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Anitha A, Banerjee M, Thanseem I, Prakash A, Melempatt N, Sumitha PS, Iype M, Thomas SV. Rare Pathogenic Variants Identified in Whole Exome Sequencing of Monozygotic Twins With Autism Spectrum Disorder. Pediatr Neurol 2024; 158:113-123. [PMID: 39038432 DOI: 10.1016/j.pediatrneurol.2024.06.003] [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: 12/28/2023] [Revised: 05/07/2024] [Accepted: 06/09/2024] [Indexed: 07/24/2024]
Abstract
BACKGROUND Autism spectrum disorder (ASD) is a childhood-onset complex neurodevelopmental disorder characterized by problems with communication and social interaction and restricted, repetitive, stereotyped behavior. The prevalence of ASD is one in 36 children. The genetic architecture of ASD is complex in spite of its high heritability. To identify the potential candidate genes of ASD, we carried out a comprehensive genetic study of monozygotic (MZ) twins concordant or discordant for ASD. METHODS Five MZ twins and their parents were recruited for the study. Four of the twins were concordant, whereas one was discordant for ASD. Whole exome sequencing was conducted for the twins and their parents. The exome DNA was enriched using Twist Human Customized Core Exome Kit, and paired-end sequencing was performed on HiSeq system. RESULTS We identified several rare and pathogenic variants (homozygous recessive, compound heterozygous, de novo) in ASD-affected individuals. CONCLUSION We report novel variants in individuals diagnosed with ASD. Several of these genes are involved in brain-related functions and not previously reported in ASD. Intriguingly, some of the variants were observed in the genes involved in sensory perception (auditory [MYO15A, PLEC, CDH23, UBR3, GPSM2], olfactory [OR9K2], gustatory [TAS2R31], and visual [CDH23, UBR3]). This is the first comprehensive genetic study of MZ twins in an Indian population. Further validation is required to determine whether these variants are associated with ASD.
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Affiliation(s)
- Ayyappan Anitha
- Department of Neurogenetics, Institute for Communicative and Cognitive Neurosciences (ICCONS), Palakkad, Kerala, India.
| | - Moinak Banerjee
- Department of Neurobiology, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
| | - Ismail Thanseem
- Department of Neurogenetics, Institute for Communicative and Cognitive Neurosciences (ICCONS), Palakkad, Kerala, India
| | - Anil Prakash
- Department of Neurobiology, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
| | - Nisha Melempatt
- Department of Audiology and Speech Language Pathology (ASLP), ICCONS, Palakkad, Kerala, India
| | - P S Sumitha
- Department of Neurogenetics, Institute for Communicative and Cognitive Neurosciences (ICCONS), Palakkad, Kerala, India
| | - Mary Iype
- Department of Neurology, ICCONS, Thiruvananthapuram, Kerala, India; Department of Neurology, ICCONS, Shoranur, Kerala, India; Department of Pediatric Neurology, Government Medical College, Thiruvananthapuram, Kerala, India
| | - Sanjeev V Thomas
- Department of Neurology, ICCONS, Thiruvananthapuram, Kerala, India; Department of Neurology, ICCONS, Shoranur, Kerala, India
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Sheth J, Nair A, Sheth F, Ajagekar M, Dhondekar T, Panigrahi I, Bavdekar A, Nampoothiri S, Datar C, Gandhi A, Muranjan M, Kaur A, Desai M, Mistri M, Patel C, Naik P, Shah M, Godbole K, Kapoor S, Gupta N, Bijarnia-Mahay S, Kadam S, Solanki D, Desai S, Iyer A, Patel K, Patel H, Shah RC, Mehta S, Shah R, Bhavsar R, Shah J, Pandya M, Patel B, Shah S, Shah H, Shah S, Bajaj S, Shah S, Thaker N, Kalane U, Kamate M, Kn VR, Tayade N, Jagadeesan S, Jain D, Chandarana M, Singh J, Mehta S, Suresh B, Sheth H. Burden of rare genetic disorders in India: twenty-two years' experience of a tertiary centre. Orphanet J Rare Dis 2024; 19:295. [PMID: 39138584 PMCID: PMC11323464 DOI: 10.1186/s13023-024-03300-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 07/31/2024] [Indexed: 08/15/2024] Open
Abstract
BACKGROUND Rare disorders comprise of ~ 7500 different conditions affecting multiple systems. Diagnosis of rare diseases is complex due to dearth of specialized medical professionals, testing labs and limited therapeutic options. There is scarcity of data on the prevalence of rare diseases in different populations. India being home to a large population comprising of 4600 population groups, of which several thousand are endogamous, is likely to have a high burden of rare diseases. The present study provides a retrospective overview of a cohort of patients with rare genetic diseases identified at a tertiary genetic test centre in India. RESULTS Overall, 3294 patients with 305 rare diseases were identified in the present study cohort. These were categorized into 14 disease groups based on the major organ/ organ system affected. Highest number of rare diseases (D = 149/305, 48.9%) were identified in the neuromuscular and neurodevelopmental (NMND) group followed by inborn errors of metabolism (IEM) (D = 47/305; 15.4%). Majority patients in the present cohort (N = 1992, 61%) were diagnosed under IEM group, of which Gaucher disease constituted maximum cases (N = 224, 11.2%). Under the NMND group, Duchenne muscular dystrophy (N = 291/885, 32.9%), trinucleotide repeat expansion disorders (N = 242/885; 27.3%) and spinal muscular atrophy (N = 141/885, 15.9%) were the most common. Majority cases of β-thalassemia (N = 120/149, 80.5%) and cystic fibrosis (N = 74/75, 98.7%) under the haematological and pulmonary groups were observed, respectively. Founder variants were identified for Tay-Sachs disease and mucopolysaccharidosis IVA diseases. Recurrent variants for Gaucher disease (GBA:c.1448T > C), β-thalassemia (HBB:c.92.+5G > C), non-syndromic hearing loss (GJB2:c.71G > A), albinism (TYR:c.832 C > T), congenital adrenal hyperplasia (CYP21A2:c.29-13 C > G) and progressive pseudo rheumatoid dysplasia (CCN6:c.298T > A) were observed in the present study. CONCLUSION The present retrospective study of rare disease patients diagnosed at a tertiary genetic test centre provides first insight into the distribution of rare genetic diseases across the country. This information will likely aid in drafting future health policies, including newborn screening programs, development of target specific panel for affordable diagnosis of rare diseases and eventually build a platform for devising novel treatment strategies for rare diseases.
