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Zhang X, Lu H, Yang H, Ji Y, Liu H, Liu W, Li J, Yang Z, Sun W. Genotype-phenotype correlation of deletions and duplications of 4p: case reports and literature review. Front Genet 2023; 14:1174314. [PMID: 37388934 PMCID: PMC10300434 DOI: 10.3389/fgene.2023.1174314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 05/30/2023] [Indexed: 07/01/2023] Open
Abstract
Structural rearrangements of chromosome 4p gives rise to a group of rare genomic disorders that mainly result in two different clinical entities: Wolf-Hirschhorn syndrome (WHS) and partial 4p trisomy. The severity of the phenotype depends on the size of the deletion or locus duplication. Here, we present two unrelated individuals with a copy number variation of chromosome 4p. Inverted duplication deletions (inv dup-del) in 4p are particularly rare. Case 1 describes a 15-year-old girl with a 1.055 Mb deletion of terminal 4p, distal to the recognized critical region of WHS, and a large duplication of 9.6 Mb in size from 4p16.3 to p16.1. She had postnatal development delay, intellectual disability (especially pronounced in speech), seizure/electroencephalogram anomalies, and facial dysmorphic features. This unusual chromosomal imbalance resulted in the WHS phenotype rather than the 4p trisomy syndrome phenotype. Case 2 describes a 21-month-old boy with a 1.386 Mb terminal 4p deletion who presented with slight developmental delay, borderline intellectual disability, and seizures. Combined with previous reported cases of 4 pter del-dup or pure 4p terminal deletions, our observations suggest that terminal chromosome 4p deletion is more pathogenic than the concomitant partial 4p duplication, and some regions of the 4p terminal may have regulatory effects on the remaining region of 4p. About nine cases have been reported thus far to date, and our study delineates further genotype-phenotype correlations about terminal 4p duplication-deletions for predicting disease prognosis and patient counseling.
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Affiliation(s)
- Xuan Zhang
- Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Hongjuan Lu
- Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Hanran Yang
- Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing, China
| | | | - Huixin Liu
- Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Wenjian Liu
- Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Jiayi Li
- Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Zhixian Yang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Wei Sun
- Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing, China
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2
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Rjiba K, Ayech H, Kraiem O, Slimani W, Jelloul A, Ben Hadj Hmida I, Mahdhaoui N, Saad A, Mougou-Zerelli S. Disorders of sex development in Wolf-Hirschhorn syndrome: a genotype-phenotype correlation and MSX1 as candidate gene. Mol Cytogenet 2021; 14:12. [PMID: 33627176 PMCID: PMC7905666 DOI: 10.1186/s13039-021-00531-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 01/28/2021] [Indexed: 05/30/2023] Open
Abstract
BACKGROUND Wolf-Hirschhorn (WHS) is a set of congenital physical anomalies and mental retardation associated with a partial deletion of the short arm of chromosome 4. To establish a genotype-phenotype correlation; we carried out a molecular cytogenetic analysis on two Tunisian WHS patients. Patient 1 was a boy of 1-year-old, presented a typical WHS phenotype while patient 2, is a boy of 2 days presented an hypospadias, a micropenis and a cryptorchidie in addition to the typical WHS phenotype. Both the array comparative genomic hybridization and fluorescence in situ hybridization techniques were used. RESULTS Results of the analysis showed that patient 2 had a greater deletion size (4.8 Mb) of chromosome 4 than patient 1 (3.4 Mb). Here, we notice that the larger the deletion, the more genes are likely to be involved, and the more severe the phenotype is likely to be. If we analyze the uncommon deleted region between patient1 and patient 2 we found that the Muscle Segment Homeobox (MSX1) gene is included in this region. MSX1 is a critical transcriptional repressor factor, expressed in the ventral side of the developing anterior pituitary and implicated in gonadotrope differentiation. Msx1 acts as a negative regulatory pituitary development by repressing the gonadotropin releasing hormone (GnRH) genes during embryogenesis. We hypothesized that the deletion of MSX1 in our patient may deregulate the androgen synthesis. CONCLUSION Based on the MSX1 gene function, its absence might be indirectly responsible for the hypospadias phenotype by contributing to the spatiotemporal regulation of GnRH transcription during development.
