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Kautiainen R, Aleksonis H, King TZ. A Systematic Review of Host Genomic Variation and Neuropsychological Outcomes for Pediatric Cancer Survivors. Neuropsychol Rev 2023; 33:278-306. [PMID: 35305234 DOI: 10.1007/s11065-022-09539-2] [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: 05/26/2021] [Accepted: 01/25/2022] [Indexed: 10/18/2022]
Abstract
Pediatric survivors of brain tumors and acute lymphoblastic leukemia (ALL) are at risk for long-term deficits in their neuropsychological functioning. Researchers have begun examining associations between germline single nucleotide polymorphisms (SNPs), which interact with cancer treatment, and neuropsychological outcomes. This review synthesizes the impact of treatment-related toxicity from germline SNPs by neuropsychological domain (i.e., working memory, processing speed, psychological functioning) in pediatric survivors. By focusing on specific neuropsychological domains, this review will examine outcome measurement and critique methodology. Fourteen studies were identified and included in this review using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA). All studies were published in peer-reviewed journals in English by November 24th, 2021. Reviewed studies were not of sufficient quality for a meta-analysis due to varying measurement strategies, gaps in reported descriptive variables, and low power. All neuropsychological domains evaluated in this review had associations with SNPs, except fine motor and visual integration abilities. Only five SNPs had consistent neuropsychological findings in more than one study or cohort. Future research and replication studies should use validated measures of discrete skills that are central to empirically validated models of survivors' long-term outcomes (i.e., attention, working memory, processing speed). Researchers should examine SNPs across pathophysiological pathways to investigate additive genetic risk in pediatric cancer survivors. Two SNPs were identified that confer resiliency in neuropsychological functioning, and future work should investigate resiliency genotypes and their underlying biological mechanisms.
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Affiliation(s)
- Rella Kautiainen
- Department of Psychology, Georgia State University, Atlanta, Georgia
| | - Holly Aleksonis
- Department of Psychology, Georgia State University, Atlanta, Georgia
| | - Tricia Z King
- Department of Psychology and the Neuroscience Institute, Georgia State University, Atlanta, Georgia.
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2
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Akter H, Rahman MM, Sarker S, Basiruzzaman M, Islam MM, Rahaman MA, Rahaman MA, Eshaque TB, Dity NJ, Sarker S, Amin MR, Hossain MM, Lopa M, Jahan N, Hossain S, Islam A, Mondol A, Faruk MO, Saha N, Kundu GK, Kanta SI, Kazal RK, Fatema K, Rahman MA, Hasan M, Hossain Mollah MA, Hosen MI, Karuvantevida N, Begum G, Zehra B, Nassir N, Nabi AHMN, Uddin KMF, Uddin M. Construction of copy number variation landscape and characterization of associated genes in a Bangladeshi cohort of neurodevelopmental disorders. Front Genet 2023; 14:955631. [PMID: 36959829 PMCID: PMC10028086 DOI: 10.3389/fgene.2023.955631] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 02/14/2023] [Indexed: 03/09/2023] Open
Abstract
Introduction: Copy number variations (CNVs) play a critical role in the pathogenesis of neurodevelopmental disorders (NDD) among children. In this study, we aim to identify clinically relevant CNVs, genes and their phenotypic characteristics in an ethnically underrepresented homogenous population of Bangladesh. Methods: We have conducted chromosomal microarray analysis (CMA) for 212 NDD patients with male to female ratio of 2.2:1.0 to identify rare CNVs. To identify candidate genes within the rare CNVs, gene constraint metrics [i.e., "Critical-Exon Genes (CEGs)"] were applied to the population data. Autism Diagnostic Observation Schedule-Second Edition (ADOS-2) was followed in a subset of 95 NDD patients to assess the severity of autism and all statistical tests were performed using the R package. Results: Of all the samples assayed, 12.26% (26/212) and 57.08% (121/212) patients carried pathogenic and variant of uncertain significance (VOUS) CNVs, respectively. While 2.83% (6/212) patients' pathogenic CNVs were found to be located in the subtelomeric regions. Further burden test identified females are significant carriers of pathogenic CNVs compared to males (OR = 4.2; p = 0.0007). We have observed an increased number of Loss of heterozygosity (LOH) within cases with 23.85% (26/109) consanguineous parents. Our analyses on imprinting genes show, 36 LOH variants disrupting 69 unique imprinted genes and classified these variants as VOUS. ADOS-2 subset shows severe social communication deficit (p = 0.014) and overall ASD symptoms severity (p = 0.026) among the patients carrying duplication CNV compared to the CNV negative group. Candidate gene analysis identified 153 unique CEGs in pathogenic CNVs and 31 in VOUS. Of the unique genes, 18 genes were found to be in smaller (<1 MB) focal CNVs in our NDD cohort and we identified PSMC3 gene as a strong candidate gene for Autism Spectrum Disorder (ASD). Moreover, we hypothesized that KMT2B gene duplication might be associated with intellectual disability. Conclusion: Our results show the utility of CMA for precise genetic diagnosis and its integration into the diagnosis, therapy and management of NDD patients.
