UT
| | - Amy L McGuire
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX
| | - Cinnamon S Bloss
- Herbert Wertheim School of Public Health, University of California San Diego, San Diego, CA
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11
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Lewis SA, Ruttenberg A, Iyiyol T, Kong N, Jin SC, Kruer MC. Potential clinical applications of advanced genomic analysis in cerebral palsy. EBioMedicine 2024; 106:105229. [PMID: 38970919 PMCID: PMC11282942 DOI: 10.1016/j.ebiom.2024.105229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 04/26/2024] [Accepted: 06/20/2024] [Indexed: 07/08/2024] Open
Abstract
Cerebral palsy (CP) has historically been attributed to acquired insults, but emerging research suggests that genetic variations are also important causes of CP. While microarray and whole-exome sequencing based studies have been the primary methods for establishing new CP-gene relationships and providing a genetic etiology for individual patients, the cause of their condition remains unknown for many patients with CP. Recent advancements in genomic technologies offer additional opportunities to uncover variations in human genomes, transcriptomes, and epigenomes that have previously escaped detection. In this review, we outline the use of these state-of-the-art technologies to address the molecular diagnostic challenges experienced by individuals with CP. We also explore the importance of identifying a molecular etiology whenever possible, given the potential for genomic medicine to provide opportunities to treat patients with CP in new and more precise ways.
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Affiliation(s)
- Sara A Lewis
- Pediatric Movement Disorders Program, Barrow Neurological Institute, Phoenix Children's Hospital, Phoenix, AZ, United States; Departments of Child Health, Neurology, and Cellular & Molecular Medicine and Program in Genetics, University of Arizona College of Medicine, Phoenix, AZ, United States
| | - Andrew Ruttenberg
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, United States
| | - Tuğçe Iyiyol
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, United States
| | - Nahyun Kong
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, United States
| | - Sheng Chih Jin
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, United States; Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, United States.
| | - Michael C Kruer
- Pediatric Movement Disorders Program, Barrow Neurological Institute, Phoenix Children's Hospital, Phoenix, AZ, United States; Departments of Child Health, Neurology, and Cellular & Molecular Medicine and Program in Genetics, University of Arizona College of Medicine, Phoenix, AZ, United States; Programs in Neuroscience and Molecular & Cellular Biology, School of Life Sciences, Arizona State University, Tempe, AZ, United States.
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12
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Nurchis MC, Radio FC, Salmasi L, Heidar Alizadeh A, Raspolini GM, Altamura G, Tartaglia M, Dallapiccola B, Damiani G. Bayesian cost-effectiveness analysis of Whole genome sequencing versus Whole exome sequencing in a pediatric population with suspected genetic disorders. THE EUROPEAN JOURNAL OF HEALTH ECONOMICS : HEPAC : HEALTH ECONOMICS IN PREVENTION AND CARE 2024; 25:999-1011. [PMID: 37975990 PMCID: PMC11283423 DOI: 10.1007/s10198-023-01644-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 10/25/2023] [Indexed: 11/19/2023]
Abstract
Genetic diseases are medical conditions caused by sequence or structural changes in an individual's genome. Whole exome sequencing (WES) and whole genome sequencing (WGS) are increasingly used for diagnosing suspected genetic conditions in children to reduce the diagnostic delay and accelerating the implementation of appropriate treatments. While more information is becoming available on clinical efficacy and economic sustainability of WES, the broad implementation of WGS is still hindered by higher complexity and economic issues. The aim of this study is to estimate the cost-effectiveness of WGS versus WES and standard testing for pediatric patients with suspected genetic disorders. A Bayesian decision tree model was set up. Model parameters were retrieved both from hospital administrative datasets and scientific literature. The analysis considered a lifetime time frame and adopted the perspective of the Italian National Health Service (NHS). Bayesian inference was performed using the Markov Chain Monte Carlo simulation method. Uncertainty was explored through a probabilistic sensitivity analysis (PSA) and a value of information analysis (VOI). The present analysis showed that implementing first-line WGS would be a cost-effective strategy, against the majority of the other tested alternatives at a threshold of €30,000-50,000, for diagnosing outpatient pediatric patients with suspected genetic disorders. According to the sensitivity analyses, the findings were robust to most assumption and parameter uncertainty. Lessons learnt from this modeling study reinforces the adoption of first-line WGS, as a cost-effective strategy, depending on actual difficulties for the NHS to properly allocate limited resources.
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Affiliation(s)
- Mario Cesare Nurchis
- School of Economics, Università Cattolica del Sacro Cuore, Largo Francesco Vito 1, 00168, Rome, Italy.
- Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168, Rome, Italy.
| | | | - Luca Salmasi
- Department of Economics and Finance, Università Cattolica del Sacro Cuore, 00168, Rome, Italy
| | - Aurora Heidar Alizadeh
- Department of Health Sciences and Public Health, Section of Hygiene, Università Cattolica del Sacro Cuore, 00168, Rome, Italy
| | - Gian Marco Raspolini
- Department of Health Sciences and Public Health, Section of Hygiene, Università Cattolica del Sacro Cuore, 00168, Rome, Italy
| | - Gerardo Altamura
- Department of Health Sciences and Public Health, Section of Hygiene, Università Cattolica del Sacro Cuore, 00168, Rome, Italy
| | - Marco Tartaglia
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù IRCCS, 00146, Rome, Italy
| | - Bruno Dallapiccola
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù IRCCS, 00146, Rome, Italy
| | - Gianfranco Damiani
- Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168, Rome, Italy
- Department of Health Sciences and Public Health, Section of Hygiene, Università Cattolica del Sacro Cuore, 00168, Rome, Italy
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13
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Lang T, Geaghan S, Loh TP, Mak C, Papassotiriou I, Kyriakopoulou LG. Considerations for applying emerging technologies in paediatric laboratory medicine. Clin Chem Lab Med 2024; 0:cclm-2023-1408. [PMID: 39044644 DOI: 10.1515/cclm-2023-1408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 07/18/2024] [Indexed: 07/25/2024]
Abstract
Emerging technology in laboratory medicine can be defined as an analytical method (including biomarkers) or device (software, applications, and algorithms) that by its stage of development, translation into broad routine clinical practice, or geographical adoption and implementation has the potential to add value to clinical diagnostics. Paediatric laboratory medicine itself may be considered an emerging area of specialisation that is established relatively recently following increased appreciation and understanding of the unique physiology and healthcare needs of the children. Through four clinical (neonatal hypoglycaemia, neonatal hyperbilirubinaemia, sickle cell disorder, congenital adrenal hyperplasia) and six technological (microassays, noninvasive testing, alternative matrices, next generation sequencing, exosome analysis, machine learning) illustrations, key takeaways of application of emerging technology for each area are summarised. Additionally, nine key considerations when applying emerging technology in paediatric laboratory medicine setting are discussed.
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Affiliation(s)
- Tim Lang
- Department of Blood Sciences, Royal Victoria Infirmary, Newcastle upon Tyne, UK
| | - Sharon Geaghan
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Tze Ping Loh
- Department of Laboratory Medicine, National University Hospital, Singapore, Singapore
| | - Chloe Mak
- Division of Chemical Pathology, Hong Kong Children's Hospital, Kowloon, Hong Kong SAR, China
| | - Ioannis Papassotiriou
- First Department of Pediatrics, School of Medicine, National and Kapodistrian University of Athens, "Aghia Sophia" Children's Hospital, Athens, Greece
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14
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Eichinger J, Elger BS, McLennan S, Filges I, Koné I. Attitudes Towards Non-directiveness Among Medical Geneticists in Germany and Switzerland. JOURNAL OF BIOETHICAL INQUIRY 2024:10.1007/s11673-024-10355-x. [PMID: 39037641 DOI: 10.1007/s11673-024-10355-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 03/03/2024] [Indexed: 07/23/2024]
Abstract
The principle of non-directiveness remains an important tenet in genetics. However, the concept has encountered growing criticism over the last two decades. There is an ongoing discussion about its appropriateness for specific situations in genetics, especially in light of recent significant advancements in genetic medicine. Despite the debate surrounding non-directiveness, there is a notable lack of up-to-date international research empirically investigating the issue from the perspective of those who actually do genetic counselling. Addressing this gap, our article delves into the viewpoints and experiences of medical geneticists in Germany and Switzerland. Twenty qualitative interviews were analysed employing reflexive thematic analysis. Participants' responses revealed substantial uncertainties and divergences in their understanding and application of the concept. It seems to cause distress since many geneticists stated that the principle was difficult to put into clinical practice and was no longer ethically justified given the increasing likelihood of therapeutic implications resulting from genomic testing outcomes. The insights provided by our qualitative empirical study accord with the ongoing theoretical debate regarding the definition, legitimacy, and feasibility of the principle. An adequately nuanced understanding and application of non-directiveness seems crucial to circumvent the risks inherent in the principle, while promoting patient autonomy and beneficence.
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Affiliation(s)
- J Eichinger
- Institute for Biomedical Ethics, University of Basel, Bernoullistrasse 28, 4056, Basel, Switzerland.
| | - B S Elger
- Institute for Biomedical Ethics, University of Basel, Bernoullistrasse 28, 4056, Basel, Switzerland
- Center for legal medicine (CURML), University of Geneva, Rue Michel-Servet 1, 1211, 4, Geneva, Switzerland
| | - S McLennan
- Institute of History and Ethics in Medicine, TUM School of Medicine, Technical University of Munich, Ismaninger Straße 22, 81675, Munich, Germany
| | - I Filges
- Medical Genetics, Institute of Medical Genetics and Pathology, University Hospital Basel and University of Basel, Schönbeinstrasse 40, 4056, Basel, Switzerland
- Department of Clinical Research, University Hospital Basel and University of Basel, c/o Universitätsspital Basel, Spitalstrasse 8/12, 4031, Basel, Switzerland
| | - I Koné
- Institute for Biomedical Ethics, University of Basel, Bernoullistrasse 28, 4056, Basel, Switzerland
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15
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Slavotinek AM, Thompson ML, Martin LJ, Gelb BD. Diagnostic yield after next-generation sequencing in pediatric cardiovascular disease. HGG ADVANCES 2024; 5:100286. [PMID: 38521975 PMCID: PMC11024993 DOI: 10.1016/j.xhgg.2024.100286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 03/20/2024] [Accepted: 03/20/2024] [Indexed: 03/25/2024] Open
Abstract
Genetic testing with exome sequencing and genome sequencing is increasingly offered to infants and children with cardiovascular diseases. However, the rates of positive diagnoses after genetic testing within the different categories of cardiac disease and phenotypic subtypes of congenital heart disease (CHD) have been little studied. We report the diagnostic yield after next-generation sequencing in 500 patients with CHD from diverse population subgroups that were enrolled at three different sites in the Clinical Sequencing Evidence-Generating Research consortium. Patients were ascertained due to a primary cardiovascular issue comprising arrhythmia, cardiomyopathy, and/or CHD, and corresponding human phenotype ontology terms were selected to describe the cardiac and extracardiac findings. We examined the diagnostic yield for patients with arrhythmia, cardiomyopathy, and/or CHD and phenotypic subtypes of CHD comprising conotruncal defects, heterotaxy, left ventricular outflow tract obstruction, septal defects, and "other" heart defects. We found a significant increase in the frequency of positive findings for patients who underwent genome sequencing compared to exome sequencing and for syndromic cardiac defects compared to isolated cardiac defects. We also found significantly higher diagnostic rates for patients who presented with isolated cardiomyopathy compared to isolated CHD. For patients with syndromic presentations who underwent genome sequencing, there were significant differences in the numbers of positive diagnoses for phenotypic subcategories of CHD, ranging from 31.7% for septal defects to 60% for "other". Despite variation in the diagnostic yield at each site, our results support genetic testing in pediatric patients with syndromic and isolated cardiovascular issues and in all subtypes of CHD.
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Affiliation(s)
- Anne M Slavotinek
- Division of Medical Genetics, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA; Division of Human Genetics, Cincinnati Children's Hospital, Cincinnati, OH, USA; Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OH, USA.
| | - Michelle L Thompson
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA; Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Lisa J Martin
- Division of Human Genetics, Cincinnati Children's Hospital, Cincinnati, OH, USA; Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OH, USA
| | - Bruce D Gelb
- Mindich Child Health and Development Institute and Departments of Pediatrics and Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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16
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Trajkova S, Kerkhof J, Rossi Sebastiano M, Pavinato L, Ferrero E, Giovenino C, Carli D, Di Gregorio E, Marinoni R, Mandrile G, Palermo F, Carestiato S, Cardaropoli S, Pullano V, Rinninella A, Giorgio E, Pippucci T, Dimartino P, Rzasa J, Rooney K, McConkey H, Petlichkovski A, Pasini B, Sukarova-Angelovska E, Campbell CM, Metcalfe K, Jenkinson S, Banka S, Mussa A, Ferrero GB, Sadikovic B, Brusco A. DNA methylation analysis in patients with neurodevelopmental disorders improves variant interpretation and reveals complexity. HGG ADVANCES 2024; 5:100309. [PMID: 38751117 PMCID: PMC11216013 DOI: 10.1016/j.xhgg.2024.100309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 05/09/2024] [Accepted: 05/07/2024] [Indexed: 06/07/2024] Open
Abstract
Analysis of genomic DNA methylation by generating epigenetic signature profiles (episignatures) is increasingly being implemented in genetic diagnosis. Here we report our experience using episignature analysis to resolve both uncomplicated and complex cases of neurodevelopmental disorders (NDDs). We analyzed 97 NDDs divided into (1) a validation cohort of 59 patients with likely pathogenic/pathogenic variants characterized by a known episignature and (2) a test cohort of 38 patients harboring variants of unknown significance or unidentified variants. The expected episignature was obtained in most cases with likely pathogenic/pathogenic variants (53/59 [90%]), a revealing exception being the overlapping profile of two SMARCB1 pathogenic variants with ARID1A/B:c.6200, confirmed by the overlapping clinical features. In the test cohort, five cases showed the expected episignature, including (1) novel pathogenic variants in ARID1B and BRWD3; (2) a deletion in ATRX causing MRXFH1 X-linked mental retardation; and (3) confirmed the clinical diagnosis of Cornelia de Lange (CdL) syndrome in mutation-negative CdL patients. Episignatures analysis of the in BAF complex components revealed novel functional protein interactions and common episignatures affecting homologous residues in highly conserved paralogous proteins (SMARCA2 M856V and SMARCA4 M866V). Finally, we also found sex-dependent episignatures in X-linked disorders. Implementation of episignature profiling is still in its early days, but with increasing utilization comes increasing awareness of the capacity of this methodology to help resolve the complex challenges of genetic diagnoses.
