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Eftekhar M, Panahi Y, Eskandari MR, Pedram M. Association Study between DUF1220 Copy Number and Severity of Social Impairment in Sex-balanced Simplex Cases of Autism. Noro Psikiyatr Ars 2023; 60:43-48. [PMID: 36911566 PMCID: PMC9999218 DOI: 10.29399/npa.28020] [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: 09/16/2021] [Accepted: 04/01/2022] [Indexed: 11/07/2022] Open
Abstract
Introduction Copy number variations (CNVs), which are genetic factors responsible for human evolution, have emerged as underlying pathogenic factors for a number of diseases such as autism spectrum disorders (ASD). DUF1220 coding sequences have been shown to be positively associated with the severity of symptoms in familial/multiplex cases of autism. However, this association has not been confirmed in simplex autism, and the potential impact of gender/sex has not been studied. Methods Using saliva samples taken from Iranian children with non-syndromic simplex autism, different ethnicity/race and genetic backgrounds from previous studies, we assessed the association between DUF1220 CNVs and Autism Diagnostic Interview-Revised (ADI-R) domain scores in both males and females. Results In the male and female combined group with autism, in line with previous reports, our findings showed that there were no significant associations between DUF1220 CNVs with either total ADI-R score, social, communication, or repetitive diagnostic scores in simplex autism cases. Interestingly, however, in sex classified groups, despite the insignificant results, our findings in girls with autism showed a negative trend between DUF1220 CNVs and severity of symptoms for the social interaction and communication domains. By contrast, in male children with autism, the results showed a positive trend. Conclusion It seems that association of DUF1220 CNV with the severity of symptoms in simplex children with autism may follow a sexually dimorphic pattern that needs to be re-examined in prospective studies.
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Affiliation(s)
- Mohammad Eftekhar
- Department of Genetics and Molecular Medicine, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Yasin Panahi
- Department of Pharmacology and Toxicology, School of Pharmacy, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Mohammad Reza Eskandari
- Department of Psychiatry, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Mehrdad Pedram
- Department of Genetics and Molecular Medicine, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
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High Olfactory Receptor-Rich 11q11 Copy Number in Girls and African American Children. Genes (Basel) 2021; 12:genes12121943. [PMID: 34946892 PMCID: PMC8701364 DOI: 10.3390/genes12121943] [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: 10/08/2021] [Revised: 11/22/2021] [Accepted: 11/29/2021] [Indexed: 11/17/2022] Open
Abstract
Copy number variants (CNVs) provide numerous genetic differences between individuals, and they have been linked with multiple human diseases. Obesity is one of the highly heritable complex disorders, which is associated with copy number variance (CNV). A recent report shows that the 11q11 gene, a novel olfactory receptor, and its copy number variants are involved in the early onset of obesity. In the current study, we analyzed the 11q11 gene copy number variance (CNV) based on gender in White/European American (EA) and African American (AA) normal weight and overweight/obese children. Sixty-nine boys and fifty-eight girls between the ages of 6 and 10 years belonging to either EA or AA ethnicity were involved in this study. As per World Health Organization (WHO) guidelines, each participant’s body weight and height were recorded. DNA was extracted from saliva, and the copy number variants for the 11q11 gene were measured using digital PCR. The descriptive analysis of the 11q11 copy number showed significantly more copies in girls compared to boys; similarly, AA participants had significantly increased CNV compared to EA. The normal weight (NW) and overweight/obese (OW/OB) girls were significantly less likely to belong to the low copy number variant (LCNV) group of 11q11 compared to boys; similarly, NW and OW/OB AA children were significantly less likely to belong to the LCNV group. The AA girls in LCNV had significantly higher BMI z-scores. Our findings suggest that the 11q11 copy number in children is race and gender-specific.
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Zhang R, Chen X, Wang D, Chen X, Wang C, Zhang Y, Xu M, Yu J. Prevalence of chromosomal abnormalities identified by copy number variation sequencing in high-risk pregnancies, spontaneous abortions, and suspected genetic disorders. J Int Med Res 2019; 47:1169-1178. [PMID: 30732499 PMCID: PMC6421393 DOI: 10.1177/0300060518818020] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Objective High-throughput sequencing based on copy number variation (CNV-seq) is
commonly used to detect chromosomal abnormalities including aneuploidy. This
study provides evidence for the prevalence of chromosomal abnormalities in
target populations. Methods A total of 160 samples, including 83 high-risk pregnancies, 37 spontaneous
abortions, and 40 suspected genetic disorders, were analyzed by CNV-seq.
Relationships between the incidence of these chromosomal abnormalities and
risk factors (e.g. advanced maternal age, abnormal pregnancy history, and
family history of congenital disease) were further analyzed by subgroup. Results A total of 37 (44.6%) high-risk pregnancies, 25 (67.6%) spontaneous
abortions, and 22 (55%) suspected genetic disorders had chromosomal
abnormalities including aneuploidy and CNVs. There was an increased risk
association between the prevalence of aneuploidy and pathogenic-relevant CNV
in the fetus or abortive tissue and advanced maternal age. Moreover, a
family history of congenital disease was also positively correlated with
fetal chromosomal abnormalities in high-risk pregnancies. Conclusion A relatively high prevalence of chromosomal abnormalities was detected in
high-risk pregnancies, spontaneous abortions, and suspected genetic
disorders, indicating the importance of CNV detection in such
populations.