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Affiliation(s)
- Hosneara Akter
- Genetics and Genomic Medicine Centre, NeuroGen Healthcare, Dhaka, Bangladesh
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - Muhammad Mizanur Rahman
- Department of Paediatric Neurology, Bangabandhu Sheikh Mujib Medical University, Dhaka, Bangladesh
| | - Shaoli Sarker
- Department of Child Neurology, NeuroGen Healthcare, Dhaka, Bangladesh
- Department of Paediatric Neuroscience, Dhaka Shishu Hospital, Dhaka, Bangladesh
| | - Mohammed Basiruzzaman
- Department of Child Neurology, NeuroGen Healthcare, Dhaka, Bangladesh
- Department of Neurology, National Institute of Neurosciences and Hospital, Dhaka, Bangladesh
| | - Md. Mazharul Islam
- Department of Child Neurology, NeuroGen Healthcare, Dhaka, Bangladesh
- Department of Neurology, National Institute of Neurosciences and Hospital, Dhaka, Bangladesh
| | - Md. Atikur Rahaman
- Genetics and Genomic Medicine Centre, NeuroGen Healthcare, Dhaka, Bangladesh
| | | | | | - Nushrat Jahan Dity
- Genetics and Genomic Medicine Centre, NeuroGen Healthcare, Dhaka, Bangladesh
| | - Shouvik Sarker
- Institute of Plant Genetics, Department of Plant Biotechnology, Leibniz University Hannover, Hanover, Germany
| | - Md. Robed Amin
- Department of Medicine, Dhaka Medical College, Dhaka, Bangladesh
| | - Mohammad Monir Hossain
- Department of Paediatric Neurology, National Institute of Neuroscience and Hospital, Dhaka, Bangladesh
| | - Maksuda Lopa
- Centre for Precision Therapeutics, NeuroGen Healthcare, Dhaka, Bangladesh
| | - Nargis Jahan
- Centre for Precision Therapeutics, NeuroGen Healthcare, Dhaka, Bangladesh
| | - Shafaat Hossain
- Department of Biology and Biochemistry, University of Houston, Houston, TX, United States
| | - Amirul Islam
- Genetics and Genomic Medicine Centre, NeuroGen Healthcare, Dhaka, Bangladesh
- Cellular Intelligence Lab, GenomeArc Inc, Toronto, ON, Canada
| | | | - Md Omar Faruk
- Centre for Precision Therapeutics, NeuroGen Healthcare, Dhaka, Bangladesh
| | - Narayan Saha
- Department of Paediatric Neurology, National Institute of Neuroscience and Hospital, Dhaka, Bangladesh
| | - Gopen kumar Kundu
- Department of Child Neurology, Bangabandhu Sheikh Mujib Medical University, Dhaka, Bangladesh
| | - Shayla Imam Kanta
- Department of Paediatric Neuroscience, Dhaka Shishu Hospital, Dhaka, Bangladesh
| | - Rezaul Karim Kazal
- Department of Obstetrics and Gynaecology, Bangabandhu Sheikh Mujib Medical University, Dhaka, Bangladesh
| | - Kanij Fatema
- Department of Paediatric Neurology, Bangabandhu Sheikh Mujib Medical University, Dhaka, Bangladesh
| | - Md. Ashrafur Rahman
- Department of Pharmaceutical Sciences, Wilkes University, Pennsylvania, PA, United States
| | - Maruf Hasan
- Department of Biomedical Engineering, Military Institute of Science and Technology, Dhaka, Bangladesh
| | | | - Md. Ismail Hosen
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - Noushad Karuvantevida
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Ghausia Begum
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Binte Zehra
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Nasna Nassir
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - A. H. M. Nurun Nabi
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - K. M. Furkan Uddin
- Genetics and Genomic Medicine Centre, NeuroGen Healthcare, Dhaka, Bangladesh
- Department of Biochemistry, Holy Family Red Crescent Medical College, Dhaka, Bangladesh
| | - Mohammed Uddin
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
- Cellular Intelligence (Ci) Lab, GenomeArc Inc, Toronto, ON, Canada
- *Correspondence: Mohammed Uddin,
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3
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van der Laan L, Rooney K, Trooster TM, Mannens MM, Sadikovic B, Henneman P. DNA methylation episignatures: insight into copy number variation. Epigenomics 2022; 14:1373-1388. [PMID: 36537268 DOI: 10.2217/epi-2022-0287] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
In this review we discuss epigenetic disorders that result from aberrations in genes linked to epigenetic regulation. We describe current testing methods for the detection of copy number variants (CNVs) in Mendelian disorders, dosage sensitivity, reciprocal phenotypes and the challenges of test selection and overlapping clinical features in genetic diagnosis. We discuss aberrations of DNA methylation and propose a role for episignatures as a novel clinical testing method in CNV disorders. Finally, we postulate that episignature mapping in CNV disorders may provide novel insights into the molecular mechanisms of disease and unlock key findings of the genome-wide impact on disease gene networks.