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Affiliation(s)
- Slavica Trajkova
- Department of Neurosciences Rita Levi-Montalcini, University of Turin, Turin 10126, Italy
| | - Jennifer Kerkhof
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A5W9, Canada
| | - Matteo Rossi Sebastiano
- Molecular Biotechnology Center "Guido Tarone" University of Turin, 10126 Turin, Italy; Department of Molecular Biotechnology and Health Sciences, University of Turin, CASSMedChem, 10126 Turin, Italy
| | - Lisa Pavinato
- Department of Medical Sciences, University of Turin, 10126 Turin, Italy
| | - Enza Ferrero
- Department of Medical Sciences, University of Turin, 10126 Turin, Italy
| | - Chiara Giovenino
- Department of Medical Sciences, University of Turin, 10126 Turin, Italy
| | - Diana Carli
- Department of Medical Sciences, University of Turin, 10126 Turin, Italy
| | - Eleonora Di Gregorio
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, 10126 Turin, Italy
| | - Roberta Marinoni
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, 10126 Turin, Italy
| | - Giorgia Mandrile
- Medical Genetics Unit and Thalassemia Center, San Luigi University Hospital, Orbassano, TO 10049, Italy
| | - Flavia Palermo
- Medical Genetics Unit and Thalassemia Center, San Luigi University Hospital, Orbassano, TO 10049, Italy
| | - Silvia Carestiato
- Department of Neurosciences Rita Levi-Montalcini, University of Turin, Turin 10126, Italy
| | - Simona Cardaropoli
- Department of Public Health and Pediatric Sciences, University of Turin, 10126 Turin, Italy
| | - Verdiana Pullano
- Department of Neurosciences Rita Levi-Montalcini, University of Turin, Turin 10126, Italy
| | - Antonina Rinninella
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, 10126 Turin, Italy; Department of Biomedical and Biotechnological Sciences, Medical Genetics, University of Catania, 94124 Catania, Italy
| | - Elisa Giorgio
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy; Neurogenetics Research Center, IRCCS Mondino Foundation, 27100 Pavia, Italy
| | - Tommaso Pippucci
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy
| | - Paola Dimartino
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
| | - Jessica Rzasa
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A5W9, Canada
| | - Kathleen Rooney
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A5W9, Canada; Department of Pathology and Laboratory Medicine, Western University, London, ON N6A3K7, Canada
| | - Haley McConkey
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A5W9, Canada; Department of Pathology and Laboratory Medicine, Western University, London, ON N6A3K7, Canada
| | - Aleksandar Petlichkovski
- Department of Immunology and Human Genetics, Faculty of Medicine, University "Sv. Kiril I Metodij", Skopje 1000, Republic of Macedonia
| | - Barbara Pasini
- Department of Medical Sciences, University of Turin, 10126 Turin, Italy; Medical Genetics Unit, Città della Salute e della Scienza University Hospital, 10126 Turin, Italy
| | - Elena Sukarova-Angelovska
- Department of Endocrinology and Genetics, Faculty of Medicine, University "Sv. Kiril I Metodij", Skopje 1000, Republic of Macedonia
| | - Christopher M Campbell
- Manchester Centre for Genomic Medicine, St. Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester M13 9WL, UK
| | - Kay Metcalfe
- Manchester Centre for Genomic Medicine, St. Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester M13 9WL, UK
| | - Sarah Jenkinson
- Manchester Centre for Genomic Medicine, St. Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester M13 9WL, UK
| | - Siddharth Banka
- Manchester Centre for Genomic Medicine, St. Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester M13 9WL, UK; Division of Evolution, Infection & Genomics, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9WL, UK
| | - Alessandro Mussa
- Department of Public Health and Pediatric Sciences, University of Turin, 10126 Turin, Italy; Pediatric Clinical Genetics Unit, Regina Margherita Childrens' Hospital, 10126 Turin, Italy
| | | | - Bekim Sadikovic
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A5W9, Canada; Department of Pathology and Laboratory Medicine, Western University, London, ON N6A3K7, Canada
| | - Alfredo Brusco
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, 10126 Turin, Italy; Department of Neurosciences Rita Levi-Montalcini, University of Turin, Turin 10126, Italy.
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17
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Rodriguez-Gil JL, Nagy PL, Francke U. Optical genome mapping with genome sequencing identifies subtelomeric Xq28 deletion and inserted 7p22.3 duplication in a male with multisystem developmental disorder. Am J Med Genet A 2024:e63814. [PMID: 39011850 DOI: 10.1002/ajmg.a.63814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 03/24/2024] [Accepted: 06/27/2024] [Indexed: 07/17/2024]
Abstract
We report a 17-year-old male with supravalvular stenosis, initial failure to thrive and delayed early development, short stature, acromelia, dysmorphic facial features, hypertelorism, macrocephaly, syringomyelia, hypertension, and anxiety disorder. Fluorescent in situ hybridization (FISH), chromosomal microarray analysis (CMA), and exome sequencing (ES) were nondiagnostic. Combined optical genome mapping (OGM) and genome sequencing (GS) showed a complex rearrangement including an X chromosome with a 22.5 kb deletion in band Xq28 replaced by a 61.4 kb insertion of duplicated chromosome 7p22.3 material. The deletion removes the distal 3' untranslated region (UTR) of FUNDC2, the entire CMC4 and MTCP1, and the first five exons of BRCC3. Transcriptome analysis revealed absent expression of CMC4 and MTCP1 and BRCC3 with normal transcript level of FUNDC2. The inserted duplication includes only one known gene: UNCX. Similar overlapping Xq28 deletions have been reported to be associated with Moyamoya disease (MMD), short stature, hypergonadotropic hypogonadism (HH), and facial dysmorphism. Although he has short stature, our patient does not have signs of Moyamoya arteriopathy or hypogonadism. The structurally abnormal X chromosome was present in his mother, but not in his unaffected brother, maternal uncle, or maternal grandparents. We propose that the combination of his absent Xq28 and duplicated 7p22.3 genomic material is responsible for his phenotype. This case highlights the potential of combined OGM and GS for detecting complex structural variants compared with standard of care genetic testing such as CMA and ES.
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Affiliation(s)
- Jorge L Rodriguez-Gil
- Department of Pediatrics, Division of Medical Genetics, Stanford University School of Medicine, Stanford, California, USA
- Department of Pediatrics, Division of Neonatal and Developmental Medicine, Stanford University, Stanford, California, USA
| | | | - Uta Francke
- Department of Pediatrics, Division of Medical Genetics, Stanford University School of Medicine, Stanford, California, USA
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18
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Kolesnikov A, Cook D, Nattestad M, Brambrink L, McNulty B, Gorzynski J, Goenka S, Ashley EA, Jain M, Miga KH, Paten B, Chang PC, Carroll A, Shafin K. Local read haplotagging enables accurate long-read small variant calling. Nat Commun 2024; 15:5907. [PMID: 39003259 PMCID: PMC11246426 DOI: 10.1038/s41467-024-50079-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 06/28/2024] [Indexed: 07/15/2024] Open
Abstract
Long-read sequencing technology has enabled variant detection in difficult-to-map regions of the genome and enabled rapid genetic diagnosis in clinical settings. Rapidly evolving third-generation sequencing platforms like Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT) are introducing newer platforms and data types. It has been demonstrated that variant calling methods based on deep neural networks can use local haplotyping information with long-reads to improve the genotyping accuracy. However, using local haplotype information creates an overhead as variant calling needs to be performed multiple times which ultimately makes it difficult to extend to new data types and platforms as they get introduced. In this work, we have developed a local haplotype approximate method that enables state-of-the-art variant calling performance with multiple sequencing platforms including PacBio Revio system, ONT R10.4 simplex and duplex data. This addition of local haplotype approximation simplifies long-read variant calling with DeepVariant.
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Affiliation(s)
| | - Daniel Cook
- Google Inc, 1600 Amphitheatre Pkwy, Mountain View, CA, USA
| | | | | | - Brandy McNulty
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
| | | | | | | | - Miten Jain
- Northeastern university, Boston, MA, USA
| | - Karen H Miga
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Benedict Paten
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Pi-Chuan Chang
- Google Inc, 1600 Amphitheatre Pkwy, Mountain View, CA, USA
| | - Andrew Carroll
- Google Inc, 1600 Amphitheatre Pkwy, Mountain View, CA, USA.
| | - Kishwar Shafin
- Google Inc, 1600 Amphitheatre Pkwy, Mountain View, CA, USA.
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19
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Thorpe E, Williams T, Shaw C, Chekalin E, Ortega J, Robinson K, Button J, Jones MC, Campo MD, Basel D, McCarrier J, Keppen LD, Royer E, Foster-Bonds R, Duenas-Roque MM, Urraca N, Bosfield K, Brown CW, Lydigsen H, Mroczkowski HJ, Ward J, Sirchia F, Giorgio E, Vaux K, Salguero HP, Lumaka A, Mubungu G, Makay P, Ngole M, Lukusa PT, Vanderver A, Muirhead K, Sherbini O, Lah MD, Anderson K, Bazalar-Montoya J, Rodriguez RS, Cornejo-Olivas M, Milla-Neyra K, Shinawi M, Magoulas P, Henry D, Gibson K, Wiafe S, Jayakar P, Salyakina D, Masser-Frye D, Serize A, Perez JE, Taylor A, Shenbagam S, Abou Tayoun A, Malhotra A, Bennett M, Rajan V, Avecilla J, Warren A, Arseneault M, Kalista T, Crawford A, Ajay SS, Perry DL, Belmont J, Taft RJ. The impact of clinical genome sequencing in a global population with suspected rare genetic disease. Am J Hum Genet 2024; 111:1271-1281. [PMID: 38843839 PMCID: PMC11267518 DOI: 10.1016/j.ajhg.2024.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 05/03/2024] [Accepted: 05/06/2024] [Indexed: 07/03/2024] Open
Abstract
There is mounting evidence of the value of clinical genome sequencing (cGS) in individuals with suspected rare genetic disease (RGD), but cGS performance and impact on clinical care in a diverse population drawn from both high-income countries (HICs) and low- and middle-income countries (LMICs) has not been investigated. The iHope program, a philanthropic cGS initiative, established a network of 24 clinical sites in eight countries through which it provided cGS to individuals with signs or symptoms of an RGD and constrained access to molecular testing. A total of 1,004 individuals (median age, 6.5 years; 53.5% male) with diverse ancestral backgrounds (51.8% non-majority European) were assessed from June 2016 to September 2021. The diagnostic yield of cGS was 41.4% (416/1,004), with individuals from LMIC sites 1.7 times more likely to receive a positive test result compared to HIC sites (LMIC 56.5% [195/345] vs. HIC 33.5% [221/659], OR 2.6, 95% CI 1.9-3.4, p < 0.0001). A change in diagnostic evaluation occurred in 76.9% (514/668) of individuals. Change of management, inclusive of specialty referrals, imaging and testing, therapeutic interventions, and palliative care, was reported in 41.4% (285/694) of individuals, which increased to 69.2% (480/694) when genetic counseling and avoidance of additional testing were also included. Individuals from LMIC sites were as likely as their HIC counterparts to experience a change in diagnostic evaluation (OR 6.1, 95% CI 1.1-∞, p = 0.05) and change of management (OR 0.9, 95% CI 0.5-1.3, p = 0.49). Increased access to genomic testing may support diagnostic equity and the reduction of global health care disparities.
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Affiliation(s)
| | | | - Chad Shaw
- Genetic and Genomic Services PBC, Houston, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Department of Statistics, Rice University, Houston, TX, USA
| | | | - Julia Ortega
- Illumina Inc, San Diego, CA, USA; C2N Diagnostics, St. Louis, MO, USA
| | | | | | - Marilyn C Jones
- Rady Children's Hospital, San Diego, CA, USA; University of California, San Diego, San Diego, CA, USA
| | - Miguel Del Campo
- Rady Children's Hospital, San Diego, CA, USA; University of California, San Diego, San Diego, CA, USA
| | - Donald Basel
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Julie McCarrier
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, USA
| | | | - Erin Royer
- Sanford Children's Specialty Clinics at Sanford Health, USD Sanford School of Medicine, Sioux Falls, SD, USA
| | | | | | - Nora Urraca
- University of Tennessee Health Science Center, Le Bonheur Children's Hospital, Memphis, TN, USA
| | - Kerri Bosfield
- University of Tennessee Health Science Center, Le Bonheur Children's Hospital, Memphis, TN, USA
| | - Chester W Brown
- University of Tennessee Health Science Center, Le Bonheur Children's Hospital, Memphis, TN, USA
| | - Holly Lydigsen
- University of Tennessee Health Science Center, Le Bonheur Children's Hospital, Memphis, TN, USA
| | - Henry J Mroczkowski
- University of Tennessee Health Science Center, Le Bonheur Children's Hospital, Memphis, TN, USA
| | - Jewell Ward
- University of Tennessee Health Science Center, Le Bonheur Children's Hospital, Memphis, TN, USA
| | - Fabio Sirchia
- Department of Molecular Medicine, University of Pavia, Pavia, Italy; Medical Genetics Unit, IRCCS San Matteo Foundation, Pavia, Italy
| | - Elisa Giorgio
- Department of Molecular Medicine, University of Pavia, Pavia, Italy; Medical Genetics Unit, IRCCS Mondino Foundation, Pavia, Italy
| | - Keith Vaux
- Point Loma Pediatrics, San Diego, CA, USA
| | | | - Aimé Lumaka
- Centre de Genetique Humaine, Universite de Kinshasa, Kinshasa, Democratic Republic of the Congo; Center for Human Genetics, Centre Hospitalier Universitaire, Liège, Belgium
| | - Gerrye Mubungu
- Centre de Genetique Humaine, Universite de Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Prince Makay
- Centre de Genetique Humaine, Universite de Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Mamy Ngole
- Centre de Genetique Humaine, Universite de Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Prosper Tshilobo Lukusa
- Centre de Genetique Humaine, Universite de Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Adeline Vanderver
- Division of Neurology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA, USA; Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Omar Sherbini
- Division of Neurology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Melissa D Lah
- Indiana University School of Medicine, Indianapolis, IN, USA
| | | | | | | | - Mario Cornejo-Olivas
- Neurogenetics Research Center, Instituto Nacional de Ciencias Neurologicas, Lima, Peru; Neurogenetics Working Group, Universidad Científica del Sur, Lima, Peru
| | - Karina Milla-Neyra
- Neurogenetics Research Center, Instituto Nacional de Ciencias Neurologicas, Lima, Peru
| | - Marwan Shinawi
- Washington University, St. Louis, MO, USA; St. Louis Children's Hospital, St. Louis, MO, USA
| | | | - Duncan Henry
- UCSF Benioff Children's Hospitals, San Francisco, CA, USA
| | - Kate Gibson
- Canterbury District Health Board, Canterbury, New Zealand
| | | | | | | | - Diane Masser-Frye
- Rady Children's Hospital, San Diego, CA, USA; San Diego-Imperial Counties Developmental Services, Inc., San Diego, CA, USA
| | | | | | - Alan Taylor
- Al Jalila Genomics Center of Excellence, Al Jalila Children's Specialty Hospital, Dubai, United Arab Emirates
| | - Shruti Shenbagam
- Al Jalila Genomics Center of Excellence, Al Jalila Children's Specialty Hospital, Dubai, United Arab Emirates
| | - Ahmad Abou Tayoun
- Al Jalila Genomics Center of Excellence, Al Jalila Children's Specialty Hospital, Dubai, United Arab Emirates; Center for Genomic Discovery, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | | | | | - Vani Rajan
- Illumina Inc, San Diego, CA, USA; Veracyte, San Diego, CA, USA
| | | | | | | | | | | | | | | | - John Belmont
- Genetic and Genomic Services PBC, Houston, TX, USA
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20
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Summers J, Baribeau D, Perlman P, Hoang N, Cui S, Krakowski A, Ambrozewicz P, Ho A, Selvanayagam T, Sándor-Bajusz KA, Palad K, Patel N, McGaughey S, Gallagher L, Scherer SW, Szatmari P, Vorstman J. An integrated clinical approach to children at genetic risk for neurodevelopmental and psychiatric conditions: interdisciplinary collaboration and research infrastructure. J Neurodev Disord 2024; 16:37. [PMID: 38970057 PMCID: PMC11229023 DOI: 10.1186/s11689-024-09552-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 06/04/2024] [Indexed: 07/07/2024] Open
Abstract
BACKGROUND A sizeable proportion of pathogenic genetic variants identified in young children tested for congenital differences are associated with neurodevelopmental psychiatric disorders (NPD). In this growing group, a genetic diagnosis often precedes the emergence of diagnosable developmental concerns. Here, we describe DAGSY (Developmental Assessment of Genetically Susceptible Youth), a novel interdisciplinary 'genetic-diagnosis-first' clinic integrating psychiatric, psychological and genetic expertise, and report our first observations and feedback from families and referring clinicians. METHODS We retrieved data on referral sources and indications, genetic and NPD diagnoses and recommendations for children seen at DAGSY between 2018 and 2022. Through a survey, we obtained feedback from twenty families and eleven referring clinicians. RESULTS 159 children (mean age 10.2 years, 57.2% males) completed an interdisciplinary (psychiatry, psychology, genetic counselling) DAGSY assessment during this period. Of these, 69.8% had a pathogenic microdeletion or microduplication, 21.5% a sequence-level variant, 4.4% a chromosomal disorder, and 4.4% a variant of unknown significance with emerging evidence of pathogenicity. One in four children did not have a prior NPD diagnosis, and referral to DAGSY was motivated by their genetic vulnerability alone. Following assessment, 76.7% received at least one new NPD diagnosis, most frequently intellectual disability (24.5%), anxiety (20.7%), autism spectrum (18.9%) and specific learning (16.4%) disorder. Both families and clinicians responding to our survey expressed satisfaction, but also highlighted some areas for potential improvement. CONCLUSIONS DAGSY addresses an unmet clinical need for children identified with genetic variants that confer increased vulnerability for NPD and provides a crucial platform for research in this area. DAGSY can serve as a model for interdisciplinary clinics integrating child psychiatry, psychology and genetics, addressing both clinical and research needs for this emerging population.
