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Yilmaz F, Gurusamy U, Mosley TJ, Hallast P, Kim K, Mostovoy Y, Purcell RH, Shaikh TH, Zwick ME, Kwok PY, Lee C, Mulle JG. High level of complexity and global diversity of the 3q29 locus revealed by optical mapping and long-read sequencing. Genome Med 2023; 15:35. [PMID: 37165454 PMCID: PMC10170684 DOI: 10.1186/s13073-023-01184-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 04/20/2023] [Indexed: 05/12/2023] Open
Abstract
BACKGROUND High sequence identity between segmental duplications (SDs) can facilitate copy number variants (CNVs) via non-allelic homologous recombination (NAHR). These CNVs are one of the fundamental causes of genomic disorders such as the 3q29 deletion syndrome (del3q29S). There are 21 protein-coding genes lost or gained as a result of such recurrent 1.6-Mbp deletions or duplications, respectively, in the 3q29 locus. While NAHR plays a role in CNV occurrence, the factors that increase the risk of NAHR at this particular locus are not well understood. METHODS We employed an optical genome mapping technique to characterize the 3q29 locus in 161 unaffected individuals, 16 probands with del3q29S and their parents, and 2 probands with the 3q29 duplication syndrome (dup3q29S). Long-read sequencing-based haplotype resolved de novo assemblies from 44 unaffected individuals, and 1 trio was used for orthogonal validation of haplotypes and deletion breakpoints. RESULTS In total, we discovered 34 haplotypes, of which 19 were novel haplotypes. Among these 19 novel haplotypes, 18 were detected in unaffected individuals, while 1 novel haplotype was detected on the parent-of-origin chromosome of a proband with the del3q29S. Phased assemblies from 44 unaffected individuals enabled the orthogonal validation of 20 haplotypes. In 89% (16/18) of the probands, breakpoints were confined to paralogous copies of a 20-kbp segment within the 3q29 SDs. In one del3q29S proband, the breakpoint was confined to a 374-bp region using long-read sequencing. Furthermore, we categorized del3q29S cases into three classes and dup3q29S cases into two classes based on breakpoints. Finally, we found no evidence of inversions in parent-of-origin chromosomes. CONCLUSIONS We have generated the most comprehensive haplotype map for the 3q29 locus using unaffected individuals, probands with del3q29S or dup3q29S, and available parents, and also determined the deletion breakpoint to be within a 374-bp region in one proband with del3q29S. These results should provide a better understanding of the underlying genetic architecture that contributes to the etiology of del3q29S and dup3q29S.
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Affiliation(s)
- Feyza Yilmaz
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, 06032, USA
| | - Umamaheswaran Gurusamy
- Cardiovascular Research Institute and Institute for Human Genetics, UCSF School of Medicine, 513 Parnassus Ave, San Francisco, CA, 94143, USA
| | - Trenell J Mosley
- Graduate Program in Genetics and Molecular Biology, Laney Graduate School, Emory University, 201 Dowman Drive, Atlanta, GA, 30322, USA
| | - Pille Hallast
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, 06032, USA
| | - Kwondo Kim
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, 06032, USA
| | - Yulia Mostovoy
- Cardiovascular Research Institute and Institute for Human Genetics, UCSF School of Medicine, 513 Parnassus Ave, San Francisco, CA, 94143, USA
| | - Ryan H Purcell
- Laboratory of Translational Cell Biology, Department of Cell Biology, Emory University School of Medicine, 100 Woodruff Circle, Atlanta, GA, 30322, USA
| | - Tamim H Shaikh
- Department of Pediatrics, Section of Genetics and Metabolism, University of Colorado School of Medicine, 13123 E 16Th Ave, Aurora, CO, 80045, USA
| | - Michael E Zwick
- Department of Genetics, Rutgers University-New Brunswick, Rutgers University, Piscataway, New Brunswick, NJ, 08901, USA
| | - Pui-Yan Kwok
- Cardiovascular Research Institute and Institute for Human Genetics, UCSF School of Medicine, 513 Parnassus Ave, San Francisco, CA, 94143, USA
- Department of Dermatology, UCSF School of Medicine, 1701 Divisadero Street, San Francisco, CA, 94115, USA
| | - Charles Lee
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, 06032, USA.
| | - Jennifer G Mulle
- Department of Psychiatry, Robert Wood Johnson Medical School, Rutgers Biomedical and Health Sciences, Rutgers University, 671 Hoes Lane, New Brunswick, NJ, 08901, USA.