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Affiliation(s)
- Liselot van der Laan
- Department of Human Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam University Medical Centers, Amsterdam, 1105 AZ, The Netherlands
| | - Kathleen Rooney
- Department of Pathology & Laboratory Medicine, Western University, London, Ontario, N5A 3K7, Canada.,Verspeeten Clinical Genome Centre, London Health Science Centre, London, Ontario, N6A 5W9, Canada
| | - Tessa Ma Trooster
- Department of Human Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam University Medical Centers, Amsterdam, 1105 AZ, The Netherlands
| | - Marcel Mam Mannens
- Department of Human Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam University Medical Centers, Amsterdam, 1105 AZ, The Netherlands
| | - Bekim Sadikovic
- Department of Pathology & Laboratory Medicine, Western University, London, Ontario, N5A 3K7, Canada.,Verspeeten Clinical Genome Centre, London Health Science Centre, London, Ontario, N6A 5W9, Canada
| | - Peter Henneman
- Department of Human Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam University Medical Centers, Amsterdam, 1105 AZ, The Netherlands
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4
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Pang H, Lin J, Luo S, Huang G, Li X, Xie Z, Zhou Z. The missing heritability in type 1 diabetes. Diabetes Obes Metab 2022; 24:1901-1911. [PMID: 35603907 PMCID: PMC9545639 DOI: 10.1111/dom.14777] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 05/04/2022] [Accepted: 05/17/2022] [Indexed: 12/15/2022]
Abstract
Type 1 diabetes (T1D) is a complex autoimmune disease characterized by an absolute deficiency of insulin. It affects more than 20 million people worldwide and imposes an enormous financial burden on patients. The underlying pathogenic mechanisms of T1D are still obscure, but it is widely accepted that both genetics and the environment play an important role in its onset and development. Previous studies have identified more than 60 susceptible loci associated with T1D, explaining approximately 80%-85% of the heritability. However, most identified variants confer only small increases in risk, which restricts their potential clinical application. In addition, there is still a so-called 'missing heritability' phenomenon. While the gap between known heritability and true heritability in T1D is small compared with that in other complex traits and disorders, further elucidation of T1D genetics has the potential to bring novel insights into its aetiology and provide new therapeutic targets. Many hypotheses have been proposed to explain the missing heritability, including variants remaining to be found (variants with small effect sizes, rare variants and structural variants) and interactions (gene-gene and gene-environment interactions; e.g. epigenetic effects). In the following review, we introduce the possible sources of missing heritability and discuss the existing related knowledge in the context of T1D.
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Affiliation(s)
- Haipeng Pang
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and EndocrinologyThe Second Xiangya Hospital of Central South UniversityChangshaChina
| | - Jian Lin
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and EndocrinologyThe Second Xiangya Hospital of Central South UniversityChangshaChina
| | - Shuoming Luo
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and EndocrinologyThe Second Xiangya Hospital of Central South UniversityChangshaChina
| | - Gan Huang
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and EndocrinologyThe Second Xiangya Hospital of Central South UniversityChangshaChina
| | - Xia Li
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and EndocrinologyThe Second Xiangya Hospital of Central South UniversityChangshaChina
| | - Zhiguo Xie
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and EndocrinologyThe Second Xiangya Hospital of Central South UniversityChangshaChina
| | - Zhiguang Zhou
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and EndocrinologyThe Second Xiangya Hospital of Central South UniversityChangshaChina
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5
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Rooney K, Sadikovic B. DNA Methylation Episignatures in Neurodevelopmental Disorders Associated with Large Structural Copy Number Variants: Clinical Implications. Int J Mol Sci 2022; 23:ijms23147862. [PMID: 35887210 PMCID: PMC9324454 DOI: 10.3390/ijms23147862] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 07/11/2022] [Accepted: 07/14/2022] [Indexed: 02/06/2023] Open
Abstract
Large structural chromosomal deletions and duplications, referred to as copy number variants (CNVs), play a role in the pathogenesis of neurodevelopmental disorders (NDDs) through effects on gene dosage. This review focuses on our current understanding of genomic disorders that arise from large structural chromosome rearrangements in patients with NDDs, as well as difficulties in overlap of clinical presentation and molecular diagnosis. We discuss the implications of epigenetics, specifically DNA methylation (DNAm), in NDDs and genomic disorders, and consider the implications and clinical impact of copy number and genomic DNAm testing in patients with suspected genetic NDDs. We summarize evidence of global methylation episignatures in CNV-associated disorders that can be used in the diagnostic pathway and may provide insights into the molecular pathogenesis of genomic disorders. Finally, we discuss the potential for combining CNV and DNAm assessment into a single diagnostic assay.
