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Sheth F, Shah J, Jain D, Shah S, Patel H, Patel K, Solanki DI, Iyer AS, Menghani B, Mhatre P, Mehta S, Bajaj S, Patel V, Pandya M, Dhami D, Patel D, Sheth J, Sheth H. Comparative yield of molecular diagnostic algorithms for autism spectrum disorder diagnosis in India: evidence supporting whole exome sequencing as first tier test. BMC Neurol 2023; 23:292. [PMID: 37543562 PMCID: PMC10403833 DOI: 10.1186/s12883-023-03341-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 07/21/2023] [Indexed: 08/07/2023] Open
Abstract
BACKGROUND Autism spectrum disorder (ASD) affects 1 in 100 children globally with a rapidly increasing prevalence. To the best of our knowledge, no data exists on the genetic architecture of ASD in India. This study aimed to identify the genetic architecture of ASD in India and to assess the use of whole exome sequencing (WES) as a first-tier test instead of chromosomal microarray (CMA) for genetic diagnosis. METHODS Between 2020 and 2022, 101 patient-parent trios of Indian origin diagnosed with ASD according to the Diagnostic and Statistical Manual, 5th edition, were recruited. All probands underwent a sequential genetic testing pathway consisting of karyotyping, Fragile-X testing (in male probands only), CMA and WES. Candidate variant validation and parental segregation analysis was performed using orthogonal methods. RESULTS Of 101 trios, no probands were identified with a gross chromosomal anomaly or Fragile-X. Three (2.9%) and 30 (29.7%) trios received a confirmed genetic diagnosis from CMA and WES, respectively. Amongst diagnosis from WES, SNVs were detected in 27 cases (90%) and CNVs in 3 cases (10%), including the 3 CNVs detected from CMA. Segregation analysis showed 66.6% (n = 3 for CNVs and n = 17 for SNVs) and 16.6% (n = 5) of the cases had de novo and recessive variants respectively, which is in concordance with the distribution of variant types and mode of inheritance observed in ASD patients of non-Hispanic white/ European ethnicity. MECP2 gene was the most recurrently mutated gene (n = 6; 20%) in the present cohort. Majority of the affected genes identified in the study cohort are involved in synaptic formation, transcription and its regulation, ubiquitination and chromatin remodeling. CONCLUSIONS Our study suggests de novo variants as a major cause of ASD in the Indian population, with Rett syndrome as the most commonly detected disorder. Furthermore, we provide evidence of a significant difference in the diagnostic yield between CMA (3%) and WES (30%) which supports the implementation of WES as a first-tier test for genetic diagnosis of ASD in India.
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Affiliation(s)
- Frenny Sheth
- FRIGE's Institute of Human Genetics, Ahmedabad, India.
| | - Jhanvi Shah
- FRIGE's Institute of Human Genetics, Ahmedabad, India
| | - Deepika Jain
- Shishu Child Development and Early Intervention Centre, Ahmedabad, India
| | - Siddharth Shah
- Royal Institute of Child Neurosciences, Ahmedabad, India
| | | | - Ketan Patel
- Specialty Homeopathic Clinic, Ahmedabad, India
| | | | | | - Bhargavi Menghani
- Children's Institute for Development and Advancement Centre, Vadodara, India
| | - Priti Mhatre
- Tender Kinds Centre for Child Development, Navi Mumbai, India
| | - Sanjiv Mehta
- Royal Institute of Child Neurosciences, Ahmedabad, India
| | | | - Vishal Patel
- Little Brain Pediatric Neurocare Centre, Vadodara, India
| | | | - Deepak Dhami
- Axon Child Neurology and Epilepsy Centre, Rajkot, India
| | - Darshan Patel
- Charotar Institute of Paramedical Sciences, Charotar University of Science and Technology, Changa, India
| | - Jayesh Sheth
- FRIGE's Institute of Human Genetics, Ahmedabad, India
| | - Harsh Sheth
- FRIGE's Institute of Human Genetics, Ahmedabad, India.
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Milone R, Scalise R, Pasquariello R, Berloffa S, Ricca I, Battini R. De Novo 1q21.3q22 Duplication Revaluation in a "Cold" Complex Neuropsychiatric Case with Syndromic Intellectual Disability. Genes (Basel) 2021; 12:genes12040511. [PMID: 33807234 PMCID: PMC8066010 DOI: 10.3390/genes12040511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 03/24/2021] [Accepted: 03/28/2021] [Indexed: 11/26/2022] Open
Abstract
Syndromic intellectual disability often obtains a genetic diagnosis due to the combination of first and next generation sequencing techniques, although their interpretation may require revaluation over the years. Here we report on a composite neuropsychiatric case whose phenotype includes moderate intellectual disability, spastic paraparesis, movement disorder, and bipolar disorder, harboring a 1.802 Mb de novo 1q21.3q22 duplication. The role of this duplication has been reconsidered in the light of negativity of many other genetic exams, and of the possible pathogenic role of many genes included in this duplication, potentially configuring a contiguous gene-duplication syndrome.
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Affiliation(s)
- Roberta Milone
- Department of Developmental Neuroscience, IRCCS Stella Maris Foundation, Calambrone, 56128 Pisa, Italy; (R.M.); (R.S.); (R.P.); (S.B.)
| | - Roberta Scalise
- Department of Developmental Neuroscience, IRCCS Stella Maris Foundation, Calambrone, 56128 Pisa, Italy; (R.M.); (R.S.); (R.P.); (S.B.)