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Affiliation(s)
- Jane Summers
- Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Psychiatry, The Hospital for Sick Children, Toronto, ON, Canada
- Autism Research Unit, The Hospital for Sick Children, Toronto, ON, Canada
| | - Danielle Baribeau
- Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
- Department of Psychiatry, The Hospital for Sick Children, Toronto, ON, Canada
- Holland Bloorview Kids Rehabilitation Hospital, Toronto, ON, Canada
- Autism Research Unit, The Hospital for Sick Children, Toronto, ON, Canada
| | - Polina Perlman
- Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
- Department of Psychiatry, The Hospital for Sick Children, Toronto, ON, Canada
- Centre for Addiction and Mental Health, Toronto, ON, Canada
- Autism Research Unit, The Hospital for Sick Children, Toronto, ON, Canada
| | - Ny Hoang
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Genetic Counselling, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- Autism Research Unit, The Hospital for Sick Children, Toronto, ON, Canada
| | - Sunny Cui
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Autism Research Unit, The Hospital for Sick Children, Toronto, ON, Canada
| | - Aneta Krakowski
- Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
- Department of Psychiatry, The Hospital for Sick Children, Toronto, ON, Canada
- Autism Research Unit, The Hospital for Sick Children, Toronto, ON, Canada
| | - Patricia Ambrozewicz
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Autism Research Unit, The Hospital for Sick Children, Toronto, ON, Canada
| | - Ariel Ho
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Autism Research Unit, The Hospital for Sick Children, Toronto, ON, Canada
| | - Thanuja Selvanayagam
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Genetic Counselling, The Hospital for Sick Children, Toronto, ON, Canada
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
- Autism Research Unit, The Hospital for Sick Children, Toronto, ON, Canada
| | - Kinga A Sándor-Bajusz
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Autism Research Unit, The Hospital for Sick Children, Toronto, ON, Canada
| | - Katrina Palad
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Autism Research Unit, The Hospital for Sick Children, Toronto, ON, Canada
| | - Nishi Patel
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Autism Research Unit, The Hospital for Sick Children, Toronto, ON, Canada
| | - Sarah McGaughey
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Autism Research Unit, The Hospital for Sick Children, Toronto, ON, Canada
| | - Louise Gallagher
- Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Psychiatry, The Hospital for Sick Children, Toronto, ON, Canada
- Centre for Addiction and Mental Health, Toronto, ON, Canada
| | - Stephen W Scherer
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
- McLaughlin Centre and Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Peter Szatmari
- Department of Psychiatry, The Hospital for Sick Children, Toronto, ON, Canada
- Centre for Addiction and Mental Health, Toronto, ON, Canada
| | - Jacob Vorstman
- Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada.
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada.
- Department of Psychiatry, The Hospital for Sick Children, Toronto, ON, Canada.
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada.
- Autism Research Unit, The Hospital for Sick Children, Toronto, ON, Canada.
- Hospital for Sick Children, Peter Gilgan Centre for Research and Learning, 686 Bay Street Room 12.9702, Toronto, ON, M5G 0A4, Canada.
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21
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Weymann D, Buckell J, Fahr P, Loewen R, Ehman M, Pollard S, Friedman JM, Stockler-Ipsiroglu S, Elliott AM, Wordsworth S, Buchanan J, Regier DA. Health Care Costs After Genome-Wide Sequencing for Children With Rare Diseases in England and Canada. JAMA Netw Open 2024; 7:e2420842. [PMID: 38985473 PMCID: PMC11238031 DOI: 10.1001/jamanetworkopen.2024.20842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 05/07/2024] [Indexed: 07/11/2024] Open
Abstract
Importance Etiologic diagnoses for rare diseases can involve a diagnostic odyssey, with repeated health care interactions and inconclusive diagnostics. Prior studies reported cost savings associated with genome-wide sequencing (GWS) compared with cytogenetic or molecular testing through rapid genetic diagnosis, but there is limited evidence on whether diagnosis from GWS is associated with reduced health care costs. Objective To measure changes in health care costs after diagnosis from GWS for Canadian and English children with suspected rare diseases. Design, Setting, and Participants This cohort study was a quasiexperimental retrospective analysis across 3 distinct English and Canadian cohorts, completed in 2023. Mixed-effects generalized linear regression was used to estimate associations between GWS and costs in the 2 years before and after GWS. Difference-in-differences regression was used to estimate associations of genetic diagnosis and costs. Costs are in 2019 US dollars. GWS was conducted in a research setting (Genomics England 100 000 Genomes Project [100KGP] and Clinical Assessment of the Utility of Sequencing and Evaluation as a Service [CAUSES] Research Clinic) or clinical outpatient setting (publicly reimbursed GWS in British Columbia [BC], Canada). Participants were children with developmental disorders, seizure disorders, or both undergoing GWS between 2014 and 2019. Data were analyzed from April 2021 to September 2023. Exposures GWS and genetic diagnosis. Main Outcomes and Measures Annual health care costs and diagnostic costs per child. Results Study cohorts included 7775 patients in 100KGP, among whom 788 children had epilepsy (mean [SD] age at GWS, 11.6 [11.1] years; 400 female [50.8%]) and 6987 children had an intellectual disability (mean [SD] age at GWS, 8.2 [8.4] years; 2750 female [39.4%]); 77 patients in CAUSES (mean [SD] age at GWS, 8.5 [4.4] years; 33 female [42.9%]); and 118 publicly reimbursed GWS recipients from BC (mean [SD] age at GWS, 5.5 [5.2] years; 58 female [49.2%]). GWS diagnostic yield was 143 children (18.1%) for those with epilepsy and 1323 children (18.9%) for those with an intellectual disability in 100KGP, 47 children (39.8%) in the BC publicly reimbursed setting, and 42 children (54.5%) in CAUSES. Mean annual per-patient spending over the study period was $5283 (95% CI, $5121-$5427) for epilepsy and $3373 (95% CI, $3322-$3424) for intellectual disability in the 100KGP, $724 (95% CI, $563-$886) in CAUSES, and $1573 (95% CI, $1372-$1773) in the BC reimbursed setting. Receiving a genetic diagnosis from GWS was not associated with changed costs in any cohort. Conclusions and Relevance In this study, receiving a genetic diagnosis was not associated with cost savings. This finding suggests that patient benefit and cost-effectiveness should instead drive GWS implementation.
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Affiliation(s)
- Deirdre Weymann
- Cancer Control Research, BC Cancer Research Institute, Vancouver, British Columbia, Canada
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - John Buckell
- Health Economics Research Centre, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
- Nuffield Department of Primary Health Care Sciences, University of Oxford, Oxford, United Kingdom
- National Institute for Health Research Biomedical Research Centre, Oxford, United Kingdom
| | - Patrick Fahr
- Health Economics Research Centre, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
| | - Rosalie Loewen
- Cancer Control Research, BC Cancer Research Institute, Vancouver, British Columbia, Canada
| | - Morgan Ehman
- Cancer Control Research, BC Cancer Research Institute, Vancouver, British Columbia, Canada
| | - Samantha Pollard
- Cancer Control Research, BC Cancer Research Institute, Vancouver, British Columbia, Canada
| | - Jan M. Friedman
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
- BC Children’s Hospital Research Institute, Vancouver, British Columbia, Canada
| | - Sylvia Stockler-Ipsiroglu
- BC Children’s Hospital Research Institute, Vancouver, British Columbia, Canada
- Department of Pediatrics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- Division of Biochemical Genetics, BC Children’s Hospital, Vancouver, British Columbia, Canada
| | - Alison M. Elliott
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
- BC Children’s Hospital Research Institute, Vancouver, British Columbia, Canada
| | - Sarah Wordsworth
- Health Economics Research Centre, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
- National Institute for Health Research Biomedical Research Centre, Oxford, United Kingdom
| | - James Buchanan
- Health Economics Research Centre, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
- National Institute for Health Research Biomedical Research Centre, Oxford, United Kingdom
| | - Dean A. Regier
- Cancer Control Research, BC Cancer Research Institute, Vancouver, British Columbia, Canada
- School of Population and Public Health, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
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22
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Khalaf T, Al Ojaimi M, Saleh DA, Sulaiman A, Sohal AP, Khan A, El-Hattab AW. The utility of exome sequencing in diagnosing pediatric neurodevelopmental disorders in a highly consanguineous population. Clin Genet 2024; 106:82-89. [PMID: 38438125 DOI: 10.1111/cge.14508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 02/07/2024] [Accepted: 02/08/2024] [Indexed: 03/06/2024]
Abstract
Exome sequencing (ES) has been utilized in diagnosing children with neurodevelopmental manifestations, this study aimed to investigate the utility of ES in children within a highly consanguineous population that presented with neurodevelopmental complaints. A retrospective chart review was performed for 405 children with neurodevelopmental complaints who have had ES and were evaluated in multiple centers in the United Arab Emirates over a four-year period. Within the cohort of 405 children, consanguinity was reported in 35% (144/405). The primary clinical presentations were developmental delay/cognitive impairment, distinctive facial features, hypotonia, seizures, and weakness. The diagnostic yield was 57% (231/405). Novel variants were identified in 54% (125/231) of positive cases. Within the positive cases, specific treatment was available in 6% (13/231) and copy number variants (CNV) were reported in 3% (8/231) of cases. In eight children, variants in genes that have not yet been linked to human disease that could potentially be the cause of the observed phenotype "candidate genes" were identified. ES was utilized effectively within this cohort with a high diagnostic yield and through the identification of novel gene variants, CNVs, candidate genes and secondary findings as well as the alteration of the treatment plan in cases where treatment was available.
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Affiliation(s)
- Tamam Khalaf
- Genetic Counseling Division, Igenomix, Dubai, UAE
| | - Mode Al Ojaimi
- Department of Clinical Sciences, College of Medicine, University of Sharjah, Sharjah, UAE
- Department of Pediatrics, University Hospital Sharjah, Sharjah, UAE
| | - Dina Amin Saleh
- Pediatric Neurology Division, American Center for Psychiatry and Neurology, Abu Dhabi, UAE
- Department of Pediatrics, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Alena Sulaiman
- Pediatric Division, KidsHeart Medical Center, Abu Dhabi, UAE
| | - Aman P Sohal
- Pediatric Neurology Division, Neuropedia Children's Neuroscience Center, Dubai, UAE
- Pediatric Neurology Division, Al Qassimi Women and Children's Hospital, Sharjah, UAE
| | - Arif Khan
- Pediatric Neurology Division, Neuropedia Children's Neuroscience Center, Dubai, UAE
- Pediatric Division, Kings College Hospital London, Dubai, UAE
- Pediatric Neurology Division, Kids Neuro Clinic and Rehab Center, Dubai, UAE
| | - Ayman W El-Hattab
- Department of Clinical Sciences, College of Medicine, University of Sharjah, Sharjah, UAE
- Department of Pediatrics, University Hospital Sharjah, Sharjah, UAE
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23
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Gupta N, Kabra M. Unexplained Intellectual Disability: Diagnostic Workflow Moving Towards "Exome Sequencing First Approach"? Indian J Pediatr 2024; 91:653-654. [PMID: 38814510 DOI: 10.1007/s12098-024-05173-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Accepted: 05/16/2024] [Indexed: 05/31/2024]
Affiliation(s)
- Neerja Gupta
- Division of Genetics, Department of Pediatrics, AIIMS, New Delhi, India
| | - Madhulika Kabra
- Division of Genetics, Department of Pediatrics, AIIMS, New Delhi, India.
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24
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Hauptman AJ, Salpekar JA, Cohen JS, Asato MR. Navigating Neurogenetics for Child and Adolescent Psychiatry Practice. J Am Acad Child Adolesc Psychiatry 2024; 63:666-669. [PMID: 38325519 DOI: 10.1016/j.jaac.2023.09.555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 09/29/2023] [Accepted: 01/29/2024] [Indexed: 02/09/2024]
Abstract
Neurodevelopmental disorders (NDDs) are a group of conditions characterized by impairments of brain processes that impact cognition, communication, motor abilities, and/or behavior during development. These conditions typically have significant effects across the life span and impact personal, social, academic, or occupational functioning. The US Centers for Disease Control and report that 1 in 6 children has a developmental disability, making it highly likely for child and adolescent psychiatrists to encounter children with NDDs in daily practice.1 While the etiologies of NDDs are broad, genetic syndromes are a common cause of NDDs. The diagnostic yield of thorough genetic testing for NDDs as a group is about 40% based on meta-analysis, including 30% to 50% yield in patients with global developmental delay (GDD) or intellectual disability (ID) and 15% to 20% yield in patients with in autism spectrum disorder.1-3 The findings are extremely heterogeneous, including chromosomal copy number variants (CNVs) and more than 2,000 known monogenic disorders associated with NDDs.3 Diagnostic yields will increase over time with advances in technology and disease gene discovery.3.