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Affiliation(s)
- Khouloud Rjiba
- Laboratory of Human Cytogenetics, Molecular Genetics and Biology of Reproduction, Farhat Hached University Teaching Hospital, Sousse, Tunisia.,Higher Institute of Biotechnology, Monastir University, Monastir, Tunisia.,Unité de Services Communs en Génétique Humaine, Faculté de Médecine de Sousse, Université de Sousse, Sousse, Tunisia
| | - Hédia Ayech
- Pediatric Department, Farhat Hached University Teaching Hospital, Sousse, Tunisia
| | - Olfa Kraiem
- Pediatric Department, Regional Hospital, Kairouan, Tunisia
| | - Wafa Slimani
- Laboratory of Human Cytogenetics, Molecular Genetics and Biology of Reproduction, Farhat Hached University Teaching Hospital, Sousse, Tunisia.,Higher Institute of Biotechnology, Monastir University, Monastir, Tunisia.,Unité de Services Communs en Génétique Humaine, Faculté de Médecine de Sousse, Université de Sousse, Sousse, Tunisia
| | - Afef Jelloul
- Laboratory of Human Cytogenetics, Molecular Genetics and Biology of Reproduction, Farhat Hached University Teaching Hospital, Sousse, Tunisia
| | - Imen Ben Hadj Hmida
- Laboratory of Human Cytogenetics, Molecular Genetics and Biology of Reproduction, Farhat Hached University Teaching Hospital, Sousse, Tunisia
| | - Nabiha Mahdhaoui
- Pediatric Department, Farhat Hached University Teaching Hospital, Sousse, Tunisia
| | - Ali Saad
- Laboratory of Human Cytogenetics, Molecular Genetics and Biology of Reproduction, Farhat Hached University Teaching Hospital, Sousse, Tunisia.,Unité de Services Communs en Génétique Humaine, Faculté de Médecine de Sousse, Université de Sousse, Sousse, Tunisia
| | - Soumaya Mougou-Zerelli
- Laboratory of Human Cytogenetics, Molecular Genetics and Biology of Reproduction, Farhat Hached University Teaching Hospital, Sousse, Tunisia. .,Unité de Services Communs en Génétique Humaine, Faculté de Médecine de Sousse, Université de Sousse, Sousse, Tunisia.
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3
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Liu J, Zhou Y, Liu S, Song X, Yang XZ, Fan Y, Chen W, Akdemir ZC, Yan Z, Zuo Y, Du R, Liu Z, Yuan B, Zhao S, Liu G, Chen Y, Zhao Y, Lin M, Zhu Q, Niu Y, Liu P, Ikegawa S, Song YQ, Posey JE, Qiu G, Zhang F, Wu Z, Lupski JR, Wu N. The coexistence of copy number variations (CNVs) and single nucleotide polymorphisms (SNPs) at a locus can result in distorted calculations of the significance in associating SNPs to disease. Hum Genet 2018; 137:553-567. [PMID: 30019117 DOI: 10.1007/s00439-018-1910-3] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Accepted: 07/07/2018] [Indexed: 01/25/2023]
Abstract
With the recent advance in genome-wide association studies (GWAS), disease-associated single nucleotide polymorphisms (SNPs) and copy number variants (CNVs) have been extensively reported. Accordingly, the issue of incorrect identification of recombination events that can induce the distortion of multi-allelic or hemizygous variants has received more attention. However, the potential distorted calculation bias or significance of a detected association in a GWAS due to the coexistence of CNVs and SNPs in the same genomic region may remain under-recognized. Here we performed the association study within a congenital scoliosis (CS) cohort whose genetic etiology was recently elucidated as a compound inheritance model, including mostly one rare variant deletion CNV null allele and one common variant non-coding hypomorphic haplotype of the TBX6 gene. We demonstrated that the existence of a deletion in TBX6 led to an overestimation of the contribution of the SNPs on the hypomorphic allele. Furthermore, we generalized a model to explain the calculation bias, or distorted significance calculation for an association study, that can be 'induced' by CNVs at a locus. Meanwhile, overlapping between the disease-associated SNPs from published GWAS and common CNVs (overlap 10%) and pathogenic/likely pathogenic CNVs (overlap 99.69%) was significantly higher than the random distribution (p < 1 × 10-6 and p = 0.034, respectively), indicating that such co-existence of CNV and SNV alleles might generally influence data interpretation and potential outcomes of a GWAS. We also verified and assessed the influence of colocalizing CNVs to the detection sensitivity of disease-associated SNP variant alleles in another adolescent idiopathic scoliosis (AIS) genome-wide association study. We proposed that detecting co-existent CNVs when evaluating the association signals between SNPs and disease traits could improve genetic model analyses and better integrate GWAS with robust Mendelian principles.