- Tuscan PhD Program of Neuroscience, University of Florence, Pisa and Siena, 50139 Florence, Italy
| | - Rosa Pasquariello
- Department of Developmental Neuroscience, IRCCS Stella Maris Foundation, Calambrone, 56128 Pisa, Italy; (R.M.); (R.S.); (R.P.); (S.B.)
| | - Stefano Berloffa
- Department of Developmental Neuroscience, IRCCS Stella Maris Foundation, Calambrone, 56128 Pisa, Italy; (R.M.); (R.S.); (R.P.); (S.B.)
| | - Ivana Ricca
- Molecular Medicine, IRCCS Stella Maris Foundation, 56128 Pisa, Italy;
| | - Roberta Battini
- Department of Developmental Neuroscience, IRCCS Stella Maris Foundation, Calambrone, 56128 Pisa, Italy; (R.M.); (R.S.); (R.P.); (S.B.)
- Department of Clinical and Experimental Medicine, University of Pisa, 56125 Pisa, Italy
- Correspondence: ; Tel.: +39-050886229; Fax: +39-050886247
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Ornelas-Arana ML, Pérez-Garcia G, Robles-Espinoza CD, Rangel-Sosa MM, Castaneda-Garcia C, Juárez-Vázquez CI, López-Pérez LG, Pérez-Ornelas C, Hernández-Zaragoza G, Lara-Aguilar RA, Córdova-Fletes C. Genomic Characterization of a Rare, de Novo Unbalanced ins(3;1)(p25.3;q21.3q23.3) in a Female Child with Multiple Congenital Anomalies. Cytogenet Genome Res 2020; 160:579-588. [PMID: 33152732 DOI: 10.1159/000511234] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 08/26/2020] [Indexed: 11/19/2022] Open
Abstract
"Simple" 1-way interchromosomal insertions involving an interstitial 1q segment are rare, and therefore, their characterization at the base pair level remains understudied. Here, we describe the genomic characterization of a previously unreported de novo interchromosomal insertion (3;1) entailing an about 12-Mb pure gain of 1q21.3q23.3 that causes typical (microcephaly, developmental delay, and facial dysmorphism) and atypical (interauricular communication, small feet with bilateral deep plantar creases, syndactyly of II-IV toes, and mild pachyonychia of all toes) clinical manifestations associated with this region. Based on our analyses, we hypothesize that the duplication of a subset of morbid genes (including LMNA, USF1, VANGL2, LOR, and POGZ) could account for most clinical findings in our patient. Furthermore, the apparent disruption of a promoter region (between CPNE9 and BRPF1) and a topologically associated domain also suggests likely pathogenic reconfiguration/position effects to contribute to the patient's phenotype. In addition to further expanding the clinical spectrum of proximal 1q duplications and evidencing the phenotypical heterogeneity among similar carriers, our genomic findings and observations suggest that randomness - rather than lethality issues - may account for the paucity of "simple" interchromosomal insertions involving the 1q21.3q23.3 region as genomic donor and distal 3p25.3 as receptor. Moreover, the microhomology sequence found at the insertion breakpoint is consistent with a simple nonhomologous end-joining mechanism, in contrast to a chromothripsis-like event, which has previously been seen in other nonrecurrent insertions. Taken together, the data gathered in this study allowed us to inform this family about the low recurrence risk but not to predict the reproductive prognosis for hypothetical carriers. We highlight that genomic-level assessment is a powerful tool that allows the visualization of the full landscape of sporadic chromosomal injuries and can be used to improve genetic counseling.
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Affiliation(s)
- Martha L Ornelas-Arana
- Laboratorio de Bioquímica, Cuerpo académico UDG-CA-80, Departamento de Biología Molecular y Genómica, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
| | - Guillermo Pérez-Garcia
- Laboratorio de Bioquímica, Cuerpo académico UDG-CA-80, Departamento de Biología Molecular y Genómica, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico.,Servicio de Genética, Hospital Civil de Guadalajara "Fray Antonio Alcalde", Guadalajara, Mexico
| | - Carla D Robles-Espinoza
- Laboratorio Internacional de Investigación Sobre el Genoma Humano, Universidad Nacional Autónoma de México, Campus Juriquilla, Santiago de Querétaro, Mexico.,Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Martha M Rangel-Sosa
- Laboratorio de Citogenómica y Microarreglos, Departamento de Bioquímica y Medicina Molecular, Facultad de Medicina, Universidad Autónoma de Nuevo León, Monterrey, Mexico
| | - Carolina Castaneda-Garcia
- Laboratorio Internacional de Investigación Sobre el Genoma Humano, Universidad Nacional Autónoma de México, Campus Juriquilla, Santiago de Querétaro, Mexico
| | | | - Leopoldo G López-Pérez
- Laboratorio de Bioquímica, Cuerpo académico UDG-CA-80, Departamento de Biología Molecular y Genómica, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
| | - Carolina Pérez-Ornelas
- Laboratorio de Bioquímica, Cuerpo académico UDG-CA-80, Departamento de Biología Molecular y Genómica, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico.,Servicio de Pediatría, Hospital General de Occidente, Zapopan, Jalisco, Mexico
| | - Guillermo Hernández-Zaragoza
- Laboratorio de Bioquímica, Cuerpo académico UDG-CA-80, Departamento de Biología Molecular y Genómica, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
| | | | - Carlos Córdova-Fletes
- Laboratorio de Citogenómica y Microarreglos, Departamento de Bioquímica y Medicina Molecular, Facultad de Medicina, Universidad Autónoma de Nuevo León, Monterrey, Mexico,
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