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Affiliation(s)
- Kathleen Rooney
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada;
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada
| | - Bekim Sadikovic
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada;
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada
- Correspondence: ; Tel.: +1-519-685-8500 (ext. 53074)
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6
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Pagni S, Mills JD, Frankish A, Mudge JM, Sisodiya SM. Non-coding regulatory elements: Potential roles in disease and the case of epilepsy. Neuropathol Appl Neurobiol 2021; 48:e12775. [PMID: 34820881 DOI: 10.1111/nan.12775] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 10/04/2021] [Accepted: 11/16/2021] [Indexed: 12/27/2022]
Abstract
Non-coding DNA (ncDNA) refers to the portion of the genome that does not code for proteins and accounts for the greatest physical proportion of the human genome. ncDNA includes sequences that are transcribed into RNA molecules, such as ribosomal RNAs (rRNAs), microRNAs (miRNAs), long non-coding RNAs (lncRNAs) and un-transcribed sequences that have regulatory functions, including gene promoters and enhancers. Variation in non-coding regions of the genome have an established role in human disease, with growing evidence from many areas, including several cancers, Parkinson's disease and autism. Here, we review the features and functions of the regulatory elements that are present in the non-coding genome and the role that these regions have in human disease. We then review the existing research in epilepsy and emphasise the potential value of further exploring non-coding regulatory elements in epilepsy. In addition, we outline the most widely used techniques for recognising regulatory elements throughout the genome, current methodologies for investigating variation and the main challenges associated with research in the field of non-coding DNA.
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Affiliation(s)
- Susanna Pagni
- Department of Clinical and Experimental Epilepsy, UCL Queen Square Institute of Neurology, London, UK.,Chalfont Centre for Epilepsy, Chalfont St Peter, UK
| | - James D Mills
- Department of Clinical and Experimental Epilepsy, UCL Queen Square Institute of Neurology, London, UK.,Chalfont Centre for Epilepsy, Chalfont St Peter, UK.,Amsterdam UMC, Department of (Neuro)Pathology, Amsterdam Neuroscience, University of Amsterdam, Amsterdam, Netherlands
| | - Adam Frankish
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | - Jonathan M Mudge
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | - Sanjay M Sisodiya
- Department of Clinical and Experimental Epilepsy, UCL Queen Square Institute of Neurology, London, UK.,Chalfont Centre for Epilepsy, Chalfont St Peter, UK
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7
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Sun Y, Liu F, Fan C, Wang Y, Song L, Fang Z, Han R, Wang Z, Wang X, Yang Z, Xu Z, Peng J, Shi C, Zhang H, Dong W, Huang H, Li Y, Le Y, Sun J, Peng Z. Characterizing sensitivity and coverage of clinical WGS as a diagnostic test for genetic disorders. BMC Med Genomics 2021; 14:102. [PMID: 33849535 PMCID: PMC8045368 DOI: 10.1186/s12920-021-00948-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 03/31/2021] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Due to its reduced cost and incomparable advantages, WGS is likely to lead to changes in clinical diagnosis of rare and undiagnosed diseases. However, the sensitivity and breadth of coverage of clinical WGS as a diagnostic test for genetic disorders has not been fully evaluated. METHODS Here, the performance of WGS in NA12878, the YH cell line, and the Chinese trios were measured by assessing their sensitivity, PPV, depth and breadth of coverage using MGISEQ-2000. We also compared the performance of WES and WGS using NA12878. The sensitivity and PPV were tested using the family-based trio design for the Chinese trios. We further developed a systematic WGS pipeline for the analysis of 8 clinical cases. RESULTS In general, the sensitivity and PPV for SNV/indel detection increased with mean depth and reached a plateau at an ~ 40X mean depth using down-sampling samples of NA12878. With a mean depth of 40X, the sensitivity of homozygous and heterozygous SNPs of NA12878 was > 99.25% and > 99.50%, respectively, and the PPV was 99.97% and 98.96%. Homozygous and heterozygous indels showed lower sensitivity and PPV. The sensitivity and PPV were still not 100% even with a mean depth of ~ 150X. We also observed a substantial variation in the sensitivity of CNV detection across different tools, especially in CNVs with a size less than 1 kb. In general, the breadth of coverage for disease-associated genes and CNVs increased with mean depth. The sensitivity and coverage of WGS (~ 40X) was better than WES (~ 120X). Among the Chinese trios with an ~ 40X mean depth, the sensitivity among offspring was > 99.48% and > 96.36% for SNP and indel detection, and the PPVs were 99.86% and 97.93%. All 12 previously validated variants in the 8 clinical cases were successfully detected using our WGS pipeline. CONCLUSIONS The current standard of a mean depth of 40X may be sufficient for SNV/indel detection and identification of most CNVs. It would be advisable for clinical scientists to determine the range of sensitivity and PPV for different classes of variants for a particular WGS pipeline, which would be useful when interpreting and delivering clinical reports.