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Affiliation(s)
- Aaron J Hauptman
- Kennedy Krieger Institute, Baltimore, Maryland, and Johns Hopkins University School of Medicine, Baltimore, Maryland.
| | - Jay A Salpekar
- Kennedy Krieger Institute, Baltimore, Maryland, and Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Julie S Cohen
- Kennedy Krieger Institute, Baltimore, Maryland, and Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Miya R Asato
- Kennedy Krieger Institute, Baltimore, Maryland, and Johns Hopkins University School of Medicine, Baltimore, Maryland
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25
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Marchionni E, Guadagnolo D, Mastromoro G, Pizzuti A. Prenatal Genome-Wide Sequencing analysis (Exome or Genome) in detecting pathogenic Single Nucleotide Variants in fetal Central Nervous System Anomalies: systematic review and meta-analysis. Eur J Hum Genet 2024; 32:759-769. [PMID: 38486024 PMCID: PMC11219734 DOI: 10.1038/s41431-024-01590-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 02/04/2024] [Accepted: 03/05/2024] [Indexed: 03/20/2024] Open
Abstract
Prenatal Exome (pES) or Genome (pGS) Sequencing analysis showed a significant incremental diagnostic yield over karyotype and chromosomal microarray analysis (CMA) in fetal structural anomalies. Optimized indications and detection rates in different fetal anomalies are still under investigation. The aim of this study was to assess the incremental diagnostic yield in prenatally diagnosed Central Nervous System (CNS) anomalies. A systematic review on antenatal CNS anomalies was performed according to PRISMA guidelines, including n = 12 paper, accounting for 428 fetuses. Results were pooled in a meta-analysis fitting a logistic random mixed-effect model. The effect of interest was the incremental diagnostic rate of pES over karyotype/CMA in detecting likely pathogenic/pathogenic Single Nucleotide Variants (SNVs). A further meta-analysis adding the available pGS studies (including diagnostic coding SNVs only) and submeta-analysis on three CNS subcategories were also performed. The pooled incremental diagnostic yield estimate of pES studies was 38% (95% C.I.: [29%;47%]) and 36% (95% C.I.: [28%;45%]) when including diagnostic SNVs of pGS studies. The point estimate of the effect resulted 22% (95% C.I.: [15%;31%]) in apparently isolated anomalies, 33% (95% C.I.: [22%;46%]) in CNS-only related anomalies (≥1) and 46% (95% C.I.: [38%;55%]) in non-isolated anomalies (either ≥ 2 anomalies in CNS, or CNS and extra-CNS). Meta-analysis showed a substantial diagnostic improvement in performing Prenatal Genome-Wide Sequencing analysis (Exome or Genome) over karyotype and CMA in CNS anomalies.
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Affiliation(s)
- Enrica Marchionni
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy.
| | - Daniele Guadagnolo
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Gioia Mastromoro
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Antonio Pizzuti
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
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Sandal S, Verma IC, Mahay SB, Dubey S, Sabharwal RK, Kulshrestha S, Saxena R, Suman P, Kumar P, Puri RD. Next-Generation Sequencing in Unexplained Intellectual Disability. Indian J Pediatr 2024; 91:682-695. [PMID: 37804371 DOI: 10.1007/s12098-023-04820-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Accepted: 06/23/2023] [Indexed: 10/09/2023]
Abstract
OBJECTIVES To determine the diagnostic yield of next generation sequencing (NGS) in patients with moderate/severe/profound intellectual disability (ID) unexplained by conventional tests and to assess the impact of definitive diagnosis on the clinical management and genetic counselling of these families. METHODS This was a ambi-directional study conducted at Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi. The study comprised 227 patients (prospective cohort - 126, retrospective cohort - 101) in whom NGS based tests were performed. RESULTS The mean age of study cohort was 4.5 ± 4.4 y (2.5 mo to 37.3 y). The male: female ratio was 1.6:1. The overall diagnostic yield of NGS was 53.3% (121/227) with causative variants identified in 84 known ID genes. Autosomal recessive intellectual disability (ARID) (23.3%, 53/227) was the most common followed by autosomal dominant intellectual disability (ADID) (20.7%, 47/227) and X-linked intellectual disability (XLID) (9.2%, 21/227). The diagnostic yield was notably higher for ID plus associated condition group (55.6% vs. 20%) (p = 0.0075, Fisher's exact test) compared to isolated ID group. The impact of diagnosis on active or long-term management was observed in 17/121 (14%) and on reproductive outcomes in 26/121 (21.4%) families. CONCLUSIONS There is paucity of data on molecular genetic spectrum of ID from India. The current study identifies extensive genetic heterogeneity and the impact of NGS in patients with ID unexplained by standard genetic tests. The study identified ARID as the most common cause of ID with additional implications for reproductive outcomes. It reiterates the importance of phenotype in genetic testing.
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Affiliation(s)
- Sapna Sandal
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Ishwar Chander Verma
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Sunita Bijarnia Mahay
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Sudhisha Dubey
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - R K Sabharwal
- Department of Pediatric Neurology, Sir Ganga Ram Hospital, New Delhi, India
| | - Samarth Kulshrestha
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Renu Saxena
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Praveen Suman
- Department of Developmental Pediatrics, Sir Ganga Ram Hospital, New Delhi, India
| | - Praveen Kumar
- Department of Pediatric Neurology, Sir Ganga Ram Hospital, New Delhi, India
| | - Ratna Dua Puri
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India.
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Fortin O, Mulkey SB, Fraser JL. Advancing fetal diagnosis and prognostication using comprehensive prenatal phenotyping and genetic testing. Pediatr Res 2024:10.1038/s41390-024-03343-9. [PMID: 38937640 DOI: 10.1038/s41390-024-03343-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 05/14/2024] [Accepted: 06/04/2024] [Indexed: 06/29/2024]
Abstract
Prenatal diagnoses of congenital malformations have increased significantly in recent years with use of high-resolution prenatal imaging. Despite more precise radiological diagnoses, discussions with expectant parents remain challenging because congenital malformations are associated with a wide spectrum of outcomes. Comprehensive prenatal genetic testing has become an essential tool that improves the accuracy of prognostication. Testing strategies include chromosomal microarray, exome sequencing, and genome sequencing. The diagnostic yield varies depending on the specific malformations, severity of the abnormalities, and multi-organ involvement. The utility of prenatal genetic diagnosis includes increased diagnostic clarity for clinicians and families, informed pregnancy decision-making, neonatal care planning, and reproductive planning. Turnaround time for results of comprehensive genetic testing remains a barrier, especially for parents that are decision-making, although this has improved over time. Uncertainty inherent to many genetic testing results is a challenge. Appropriate genetic counseling is essential for parents to understand the diagnosis and prognosis and to make informed decisions. Recent research has investigated the yield of exome or genome sequencing in structurally normal fetuses, both with non-invasive screening methods and invasive diagnostic testing; the prenatal diagnostic community must evaluate and analyze the significant ethical considerations associated with this practice prior to generalizing its use. IMPACT: Reviews available genetic testing options during the prenatal period in detail. Discusses the impact of prenatal genetic testing on care using case-based examples. Consolidates the current literature on the yield of genetic testing for prenatal diagnosis of congenital malformations.
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Affiliation(s)
- Olivier Fortin
- Zickler Family Prenatal Pediatrics Institute, Children's National Hospital, Washington, DC, USA
| | - Sarah B Mulkey
- Zickler Family Prenatal Pediatrics Institute, Children's National Hospital, Washington, DC, USA
- Department of Neurology and Rehabilitation Medicine, George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Jamie L Fraser
- Zickler Family Prenatal Pediatrics Institute, Children's National Hospital, Washington, DC, USA.
- Rare Disease Institute, Children's National Hospital, Washington, DC, USA.
- Center for Genetic Medicine Research, Children's National Hospital, Washington, DC, USA.
- Department of Pediatrics, George Washington University School of Medicine and Health Sciences, Washington, DC, USA.
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28
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Chong JX, Berger SI, Baxter S, Smith E, Xiao C, Calame DG, Hawley MH, Rivera-Munoz EA, DiTroia S, Bamshad MJ, Rehm HL. Considerations for reporting variants in novel candidate genes identified during clinical genomic testing. Genet Med 2024; 26:101199. [PMID: 38944749 DOI: 10.1016/j.gim.2024.101199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 06/18/2024] [Accepted: 06/21/2024] [Indexed: 07/01/2024] Open
Abstract
Since the first novel gene discovery for a Mendelian condition was made via exome sequencing, the rapid increase in the number of genes known to underlie Mendelian conditions coupled with the adoption of exome (and more recently, genome) sequencing by diagnostic testing labs has changed the landscape of genomic testing for rare diseases. Specifically, many individuals suspected to have a Mendelian condition are now routinely offered clinical ES. This commonly results in a precise genetic diagnosis but frequently overlooks the identification of novel candidate genes. Such candidates are also less likely to be identified in the absence of large-scale gene discovery research programs. Accordingly, clinical laboratories have both the opportunity, and some might argue a responsibility, to contribute to novel gene discovery, which should, in turn, increase the diagnostic yield for many conditions. However, clinical diagnostic laboratories must necessarily balance priorities for throughput, turnaround time, cost efficiency, clinician preferences, and regulatory constraints and often do not have the infrastructure or resources to effectively participate in either clinical translational or basic genome science research efforts. For these and other reasons, many laboratories have historically refrained from broadly sharing potentially pathogenic variants in novel genes via networks such as Matchmaker Exchange, much less reporting such results to ordering providers. Efforts to report such results are further complicated by a lack of guidelines for clinical reporting and interpretation of variants in novel candidate genes. Nevertheless, there are myriad benefits for many stakeholders, including patients/families, clinicians, and researchers, if clinical laboratories systematically and routinely identify, share, and report novel candidate genes. To facilitate this change in practice, we developed criteria for triaging, sharing, and reporting novel candidate genes that are most likely to be promptly validated as underlying a Mendelian condition and translated to use in clinical settings.
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Affiliation(s)
- Jessica X Chong
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA; Brotman-Baty Institute for Precision Medicine, Seattle, WA.
| | - Seth I Berger
- Center for Genetic Medicine Research, Children's National Research Institute, Washington, DC
| | - Samantha Baxter
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Erica Smith
- Department of Clinical Diagnostics, Ambry Genetics, Aliso Viejo, CA
| | - Changrui Xiao
- Department of Neurology, University of California Irvine, Orange, CA
| | - Daniel G Calame
- Department of Pediatrics, Division of Pediatric Neurology and Developmental Neurosciences, Baylor College of Medicine, Houston, TX
| | | | | | - Stephanie DiTroia
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Michael J Bamshad
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA; Brotman-Baty Institute for Precision Medicine, Seattle, WA; Department of Pediatrics, Division of Genetic Medicine, Seattle Children's Hospital, Seattle, WA
| | - Heidi L Rehm
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
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29
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Coleman TF, Pugh J, Kelley WV, East KM, Greve V, Finnila CR, Henson A, Korf BR, Barsh GS, Cooper GM, Cochran ME. Errors in genome sequencing result disclosures: A randomized controlled trial comparing neonatology non-genetics healthcare professionals and genetic counselors. Genet Med 2024; 26:101198. [PMID: 38943479 DOI: 10.1016/j.gim.2024.101198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 06/18/2024] [Accepted: 06/21/2024] [Indexed: 07/01/2024] Open
Abstract
PURPOSE We compared the rate of errors in genome sequencing (GS) result disclosures by genetic counselors (GC) and trained non-genetics healthcare professionals (NGHPs) in SouthSeq, a randomized trial utilizing GS in critically ill infants. METHODS Over 400 recorded GS result disclosures were analyzed for major and minor errors. We used Fisher's exact test to compare error rates between GCs and NGHPs and performed a qualitative content analysis to characterize error themes. RESULTS Major errors were identified in 7.5% of disclosures by NGHPs and in no disclosures by GCs. Minor errors were identified in 32.1% of disclosures by NGHPs and in 11.4% of disclosures by GCs. Although most disclosures lacked errors, NGHPs were significantly more likely to make any error than GCs for all result types (positive, negative, or uncertain). Common major error themes include omission of critical information, overstating a negative result, and overinterpreting an uncertain result. The most common minor error was failing to disclose negative secondary findings. CONCLUSION Trained NGHPs made clinically significant errors in GS result disclosures. Characterizing common errors in result disclosure can illuminate gaps in education to inform the development of future genomics training and alternative service delivery models.
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Affiliation(s)
| | - Jada Pugh
- HudsonAlpha Institute for Biotechnology, Huntsville, AL
| | | | - Kelly M East
- HudsonAlpha Institute for Biotechnology, Huntsville, AL
| | | | | | - Ava Henson
- HudsonAlpha Institute for Biotechnology, Huntsville, AL; Graduate School of Biomedical Sciences, University of Texas MD Anderson Cancer Center UTHealth Houston, Houston, TX
| | - Bruce R Korf
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL
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30
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Velasco HM, Bertoli-Avella A, Jaramillo CJ, Cardona DS, González LA, Vanegas MN, Arango JPV, Buitrago CA, González JAG, Marcello J, Bauer P, Moncada JE. Facing the challenges to shorten the diagnostic odyssey: first Whole Genome Sequencing experience of a Colombian cohort with suspected rare diseases. Eur J Hum Genet 2024:10.1038/s41431-024-01609-8. [PMID: 38909121 DOI: 10.1038/s41431-024-01609-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 03/04/2024] [Accepted: 04/10/2024] [Indexed: 06/24/2024] Open
Abstract
Exome and genome sequencing (ES/GS) are routinely used for the diagnosis of genetic diseases in developed countries. However, their implementation is limited in countries from Latin America. We aimed to describe the results of GS in patients with suspected rare genetic diseases in Colombia. We studied 501 patients from 22 healthcare sites from January to December 2022. GS was performed in the index cases using dried blood spots on filtercards. Ancestry analysis was performed under iAdmix. Multiomic testing was performed when needed (biomarker, enzymatic activity, RNA-seq). All tests were performed at an accredited genetic laboratory. Ethnicity prediction data confirmed that 401 patients (80%) were mainly of Amerindian origin. A genetic diagnosis was established for 142 patients with a 28.3% diagnostic yield. The highest diagnostic yield was achieved for pathologies with a metabolic component and syndromic disorders (p < 0.001). Young children had a median of 1 year of diagnostic odyssey, while the median time for adults was significantly longer (15 years). Patients with genetic syndromes have spent more than 75% of their life without a diagnosis, while for patients with neurologic and neuromuscular diseases, the time of the diagnostic odyssey tended to decrease with age. Previous testing, specifically karyotyping or chromosomal microarray were significantly associated with a longer time to reach a definitive diagnosis (p < 0.01). Furthermore, one out of five patients that had an ES before could be diagnosed by GS. The Colombian genome project is the first Latin American study reporting the experience of systematic use of diagnostic GS in rare diseases.
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Affiliation(s)
- Harvy Mauricio Velasco
- Personalized Medicine Group, Unidad de Bioentendimiento, Bioscience Center, Ayudas Diagnósticas SURA, Medellín, Colombia.
| | | | - Carolina Jaramillo Jaramillo
- Sura Omics Science Center, Unidad de Bioentendimiento, Bioscience Center, Ayudas Diagnósticas SURA, Medellín, Colombia
| | - Danny Styvens Cardona
- Data Science Department, Bioscience Center, Ayudas Diagnósticas SURA, Medellín, Colombia
| | - Leonel Andrés González
- Personalized Medicine Group, Unidad de Bioentendimiento, Bioscience Center, Ayudas Diagnósticas SURA, Medellín, Colombia
| | - Melisa Naranjo Vanegas
- Medical Imaging & AI in Health SURA, Bioscience Center, Ayudas Diagnósticas SURA, Medellín, Colombia
| | | | - Cesar Augusto Buitrago
- Personalized Medicine Group, Unidad de Bioentendimiento, Bioscience Center, Ayudas Diagnósticas SURA, Medellín, Colombia
| | | | | | - Peter Bauer
- CENTOGENE GmbH, Rostock, Germany
- University Hospital of Rostock, Hematology, Oncology, and Palliative Medicine, Rostock, Germany
| | - Juliana Espinosa Moncada
- Sura Omics Science Center, Unidad de Bioentendimiento, Bioscience Center, Ayudas Diagnósticas SURA, Medellín, Colombia
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31
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Chong JX, Berger SI, Baxter S, Smith E, Xiao C, Calame DG, Hawley MH, Rivera-Munoz EA, DiTroia S, Bamshad MJ, Rehm HL. Considerations for reporting variants in novel candidate genes identified during clinical genomic testing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.05.579012. [PMID: 38370830 PMCID: PMC10871197 DOI: 10.1101/2024.02.05.579012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Since the first novel gene discovery for a Mendelian condition was made via exome sequencing (ES), the rapid increase in the number of genes known to underlie Mendelian conditions coupled with the adoption of exome (and more recently, genome) sequencing by diagnostic testing labs has changed the landscape of genomic testing for rare disease. Specifically, many individuals suspected to have a Mendelian condition are now routinely offered clinical ES. This commonly results in a precise genetic diagnosis but frequently overlooks the identification of novel candidate genes. Such candidates are also less likely to be identified in the absence of large-scale gene discovery research programs. Accordingly, clinical laboratories have both the opportunity, and some might argue a responsibility, to contribute to novel gene discovery which should in turn increase the diagnostic yield for many conditions. However, clinical diagnostic laboratories must necessarily balance priorities for throughput, turnaround time, cost efficiency, clinician preferences, and regulatory constraints, and often do not have the infrastructure or resources to effectively participate in either clinical translational or basic genome science research efforts. For these and other reasons, many laboratories have historically refrained from broadly sharing potentially pathogenic variants in novel genes via networks like Matchmaker Exchange, much less reporting such results to ordering providers. Efforts to report such results are further complicated by a lack of guidelines for clinical reporting and interpretation of variants in novel candidate genes. Nevertheless, there are myriad benefits for many stakeholders, including patients/families, clinicians, researchers, if clinical laboratories systematically and routinely identify, share, and report novel candidate genes. To facilitate this change in practice, we developed criteria for triaging, sharing, and reporting novel candidate genes that are most likely to be promptly validated as underlying a Mendelian condition and translated to use in clinical settings.