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Affiliation(s)
- Jayesh Sheth
- FRIGE Institute of Human Genetics, FRIGE House, Ahmedabad, India.
| | - Aadhira Nair
- FRIGE Institute of Human Genetics, FRIGE House, Ahmedabad, India
| | - Frenny Sheth
- FRIGE Institute of Human Genetics, FRIGE House, Ahmedabad, India
| | - Manali Ajagekar
- FRIGE Institute of Human Genetics, FRIGE House, Ahmedabad, India
| | | | - Inusha Panigrahi
- Postgraduate Institute of Medical Education and Research, PGIMER, Chandigarh, India
| | | | | | - Chaitanya Datar
- Bharati Hospital and Research Centre, Dhankawadi, Pune, India
| | | | - Mamta Muranjan
- Department of Pediatrics, KEM Hospital, Parel, Mumbai, India
| | - Anupriya Kaur
- Postgraduate Institute of Medical Education and Research, PGIMER, Chandigarh, India
| | - Manisha Desai
- FRIGE Institute of Human Genetics, FRIGE House, Ahmedabad, India
| | - Mehul Mistri
- FRIGE Institute of Human Genetics, FRIGE House, Ahmedabad, India
| | - Chitra Patel
- FRIGE Institute of Human Genetics, FRIGE House, Ahmedabad, India
| | - Premal Naik
- Rainbow Super speciality Hospital, Ahmedabad, India
| | | | - Koumudi Godbole
- Deenanath Mangeshkar Hospital & Research Centre, Pune, India
| | - Seema Kapoor
- Division of Genetics & Metabolism Department of Pediatrics, Lok Nayak Hospital and Maulana Azad Medical College, New Delhi, India
| | - Neerja Gupta
- Division of Genetics, Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Sunita Bijarnia-Mahay
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Sandeep Kadam
- Department of Pediatrics, K.E.M Hospital, Pune, India
| | | | - Soham Desai
- Shree Krishna Hospital, Karamsad, Anand, India
| | | | - Ketan Patel
- Himalaya Arcade, Homeopathy Clinic, Vastrapur, Ahmedabad, India
| | - Harsh Patel
- Zydus Hospital & Healthcare Research Pvt Ltd, Ahmedabad, India
| | - Raju C Shah
- Ankur Neonatal Hospital, Ashram Road, Ahmedabad, India
| | | | | | - Riddhi Bhavsar
- FRIGE Institute of Human Genetics, FRIGE House, Ahmedabad, India
| | - Jhanvi Shah
- FRIGE Institute of Human Genetics, FRIGE House, Ahmedabad, India
| | - Mili Pandya
- FRIGE Institute of Human Genetics, FRIGE House, Ahmedabad, India
| | | | | | - Heli Shah
- Ansa Clinic, S. G. Highway, Ahmedabad, India
| | - Shalin Shah
- Ansa Clinic, S. G. Highway, Ahmedabad, India
| | - Shruti Bajaj
- The Purple Gene Clinic, Simplex Khushaangan, SV Road, Malad West, Mumbai, India
| | | | | | - Umesh Kalane
- Deenanath Mangeshkar Hospital & Research Centre, Pune, India
| | | | - Vykunta Raju Kn
- Department of Pediatric Neurology, Indira Gandhi Institute of Child Health, Bangalore, India
| | - Naresh Tayade
- Department of Paediatrics, Dr. Panjabrao Deshmukh Memorial Medical College, Amravati, India
| | - Sujatha Jagadeesan
- Department of Clinical Genetics & Genetic Counselling, Mediscan Systems, Chennai, India
| | - Deepika Jain
- Shishu Child Development and Early Intervention Centre, Ahmedabad, India
| | - Mitesh Chandarana
- Medisquare Superspeciality Hospital and Research Institute, Ahmedabad, India
| | - Jitendra Singh
- Neurology Clinic, Shivranjini Cross Road, Satellite, Ahmedabad, India
| | | | - Beena Suresh
- Department of Clinical Genetics & Genetic Counselling, Mediscan Systems, Chennai, India
| | - Harsh Sheth
- FRIGE Institute of Human Genetics, FRIGE House, Ahmedabad, India.
