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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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Rajan-Babu IS, Dolzhenko E, Eberle MA, Friedman JM. Sequence composition changes in short tandem repeats: heterogeneity, detection, mechanisms and clinical implications. Nat Rev Genet 2024; 25:476-499. [PMID: 38467784 DOI: 10.1038/s41576-024-00696-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/19/2024] [Indexed: 03/13/2024]
Abstract
Short tandem repeats (STRs) are a class of repetitive elements, composed of tandem arrays of 1-6 base pair sequence motifs, that comprise a substantial fraction of the human genome. STR expansions can cause a wide range of neurological and neuromuscular conditions, known as repeat expansion disorders, whose age of onset, severity, penetrance and/or clinical phenotype are influenced by the length of the repeats and their sequence composition. The presence of non-canonical motifs, depending on the type, frequency and position within the repeat tract, can alter clinical outcomes by modifying somatic and intergenerational repeat stability, gene expression and mutant transcript-mediated and/or protein-mediated toxicities. Here, we review the diverse structural conformations of repeat expansions, technological advances for the characterization of changes in sequence composition, their clinical correlations and the impact on disease mechanisms.
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Affiliation(s)
- Indhu-Shree Rajan-Babu
- Department of Medical Genetics, The University of British Columbia, and Children's & Women's Hospital, Vancouver, British Columbia, Canada.
| | | | | | - Jan M Friedman
- Department of Medical Genetics, The University of British Columbia, and Children's & Women's Hospital, Vancouver, British Columbia, Canada
- BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada
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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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Ciobanu CG, Nucă I, Popescu R, Antoci LM, Caba L, Ivanov AV, Cojocaru KA, Rusu C, Mihai CT, Pânzaru MC. Narrative Review: Update on the Molecular Diagnosis of Fragile X Syndrome. Int J Mol Sci 2023; 24:ijms24119206. [PMID: 37298158 DOI: 10.3390/ijms24119206] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 04/30/2023] [Accepted: 05/20/2023] [Indexed: 06/12/2023] Open
Abstract
The diagnosis and management of fragile X syndrome (FXS) have significantly improved in the last three decades, although the current diagnostic techniques are not yet able to precisely identify the number of repeats, methylation status, level of mosaicism, and/or the presence of AGG interruptions. A high number of repeats (>200) in the fragile X messenger ribonucleoprotein 1 gene (FMR1) results in hypermethylation of promoter and gene silencing. The actual molecular diagnosis is performed using a Southern blot, TP-PCR (Triplet-Repeat PCR), MS-PCR (Methylation-Specific PCR), and MS-MLPA (Methylation-Specific MLPA) with some limitations, with multiple assays being necessary to completely characterise a patient with FXS. The actual gold standard diagnosis uses Southern blot; however, it cannot accurately characterise all cases. Optical genome mapping is a new technology that has also been developed to approach the diagnosis of fragile X syndrome. Long-range sequencing represented by PacBio and Oxford Nanopore has the potential to replace the actual diagnosis and offers a complete characterization of molecular profiles in a single test. The new technologies have improved the diagnosis of fragile X syndrome and revealed unknown aberrations, but they are a long way from being used routinely in clinical practice.