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Affiliation(s)
- Jessica X. Chong
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, 1959 NE Pacific Street, Box 357371, Seattle, WA, 98195, USA
- Brotman-Baty Institute for Precision Medicine, 1959 NE Pacific Street, Box 357657, Seattle, WA, 98195, USA
| | - Seth I. Berger
- Center for Genetic Medicine Research, Children’s National Research Institute, 111 Michigan Ave, NW, Washington, DC, 20010, USA
| | - Samantha Baxter
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02141, USA
| | - Erica Smith
- Department of Clinical Diagnostics, Ambry Genetics, 15 Argonaut, Aliso Viejo, CA, 92656, USA
| | - Changrui Xiao
- Department of Neurology, University of California Irvine, 200 South Manchester Ave. St 206E, Orange, CA, 92868, USA
| | - Daniel G. Calame
- Department of Pediatrics, Division of Pediatric Neurology and Developmental Neurosciences, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Megan H. Hawley
- Clinical Operations, Invitae, 485F US-1 Suite 110, Iselin, NJ, 08830, USA
| | - E. Andres Rivera-Munoz
- Department of Molecular and Human Genetics, Baylor College of Medicine, 1 Baylor Plaza T605, Houston, TX, 77030, USA
| | - Stephanie DiTroia
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02141, USA
| | | | - Michael J. Bamshad
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, 1959 NE Pacific Street, Box 357371, Seattle, WA, 98195, USA
- Brotman-Baty Institute for Precision Medicine, 1959 NE Pacific Street, Box 357657, Seattle, WA, 98195, USA
- Department of Pediatrics, Division of Genetic Medicine, Seattle Children’s Hospital, Seattle, WA, 98195, USA
| | - Heidi L. Rehm
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02141, USA
- Center for Genomic Medicine, Massachusetts General Hospital, 185 Cambridge St, Boston, MA, 02114, USA
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32
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Zhang F, Gu Q, Song J, Zhao Y, Wang Z, Men S, Wang L. Prenatal diagnosis and family analysis of 17q12 microdeletion syndrome with fetal renal abnormalities. Front Genet 2024; 15:1401315. [PMID: 38957807 PMCID: PMC11217314 DOI: 10.3389/fgene.2024.1401315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 05/23/2024] [Indexed: 07/04/2024] Open
Abstract
Purpose To analyze the prenatal diagnosis, parental verification, and pregnancy outcomes of three fetuses with 17ql2 microdeletion syndrome. Methods We retrospectively reviewed 46 singleton pregnancies with anomalies in the urinary system who underwent amniocentesis from Feb 2022 to October 2023 in the Prenatal Diagnosis Center of Lianyungang Maternal and Child Health Hospital. These fetuses were subjected to chromosomal microarray analysis (CMA) and/or trio whole-exome sequencing (Trio-WES). We specifically evaluated these cases' prenatal renal ultrasound findings and clinical characteristics of the affected parents. Results Three fetuses were diagnosed as 17q12 microdeletions, and the detection rate was 6.5% in fetuses with anomalies in the urinary system (3/46). The heterogeneous deletions range from 1.494 to 1.66 Mb encompassing the complete hepatocyte nuclear factor 1 homeobox B (HNF1B) gene. Fetuses with 17q12 deletion exhibited varied renal phenotypes. Moreover, the clinical phenotypes of the affected parents differed greatly in the two cases (case 2 and case 3) in which the deletion was inherited. For case 3, the mother manifested classic symptoms of 17q12 deletion syndrome as well as unreported characteristics, such as very high myopia. Conclusion Our findings demonstrate the necessity and significance of offering prenatal genetic testing when various renal anomalies are detected. In addition, our study broadens the phenotypic spectrum of 17q12 deletions. Most importantly, our findings may allow timely supportive genetic counseling and guidance for pregnancy in affected families, e.g., with the help of preimplantation genetic testing (PGT).
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Affiliation(s)
| | | | | | | | | | | | - Leilei Wang
- Department of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, China
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33
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Ilic N, Maric N, Maver A, Armengol L, Kravljanac R, Cirkovic J, Krstic J, Radivojevic D, Cirkovic S, Ostojic S, Krasic S, Paripovic A, Vukomanovic V, Peterlin B, Maric G, Sarajlija A. Reverse Phenotyping after Whole-Exome Sequencing in Children with Developmental Delay/Intellectual Disability-An Exception or a Necessity? Genes (Basel) 2024; 15:789. [PMID: 38927725 PMCID: PMC11203244 DOI: 10.3390/genes15060789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Revised: 06/11/2024] [Accepted: 06/12/2024] [Indexed: 06/28/2024] Open
Abstract
This study delves into the diagnostic yield of whole-exome sequencing (WES) in pediatric patients presenting with developmental delay/intellectual disability (DD/ID), while also exploring the utility of Reverse Phenotyping (RP) in refining diagnoses. A cohort of 100 pediatric patients underwent WES, yielding a diagnosis in 66% of cases. Notably, RP played a significant role in cases with negative prior genetic testing, underscoring its significance in complex diagnostic scenarios. The study revealed a spectrum of genetic conditions contributing to DD/ID, illustrating the heterogeneity of etiological factors. Despite challenges, WES demonstrated effectiveness, particularly in cases with metabolic abnormalities. Reverse phenotyping was indicated in half of the patients with positive WES findings. Neural network models exhibited moderate-to-exceptional predictive abilities for aiding in patient selection for WES and RP. These findings emphasize the importance of employing comprehensive genetic approaches and RP in unraveling the genetic underpinnings of DD/ID, thereby facilitating personalized management and genetic counseling for affected individuals and families. This research contributes insights into the genetic landscape of DD/ID, enhancing our understanding and guiding clinical practice in this particular field of clinical genetics.
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Affiliation(s)
- Nikola Ilic
- Clinical Genetics Outpatient Clinic, Mother and Child Health Care Institute of Serbia “Dr Vukan Cupic”, 11070 Belgrade, Serbia; (N.I.); (J.C.); (J.K.)
| | - Nina Maric
- Clinic for Children Diseases, University Clinical Center of the Republic of Srpska, Banja Luka 78000, Bosnia and Herzegovina;
| | - Ales Maver
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia; (A.M.); (B.P.)
| | - Lluis Armengol
- CIBER en Epidemiología y Salud Pública (CIBERESP), Genes and Disease Program, Center for Genomic Regulation (CRG-UPF), 08003 Barcelona, Spain;
| | - Ruzica Kravljanac
- Department of Neurology, Mother and Child Health Care Institute of Serbia “Dr Vukan Cupic”, 11070 Belgrade, Serbia; (R.K.); (S.O.)
- Department of Pediatrics, Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia; (A.P.); (V.V.)
| | - Jana Cirkovic
- Clinical Genetics Outpatient Clinic, Mother and Child Health Care Institute of Serbia “Dr Vukan Cupic”, 11070 Belgrade, Serbia; (N.I.); (J.C.); (J.K.)
| | - Jovana Krstic
- Clinical Genetics Outpatient Clinic, Mother and Child Health Care Institute of Serbia “Dr Vukan Cupic”, 11070 Belgrade, Serbia; (N.I.); (J.C.); (J.K.)
| | - Danijela Radivojevic
- Laboratory of Medical Genetics, Mother and Child Health Care Institute of Serbia “Dr Vukan Cupic”, 11070 Belgrade, Serbia; (D.R.); (S.C.)
| | - Sanja Cirkovic
- Laboratory of Medical Genetics, Mother and Child Health Care Institute of Serbia “Dr Vukan Cupic”, 11070 Belgrade, Serbia; (D.R.); (S.C.)
| | - Slavica Ostojic
- Department of Neurology, Mother and Child Health Care Institute of Serbia “Dr Vukan Cupic”, 11070 Belgrade, Serbia; (R.K.); (S.O.)
- Department of Pediatrics, Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia; (A.P.); (V.V.)
| | - Stasa Krasic
- Department of Cardiology, Mother and Child Health Care Institute of Serbia “Dr Vukan Cupic”, 11070 Belgrade, Serbia;
| | - Aleksandra Paripovic
- Department of Pediatrics, Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia; (A.P.); (V.V.)
- Department of Nephrology, Mother and Child Health Care Institute of Serbia “Dr Vukan Cupic”, 11070 Belgrade, Serbia
| | - Vladislav Vukomanovic
- Department of Pediatrics, Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia; (A.P.); (V.V.)
- Department of Cardiology, Mother and Child Health Care Institute of Serbia “Dr Vukan Cupic”, 11070 Belgrade, Serbia;
| | - Borut Peterlin
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia; (A.M.); (B.P.)
| | - Gorica Maric
- Institute of Epidemiology, Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia;
| | - Adrijan Sarajlija
- Clinical Genetics Outpatient Clinic, Mother and Child Health Care Institute of Serbia “Dr Vukan Cupic”, 11070 Belgrade, Serbia; (N.I.); (J.C.); (J.K.)
- Department of Pediatrics, Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia; (A.P.); (V.V.)
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Freeman M, Fakhori N, Monteil D. Progressive spasticity and developmental delay in an infant with a CTNNB1 mutation. BMJ Case Rep 2024; 17:e260856. [PMID: 38871641 DOI: 10.1136/bcr-2024-260856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2024] Open
Abstract
We present an infant referred to Developmental Paediatrics for delays, slow growth, hypotonia, esotropia and spasticity. Over the course of 2 months, the infant's exam progressed, demonstrating worsening spasticity and tonal changes in the setting of a normal brain MRI with acquired microcephaly. Genetic testing demonstrated a pathogenic CTNNB1 nonsense mutation. Following the discovery of the underlying cause for the child's clinical picture, the child was evaluated by therapeutic services and neurology, which was initially only available via asynchronous telehealth, due to a resource limited area. Cerebral palsy is a nonprogressive neurodevelopmental disorder and, when associated with developmental delay, qualifies for further genetic investigation into the underlying aetiology. Genetic testing recommendations exist for developmental delay, but there is no current algorithm regarding testing for cerebral palsy. Education and clear guidelines on genetic testing allow for better prognostication and potential treatment in cases of cerebral palsy, especially when associated with other disorders.
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Affiliation(s)
- Meagan Freeman
- Pediatrics, Landstuhl Regional Medical Center, Landstuhl Kirchberg, Germany
| | - Nina Fakhori
- U.S.Army Health Clinic Vilseck, Vilseck, Germany
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35
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Harrington CN, Morales A, Bernstein JA, Calderwood L. Implications of Provider Specialty, Test Type, and Demographic Factors on Genetic Testing Outcomes for Patients with Autism Spectrum Disorder. J Autism Dev Disord 2024:10.1007/s10803-024-06423-1. [PMID: 38858309 DOI: 10.1007/s10803-024-06423-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/23/2024] [Indexed: 06/12/2024]
Abstract
A minority of patients with autism spectrum disorder (ASD) are offered genetic testing by their providers or referred for genetics evaluation despite published guidelines and consensus statements supporting genetics-informed care for this population. This study aimed to investigate the ordering habits of providers of different specialties and to additionally assess the diagnostic utility of genetic testing by test type, patient sex, and race and ethnicity. We retrospectively analyzed data associated with orders for the indication of ASD from a large clinical laboratory over 6 years (2017-2022). Geneticists and neurologists were more likely than other specialists to order exome sequencing and neurodevelopmental (NDD) panel testing while other providers were more likely to order chromosomal microarray (CMA) and Fragile X testing. Exome had the highest diagnostic yield (24.5%), followed by NDD panel (6.4%), CMA (6.2%), and Fragile X testing (0.4%). Females were 1.4x (95% CI: 1.2-1.7) more likely than males to receive a genetic diagnosis. However, for Fragile X, males had a higher diagnostic yield than females (0.4% vs 0.2%). Our findings highlight the need to enable non-genetics providers to order comprehensive genetic testing or promote referral to genetics following negative CMA and/or Fragile X testing. Our data supports that ASD testing should include exome, CMA, and other clinically indicated tests, as first-tier tests, with the consideration of panel testing, in cases where exome sequencing is not an option. Lastly, our study helps to inform expectations for genetic testing yield by test type and patient presentation.
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Affiliation(s)
- Caitlin N Harrington
- Department of Pediatrics, Division of Medical Genetics, Stanford University School of Medicine, Stanford, CA, USA.
- Stanford Medicine Children's Health, Stanford, CA, USA.
| | - Ana Morales
- Translational Health Sciences Program, School of Medicine and Health Sciences, The George Washington University, Washington, DC, USA
| | - Jonathan A Bernstein
- Department of Pediatrics, Division of Medical Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Medicine Children's Health, Stanford, CA, USA
| | - Laurel Calderwood
- Department of Pediatrics, Division of Medical Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Medicine Children's Health, Stanford, CA, USA
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Hansford JR, Das A, McGee RB, Nakano Y, Brzezinski J, Scollon SR, Rednam SP, Schienda J, Michaeli O, Kim SY, Greer MLC, Weksberg R, Stewart DR, Foulkes WD, Tabori U, Pajtler KW, Pfister SM, Brodeur GM, Kamihara J. Update on Cancer Predisposition Syndromes and Surveillance Guidelines for Childhood Brain Tumors. Clin Cancer Res 2024; 30:2342-2350. [PMID: 38573059 PMCID: PMC11147702 DOI: 10.1158/1078-0432.ccr-23-4033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 02/27/2024] [Accepted: 04/04/2024] [Indexed: 04/05/2024]
Abstract
Tumors of the central nervous system (CNS) comprise the second most common group of neoplasms in childhood. The incidence of germline predisposition among children with brain tumors continues to grow as our knowledge on disease etiology increases. Some children with brain tumors may present with nonmalignant phenotypic features of specific syndromes (e.g., nevoid basal cell carcinoma syndrome, neurofibromatosis type 1 and type 2, DICER1 syndrome, and constitutional mismatch-repair deficiency), while others may present with a strong family history of cancer (e.g., Li-Fraumeni syndrome) or with a rare tumor commonly found in the context of germline predisposition (e.g., rhabdoid tumor predisposition syndrome). Approximately 50% of patients with a brain tumor may be the first in a family identified to have a predisposition. The past decade has witnessed a rapid expansion in our molecular understanding of CNS tumors. A significant proportion of CNS tumors are now well characterized and known to harbor specific genetic changes that can be found in the germline. Additional novel predisposition syndromes are also being described. Identification of these germline syndromes in individual patients has not only enabled cascade testing of family members and early tumor surveillance but also increasingly affected cancer management in those patients. Therefore, the AACR Cancer Predisposition Working Group chose to highlight these advances in CNS tumor predisposition and summarize and/or generate surveillance recommendations for established and more recently emerging pediatric brain tumor predisposition syndromes.