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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: 2] [Impact Index Per Article: 2.0] [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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Huang Y, Tian R, Xu J, Ji Z, Zhang Y, Zhao L, Yang C, Li P, Zhi E, Bai H, Han S, Luo J, Zhao J, Zhang J, Zhou Z, Li Z, Yao C. Novel copy number variations within SYCE1 caused meiotic arrest and non-obstructive azoospermia. BMC Med Genomics 2022; 15:137. [PMID: 35718780 PMCID: PMC9208180 DOI: 10.1186/s12920-022-01288-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 06/06/2022] [Indexed: 01/26/2023] Open
Abstract
Background Non-obstructive azoospermia (NOA) is the most severe disease in male infertility, but the genetic causes for majority of NOA remain unknown. Methods Two Chinese NOA-affected patients were recruited to identify the genetic causal factor of infertility. Whole-exome sequencing (WES) was conducted in the two patients with NOA. Sanger sequencing and CNV array were used to ascertain the WES results. Hematoxylin and eosin (H&E) staining and immunofluorescence (IF) were carried out to evaluate the stage of spermatogenesis arrested in the affected cases. Results Novel heterozygous deletion (LOH) within SYCE1 (seq[GRCh37] del(10)(10q26.3)chr10:g.135111754_135427143del) and heterozygous loss of function (LoF) variant in SYCE1 (NM_001143763: c.689_690 del:p.F230fs) were identified in one NOA-affected patient. While homozygous deletion within SYCE1 (seq[GRCh37] del(10)(10q26.3)chr10:g.135340247_135379115del) was detected in the other patient with meiotic arrest. H&E and IF staining demonstrated that the spermatogenesis was arrested at pachytene stage in the two patients with NOA, suggesting these two novel CNVs within SYCE1 could lead to meiotic defect and NOA. Conclusions We identified that two novel CNVs within SYCE1 are associated with meiotic arrest and male infertility. Thus, our study expands the knowledge of variants in SYCE1 and provides a new insight to understand the genetic etiologies of NOA. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-022-01288-8.
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Affiliation(s)
- Yuhua Huang
- Department of Andrology, Shanghai Key Laboratory of Reproductive Medicine, The Center for Men's Health, Urologic Medical Center, Shanghai General Hospital, Shanghai Jiao Tong University, Shanghai, 200080, China
| | - Ruhui Tian
- Department of Andrology, Shanghai Key Laboratory of Reproductive Medicine, The Center for Men's Health, Urologic Medical Center, Shanghai General Hospital, Shanghai Jiao Tong University, Shanghai, 200080, China
| | - Junwei Xu
- Department of Andrology, Shanghai Key Laboratory of Reproductive Medicine, The Center for Men's Health, Urologic Medical Center, Shanghai General Hospital, Shanghai Jiao Tong University, Shanghai, 200080, China
| | - Zhiyong Ji
- State Key Lab of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Yuxiang Zhang
- Department of Andrology, Shanghai Key Laboratory of Reproductive Medicine, The Center for Men's Health, Urologic Medical Center, Shanghai General Hospital, Shanghai Jiao Tong University, Shanghai, 200080, China
| | - Liangyu Zhao
- Department of Andrology, Shanghai Key Laboratory of Reproductive Medicine, The Center for Men's Health, Urologic Medical Center, Shanghai General Hospital, Shanghai Jiao Tong University, Shanghai, 200080, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Chao Yang
- Department of Andrology, Shanghai Key Laboratory of Reproductive Medicine, The Center for Men's Health, Urologic Medical Center, Shanghai General Hospital, Shanghai Jiao Tong University, Shanghai, 200080, China
| | - Peng Li
- Department of Andrology, Shanghai Key Laboratory of Reproductive Medicine, The Center for Men's Health, Urologic Medical Center, Shanghai General Hospital, Shanghai Jiao Tong University, Shanghai, 200080, China
| | - Erlei Zhi
- Department of Andrology, Shanghai Key Laboratory of Reproductive Medicine, The Center for Men's Health, Urologic Medical Center, Shanghai General Hospital, Shanghai Jiao Tong University, Shanghai, 200080, China
| | - Haowei Bai
- Department of Andrology, Shanghai Key Laboratory of Reproductive Medicine, The Center for Men's Health, Urologic Medical Center, Shanghai General Hospital, Shanghai Jiao Tong University, Shanghai, 200080, China
| | - Sha Han
- Department of Andrology, Shanghai Key Laboratory of Reproductive Medicine, The Center for Men's Health, Urologic Medical Center, Shanghai General Hospital, Shanghai Jiao Tong University, Shanghai, 200080, China
| | - Jiaqiang Luo
- Department of Andrology, Shanghai Key Laboratory of Reproductive Medicine, The Center for Men's Health, Urologic Medical Center, Shanghai General Hospital, Shanghai Jiao Tong University, Shanghai, 200080, China
| | - Jingpeng Zhao
- State Key Lab of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Jing Zhang
- Reproductive Medicine Research Center, The Sixth Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510620, China
| | - Zhi Zhou
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
| | - Zheng Li
- Department of Andrology, Shanghai Key Laboratory of Reproductive Medicine, The Center for Men's Health, Urologic Medical Center, Shanghai General Hospital, Shanghai Jiao Tong University, Shanghai, 200080, China. .,State Key Lab of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, China.
