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Vaseghi P, Habibi L, Neidich JA, Cao Y, Fattahi N, Rashidi-Nezhad R, Salehnezhad T, Dalili H, Rahimi Sharbaf F, Zarkesh MR, Malekian M, Mokhberdezfuli M, Mehrtash A, Ardeshirdavani A, Kariminejad R, Ghorbansabagh V, Sadeghimoghadam P, Naddaf A, Esmaeilnia Shirvany T, Mosayebi Z, Sahebdel B, Golshahi F, Shirazi M, Shamel S, Moeini R, Heidari A, Daneshmand MA, Ghasemi R, Akrami SM, Rashidi-Nezhad A. Towards solving the genetic diagnosis odyssey in Iranian patients with congenital anomalies. Eur J Hum Genet 2024:10.1038/s41431-024-01533-x. [PMID: 38278869 DOI: 10.1038/s41431-024-01533-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 11/23/2023] [Accepted: 12/12/2023] [Indexed: 01/28/2024] Open
Abstract
Understanding the underlying causes of congenital anomalies (CAs) can be a complex diagnostic journey. We aimed to assess the efficiency of exome sequencing (ES) and chromosomal microarray analysis (CMA) in patients with CAs among a population with a high fraction of consanguineous marriage. Depending on the patient's symptoms and family history, karyotype/Quantitative Fluorescence- Polymerase Chain Reaction (QF-PCR) (n = 84), CMA (n = 81), ES (n = 79) or combined CMA and ES (n = 24) were performed on 168 probands (66 prenatal and 102 postnatal) with CAs. Twelve (14.28%) probands were diagnosed by karyotype/QF-PCR and seven (8.64%) others were diagnosed by CMA. ES findings were conclusive in 39 (49.36%) families, and 61.90% of them were novel variants. Also, 64.28% of these variants were identified in genes that follow recessive inheritance in CAs. The diagnostic rate (DR) of ES was significantly higher than that of CMA in children from consanguineous families (P = 0·0001). The highest DR by CMA was obtained in the non-consanguineous postnatal subgroup and by ES in the consanguineous prenatal subgroup. In a population that is highly consanguineous, our results suggest that ES may have a higher diagnostic yield than CMA and should be considered as the first-tier test in the evaluation of patients with congenital anomalies.
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Affiliation(s)
- Parisa Vaseghi
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
- Department of Photo Healing and Regeneration, Medical Laser Research Center, Yara Institute, ACECR, Tehran, Iran
| | - Laleh Habibi
- Ronash Medical Genetics Laboratory, Tehran, Iran
| | - Julie A Neidich
- Department of Pathology & Immunology, Division of Laboratory & Genomic Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - Yang Cao
- Department of Pathology & Immunology, Division of Laboratory & Genomic Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Neda Fattahi
- Ronash Medical Genetics Laboratory, Tehran, Iran
| | | | | | - Hossein Dalili
- Breastfeeding Research Center, Family Health Research Institute, Tehran University of Medical Sciences, Tehran, Iran
- Department of Pediatrics, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Fatemeh Rahimi Sharbaf
- Department of Obstetrics and Gynecology, School of Medicine, Yas Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Zarkesh
- Department of Neonatology, Yas Hospital Complex, Tehran university of medical sciences, Tehran, Iran
| | | | - Mahdieh Mokhberdezfuli
- Ronash Medical Genetics Laboratory, Tehran, Iran
- Multiple Sclerosis Research Center, Neuroscience Institute, Tehran University of Medical Sciences, Tehran, Iran
| | | | | | | | - Vafa Ghorbansabagh
- Department of Pediatrics, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
- Maternal, Fetal and Neonatal Research Center, Family Health Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Parvane Sadeghimoghadam
- Department of Pediatrics, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
- Maternal, Fetal and Neonatal Research Center, Family Health Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Amir Naddaf
- Department of Pediatrics, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
- Maternal, Fetal and Neonatal Research Center, Family Health Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Tahereh Esmaeilnia Shirvany
- Department of Pediatrics, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
- Maternal, Fetal and Neonatal Research Center, Family Health Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Ziba Mosayebi
- Department of Pediatrics, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
- Maternal, Fetal and Neonatal Research Center, Family Health Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Behrokh Sahebdel
- Department of Obstetrics and Gynecology, School of Medicine, Yas Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran
| | - Fatemeh Golshahi
- Department of Obstetrics and Gynecology, School of Medicine, Yas Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran
| | - Mahboobeh Shirazi
- Department of Obstetrics and Gynecology, School of Medicine, Yas Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran
| | - Shirin Shamel
- Department of Neonatology, Yas Hospital Complex, Tehran university of medical sciences, Tehran, Iran
| | - Roksana Moeini
- Department of Neonatology, Yas Hospital Complex, Tehran university of medical sciences, Tehran, Iran
| | | | | | - Reza Ghasemi
- Department of Pathology & Immunology, Division of Laboratory & Genomic Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Seyed Mohammad Akrami
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.
| | - Ali Rashidi-Nezhad
- Maternal, Fetal and Neonatal Research Center, Family Health Research Institute, Tehran University of Medical Sciences, Tehran, Iran.
- Genetics Ward, Yas Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran.
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Aygün N, Krupa O, Mory J, Le B, Valone J, Liang D, Love MI, Stein JL. Genetics of cell-type-specific post-transcriptional gene regulation during human neurogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.30.555019. [PMID: 37693528 PMCID: PMC10491258 DOI: 10.1101/2023.08.30.555019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
The function of some genetic variants associated with brain-relevant traits has been explained through colocalization with expression quantitative trait loci (eQTL) conducted in bulk post-mortem adult brain tissue. However, many brain-trait associated loci have unknown cellular or molecular function. These genetic variants may exert context-specific function on different molecular phenotypes including post-transcriptional changes. Here, we identified genetic regulation of RNA-editing and alternative polyadenylation (APA), within a cell-type-specific population of human neural progenitors and neurons. More RNA-editing and isoforms utilizing longer polyadenylation sequences were observed in neurons, likely due to higher expression of genes encoding the proteins mediating these post-transcriptional events. We also detected hundreds of cell-type-specific editing quantitative trait loci (edQTLs) and alternative polyadenylation QTLs (apaQTLs). We found colocalizations of a neuron edQTL in CCDC88A with educational attainment and a progenitor apaQTL in EP300 with schizophrenia, suggesting genetically mediated post-transcriptional regulation during brain development lead to differences in brain function.
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Affiliation(s)
- Nil Aygün
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- UNC Neuroscience Center University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Oleh Krupa
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- UNC Neuroscience Center University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jessica Mory
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- UNC Neuroscience Center University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Brandon Le
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- UNC Neuroscience Center University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jordan Valone
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- UNC Neuroscience Center University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Dan Liang
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- UNC Neuroscience Center University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Michael I. Love
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jason L. Stein
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- UNC Neuroscience Center University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Lead contact
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