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Affiliation(s)
- Yan Sun
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Fengxia Liu
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
- Binhai Genomics Institute, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Chunna Fan
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
- Binhai Genomics Institute, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Yaoshen Wang
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
- Binhai Genomics Institute, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Lijie Song
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
- Binhai Genomics Institute, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Zhonghai Fang
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
- Binhai Genomics Institute, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Rui Han
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
- Binhai Genomics Institute, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Zhonghua Wang
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
- Binhai Genomics Institute, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Xiaodan Wang
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
- Binhai Genomics Institute, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Ziying Yang
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
- Binhai Genomics Institute, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Zhenpeng Xu
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Jiguang Peng
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Chaonan Shi
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
- Binhai Genomics Institute, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | | | - Wei Dong
- BGI-Beijing Clinical Laboratories, BGI-Shenzhen, Beijing, 101300, China
| | - Hui Huang
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Yun Li
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Yanqun Le
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Jun Sun
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China.
- Binhai Genomics Institute, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China.
| | - Zhiyu Peng
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China.
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8
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Dewey D. What Is Comorbidity and Why Does It Matter in Neurodevelopmental Disorders? CURRENT DEVELOPMENTAL DISORDERS REPORTS 2018. [DOI: 10.1007/s40474-018-0152-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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9
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Zhou B, Ho SS, Zhang X, Pattni R, Haraksingh RR, Urban AE. Whole-genome sequencing analysis of CNV using low-coverage and paired-end strategies is efficient and outperforms array-based CNV analysis. J Med Genet 2018; 55:735-743. [PMID: 30061371 DOI: 10.1136/jmedgenet-2018-105272] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 05/16/2018] [Accepted: 06/26/2018] [Indexed: 11/03/2022]
Abstract
BACKGROUND Copy number variation (CNV) analysis is an integral component of the study of human genomes in both research and clinical settings. Array-based CNV analysis is the current first-tier approach in clinical cytogenetics. Decreasing costs in high-throughput sequencing and cloud computing have opened doors for the development of sequencing-based CNV analysis pipelines with fast turnaround times. We carry out a systematic and quantitative comparative analysis for several low-coverage whole-genome sequencing (WGS) strategies to detect CNV in the human genome. METHODS We compared the CNV detection capabilities of WGS strategies (short insert, 3 kb insert mate pair and 5 kb insert mate pair) each at 1×, 3× and 5× coverages relative to each other and to 17 currently used high-density oligonucleotide arrays. For benchmarking, we used a set of gold standard (GS) CNVs generated for the 1000 Genomes Project CEU subject NA12878. RESULTS Overall, low-coverage WGS strategies detect drastically more GS CNVs compared with arrays and are accompanied with smaller percentages of CNV calls without validation. Furthermore, we show that WGS (at ≥1× coverage) is able to detect all seven GS deletion CNVs >100 kb in NA12878, whereas only one is detected by most arrays. Lastly, we show that the much larger 15 Mbp Cri du chat deletion can be readily detected with short-insert paired-end WGS at even just 1× coverage. CONCLUSIONS CNV analysis using low-coverage WGS is efficient and outperforms the array-based analysis that is currently used for clinical cytogenetics.
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Affiliation(s)
- Bo Zhou
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, California, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Steve S Ho
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, California, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Xianglong Zhang
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, California, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Reenal Pattni
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, California, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Rajini R Haraksingh
- Department of Life Sciences, The University of the West Indies, Saint Augustine, Trinidad and Tobago
| | - Alexander E Urban
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, California, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, California, USA.,Program on Genetics of Brain Function, Stanford Center for Genomics and Personalized Medicine, Tasha and John Morgridge Faculty Scholar, Stanford Child Health Research Institute, Stanford University, Stanford, California, USA
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10
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Comprehensive performance comparison of high-resolution array platforms for genome-wide Copy Number Variation (CNV) analysis in humans. BMC Genomics 2017; 18:321. [PMID: 28438122 PMCID: PMC5402652 DOI: 10.1186/s12864-017-3658-x] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 03/25/2017] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND High-resolution microarray technology is routinely used in basic research and clinical practice to efficiently detect copy number variants (CNVs) across the entire human genome. A new generation of arrays combining high probe densities with optimized designs will comprise essential tools for genome analysis in the coming years. We systematically compared the genome-wide CNV detection power of all 17 available array designs from the Affymetrix, Agilent, and Illumina platforms by hybridizing the well-characterized genome of 1000 Genomes Project subject NA12878 to all arrays, and performing data analysis using both manufacturer-recommended and platform-independent software. We benchmarked the resulting CNV call sets from each array using a gold standard set of CNVs for this genome derived from 1000 Genomes Project whole genome sequencing data. RESULTS The arrays tested comprise both SNP and aCGH platforms with varying designs and contain between ~0.5 to ~4.6 million probes. Across the arrays CNV detection varied widely in number of CNV calls (4-489), CNV size range (~40 bp to ~8 Mbp), and percentage of non-validated CNVs (0-86%). We discovered strikingly strong effects of specific array design principles on performance. For example, some SNP array designs with the largest numbers of probes and extensive exonic coverage produced a considerable number of CNV calls that could not be validated, compared to designs with probe numbers that are sometimes an order of magnitude smaller. This effect was only partially ameliorated using different analysis software and optimizing data analysis parameters. CONCLUSIONS High-resolution microarrays will continue to be used as reliable, cost- and time-efficient tools for CNV analysis. However, different applications tolerate different limitations in CNV detection. Our study quantified how these arrays differ in total number and size range of detected CNVs as well as sensitivity, and determined how each array balances these attributes. This analysis will inform appropriate array selection for future CNV studies, and allow better assessment of the CNV-analytical power of both published and ongoing array-based genomics studies. Furthermore, our findings emphasize the importance of concurrent use of multiple analysis algorithms and independent experimental validation in array-based CNV detection studies.