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Affiliation(s)
- Cristian-Gabriel Ciobanu
- Medical Genetics Department, Faculty of Medicine, "Grigore T. Popa" University of Medicine and Pharmacy, University Street No 16, 700115 Iasi, Romania
| | - Irina Nucă
- Medical Genetics Department, Faculty of Medicine, "Grigore T. Popa" University of Medicine and Pharmacy, University Street No 16, 700115 Iasi, Romania
- Investigatii Medicale Praxis, St. Moara de Vant No 35, 700376 Iasi, Romania
| | - Roxana Popescu
- Medical Genetics Department, Faculty of Medicine, "Grigore T. Popa" University of Medicine and Pharmacy, University Street No 16, 700115 Iasi, Romania
- Medical Genetics Department, "Saint Mary" Emergency Children's Hospital, St. Vasile Lupu No 62, 700309 Iasi, Romania
| | - Lucian-Mihai Antoci
- Medical Genetics Department, Faculty of Medicine, "Grigore T. Popa" University of Medicine and Pharmacy, University Street No 16, 700115 Iasi, Romania
| | - Lavinia Caba
- Medical Genetics Department, Faculty of Medicine, "Grigore T. Popa" University of Medicine and Pharmacy, University Street No 16, 700115 Iasi, Romania
| | - Anca Viorica Ivanov
- Pediatrics Department, "Grigore T. Popa" University of Medicine and Pharmacy, University Street No 16, 700115 Iasi, Romania
| | - Karina-Alexandra Cojocaru
- Department of Biochemistry, Faculty of Dental Medicine, "Grigore T. Popa" University of Medicine and Pharmacy, University Street No 16, 700115 Iasi, Romania
| | - Cristina Rusu
- Medical Genetics Department, Faculty of Medicine, "Grigore T. Popa" University of Medicine and Pharmacy, University Street No 16, 700115 Iasi, Romania
- Medical Genetics Department, "Saint Mary" Emergency Children's Hospital, St. Vasile Lupu No 62, 700309 Iasi, Romania
| | | | - Monica-Cristina Pânzaru
- Medical Genetics Department, Faculty of Medicine, "Grigore T. Popa" University of Medicine and Pharmacy, University Street No 16, 700115 Iasi, Romania
- Medical Genetics Department, "Saint Mary" Emergency Children's Hospital, St. Vasile Lupu No 62, 700309 Iasi, Romania
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Rajan-Babu IS, Lian M, Chong SS. Triplet-Primed PCR Assays for Accurate Screening of FMR1 CGG Repeat Expansion and Genotype Verification. Curr Protoc 2022; 2:e427. [PMID: 35609145 DOI: 10.1002/cpz1.427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Fragile X syndrome and other fragile X-associated disorders are caused by the full-mutation (>200 copies) and premutation (55 to 200 copies) expansion, respectively, of the CGG short tandem repeat in the fragile X messenger ribonucleoprotein 1 (FMR1) gene. Clinical diagnostic laboratories use Southern blot analysis and polymerase chain reaction (PCR)-based tests to detect and/or size the FMR1 CGG repeats. The development of sensitive and high-throughput triplet-primed PCR (TP-PCR) assays has diminished the need to subject all samples to Southern blot analysis, which is both labor- and time-intensive. In this article, we describe two direct TP-PCR (dTP-PCR) assays for the detection of FMR1 CGG repeat expansions. We outline a protocol that is based on melting curve analysis of dTP-PCR amplicons for a rapid and cost-effective first-tier screening and identification of individuals with premutation and full-mutation expansions. We also describe a protocol that employs capillary electrophoresis to resolve the dTP-PCR amplicon fragments and to estimate the repeat sizes of normal (5 to 44 copies), intermediate (45 to 54 copies), and premutation alleles, as well as to detect full mutations and determine the structure of the FMR1 alleles. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Direct triplet-primed PCR master mix preparation and amplification of the FMR1 CGG repeat locus for melting curve analysis Basic Protocol 2: Melting curve analysis of direct triplet-primed PCR amplicons on the Rotor-Gene Q MD × 5plex high-resolution melt platform Alternate Protocol: Melting curve analysis of direct triplet-primed PCR amplicons on the LightCycler 480 system Basic Protocol 3: Generation of direct triplet-primed PCR melting curve analysis profiles Basic Protocol 4: Direct triplet-primed PCR master mix preparation and amplification of the FMR1 CGG repeat locus for capillary electrophoresis Basic Protocol 5: Generation of control FMR1 plasmids for direct triplet-primed PCR melting curve analysis Basic Protocol 6: Sanger sequencing assay to verify FMR1 CGG repeat size and structure of plasmid DNA controls.