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Affiliation(s)
- Jordan R Hansford
- Michael Rice Children's Hematology and Oncology Center, Women's and Children's Hospital; South Australia Health and Medical Research Institute; South Australia ImmunoGenomics Cancer Institute, University of Adelaide, Adelaide, South Australia, Australia
| | - Anirban Das
- Division of Hematology/Oncology, The Hospital for Sick Children; SickKids Research Institute; Department of Pediatrics, University of Toronto, Toronto, Ontario, Canada
| | - Rose B McGee
- Department of Oncology, Division of Cancer Predisposition, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Yoshiko Nakano
- Department of Pediatrics, Division of Hematology/Oncology, Baylor College of Medicine, Houston, Texas
| | - Jack Brzezinski
- Division of Hematology/Oncology, The Hospital for Sick Children; SickKids Research Institute; Department of Pediatrics, University of Toronto, Toronto, Ontario, Canada
| | - Sarah R Scollon
- Department of Pediatrics, Division of Hematology/Oncology, Baylor College of Medicine, Houston, Texas
| | - Surya P Rednam
- Department of Pediatrics, Division of Hematology/Oncology, Baylor College of Medicine, Houston, Texas
| | - Jaclyn Schienda
- Department of Pediatric Oncology, Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School, Boston, Massachusetts
| | - Orli Michaeli
- Division of Hematology/Oncology, Schneider Children's Medical Center of Israel, Petach Tikva, Israel
| | - Sun Young Kim
- Division of Human Genetics, Department of Pediatrics, Cincinnati Children's Hospital Center, Cincinnati, Ohio
| | - Mary-Louise C Greer
- Department of Diagnostic and Interventional Radiology, The Hospital for Sick Children/Department of Medical Imaging, University of Toronto, Toronto, Ontario, Canada
| | - Rosanna Weksberg
- Division of Clinical and Metabolic Genetics, Department of Pediatrics, Hospital for Sick Children and University of Toronto, Toronto, Ontario, Canada
| | - Douglas R Stewart
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland
| | - William D Foulkes
- Department of Human Genetics, McGill University, and Division of Medical Genetics, Departments of Specialized Medicine, McGill University Health Centre and Jewish General Hospital, Montreal, Quebec, Canada
| | - Uri Tabori
- Division of Hematology/Oncology, The Hospital for Sick Children; SickKids Research Institute; Department of Pediatrics, University of Toronto, Toronto, Ontario, Canada
| | - Kristian W Pajtler
- Division of Pediatric Neurooncology, Hopp Children's Cancer Center Heidelberg (KiTZ); German Cancer Research Center Heidelberg (DKFZ) and Heidelberg University Hospital, Heidelberg; National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Stefan M Pfister
- Division of Pediatric Neurooncology, Hopp Children's Cancer Center Heidelberg (KiTZ); German Cancer Research Center Heidelberg (DKFZ) and Heidelberg University Hospital, Heidelberg; National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Garrett M Brodeur
- Department of Pediatrics, Division of Oncology, the Children's Hospital of Philadelphia, and the University of Pennsylvania/Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Junne Kamihara
- Department of Pediatric Oncology, Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School, Boston, Massachusetts
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Zhang J, Xu Y, Liu Y, Yue L, Jin H, Chen Y, Wang D, Wang M, Chen G, Yang L, Zhang G, Zhang X, Li S, Zhao H, Zhao Y, Niu G, Gao Y, Cai Z, Yang F, Zhu C, Zhu D. Genetic Testing for Global Developmental Delay in Early Childhood. JAMA Netw Open 2024; 7:e2415084. [PMID: 38837156 PMCID: PMC11154162 DOI: 10.1001/jamanetworkopen.2024.15084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Accepted: 04/03/2024] [Indexed: 06/06/2024] Open
Abstract
Importance Global developmental delay (GDD) is characterized by a complex etiology, diverse phenotypes, and high individual heterogeneity, presenting challenges for early clinical etiologic diagnosis. Cognitive impairment is the core symptom, and despite the pivotal role of genetic factors in GDD development, the understanding of them remains limited. Objectives To assess the utility of genetic detection in patients with GDD and to examine the potential molecular pathogenesis of GDD to identify targets for early intervention. Design, Setting, and Participants This multicenter, prospective cohort study enrolled patients aged 12 to 60 months with GDD from 6 centers in China from July 4, 2020, to August 31, 2023. Participants underwent trio whole exome sequencing (trio-WES) coupled with copy number variation sequencing (CNV-seq). Bioinformatics analysis was used to unravel pathogenesis and identify therapeutic targets. Main Outcomes and Measures The main outcomes of this study involved enhancing the rate of positive genetic diagnosis for GDD, broadening the scope of genetic testing indications, and investigating the underlying pathogenesis. The classification of children into levels of cognitive impairment was based on the developmental quotient assessed using the Gesell scale. Results The study encompassed 434 patients with GDD (262 [60%] male; mean [SD] age, 25.75 [13.24] months) with diverse degrees of cognitive impairment: mild (98 [23%]), moderate (141 [32%]), severe (122 [28%]), and profound (73 [17%]). The combined use of trio-WES and CNV-seq resulted in a 61% positive detection rate. Craniofacial abnormalities (odds ratio [OR], 2.27; 95% CI, 1.45-3.56), moderate or severe cognitive impairment (OR, 1.69; 95% CI, 1.05-2.70), and age between 12 and 24 months (OR, 1.57; 95% CI, 1.05-2.35) were associated with a higher risk of carrying genetic variants. Additionally, bioinformatics analysis suggested that genetic variants may induce alterations in brain development and function, which may give rise to cognitive impairment. Moreover, an association was found between the dopaminergic pathway and cognitive impairment. Conclusions and Relevance In this cohort study of patients with GDD, combining trio-WES with CNV-seq was a demonstrable, instrumental strategy for advancing the diagnosis of GDD. The close association among genetic variations, brain development, and clinical phenotypes contributed valuable insights into the pathogenesis of GDD. Notably, the dopaminergic pathway emerged as a promising focal point for potential targets in future precision medical interventions for GDD.
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Affiliation(s)
- Jiamei Zhang
- Department of Rehabilitation Medicine, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yiran Xu
- Henan Key Laboratory of Child Brain Injury and Henan Pediatric Clinical Research Center, Institute of Neuroscience and Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yun Liu
- Kunming Children’s Hospital, Kunming, China
| | - Ling Yue
- Department of Neurological Rehabilitation, Children’s Hospital of Hebei Province, Shijiazhuang, China
| | - Hongfang Jin
- Qinghai Provincial Women and Children’s Hospital, Xining, China
| | | | - Dong Wang
- Department of Pediatric Neurology, Xi’an Children’s Hospital, Xi’an, China
| | - Mingmei Wang
- Department of Rehabilitation Medicine, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Gongxun Chen
- Department of Rehabilitation Medicine, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Lei Yang
- Department of Rehabilitation Medicine, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Guangyu Zhang
- Department of Rehabilitation Medicine, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xiaoli Zhang
- Department of Pediatric Neurology, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Sansong Li
- Department of Rehabilitation Medicine, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Huiling Zhao
- Department of Rehabilitation Medicine, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yunxia Zhao
- Department of Rehabilitation Medicine, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Guohui Niu
- Department of Rehabilitation Medicine, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yongqiang Gao
- Department of Rehabilitation Medicine, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zhijun Cai
- Department of Rehabilitation Medicine, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | | | - Changlian Zhu
- Henan Key Laboratory of Child Brain Injury and Henan Pediatric Clinical Research Center, Institute of Neuroscience and Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Center for Brain Repair and Rehabilitation, Institute of Neuroscience and Physiology, University of Gothenburg, Gothenburg, Sweden
| | - Dengna Zhu
- Department of Rehabilitation Medicine, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Key Laboratory of Child Brain Injury and Henan Pediatric Clinical Research Center, Institute of Neuroscience and Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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38
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Vuocolo B, German RJ, Lalani SR, Murali CN, Bacino CA, Baskin S, Littlejohn R, Odom JD, McLean S, Schmid C, Nutter M, Stuebben M, Magness E, Juarez O, El Achi D, Mitchell B, Glinton KE, Robak L, Nagamani SCS, Saba L, Ritenour A, Zhang L, Streff H, Chan K, Kemere KJ, Carter K, Owen N, Vossaert L, Liu P, Bellen H, Wangler MF. Improving access to exome sequencing in a medically underserved population through the Texome Project. Genet Med 2024; 26:101102. [PMID: 38431799 PMCID: PMC11161315 DOI: 10.1016/j.gim.2024.101102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 02/16/2024] [Accepted: 02/21/2024] [Indexed: 03/05/2024] Open
Abstract
PURPOSE Genomic medicine can end diagnostic odysseys for patients with complex phenotypes; however, limitations in insurance coverage and other systemic barriers preclude individuals from accessing comprehensive genetics evaluation and testing. METHODS The Texome Project is a 4-year study that reduces barriers to genomic testing for individuals from underserved and underrepresented populations. Participants with undiagnosed, rare diseases who have financial barriers to obtaining exome sequencing (ES) clinically are enrolled in the Texome Project. RESULTS We highlight the Texome Project process and describe the outcomes of the first 60 ES results for study participants. Participants received a genetic evaluation, ES, and return of results at no cost. We summarize the psychosocial or medical implications of these genetic diagnoses. Thus far, ES provided molecular diagnoses for 18 out of 60 (30%) of Texome participants. Plus, in 11 out of 60 (18%) participants, a partial or probable diagnosis was identified. Overall, 5 participants had a change in medical management. CONCLUSION To date, the Texome Project has recruited a racially, ethnically, and socioeconomically diverse cohort. The diagnostic rate and medical impact in this cohort support the need for expanded access to genetic testing and services. The Texome Project will continue reducing barriers to genomic care throughout the future study years.
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Affiliation(s)
- Blake Vuocolo
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX
| | - Ryan J German
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX
| | - Seema R Lalani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Chaya N Murali
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Carlos A Bacino
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Stephanie Baskin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Department of Pediatrics, Baylor College of Medicine, San Antonio, TX
| | | | - John D Odom
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Department of Pediatrics, Baylor College of Medicine, San Antonio, TX
| | - Scott McLean
- Department of Pediatrics, Baylor College of Medicine, San Antonio, TX
| | - Carrie Schmid
- Department of Pediatrics, Baylor College of Medicine, San Antonio, TX
| | - Morgan Nutter
- Department of Pediatrics, Baylor College of Medicine, San Antonio, TX
| | - Melissa Stuebben
- Department of Pediatrics, Baylor College of Medicine, San Antonio, TX
| | - Emily Magness
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Olivia Juarez
- Department of Pediatrics, Baylor College of Medicine, San Antonio, TX
| | - Dina El Achi
- Department of Pediatrics, Baylor College of Medicine, San Antonio, TX
| | - Bailey Mitchell
- Department of Pediatrics, Baylor College of Medicine, San Antonio, TX
| | - Kevin E Glinton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Laurie Robak
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Sandesh C S Nagamani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Texas Children's Hospital Department of Pathology, Houston, TX
| | - Lisa Saba
- Texas Children's Hospital Department of Pathology, Houston, TX
| | - Adasia Ritenour
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Lilei Zhang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Haley Streff
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Texas Children's Hospital Department of Pathology, Houston, TX
| | - Katie Chan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - K Jordan Kemere
- Department of Internal Medicine, Section Transition Medicine, Baylor College of Medicine and Texas Children's Hospital, Houston, TX
| | - Kent Carter
- Department of Pediatrics, University of Texas Rio Grande Valley, Harlingen, TX
| | | | | | | | - Hugo Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX
| | - Michael F Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX.
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Pucel J, Briere LC, Reuter C, Gochyyev P, LeBlanc K. Exome and genome sequencing in a heterogeneous population of patients with rare disease: Identifying predictors of a diagnosis. Genet Med 2024; 26:101115. [PMID: 38436216 PMCID: PMC11161308 DOI: 10.1016/j.gim.2024.101115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 02/24/2024] [Accepted: 02/27/2024] [Indexed: 03/05/2024] Open
Abstract
PURPOSE Exome (ES) and genome sequencing (GS) are increasingly being utilized for individuals with rare and undiagnosed diseases; however, guidelines on their use remain limited. This study aimed to identify factors associated with diagnosis by ES and/or GS in a heterogeneous population of patients with rare and undiagnosed diseases. METHODS In this case control study, we reviewed data from 400 diagnosed and 400 undiagnosed randomly selected participants in the Undiagnosed Diseases Network, all of whom had undergone ES and/or GS. We analyzed factors associated with receiving a diagnosis by ES and/or GS. RESULTS Factors associated with a decreased odds of being diagnosed included adult symptom onset, singleton sequencing, and having undergone ES and/or GS before acceptance to the Undiagnosed Diseases Network (48%, 51%, and 32% lower odds, respectively). Factors that increased the odds of being diagnosed by ES and/or GS included having primarily neurological symptoms and having undergone prior chromosomal microarray testing (44% and 59% higher odds, respectively). CONCLUSION We identified several factors that were associated with receiving a diagnosis by ES and/or GS. This will ideally inform the utilization of ES and/or GS and help manage expectations of individuals and families undergoing these tests.
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Affiliation(s)
- Jenna Pucel
- MGH Institute of Health Professions, Boston, MA.
| | - Lauren C Briere
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
| | - Chloe Reuter
- Stanford Center for Undiagnosed Diseases, Cardiovascular Medicine, Stanford University, Palo Alto, CA
| | | | - Kimberly LeBlanc
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA
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40
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Khan YN, Mahmud MIAM, Othman N, Radzuan HM, Basit S. Whole exome sequencing enables the correct diagnosis of Frank-Ter Haar syndrome in a Saudi family. Vavilovskii Zhurnal Genet Selektsii 2024; 28:326-331. [PMID: 38952703 PMCID: PMC11214900 DOI: 10.18699/vjgb-24-37] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 11/05/2023] [Accepted: 11/28/2023] [Indexed: 07/03/2024] Open
Abstract
Frank-Ter Haar syndrome (FTHS) is a rare genetic hereditary autosomal recessive disorder characterized by defective malformation of cardiovascular, craniofacial, and skeletal system. Mutations in the SH3PXD2B gene are a common cause in the development of FTHS. We recruited a family with two affected individuals (3-year-old female and 2-month-old male infant) having bilateral clubfoot. Family pedigree shows an autosomal recessive mode of inheritance. DNA was extracted from the blood samples of six members of the family. Whole exome sequencing was done for the two affected individuals and the variant was validated in the whole family by using Sanger sequencing approach. Whole exome sequencing (WES) data analysis identified a rare homozygous variant (c.280C>G; p.R94G) in the SH3PXD2B gene, and Sanger sequencing showed that the same variant perfectly segregates with the phenotype in the pedigree. Moreover, the variant is predicted to be damaging and deleterious by several computation tools. Revisiting the family members for detailed clinical analysis, we diagnosed the patients as having the typical phenotype of FTHS. This study enabled us to correctly diagnose the cases of FTHS in a family initially recruited for having bilateral clubfoot by using WES. Moreover, this study identified a novel homozygous missense variant (c.280C>G; p.R94G) in (NM_001308175.2) the SH3PXD2B gene as a causative variant for autosomal recessive FTHS. This finding supports the evidence that homozygous mutations in the SH3PXD2B gene are the main cause in the development of FTHS.