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Iourov IY, Vorsanova SG, Korostelev SA, Vasin KS, Zelenova MA, Kurinnaia OS, Yurov YB. [Structural variations of the genome in autistic spectrum disorders with intellectual disability]. Zh Nevrol Psikhiatr Im S S Korsakova 2016; 116:50-54. [PMID: 27500877 DOI: 10.17116/jnevro20161167150-54] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
AIM To analyze structural variations in the genome in children with autism and intellectual disability. MATERIAL AND METHODS Using high-resolution karyotyping (AffymetrixCytoScan HD Array) and original bioinformatic technology, 200 children with autism and intellectual disability were studied. RESULTS AND CONCLUSION Data on structural variations in the genome in children with autism and intellectual disability are provided. Causative genomic pathology (chromosome abnormalities and copy number variations - CNV) was determined in 97 cases (48.5%). Based on these RESULTS 24 candidate genes for autism with intellectual disability were selected. In 16 cases (8%), the chromosome mosaicism manifested as aneuploidy of whole autosomes and sex chromosomes (gonosomes) was identified. In 87 children (43.5%), there were genomic variations, which are characteristic of the so-called «grey zone» of genetic pathology in mental illnesses. Bioinformatic analysis showed that these genomic variations had a pleiotropic effect on the phenotype.
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Affiliation(s)
- I Yu Iourov
- Mental Health Research Center, Moscow, Russia; Veltishev Research and Clinical Institute for Pediatrics at the Pirogov Russian National Research Medical University, Moscow, Russia; Russian Medical Academy of Postgraduate Education, Moscow, Russia
| | - S G Vorsanova
- Mental Health Research Center, Moscow, Russia; Veltishev Research and Clinical Institute for Pediatrics at the Pirogov Russian National Research Medical University, Moscow, Russia; Moscow State University of Psychology and Education, Moscow, Russia
| | | | - K S Vasin
- Mental Health Research Center, Moscow, Russia; Veltishev Research and Clinical Institute for Pediatrics at the Pirogov Russian National Research Medical University, Moscow, Russia; Moscow State University of Psychology and Education, Moscow, Russia
| | - M A Zelenova
- Mental Health Research Center, Moscow, Russia; Veltishev Research and Clinical Institute for Pediatrics at the Pirogov Russian National Research Medical University, Moscow, Russia; Moscow State University of Psychology and Education, Moscow, Russia
| | - O S Kurinnaia
- Mental Health Research Center, Moscow, Russia; Veltishev Research and Clinical Institute for Pediatrics at the Pirogov Russian National Research Medical University, Moscow, Russia; Moscow State University of Psychology and Education, Moscow, Russia
| | - Yu B Yurov
- Mental Health Research Center, Moscow, Russia; Veltishev Research and Clinical Institute for Pediatrics at the Pirogov Russian National Research Medical University, Moscow, Russia; Moscow State University of Psychology and Education, Moscow, Russia
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Mosca SJ, Langevin LM, Dewey D, Innes AM, Lionel AC, Marshall CC, Scherer SW, Parboosingh JS, Bernier FP. Copy-number variations are enriched for neurodevelopmental genes in children with developmental coordination disorder. J Med Genet 2016; 53:812-819. [DOI: 10.1136/jmedgenet-2016-103818] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Revised: 07/08/2016] [Accepted: 07/11/2016] [Indexed: 01/24/2023]
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Brewer MH, Chaudhry R, Qi J, Kidambi A, Drew AP, Menezes MP, Ryan MM, Farrar MA, Mowat D, Subramanian GM, Young HK, Zuchner S, Reddel SW, Nicholson GA, Kennerson ML. Whole Genome Sequencing Identifies a 78 kb Insertion from Chromosome 8 as the Cause of Charcot-Marie-Tooth Neuropathy CMTX3. PLoS Genet 2016; 12:e1006177. [PMID: 27438001 PMCID: PMC4954712 DOI: 10.1371/journal.pgen.1006177] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 06/15/2016] [Indexed: 11/18/2022] Open
Abstract
With the advent of whole exome sequencing, cases where no pathogenic coding mutations can be found are increasingly being observed in many diseases. In two large, distantly-related families that mapped to the Charcot-Marie-Tooth neuropathy CMTX3 locus at chromosome Xq26.3-q27.3, all coding mutations were excluded. Using whole genome sequencing we found a large DNA interchromosomal insertion within the CMTX3 locus. The 78 kb insertion originates from chromosome 8q24.3, segregates fully with the disease in the two families, and is absent from the general population as well as 627 neurologically normal chromosomes from in-house controls. Large insertions into chromosome Xq27.1 are known to cause a range of diseases and this is the first neuropathy phenotype caused by an interchromosomal insertion at this locus. The CMTX3 insertion represents an understudied pathogenic structural variation mechanism for inherited peripheral neuropathies. Our finding highlights the importance of considering all structural variation types when studying unsolved inherited peripheral neuropathy cases with no pathogenic coding mutations.