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Affiliation(s)
- Indhu-Shree Rajan-Babu
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada.,Children's & Women's Hospital, Vancouver, British Columbia, Canada
| | - Mulias Lian
- Khoo Teck Puat-National University Children's Medical Institute, National University Hospital, Singapore, Singapore
| | - Samuel S Chong
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Department of Obstetrics and Gynecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Department of Laboratory Medicine, National University Hospital, Singapore, Singapore
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6
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Rajan-Babu IS, Phang GP, Law HY, Lee CG, Chong SS. High-Throughput Methylation-Specific Triplet-Primed PCR and Melting Curve Analysis for Selective and Reliable Identification of Actionable FMR1 Genotypes. J Mol Diagn 2022; 24:241-252. [PMID: 35038595 DOI: 10.1016/j.jmoldx.2021.11.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 10/26/2021] [Accepted: 11/23/2021] [Indexed: 11/17/2022] Open
Abstract
Methylated FMR1 full-mutation expansions cause fragile X syndrome. FMR1 premutation carriers are susceptible to other late-onset conditions, and women with premutation are at risk of transmitting a fully expanded FMR1 allele to offspring. Identification of individuals with actionable FMR1 genotypes (full-mutation males and females, and premutation females at risk for primary ovarian insufficiency and/or having fragile X-affected offspring) can enable timely access to intervention services and genetic counseling. This study presents a rapid, first-tier test based on melting curve analysis of methylation-specific triplet-primed PCR amplicons (msTP-PCR MCA) for concurrent detection of FMR1 CGG-repeat expansions and their methylation status. The msTP-PCR MCA assay was optimized on 20 fragile X reference samples, and its performance was evaluated on 111 peripheral blood-derived DNA samples from patients who have undergone prior molecular testing with PCR and/or Southern blot analysis. The msTP-PCR MCA assay detected all samples with a methylated FMR1 CGG-repeat expansion, and had sensitivity, specificity, positive predictive value, and negative predictive values of 100%, 92.06%, 91.1%, and 100%, respectively. The msTP-PCR MCA assay identified premutation/full-mutation mosaicism down to 1%, detected skewed inactivation in females with FMR1 expansions, and enabled selective identification of all individuals with an actionable FMR1 genotype. The msTP-PCR MCA assay may aid in fragile X screening of at-risk populations and newborns and voluntary carrier screening of women of reproductive age.
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Affiliation(s)
- Indhu-Shree Rajan-Babu
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Department of Medical Genetics, University of British Columbia, and Children's and Women's Hospital, Vancouver, British Columbia, Canada.
| | - Gui-Ping Phang
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Hai-Yang Law
- Department of Pediatric Medicine, KK Women's and Children's Hospital, Singapore
| | - Caroline G Lee
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Division of Cellular and Molecular Research, Humphrey Oei Institute of Cancer Research, National Cancer Centre Singapore, Singapore; Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Samuel S Chong
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Department of Obstetrics and Gynecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Department of Laboratory Medicine, National University Hospital, Singapore.
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7
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Joz Abbasalian Z, Khanahmad H, Tabatabaiefar MA. Bisulfite Treatment of CG-Rich Track of Trinucleotide Repeat Expansion Disorder: Make the Sequence Less CG Rich. Adv Biomed Res 2022; 10:46. [PMID: 35127573 PMCID: PMC8781891 DOI: 10.4103/abr.abr_144_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 08/03/2019] [Accepted: 12/15/2020] [Indexed: 11/08/2022] Open
Abstract
Background: Trinucleotide repeat (TNR) expansion is a kind of mutation with instability in the number of microsatellite repeats. This nature of mutation leads to the different kinds of neurological and neuromuscular disorders; among them, fragile-X syndrome is the main cause of intellectual disability in which the increasing number of CGG TNR in 5' untranslated region is the main reason for epigenetic silencing of Fragile X mental retardation 1 gene. The aim of this study is to decrease the CG content of the candidate region to facilitate amplification by conventional polymerase chain reaction (PCR). Bisulfite treatment of the genomic DNA results in conversion of unmethylated cytosine to uridine and may overcome the diagnostic pitfalls. Materials and Methods: The whole blood DNA was extracted and bisulfite treated. Then any simplification in PCR process of desire sequence were assayed through following conventional PCR using specifically designed primers for converted sequence. Bisulfite-treated PCR product of a nearby sequence confirmed our results as a conversion control. Results: Both the control and the candidate sequences undergoing bisulfite treatment were successfully amplified by PCR. Conclusions: Decreasing the GC content of the sequence by bisulfite treating could be a new approach to overcome difficulties in amplifying GC-rich sequences.
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Affiliation(s)
- Zahra Joz Abbasalian
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Hossein Khanahmad
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mohammad Amin Tabatabaiefar
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
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