| | - Chencheng Yao
- Department of Andrology, Shanghai Key Laboratory of Reproductive Medicine, The Center for Men's Health, Urologic Medical Center, Shanghai General Hospital, Shanghai Jiao Tong University, Shanghai, 200080, China. .,School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
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4
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Porubsky D, Höps W, Ashraf H, Hsieh P, Rodriguez-Martin B, Yilmaz F, Ebler J, Hallast P, Maria Maggiolini FA, Harvey WT, Henning B, Audano PA, Gordon DS, Ebert P, Hasenfeld P, Benito E, Zhu Q, Lee C, Antonacci F, Steinrücken M, Beck CR, Sanders AD, Marschall T, Eichler EE, Korbel JO. Recurrent inversion polymorphisms in humans associate with genetic instability and genomic disorders. Cell 2022; 185:1986-2005.e26. [PMID: 35525246 PMCID: PMC9563103 DOI: 10.1016/j.cell.2022.04.017] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 02/14/2022] [Accepted: 04/08/2022] [Indexed: 12/13/2022]
Abstract
Unlike copy number variants (CNVs), inversions remain an underexplored genetic variation class. By integrating multiple genomic technologies, we discover 729 inversions in 41 human genomes. Approximately 85% of inversions <2 kbp form by twin-priming during L1 retrotransposition; 80% of the larger inversions are balanced and affect twice as many nucleotides as CNVs. Balanced inversions show an excess of common variants, and 72% are flanked by segmental duplications (SDs) or retrotransposons. Since flanking repeats promote non-allelic homologous recombination, we developed complementary approaches to identify recurrent inversion formation. We describe 40 recurrent inversions encompassing 0.6% of the genome, showing inversion rates up to 2.7 × 10-4 per locus per generation. Recurrent inversions exhibit a sex-chromosomal bias and co-localize with genomic disorder critical regions. We propose that inversion recurrence results in an elevated number of heterozygous carriers and structural SD diversity, which increases mutability in the population and predisposes specific haplotypes to disease-causing CNVs.
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A rare familial rearrangement of chromosomes 9 and 15 associated with intellectual disability: a clinical and molecular study. Mol Cytogenet 2021; 14:47. [PMID: 34607577 PMCID: PMC8489072 DOI: 10.1186/s13039-021-00565-y] [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: 01/25/2021] [Accepted: 03/09/2021] [Indexed: 11/22/2022] Open
Abstract
Background There are many reports on rearrangements occurring separately in the regions of chromosomes 9p and 15q affected in the case under study. 15q duplication syndrome is caused by the presence of at least one extra maternally derived copy of the Prader–Willi/Angelman critical region. Trisomy 9p is the fourth most frequent chromosome anomaly with a clinically recognizable syndrome often accompanied by intellectual disability. Here we report a new case of a patient with maternally derived unique complex sSMC resulting in partial trisomy of both chromosomes 9 and 15 associated with intellectual disability. Case presentation We characterise a supernumerary derivative chromosome 15: 47,XY,+der(15)t(9;15)(p21.2;q13.2), likely resulting from 3:1 malsegregation during maternal gametogenesis. Chromosomal analysis showed that a phenotypically normal mother is a carrier of balanced translocation t(9;15)(p21.1;q13.2). Her 7-year-old son showed signs of intellectual disability and a number of physical abnormalities including bilateral cryptorchidism and congenital megaureter. The child’s magnetic resonance imaging showed changes in brain volume and in structural and functional connectivity revealing phenotypic changes caused by the presence of the extra chromosome material, whereas the mother’s brain MRI was normal. Sequence analyses of the microdissected der(15) chromosome detected two breakpoint regions: HSA9:25,928,021-26,157,441 (9p21.2 band) and HSA15:30,552,104-30,765,905 (15q13.2 band). The breakpoint region on chromosome HSA9 is poor in genetic features with several areas of high homology with the breakpoint region on chromosome 15. The breakpoint region on HSA15 is located in the area of a large segmental duplication. Conclusions We discuss the case of these phenotypic and brain MRI features in light of reported signatures for 9p partial trisomy and 15 duplication syndromes and analyze how the genomic characteristics of the found breakpoint regions have contributed to the origin of the derivative chromosome. We recommend MRI for all patients with a developmental delay, especially in cases with identified rearrangements, to accumulate more information on brain phenotypes related to chromosomal syndromes. Supplementary Information The online version contains supplementary material available at 10.1186/s13039-021-00565-y.