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Affiliation(s)
- Megan H. Brewer
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Concord, New South Wales, Australia
- Sydney Medical School, University of Sydney, Camperdown, New South Wales, Australia
- * E-mail:
| | - Rabia Chaudhry
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Concord, New South Wales, Australia
- Sydney Medical School, University of Sydney, Camperdown, New South Wales, Australia
| | - Jessica Qi
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Concord, New South Wales, Australia
- Discipline of Pathology, University of Sydney, Camperdown, New South Wales, Australia
| | - Aditi Kidambi
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Concord, New South Wales, Australia
| | - Alexander P. Drew
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Concord, New South Wales, Australia
| | - Manoj P. Menezes
- The Institute for Neuroscience and Muscle Research, The Children’s Hospital at Westmead, Westmead, New South Wales, Australia
- T.Y. Nelson Department of Neurology and Neurosurgery, The Children’s Hospital at Westmead, Westmead, New South Wales, Australia
- Paediatrics and Child Health, University of Sydney, Camperdown, New South Wales, Australia
| | - Monique M. Ryan
- Department of Neurology, Royal Children’s Hospital, Parkville, Victoria, Australia
- Murdoch Childrens Research Institute, Parkville, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia
| | - Michelle A. Farrar
- Department of Neurology, Sydney Children’s Hospital, Randwick, New South Wales, Australia
- School of Women’s and Children’s Health, UNSW Medicine, University of New South Wales, Kensington, New South Wales, Australia
| | - David Mowat
- School of Women’s and Children’s Health, UNSW Medicine, University of New South Wales, Kensington, New South Wales, Australia
- Department of Medical Genetics, Sydney Children’s Hospital, Randwick, New South Wales, Australia
| | - Gopinath M. Subramanian
- Department of Paediatrics, John Hunter Children’s Hospital, Newcastle, New South Wales, Australia
| | - Helen K. Young
- Department of Paediatrics, Royal North Shore Hospital, St Leonards, New South Wales, Australia
- Northern Clinical School, Sydney Medical School, University of Sydney, St Leonards, New South Wales, Australia
- Department of Neurogenetics, The Children’s Hospital at Westmead, Westmead, New South Wales, Australia
| | - Stephan Zuchner
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, United States of America
- Dr. John T. Macdonald Department of Human Genetics, University of Miami Miller School of Medicine, Miami, Florida, United States of America
| | - Stephen W. Reddel
- Department of Neurology, Concord Repatriation General Hospital, Concord, New South Wales, Australia
| | - Garth A. Nicholson
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Concord, New South Wales, Australia
- Sydney Medical School, University of Sydney, Camperdown, New South Wales, Australia
- Molecular Medicine, Concord Repatriation General Hospital, Concord, New South Wales, Australia
| | - Marina L. Kennerson
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Concord, New South Wales, Australia
- Sydney Medical School, University of Sydney, Camperdown, New South Wales, Australia
- Molecular Medicine, Concord Repatriation General Hospital, Concord, New South Wales, Australia
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Dewey D, Bernier FP. The Concept of Atypical Brain Development in Developmental Coordination Disorder (DCD)—a New Look. CURRENT DEVELOPMENTAL DISORDERS REPORTS 2016. [DOI: 10.1007/s40474-016-0086-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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15
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Genotyping of single nucleotide polymorphisms related to attention-deficit hyperactivity disorder. Anal Bioanal Chem 2016; 408:2339-45. [DOI: 10.1007/s00216-016-9332-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Revised: 01/08/2016] [Accepted: 01/12/2016] [Indexed: 01/04/2023]
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16
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Wu N, Su Y. Oxytocin Receptor Gene Relates to Theory of Mind and Prosocial Behavior in Children. JOURNAL OF COGNITION AND DEVELOPMENT 2014. [DOI: 10.1080/15248372.2013.858042] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Shozu M, Fukami M, Ogata T. Understanding the pathological manifestations of aromatase excess syndrome: lessons for clinical diagnosis. Expert Rev Endocrinol Metab 2014; 9:397-409. [PMID: 25264451 PMCID: PMC4162655 DOI: 10.1586/17446651.2014.926810] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
CYP19A1 Aromatase excess syndrome is characterized by pre- or peripubertal onset of gynecomastia due to estrogen excess because of a gain-of-function mutation in the aromatase gene (CYP19A1). Subchromosomal recombination events including duplication, deletion, and inversion has been identified. The latter two recombinations recruit novel promoters for CYP19A1 through a unique mechanism. Gynecomastia continues for life, and although the general condition is well preserved, it may cause psychological issues. Minor symptoms (variably advanced bone age and short adult height), if present, are exclusively because of estrogen excess. Serum estradiol levels are elevated in 48% of affected males, but are not necessarily useful for diagnosis. Molecular analysis of CYP19A1 mutations is mandatory to confirm aromatase excess syndrome diagnosis. Furthermore, the use of an aromatase inhibitor can ameliorate gynecomastia.