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Affiliation(s)
- Rui Zhang
- 1 Prenatal Diagnosis Center, The Second Affiliated Hospital of Harbin Medical University, Harbin, China.,2 Scientific Research Centre, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | | | - Dong Wang
- 2 Scientific Research Centre, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xuan Chen
- 4 Department of Obstetrics, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Chao Wang
- 1 Prenatal Diagnosis Center, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yuhong Zhang
- 1 Prenatal Diagnosis Center, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | | | - Jingcui Yu
- 2 Scientific Research Centre, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
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Butcher NJ, Horne MK, Mellick GD, Fowler CJ, Masters CL, Minchin RF. Sulfotransferase 1A3/4 copy number variation is associated with neurodegenerative disease. THE PHARMACOGENOMICS JOURNAL 2017; 18:209-214. [DOI: 10.1038/tpj.2017.4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 12/12/2016] [Accepted: 01/17/2017] [Indexed: 12/14/2022]
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Global patterns of large copy number variations in the human genome reveal complexity in chromosome organization. Genet Res (Camb) 2015; 97:e18. [PMID: 26390810 DOI: 10.1017/s0016672315000191] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Global patterns of copy number variations (CNVs) in chromosomes are required to understand the dynamics of genome organization and complexity. For this study, analysis was performed using the Affymetrix Genome-Wide Human SNP Array 6.0 chip and CytoScan High-Density arrays. We identified a total of 44 109 CNVs from 1715 genomes with a mean of 25 CNVs in an individual, which established the first drafts of population-specific CNV maps providing a rationale for prioritizing chromosomal regions. About 19 905 ancient CNVs were identified across all chromosomes and populations at varying frequencies. CNV count, and sometimes CNV size, contributed to the bulk CNV size of the chromosome. Population specific lengthening and shortening of chromosomal length was observed. Sex bias for CNV presence was largely dependent on ethnicity. Lower CNV inheritance rate was observed for India, compared to YRI and CEU. A total of 33 candidate CNV hotspots from 5382 copy number (CN) variable region (CNVR) clusters were identified. Population specific CNV distribution patterns in p and q arms disturbed the assumption that CNV counts in the p arm are less common compared to long arms, and the CNV occurrence and distribution in chromosomes is length independent. This study unraveled the force of independent evolutionary dynamics on genome organization and complexity across chromosomes and populations.
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Veerappa AM, N MM, Vishweswaraiah S, Lingaiah K, Suresh RV, Nachappa SA, Prashali N, Yadav SN, Srikanta MA, Manjegowda DS, Seshachalam KB, Ramachandra NB. Copy number variations burden on miRNA genes reveals layers of complexities involved in the regulation of pathways and phenotypic expression. PLoS One 2014; 9:e90391. [PMID: 24587348 PMCID: PMC3938728 DOI: 10.1371/journal.pone.0090391] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Accepted: 01/28/2014] [Indexed: 12/21/2022] Open
Abstract
MicroRNAs are involved in post-transcriptional down-regulation of gene expression. Variations in miRNA genes can severely affect downstream-regulated genes and their pathways. However, population-specific burden of CNVs on miRNA genes and the complexities created towards the phenotype is not known. From a total of 44109 CNVs investigated from 1715 individuals across 12 populations using high-throughput arrays, 4007 miRNA-CNVs (∼ 9%) consisting 6542 (∼ 5%) miRNA genes with a total of 333 (∼ 5%) singleton miRNA genes were identified. We found miRNA-CNVs across the genomes of individuals showing multiple hits in many targets, co-regulated under the same pathway. This study proposes four mechanisms unraveling the many complexities in miRNA genes, targets and co-regulated miRNA genes towards establishment of phenotypic diversity.
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Affiliation(s)
- Avinash M. Veerappa
- Genetics and Genomics Lab, Department of Studies in Zoology, University of Mysore, Manasagangotri, Mysore, Karnataka, India
| | - Megha Murthy N
- Genetics and Genomics Lab, Department of Studies in Zoology, University of Mysore, Manasagangotri, Mysore, Karnataka, India
| | - Sangeetha Vishweswaraiah
- Genetics and Genomics Lab, Department of Studies in Zoology, University of Mysore, Manasagangotri, Mysore, Karnataka, India
| | - Kusuma Lingaiah
- Genetics and Genomics Lab, Department of Studies in Zoology, University of Mysore, Manasagangotri, Mysore, Karnataka, India
| | - Raviraj V. Suresh
- Genetics and Genomics Lab, Department of Studies in Zoology, University of Mysore, Manasagangotri, Mysore, Karnataka, India
| | - Somanna Ajjamada Nachappa
- Genetics and Genomics Lab, Department of Studies in Zoology, University of Mysore, Manasagangotri, Mysore, Karnataka, India
| | - Nelchi Prashali
- Genetics and Genomics Lab, Department of Studies in Zoology, University of Mysore, Manasagangotri, Mysore, Karnataka, India
| | - Sangeetha Nuggehalli Yadav
- Genetics and Genomics Lab, Department of Studies in Zoology, University of Mysore, Manasagangotri, Mysore, Karnataka, India
| | - Manjula Arsikere Srikanta
- Genetics and Genomics Lab, Department of Studies in Zoology, University of Mysore, Manasagangotri, Mysore, Karnataka, India
| | - Dinesh S. Manjegowda
- Department of Anatomy, Yenepoya Medical College, Yenepoya University, Mangalore, Karnataka, India
- Nitte University Centre for Science Education & Research, K S Hegde Medical Academy, Nitte University, Deralakatte, Mangalore, Karnataka, India
| | | | - Nallur B. Ramachandra
- Genetics and Genomics Lab, Department of Studies in Zoology, University of Mysore, Manasagangotri, Mysore, Karnataka, India
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