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Rahman MM, Uddin KF, Al Jezawi NK, Karuvantevida N, Akter H, Dity NJ, Rahaman MA, Begum M, Rahaman MA, Baqui MA, Salwa Z, Islam S, Woodbury-Smith M, Basiruzzaman M, Uddin M. Gonadal mosaicism of large terminal de novo duplication and deletion in siblings with variable intellectual disability phenotypes. Mol Genet Genomic Med 2019; 7:e00954. [PMID: 31475484 PMCID: PMC6785528 DOI: 10.1002/mgg3.954] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 08/08/2019] [Accepted: 08/09/2019] [Indexed: 12/15/2022] Open
Abstract
Background Intellectual disability (ID) is a complex condition that can impact multiple domains of development. The genetic contribution to ID’s etiology is significant, with more than 100 implicated genes and loci currently identified. The majority of such variants are rare and de novo genetic mutations. Methods We have applied whole‐genome microarray to identify large, rare, clinically relevant copy number variants (CNVs). We have applied well‐established algorithms for variants call. Quantitative polymerase chain reaction (qPCR) was applied to validate the variants using three technical replicates for each family member. To assess whether the copy number variation was due to balanced translocation or mosaicism, we further conducted droplet digital PCR (ddPCR) on the whole family. We have, as well, applied “critical‐exon” mapping, human developmental brain transcriptome, and a database of known associated neurodevelopmental disorder variants to identify candidate genes. Results Here we present two siblings who are both impacted by a large terminal duplication and a deletion. Whole‐genome microarray revealed an 18.82 megabase (MB) duplication at terminal locus (7q34‐q36.3) of chromosome 7 and a 3.90 MB deletion impacting the terminal locus (15q26.3) of chromosome 15. qPCR and ddPCR experiments confirmed the de novo origin of the variants and the co‐occurrence of these two de novo events among the siblings, but their absence in both parents, implicates an unbalanced translocation that could have mal‐segregated among the siblings or a possible germline mosaicism. These terminal events impact IGF1R, CNTNAP2, and DPP6, shown to be strongly associated with neurodevelopmental disorders. Detailed clinical examination of the siblings revealed the presence of both shared and distinct phenotypic features. Conclusions This study identified two large rare terminal de novo events impacting two siblings. Further phenotypic investigation highlights that even in the presence of identical large high penetrant variants, spectrum of clinical features can be different between the siblings.
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Affiliation(s)
| | - Km Furkan Uddin
- NeuroGen Technologies Ltd., Dhaka, Bangladesh.,Holy Family Red Crescent Medical College, Dhaka, Bangladesh
| | - Nesreen K Al Jezawi
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Noushad Karuvantevida
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates.,Department of Biotechnology, Bharathidasan University, Tiruchirappalli, India
| | | | | | | | | | | | - Md Abdul Baqui
- NeuroGen Technologies Ltd., Dhaka, Bangladesh.,Holy Family Red Crescent Medical College, Dhaka, Bangladesh
| | | | | | - Marc Woodbury-Smith
- Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, UK.,The Centre for Applied Genomics, Department of Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Mohammed Basiruzzaman
- NeuroGen Technologies Ltd., Dhaka, Bangladesh.,Department of Neurology, Dhaka Medical College Hospital, Dhaka, Bangladesh
| | - Mohammed Uddin
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates.,The Centre for Applied Genomics, Department of Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
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7
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Interplay of interlocus gene conversion and crossover in segmental duplications under a neutral scenario. G3-GENES GENOMES GENETICS 2014; 4:1479-89. [PMID: 24906640 PMCID: PMC4132178 DOI: 10.1534/g3.114.012435] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Interlocus gene conversion is a major evolutionary force that drives the concerted evolution of duplicated genomic regions. Theoretical models successfully have addressed the effects of interlocus gene conversion and the importance of crossover in the evolutionary fate of gene families and duplications but have not considered complex recombination scenarios, such as the presence of hotspots. To study the interplay between interlocus gene conversion and crossover, we have developed a forward-time simulator that allows the exploration of a wide range of interlocus gene conversion rates under different crossover models. Using it, we have analyzed patterns of nucleotide variation and linkage disequilibrium within and between duplicate regions, focusing on a neutral scenario with constant population size and validating our results with the existing theoretical models. We show that the interaction of gene conversion and crossover is nontrivial and that the location of crossover junctions is a fundamental determinant of levels of variation and linkage disequilibrium in duplicated regions. We also show that if crossover activity between duplications is strong enough, recurrent interlocus gene conversion events can break linkage disequilibrium within duplicates. Given the complex nature of interlocus gene conversion and crossover, we provide a framework to explore their interplay to help increase knowledge on molecular evolution within segmental duplications under more complex scenarios, such as demographic changes or natural selection.