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Affiliation(s)
- Makio Shozu
- Department of Reproductive Medicine, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba City 260-8670, Japan
| | - Maki Fukami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, 2-10-1 Ohkura, Setagaya, Tokyo 157-8535, Japan
| | - Tsutomu Ogata
- Department of Pediatrics, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, Shizuoka, 431-3192, Japan
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Hannibal RL, Chuong EB, Rivera-Mulia JC, Gilbert DM, Valouev A, Baker JC. Copy number variation is a fundamental aspect of the placental genome. PLoS Genet 2014; 10:e1004290. [PMID: 24785991 PMCID: PMC4006706 DOI: 10.1371/journal.pgen.1004290] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 02/20/2014] [Indexed: 11/19/2022] Open
Abstract
Discovery of lineage-specific somatic copy number variation (CNV) in mammals has led to debate over whether CNVs are mutations that propagate disease or whether they are a normal, and even essential, aspect of cell biology. We show that 1,000N polyploid trophoblast giant cells (TGCs) of the mouse placenta contain 47 regions, totaling 138 Megabases, where genomic copies are underrepresented (UR). UR domains originate from a subset of late-replicating heterochromatic regions containing gene deserts and genes involved in cell adhesion and neurogenesis. While lineage-specific CNVs have been identified in mammalian cells, classically in the immune system where V(D)J recombination occurs, we demonstrate that CNVs form during gestation in the placenta by an underreplication mechanism, not by recombination nor deletion. Our results reveal that large scale CNVs are a normal feature of the mammalian placental genome, which are regulated systematically during embryogenesis and are propagated by a mechanism of underreplication. Generally, every mammalian cell has the same complement of each part of its genome. However, copy number variation (CNV) can occur, where, compared to the rest of its genome, a cell has either more or less of a specific genomic region. It is unknown whether CNVs cause disease, or whether they are a normal aspect of cell biology. We investigated CNVs in polyploid trophoblast giant cells (TGCs) of the mouse placenta, which have up to 1,000 copies of the genome in each cell. We found that there are 47 regions with decreased copy number in TGCs, which we call underrepresented (UR) domains. These domains are marked in the TGC progenitor cells and we suggest that they gradually form during gestation due to slow replication versus fast replication of the rest of the genome. While UR domains contain cell adhesion and neuronal genes, they also contain significantly fewer genes than other genomic regions. Our results demonstrate that CNVs are a normal feature of the mammalian placental genome, which are regulated systematically during pregnancy.
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Affiliation(s)
- Roberta L. Hannibal
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Edward B. Chuong
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Juan Carlos Rivera-Mulia
- Department of Biological Science, Florida State University, Tallahassee, Tallahassee Florida, United States of America
| | - David M. Gilbert
- Department of Biological Science, Florida State University, Tallahassee, Tallahassee Florida, United States of America
| | - Anton Valouev
- Division of Bioinformatics, Department of Preventive Medicine, University of Southern California Keck School of Medicine, Los Angeles, California, United States of America
| | - Julie C. Baker
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
- * E-mail:
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Impacts of variation in the human genome on gene regulation. J Mol Biol 2013; 425:3970-7. [PMID: 23871684 DOI: 10.1016/j.jmb.2013.07.015] [Citation(s) in RCA: 95] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Revised: 07/10/2013] [Accepted: 07/10/2013] [Indexed: 11/22/2022]
Abstract
Recent advances in fast and inexpensive DNA sequencing have enabled the extensive study of genomic and transcriptomic variation in humans. Human genomic variation is composed of sequence and structural changes including single-nucleotide and multinucleotide variants, short insertions or deletions (indels), larger copy number variants, and similarly sized copy neutral inversions and translocations. It is now well established that any two genomes differ extensively and that structural changes constitute a prominent source of this variation. There have also been major technological advances in RNA sequencing to globally quantify and describe diversity in transcripts. Large consortia such as the 1000 Genomes Project and the ENCODE (ENCyclopedia Of DNA Elements) Project are producing increasingly comprehensive maps outlining the regions of the human genome containing variants and functional elements, respectively. Integration of genetic variation data and extensive annotation of functional genomic elements, along with the ability to measure global transcription, allow the impacts of genetic variants on gene expression to be resolved. There are several well-established models by which genetic variants affect gene regulation depending on the type, nature, and position of the variant with respect to the affected genes. These effects can be manifested in two ways: changes to transcript sequences and isoforms by coding variants, and changes to transcript abundance by dosage or regulatory variants. Here, we review the current state of how genetic variations impact gene regulation locally and globally in the human genome.
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