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Affiliation(s)
- Y N Khan
- Department of Basic Medical Sciences, Faculty of Medicine, International Islamic University Malaysia
| | - M Imad A M Mahmud
- Department of Basic Medical Sciences, Faculty of Medicine, International Islamic University Malaysia
| | - N Othman
- Department of Basic Medical Sciences, Faculty of Medicine, International Islamic University Malaysia
| | - H M Radzuan
- Department of Basic Medical Sciences, Faculty of Medicine, International Islamic University Malaysia
| | - S Basit
- Department of Biochemistry and Molecular Medicine, College of Medicine, Taibah University Al Madinah Al Munawara, Saudi Arabia Center for Genetics and Inherited Diseases, Taibah University Al Madinah Al Munawara, Saudi Arabia
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Hung KL. Genetic Diagnosis in Children with Developmental Delay. CHILDREN (BASEL, SWITZERLAND) 2024; 11:669. [PMID: 38929248 PMCID: PMC11201514 DOI: 10.3390/children11060669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 03/05/2024] [Indexed: 06/28/2024]
Abstract
Developmental delay (DD) has a great impact on children at the developmental stage, and is often manifested by varying degrees of motor delays, intellectual disabilities, and other defects [...].
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Affiliation(s)
- Kun-Long Hung
- Department of Pediatrics, Fu-Jen Catholic University Hospital, New Taipei City 243, Taiwan; or ; Tel.: +886-2-8512-8704; Fax: +886-2-2904-6422
- School of Medicine, Fu-Jen Catholic University, New Taipei City 242, Taiwan
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42
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Dreikorn EN, Munro C, Robin Berman N, Kunovac A, Bellissimo D, Massart MB. Case report: Early use of whole exome sequencing unveils HNRNPU-related neurodevelopmental disorder and answers additional clinical questions through reanalysis. Front Genet 2024; 15:1380552. [PMID: 38846959 PMCID: PMC11153700 DOI: 10.3389/fgene.2024.1380552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 04/26/2024] [Indexed: 06/09/2024] Open
Abstract
This case report chronicles the diagnostic odyssey and resolution of a 27-year-old female with a complex neurodevelopmental disorder (NDD) using Whole Exome Sequencing (WES). The patient presented to a precision medicine clinic with multiple diagnoses including intellectual disability, autism spectrum disorder (ASD), obsessive-compulsive disorder (OCD), tics, seizures, and pediatric autoimmune neuropsychiatric disorders associated with streptococcal infections (PANDAS). Although this patient previously had chromosomal microarray and several single-gene tests, the underlying cause of this patient's symptoms remained elusive. WES revealed a pathogenic missense mutation in the HNRNPU gene, associated with HNRNPU-related neurodevelopmental disorder (HNRNPU-NDD) and developmental and epileptic encephalopathy-54 (DEE54, OMIM: # 617391). Following this diagnoses, other treating clinicians identified additional indications for genetic testing, however, as the WES data was readily available, the clinical team was able to re-analyze the WES data to address their inquiries without requiring additional tests. This emphasizes the pivotal role of WES in expediting diagnoses, reducing costs, and providing ongoing clinical utility throughout a patient's life. Accessible WES data in primary care settings can enhance patient care by informing future genetic inquiries, enhancing coordination of care, and facilitating precision medicine interventions, thereby mitigating the burden on families and the healthcare system.
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Affiliation(s)
- Erika Nicole Dreikorn
- Primary Care Precision Medicine Clinic, UPMC, Pittsburgh, PA, United States
- Department of Family Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Christine Munro
- Primary Care Precision Medicine Clinic, UPMC, Pittsburgh, PA, United States
- Department of Family Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Natasha Robin Berman
- Primary Care Precision Medicine Clinic, UPMC, Pittsburgh, PA, United States
- Department of Family Medicine, University of Pittsburgh, Pittsburgh, PA, United States
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Zhang R, Cui X, Zhang Y, Ma H, Gao J, Zhang Y, Shu J, Cai C, Liu Y. Whole-exome sequencing as the first-tier test for patients in neonatal intensive care unit: a Chinese single-center study. BMC Pediatr 2024; 24:351. [PMID: 38778310 PMCID: PMC11110365 DOI: 10.1186/s12887-024-04820-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Accepted: 05/08/2024] [Indexed: 05/25/2024] Open
Abstract
BACKGROUND Genetic disorders significantly affect patients in neonatal intensive care units, where establishing a diagnosis can be challenging through routine tests and supplementary examinations. Whole-exome sequencing offers a molecular-based approach for diagnosing genetic disorders. This study aimed to assess the importance of whole-exome sequencing for neonates in intensive care through a retrospective observational study within a Chinese cohort. METHODS We gathered data from neonatal patients at Tianjin Children's Hospital between January 2018 and April 2021. These patients presented with acute illnesses and were suspected of having genetic disorders, which were investigated using whole-exome sequencing. Our retrospective analysis covered clinical data, genetic findings, and the correlation between phenotypes and genetic variations. RESULTS The study included 121 neonates. Disorders affected multiple organs or systems, predominantly the metabolic, neurological, and endocrine systems. The detection rate for whole-exome sequencing was 52.9% (64 out of 121 patients), identifying 84 pathogenic or likely pathogenic genetic variants in 64 neonates. These included 13 copy number variations and 71 single-nucleotide variants. The most frequent inheritance pattern was autosomal recessive (57.8%, 37 out of 64), followed by autosomal dominant (29.7%, 19 out of 64). In total, 40 diseases were identified through whole-exome sequencing. CONCLUSION This study underscores the value and clinical utility of whole-exome sequencing as a primary diagnostic tool for neonates in intensive care units with suspected genetic disorders. Whole-exome sequencing not only aids in diagnosis but also offers significant benefits to patients and their families by providing clarity in uncertain diagnostic situations.
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Affiliation(s)
- Ruiping Zhang
- Department of Neonatology, Tianjin Children's Hospital/Tianjin University Children's Hospital, Beichen District, Tianjin, China
| | - Xiaoyu Cui
- Department of Neonatology, Tianjin Children's Hospital/Tianjin University Children's Hospital, Beichen District, Tianjin, China
| | - Yan Zhang
- Department of Neonatology, Tianjin Children's Hospital/Tianjin University Children's Hospital, Beichen District, Tianjin, China
- Graduate College, Tianjin Medical University, Heping District, Tianjin, China
| | - Huiqing Ma
- Graduate College, Tianjin Medical University, Heping District, Tianjin, China
| | - Jing Gao
- Graduate College, Tianjin Medical University, Heping District, Tianjin, China
| | - Ying Zhang
- Department of Neonatology, Tianjin Children's Hospital/Tianjin University Children's Hospital, Beichen District, Tianjin, China
| | - Jianbo Shu
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital/Tianjin University Children's Hospital, Beichen District, Tianjin, China.
- Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Beichen District, Tianjin, China.
| | - Chunquan Cai
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital/Tianjin University Children's Hospital, Beichen District, Tianjin, China.
- Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Beichen District, Tianjin, China.
| | - Yang Liu
- Department of Neonatology, Tianjin Children's Hospital/Tianjin University Children's Hospital, Beichen District, Tianjin, China.
- The Pediatric Clinical College in Tianjin Medical University, Heping District, Tianjin, China.
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44
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Wu R, Li X, Meng Z, Li P, He Z, Liang L. Phenotypic and genetic analysis of children with unexplained neurodevelopmental delay and neurodevelopmental comorbidities in a Chinese cohort using trio-based whole-exome sequencing. Orphanet J Rare Dis 2024; 19:205. [PMID: 38764027 PMCID: PMC11103872 DOI: 10.1186/s13023-024-03214-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 05/10/2024] [Indexed: 05/21/2024] Open
Abstract
BACKGROUND Trio-based whole-exome sequencing (trio-WES) enables identification of pathogenic variants, including copy-number variants (CNVs), in children with unexplained neurodevelopmental delay (NDD) and neurodevelopmental comorbidities (NDCs), including autism spectrum disorder (ASD), epilepsy, and attention deficit hyperactivity disorder. Further phenotypic and genetic analysis on trio-WES-tested NDD-NDCs cases may help to identify key phenotypic factors related to higher diagnostic yield of using trio-WES and novel risk genes associated with NDCs in clinical settings. METHODS In this study, we retrospectively performed phenotypic analysis on 163 trio-WES-tested NDD-NDCs children to determine the phenotypic differences between genetically diagnosed and non-genetically diagnosed groups. Additionally, we conducted genetic analysis of ASD genes with the help of Simons Foundation for Autism Research Institute (SFARI) Gene database to identify novel possible ASD-risk genes underlying genetic NDD conditions. RESULTS Among these 163 patients, pathogenic variants were identified in 82 cases (82/163, 50.3%), including 20 cases with CNVs. By comparing phenotypic variables between genetically diagnosed group (82 cases) and non-genetically diagnosed group (81 cases) with multivariate binary logistic regression analysis, we revealed that NDD-NDCs cases presenting with severe-profound NDD [53/82 vs 17/81, adjusted-OR (95%CI): 4.865 (2.213 - 10.694), adjusted-P < 0.001] or having multiple NDCs [26/82 vs 8/81, adjusted-OR (95%CI): 3.731 (1.399 - 9.950), adjusted-P = 0.009] or accompanying ASD [64/82 vs 35/81, adjusted-OR (95%CI): 3.256 (1.479 - 7.168), adjusted-P = 0.003] and head circumference abnormality [33/82 vs 11/81, adjusted-OR (95%CI): 2.788 (1.148 - 6.774), adjusted-P = 0.024] were more likely to have a genetic diagnosis using trio-WES. Moreover, 37 genes with monogenetic variants were identified in 48 patients genetically diagnosed with NDD-ASD, and 15 dosage-sensitive genes were identified in 16 individuals with NDD-ASD carrying CNVs. Most of those genes had been proven to be ASD-related genes. However, some of them (9 genes) were not proven sufficiently to correlate with ASD. By literature review and constructing protein-protein interaction networks among these 9 candidate ASD-risk genes and 102 established ASD genes obtained from the SFARI Gene database, we identified CUL4B, KCNH1, and PLA2G6 as novel possible ASD-risk genes underlying genetic NDD conditions. CONCLUSIONS Trio-WES testing is recommended for patients with unexplained NDD-NDCs that have severe-profound NDD or multiple NDCs, particularly those with accompanying ASD and head circumference abnormality, as these independent factors may increase the likelihood of genetic diagnosis using trio-WES. Moreover, NDD patients with pathogenic variants in CUL4B, KCNH1 and PLA2G6 should be aware of potential risks of developing ASD during their disease courses.
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Affiliation(s)
- Ruohao Wu
- Department of Children's Neuro-endocrinology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, Guangdong, China
- Children's Medical Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou Guangdong, 510120, China
| | - Xiaojuan Li
- Department of Research and Molecular Diagnostics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, Guangdong, China
| | - Zhe Meng
- Department of Children's Neuro-endocrinology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, Guangdong, China
- Children's Medical Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou Guangdong, 510120, China
| | - Pinggan Li
- Department of Children's Neuro-endocrinology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, Guangdong, China
- Children's Medical Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou Guangdong, 510120, China
| | - Zhanwen He
- Department of Children's Neuro-endocrinology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, Guangdong, China.
- Children's Medical Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou Guangdong, 510120, China.
| | - Liyang Liang
- Department of Children's Neuro-endocrinology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, Guangdong, China.
- Children's Medical Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou Guangdong, 510120, China.
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Godown J, Kim EH, Everitt MD, Chung WK, Lytrivi ID, Kirmani S, Kantor PF, Ware SM, Ballweg JA, Lal AK, Bansal N, Towbin J, Lipshultz SE, Lee TM. Genetic Testing Resources and Practice Patterns Among Pediatric Cardiomyopathy Programs. Pediatr Cardiol 2024:10.1007/s00246-024-03498-6. [PMID: 38714589 DOI: 10.1007/s00246-024-03498-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 04/11/2024] [Indexed: 05/10/2024]
Abstract
The use of genetic testing has enhanced the diagnostic accuracy of heritable genetic cardiomyopathies. However, it remains unclear how genetic information is interpreted and incorporated into clinical practice for children with cardiomyopathy. The primary aim of this study was to understand how clinical practice differs regarding sequence variant classifications amongst pediatric cardiologists who treat children with cardiomyopathy. A secondary aim was to understand the availability of genetic testing and counseling resources across participating pediatric cardiomyopathy programs. An electronic survey was distributed to pediatric heart failure, cardiomyopathy, or heart transplantation physicians between August and September 2022. A total of 106 individual providers from 68 unique centers responded to the survey. Resources for genetic testing and genetic counseling vary among large pediatric cardiomyopathy programs. A minority of centers reported having a geneticist (N = 16, 23.5%) or a genetic counselor (N = 21, 31%) on faculty within the division of pediatric cardiology. A total of 9 centers reported having both (13%). Few centers (N = 13, 19%) have a formal process in place to re-engage patients who were previously discharged from cardiology follow-up if variant reclassification would alter clinical management. Clinical practice patterns were uniform in response to pathogenic or likely pathogenic variants but were more variable for variants of uncertain significance. Efforts to better incorporate genetic expertise and resources into the clinical practice of pediatric cardiomyopathy may help to standardize the interpretation of genetic information and better inform clinical decision-making surrounding heritable cardiomyopathies.