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8
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Schierding W, Cutfield WS, O'Sullivan JM. The missing story behind Genome Wide Association Studies: single nucleotide polymorphisms in gene deserts have a story to tell. Front Genet 2014; 5:39. [PMID: 24600475 PMCID: PMC3927098 DOI: 10.3389/fgene.2014.00039] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Accepted: 01/31/2014] [Indexed: 11/13/2022] Open
Abstract
Genome wide association studies are central to the evolution of personalized medicine. However, the propensity for single nucleotide polymorphisms (SNPs) to fall outside of genes means that understanding how these polymorphisms alter cellular function requires an expanded view of human genetics. Integrating the study of genome structure (chromosome conformation capture) into its function opens up new avenues of exploration. Changes in the epigenome associated with SNPs in gene deserts will allow us to define complex diseases in a much clearer manner, and usher in a new era of disease pathway exploration.
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Affiliation(s)
| | - Wayne S. Cutfield
- Liggins Institute, University of AucklandAuckland, New Zealand
- Gravida – National Centre for Growth and DevelopmentAuckland, New Zealand
| | - Justin M. O'Sullivan
- Liggins Institute, University of AucklandAuckland, New Zealand
- Gravida – National Centre for Growth and DevelopmentAuckland, New Zealand
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9
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UGT2B17 copy number gain in a large ankylosing spondylitis multiplex family. BMC Genet 2013; 14:67. [PMID: 23927372 PMCID: PMC3751806 DOI: 10.1186/1471-2156-14-67] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Accepted: 08/03/2013] [Indexed: 01/19/2023] Open
Abstract
Background The primary objective of this study is to identify novel copy number variations (CNVs) associated with familial ankylosing spondylitis (AS). A customized genome-wide microarray was designed to detect CNVs and applied to a multiplex AS family with six (6) affected family members. CNVs were detected using the built-in DNA analytics aberration detection method-2 (ADM-2) algorithm. Gene enrichment analysis was performed to observe the segregation. Subsequent validation was performed using real time quantitative fluorescence polymerase reaction (QF-PCR). The frequency of copy number variation for the UGT2B17 gene was then performed on two well-defined AS cohorts. Fisher exact test was performed to quantify the association. Results Our family-based analysis revealed ten gene-enriched CNVs that segregate with all six family members affected with AS. Based on the proposed function and the polymorphic nature of the UGT2B17 gene, the UGT2B17 gene CNV was selected for validation using real time QF-PCR with full concordance. The frequency of two copies of the UGT2B17 gene CNV was 0.41 in the Newfoundland AS cases and 0.35 in the Newfoundland controls (OR = 1.26(0.99-1.59); p < 0.05)), whereas the frequency of two (2) copies of the UGT2B17 gene CNV was 0.40 in the Alberta AS cases and 0.39 in the Alberta controls (OR = 1.05(95% CI: 0.83-1.33); p < 0.71)). Conclusions A genome-wide microarray interrogation of a large multiplex AS family revealed segregation of the UGT2B17 gene CNV among all affected family members. The association of the UGT2B17 CNV with AS is particularly interesting given the recent association of this CNV with osteoporosis and the proposed function as it encodes a key enzyme that inhibits androgens. However, two copies of the UGT2B17 gene CNV were only marginally significant in a uniplex AS cohort from Newfoundland but not in a uniplex AS cohort from Alberta.
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