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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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Bar O, Vahey E, Mintz M, Frye RE, Boles RG. Reanalysis of Trio Whole-Genome Sequencing Data Doubles the Yield in Autism Spectrum Disorder: De Novo Variants Present in Half. Int J Mol Sci 2024; 25:1192. [PMID: 38256266 PMCID: PMC10816071 DOI: 10.3390/ijms25021192] [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: 12/24/2023] [Revised: 01/14/2024] [Accepted: 01/16/2024] [Indexed: 01/24/2024] Open
Abstract
Autism spectrum disorder (ASD) is a common condition with lifelong implications. The last decade has seen dramatic improvements in DNA sequencing and related bioinformatics and databases. We analyzed the raw DNA sequencing files on the Variantyx® bioinformatics platform for the last 50 ASD patients evaluated with trio whole-genome sequencing (trio-WGS). "Qualified" variants were defined as coding, rare, and evolutionarily conserved. Primary Diagnostic Variants (PDV), additionally, were present in genes directly linked to ASD and matched clinical correlation. A PDV was identified in 34/50 (68%) of cases, including 25 (50%) cases with heterozygous de novo and 10 (20%) with inherited variants. De novo variants in genes directly associated with ASD were far more likely to be Qualifying than non-Qualifying versus a control group of genes (p = 0.0002), validating that most are indeed disease related. Sequence reanalysis increased diagnostic yield from 28% to 68%, mostly through inclusion of de novo PDVs in genes not yet reported as ASD associated. Thirty-three subjects (66%) had treatment recommendation(s) based on DNA analyses. Our results demonstrate a high yield of trio-WGS for revealing molecular diagnoses in ASD, which is greatly enhanced by reanalyzing DNA sequencing files. In contrast to previous reports, de novo variants dominate the findings, mostly representing novel conditions. This has implications to the cause and rising prevalence of autism.
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Affiliation(s)
- Omri Bar
- NeurAbilities Healthcare, Voorhees, NJ 08043, USA; (O.B.); (E.V.); (M.M.)
| | - Elizabeth Vahey
- NeurAbilities Healthcare, Voorhees, NJ 08043, USA; (O.B.); (E.V.); (M.M.)
| | - Mark Mintz
- NeurAbilities Healthcare, Voorhees, NJ 08043, USA; (O.B.); (E.V.); (M.M.)
| | - Richard E. Frye
- Autism Discovery and Treatment Foundation, Phoenix, AZ 85050, USA;
| | - Richard G. Boles
- NeurAbilities Healthcare, Voorhees, NJ 08043, USA; (O.B.); (E.V.); (M.M.)
- NeuroNeeds, Old Lyme, CT 06371, USA
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Louw N, Carstens N, Lombard Z. Incorporating CNV analysis improves the yield of exome sequencing for rare monogenic disorders-an important consideration for resource-constrained settings. Front Genet 2023; 14:1277784. [PMID: 38155715 PMCID: PMC10753787 DOI: 10.3389/fgene.2023.1277784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 11/22/2023] [Indexed: 12/30/2023] Open
Abstract
Exome sequencing (ES) is a recommended first-tier diagnostic test for many rare monogenic diseases. It allows for the detection of both single-nucleotide variants (SNVs) and copy number variants (CNVs) in coding exonic regions of the genome in a single test, and this dual analysis is a valuable approach, especially in limited resource settings. Single-nucleotide variants are well studied; however, the incorporation of copy number variant analysis tools into variant calling pipelines has not been implemented yet as a routine diagnostic test, and chromosomal microarray is still more widely used to detect copy number variants. Research shows that combined single and copy number variant analysis can lead to a diagnostic yield of up to 58%, increasing the yield with as much as 18% from the single-nucleotide variant only pipeline. Importantly, this is achieved with the consideration of computational costs only, without incurring any additional sequencing costs. This mini review provides an overview of copy number variant analysis from exome data and what the current recommendations are for this type of analysis. We also present an overview on rare monogenic disease research standard practices in resource-limited settings. We present evidence that integrating copy number variant detection tools into a standard exome sequencing analysis pipeline improves diagnostic yield and should be considered a significantly beneficial addition, with relatively low-cost implications. Routine implementation in underrepresented populations and limited resource settings will promote generation and sharing of CNV datasets and provide momentum to build core centers for this niche within genomic medicine.
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Affiliation(s)
- Nadja Louw
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Nadia Carstens
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Genomics Platform, South African Medical Research Council, Cape Town, South Africa
| | - Zané Lombard
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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