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Affiliation(s)
- Justin Godown
- Division of Pediatric Cardiology, Monroe Carell Jr. Children's Hospital at Vanderbilt, Nashville, TN, USA
- BioMarin Pharmaceutical Inc, Novato, CA, USA
| | - Emily H Kim
- Division of Pediatric Cardiology, Monroe Carell Jr. Children's Hospital at Vanderbilt, Nashville, TN, USA
| | - Melanie D Everitt
- Department of Pediatrics, University of Colorado, Children's Hospital Colorado, Aurora, CO, USA
| | - Wendy K Chung
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Irene D Lytrivi
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - Sonya Kirmani
- Department of Pediatrics, University of Wisconsin School of Medicine, Madison, WI, USA
| | - Paul F Kantor
- Department of Pediatrics, Keck School of Medicine of USC, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Stephanie M Ware
- Department of Pediatrics and Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Jean A Ballweg
- Department of Pediatrics, Helen DeVos Children's Hospital, Grand Rapids, MI, USA
| | - Ashwin K Lal
- Division of Pediatric Cardiology, University of Utah, Primary Children's Hospital, Salt Lake City, Utah, USA
| | - Neha Bansal
- Division of Pediatric Cardiology, Mount Sinai Kravis Children's Hospital, New York, NY, USA
| | - Jeffrey Towbin
- Heart Institute, Le Bonheur Children's Hospital, Memphis, TN, USA
| | - Steven E Lipshultz
- Department of Pediatrics, Jacobs School of Medicine and Biomedical Sciences, Clinical and Translational Research Center, University at Buffalo, 875 Ellicott Street, Suite 5018, Buffalo, NY, 14203, USA.
| | - Teresa M Lee
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
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46
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Lemire G, Sanchis-Juan A, Russell K, Baxter S, Chao KR, Singer-Berk M, Groopman E, Wong I, England E, Goodrich J, Pais L, Austin-Tse C, DiTroia S, O'Heir E, Ganesh VS, Wojcik MH, Evangelista E, Snow H, Osei-Owusu I, Fu J, Singh M, Mostovoy Y, Huang S, Garimella K, Kirkham SL, Neil JE, Shao DD, Walsh CA, Argilli E, Le C, Sherr EH, Gleeson JG, Shril S, Schneider R, Hildebrandt F, Sankaran VG, Madden JA, Genetti CA, Beggs AH, Agrawal PB, Bujakowska KM, Place E, Pierce EA, Donkervoort S, Bönnemann CG, Gallacher L, Stark Z, Tan TY, White SM, Töpf A, Straub V, Fleming MD, Pollak MR, Õunap K, Pajusalu S, Donald KA, Bruwer Z, Ravenscroft G, Laing NG, MacArthur DG, Rehm HL, Talkowski ME, Brand H, O'Donnell-Luria A. Exome copy number variant detection, analysis, and classification in a large cohort of families with undiagnosed rare genetic disease. Am J Hum Genet 2024; 111:863-876. [PMID: 38565148 PMCID: PMC11080278 DOI: 10.1016/j.ajhg.2024.03.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 03/09/2024] [Accepted: 03/11/2024] [Indexed: 04/04/2024] Open
Abstract
Copy number variants (CNVs) are significant contributors to the pathogenicity of rare genetic diseases and, with new innovative methods, can now reliably be identified from exome sequencing. Challenges still remain in accurate classification of CNV pathogenicity. CNV calling using GATK-gCNV was performed on exomes from a cohort of 6,633 families (15,759 individuals) with heterogeneous phenotypes and variable prior genetic testing collected at the Broad Institute Center for Mendelian Genomics of the Genomics Research to Elucidate the Genetics of Rare Diseases consortium and analyzed using the seqr platform. The addition of CNV detection to exome analysis identified causal CNVs for 171 families (2.6%). The estimated sizes of CNVs ranged from 293 bp to 80 Mb. The causal CNVs consisted of 140 deletions, 15 duplications, 3 suspected complex structural variants (SVs), 3 insertions, and 10 complex SVs, the latter two groups being identified by orthogonal confirmation methods. To classify CNV variant pathogenicity, we used the 2020 American College of Medical Genetics and Genomics/ClinGen CNV interpretation standards and developed additional criteria to evaluate allelic and functional data as well as variants on the X chromosome to further advance the framework. We interpreted 151 CNVs as likely pathogenic/pathogenic and 20 CNVs as high-interest variants of uncertain significance. Calling CNVs from existing exome data increases the diagnostic yield for individuals undiagnosed after standard testing approaches, providing a higher-resolution alternative to arrays at a fraction of the cost of genome sequencing. Our improvements to the classification approach advances the systematic framework to assess the pathogenicity of CNVs.
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Affiliation(s)
- Gabrielle Lemire
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.
| | - Alba Sanchis-Juan
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Kathryn Russell
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Samantha Baxter
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Katherine R Chao
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Moriel Singer-Berk
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Emily Groopman
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - Isaac Wong
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Eleina England
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - Julia Goodrich
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Lynn Pais
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Christina Austin-Tse
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Stephanie DiTroia
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Emily O'Heir
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Vijay S Ganesh
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA
| | - Monica H Wojcik
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA
| | - Emily Evangelista
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Hana Snow
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ikeoluwa Osei-Owusu
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Jack Fu
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Mugdha Singh
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Yulia Mostovoy
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Steve Huang
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kiran Garimella
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Samantha L Kirkham
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - Jennifer E Neil
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA
| | - Diane D Shao
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Department of Neurology, Boston Children's Hospital, Boston, MA, USA
| | - Christopher A Walsh
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA
| | - Emanuela Argilli
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA; Institute of Human Genetics and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Carolyn Le
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA; Institute of Human Genetics and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Elliott H Sherr
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA; Institute of Human Genetics and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Joseph G Gleeson
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA; Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Shirlee Shril
- Harvard Medical School, Boston, MA, USA; Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
| | - Ronen Schneider
- Harvard Medical School, Boston, MA, USA; Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
| | - Friedhelm Hildebrandt
- Harvard Medical School, Boston, MA, USA; Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
| | - Vijay G Sankaran
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA; Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jill A Madden
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA
| | - Casie A Genetti
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA
| | - Alan H Beggs
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA
| | - Pankaj B Agrawal
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA
| | - Kinga M Bujakowska
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA; Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Boston, MA, USA
| | - Emily Place
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA; Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Boston, MA, USA
| | - Eric A Pierce
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA; Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Boston, MA, USA
| | - Sandra Donkervoort
- Neuromuscular and Neurogenetic Disorders of Childhood Section, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Carsten G Bönnemann
- Neuromuscular and Neurogenetic Disorders of Childhood Section, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Lyndon Gallacher
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Zornitza Stark
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Tiong Yang Tan
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Susan M White
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Ana Töpf
- John Walton Muscular Dystrophy Research Centre, Newcastle University and Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Volker Straub
- John Walton Muscular Dystrophy Research Centre, Newcastle University and Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Mark D Fleming
- Harvard Medical School, Boston, MA, USA; Department of Pathology, Boston Children's Hospital, Boston, MA, USA
| | - Martin R Pollak
- Harvard Medical School, Boston, MA, USA; Division of Nephrology, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Katrin Õunap
- Department of Clinical Genetics, Genetics and Personalized Medicine Clinic, Tartu University Hospital, Tartu, Estonia; Department of Genetics and Personalized Medicine, Institute of Clinical Medicine, Faculty of Medicine, University of Tartu, Tartu, Estonia
| | - Sander Pajusalu
- Department of Clinical Genetics, Genetics and Personalized Medicine Clinic, Tartu University Hospital, Tartu, Estonia; Department of Genetics and Personalized Medicine, Institute of Clinical Medicine, Faculty of Medicine, University of Tartu, Tartu, Estonia
| | - Kirsten A Donald
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital, Cape Town, South Africa; Neuroscience Institute, University of Cape Town, Cape Town, South Africa
| | - Zandre Bruwer
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital, Cape Town, South Africa; Neuroscience Institute, University of Cape Town, Cape Town, South Africa
| | - Gianina Ravenscroft
- University of Western Australia Centre for Medical Research, Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, Australia
| | - Nigel G Laing
- University of Western Australia Centre for Medical Research, Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, Australia
| | - Daniel G MacArthur
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Centre for Population Genomics, Garvan Institute of Medical Research and UNSW, Sydney, NSW, Australia; Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Heidi L Rehm
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Michael E Talkowski
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Harrison Brand
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Anne O'Donnell-Luria
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA.
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47
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Pidaparti M, Geddes GC, Durbin MD. Clinical Genetic and Genomic Testing in Congenital Heart Disease and Cardiomyopathy. J Clin Med 2024; 13:2544. [PMID: 38731073 PMCID: PMC11084871 DOI: 10.3390/jcm13092544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 04/20/2024] [Accepted: 04/21/2024] [Indexed: 05/13/2024] Open
Abstract
Congenital heart disease (CHD) and cardiomyopathies are the leading cause of morbidity and mortality worldwide. These conditions are often caused by genetic factors, and recent research has shown that genetic and genomic testing can provide valuable information for patient care. By identifying genetic causes, healthcare providers can screen for other related health conditions, offer early interventions, estimate prognosis, select appropriate treatments, and assess the risk for family members. Genetic and genomic testing is now the standard of care in patients with CHD and cardiomyopathy. However, rapid advances in technology and greater availability of testing options have led to changes in recommendations for the most appropriate testing method. Several recent studies have investigated the utility of genetic testing in this changing landscape. This review summarizes the literature surrounding the clinical utility of genetic evaluation in patients with CHD and cardiomyopathy.
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Affiliation(s)
- Mahati Pidaparti
- Division of Neonatal-Perinatal Medicine, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN 46202, USA;
| | - Gabrielle C. Geddes
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA;
| | - Matthew D. Durbin
- Division of Neonatal-Perinatal Medicine, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN 46202, USA;
- Herman B Wells Center for Pediatric Research, 1044 W. Walnut, Indianapolis, IN 46202, USA
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48
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Ma H, Zhu L, Yang X, Ao M, Zhang S, Guo M, Dai X, Ma X, Zhang X. Genetic and phenotypic analysis of 225 Chinese children with developmental delay and/or intellectual disability using whole-exome sequencing. BMC Genomics 2024; 25:391. [PMID: 38649797 PMCID: PMC11034079 DOI: 10.1186/s12864-024-10279-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 04/02/2024] [Indexed: 04/25/2024] Open
Abstract
Developmental delay (DD), or intellectual disability (ID) is a very large group of early onset disorders that affects 1-2% of children worldwide, which have diverse genetic causes that should be identified. Genetic studies can elucidate the pathogenesis underlying DD/ID. In this study, whole-exome sequencing (WES) was performed on 225 Chinese DD/ID children (208 cases were sequenced as proband-parent trio) who were classified into seven phenotype subgroups. The phenotype and genomic data of patients with DD/ID were further retrospectively analyzed. There were 96/225 (42.67%; 95% confidence interval [CI] 36.15-49.18%) patients were found to have causative single nucleotide variants (SNVs) and small insertions/deletions (Indels) associated with DD/ID based on WES data. The diagnostic yields among the seven subgroups ranged from 31.25 to 71.43%. Three specific clinical features, hearing loss, visual loss, and facial dysmorphism, can significantly increase the diagnostic yield of WES in patients with DD/ID (P = 0.005, P = 0.005, and P = 0.039, respectively). Of note, hearing loss (odds ratio [OR] = 1.86%; 95% CI = 1.00-3.46, P = 0.046) or abnormal brainstem auditory evoked potential (BAEP) (OR = 1.91, 95% CI = 1.02-3.50, P = 0.042) was independently associated with causative genetic variants in DD/ID children. Our findings enrich the variation spectrums of SNVs/Indels associated with DD/ID, highlight the value genetic testing for DD/ID children, stress the importance of BAEP screen in DD/ID children, and help to facilitate early diagnose, clinical management and reproductive decisions, improve therapeutic response to medical treatment.
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Affiliation(s)
- Heqian Ma
- The School of Public Health, Guilin Medical University, 1 Zhiyuan Road, Lingui District, 541199, Guilin, PR China
| | - Lina Zhu
- Faculty of Pediatrics, The Chinese PLA General Hospital, 100700, Beijing, China
- National Engineering Laboratory for Birth Defects Prevention and Control of Key Technology, 100700, Beijing, China
- Beijing Key Laboratory of Pediatric Organ Failure, 100700, Beijing, China
| | - Xiao Yang
- Faculty of Pediatrics, The Chinese PLA General Hospital, 100700, Beijing, China
- National Engineering Laboratory for Birth Defects Prevention and Control of Key Technology, 100700, Beijing, China
- Beijing Key Laboratory of Pediatric Organ Failure, 100700, Beijing, China
| | - Meng Ao
- The School of Public Health, Guilin Medical University, 1 Zhiyuan Road, Lingui District, 541199, Guilin, PR China
| | - Shunxiang Zhang
- The School of Public Health, Guilin Medical University, 1 Zhiyuan Road, Lingui District, 541199, Guilin, PR China
| | - Meizhen Guo
- The School of Public Health, Guilin Medical University, 1 Zhiyuan Road, Lingui District, 541199, Guilin, PR China
| | - Xuelin Dai
- The School of Public Health, Guilin Medical University, 1 Zhiyuan Road, Lingui District, 541199, Guilin, PR China
| | - Xiuwei Ma
- Faculty of Pediatrics, The Chinese PLA General Hospital, 100700, Beijing, China.
- National Engineering Laboratory for Birth Defects Prevention and Control of Key Technology, 100700, Beijing, China.
- Beijing Key Laboratory of Pediatric Organ Failure, 100700, Beijing, China.
| | - Xiaoying Zhang
- The School of Public Health, Guilin Medical University, 1 Zhiyuan Road, Lingui District, 541199, Guilin, PR China.
- The Guangxi Key Laboratory of Environmental Exposomics and Entire Lifecycle Heath, 1 Zhiyuan Road, Lingui District, 541199, Guilin, PR China.
- Guangxi Health Commission Key Laboratory of Entire Lifecycle Health and Care, 1 Zhiyuan Road, Lingui District, 541199, Guilin, PR China.
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49
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Herlin MK. Genetics of Mayer-Rokitansky-Küster-Hauser (MRKH) syndrome: advancements and implications. Front Endocrinol (Lausanne) 2024; 15:1368990. [PMID: 38699388 PMCID: PMC11063329 DOI: 10.3389/fendo.2024.1368990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 04/04/2024] [Indexed: 05/05/2024] Open
Abstract
Mayer-Rokitansky-Küster-Hauser (MRKH) syndrome is a congenital anomaly characterized by agenesis/aplasia of the uterus and upper part of the vagina in females with normal external genitalia and a normal female karyotype (46,XX). Patients typically present during adolescence with complaints of primary amenorrhea where the diagnosis is established with significant implications including absolute infertility. Most often cases appear isolated with no family history of MRKH syndrome or related anomalies. However, cumulative reports of familial recurrence suggest genetic factors to be involved. Early candidate gene studies had limited success in their search for genetic causes of MRKH syndrome. More recently, genomic investigations using chromosomal microarray and genome-wide sequencing have been successful in detecting promising genetic variants associated with MRKH syndrome, including 17q12 (LHX1, HNF1B) and 16p11.2 (TBX6) deletions and sequence variations in GREB1L and PAX8, pointing towards a heterogeneous etiology with various genes involved. With uterus transplantation as an emerging fertility treatment in MRKH syndrome and increasing evidence for genetic etiologies, the need for genetic counseling concerning the recurrence risk in offspring will likely increase. This review presents the advancements in MRKH syndrome genetics from early familial occurrences and candidate gene searches to current genomic studies. Moreover, the review provides suggestions for future genetic investigations and discusses potential implications for clinical practice.
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Affiliation(s)
- Morten Krogh Herlin
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus N, Denmark
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50
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Helm BM, Ware SM. Clinical Decision Analysis of Genetic Evaluation and Testing in 1013 Intensive Care Unit Infants with Congenital Heart Defects Supports Universal Genetic Testing. Genes (Basel) 2024; 15:505. [PMID: 38674439 PMCID: PMC11050575 DOI: 10.3390/genes15040505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 03/18/2024] [Accepted: 04/12/2024] [Indexed: 04/28/2024] Open
Abstract
Extracardiac anomalies (ECAs) are strong predictors of genetic disorders in infants with congenital heart disease (CHD), but there are no prior studies assessing performance of ECA status as a screen for genetic diagnoses in CHD patients. This retrospective cohort study assessed this in our comprehensive inpatient CHD genetics service focusing on neonates and infants admitted to the intensive care unit (ICU). The performance and diagnostic utility of using ECA status to screen for genetic disorders was assessed using decision curve analysis, a statistical tool to assess clinical utility, determining the threshold of phenotypic screening by ECA versus a Test-All approach. Over 24% of infants had genetic diagnoses identified (n = 244/1013), and ECA-positive status indicated a 4-fold increased risk of having a genetic disorder. However, ECA status had low-moderate screening performance based on predictive summary index, a compositive measure of positive and negative predictive values. For those with genetic diagnoses, nearly one-third (32%, 78/244) were ECA-negative but had cytogenetic and/or monogenic disorders identified by genetic testing. Thus, if the presence of multiple congenital anomalies is the phenotypic driver to initiate genetic testing, 13.4% (78/580) of infants with isolated CHD with identifiable genetic causes will be missed. Given the prevalence of genetic disorders and limited screening performance of ECA status, this analysis supports genetic testing in all CHD infants in intensive care settings rather than screening based on ECA.
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Affiliation(s)
- Benjamin M. Helm
- Department of Medical & Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA;
- Department of Epidemiology, Indiana University Fairbanks School of Public Health, Indianapolis, IN 46202, USA
| | - Stephanie M. Ware
- Department of Medical & Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA;
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
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