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Affiliation(s)
- Jiaqi Liu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No.1 Shuaifuyuan, Beijing, 100730, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China.,Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Yangzhong Zhou
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China.,Department of Internal Medicine, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Sen Liu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No.1 Shuaifuyuan, Beijing, 100730, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China.,Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Xiaofei Song
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Xin-Zhuang Yang
- Department of Central Laboratory, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Yanhui Fan
- School of Biomedical Sciences, The University of Hong Kong, Hong Kong, China
| | - Weisheng Chen
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No.1 Shuaifuyuan, Beijing, 100730, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China.,Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Zeynep Coban Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Zihui Yan
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No.1 Shuaifuyuan, Beijing, 100730, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China.,Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Yuzhi Zuo
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No.1 Shuaifuyuan, Beijing, 100730, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China.,Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Renqian Du
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Zhenlei Liu
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China.,Department of Neurosurgery, Xuanwu Hospital, Capital Medical University, Beijing, 100053, China
| | - Bo Yuan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Sen Zhao
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No.1 Shuaifuyuan, Beijing, 100730, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China.,Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Gang Liu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No.1 Shuaifuyuan, Beijing, 100730, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China.,Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Yixin Chen
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No.1 Shuaifuyuan, Beijing, 100730, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China.,Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Yanxue Zhao
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No.1 Shuaifuyuan, Beijing, 100730, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China.,Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Mao Lin
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No.1 Shuaifuyuan, Beijing, 100730, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China.,Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Qiankun Zhu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No.1 Shuaifuyuan, Beijing, 100730, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China.,Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Yuchen Niu
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China.,Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing, 100730, China.,Department of Central Laboratory, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Shiro Ikegawa
- Laboratory of Bone and Joint Diseases, Center for Integrative Medical Sciences, RIKEN, Tokyo, 108-8639, Japan
| | - You-Qiang Song
- School of Biomedical Sciences, The University of Hong Kong, Hong Kong, China
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Guixing Qiu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No.1 Shuaifuyuan, Beijing, 100730, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China.,Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | | | - Feng Zhang
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, 200433, China.,Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Zhihong Wu
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China.,Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing, 100730, China.,Department of Central Laboratory, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA.,Texas Children's Hospital, Houston, TX, 77030, USA
| | - Nan Wu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No.1 Shuaifuyuan, Beijing, 100730, China. .,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China. .,Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing, 100730, China.
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4
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Poot M. Syndromes Hidden within the 16p11.2 Deletion Region. Mol Syndromol 2018; 9:171-174. [PMID: 30140194 DOI: 10.1159/000490845] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/11/2018] [Indexed: 12/31/2022] Open
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5
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Poot M. Adding Insult to Injury, Complexity to Intricacy. Mol Syndromol 2017; 8:225-226. [PMID: 28878605 DOI: 10.1159/000477230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/29/2017] [Indexed: 11/19/2022] Open
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6
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Poot M. When Recessive Genes Mutate to Dominant Gene Action. Mol Syndromol 2016; 7:249-250. [PMID: 27867339 DOI: 10.1159/000449116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/11/2016] [Indexed: 11/19/2022] Open
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7
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Unmasking a novel disease gene NEO1 associated with autism spectrum disorders by a hemizygous deletion on chromosome 15 and a functional polymorphism. Behav Brain Res 2016; 300:135-42. [DOI: 10.1016/j.bbr.2015.10.041] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 10/14/2015] [Accepted: 10/21/2015] [Indexed: 11/20/2022]
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8
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Abdolrahimzadeh S, Fameli V, Mollo R, Contestabile MT, Perdicchi A, Recupero SM. Rare Diseases Leading to Childhood Glaucoma: Epidemiology, Pathophysiogenesis, and Management. BIOMED RESEARCH INTERNATIONAL 2015; 2015:781294. [PMID: 26451378 PMCID: PMC4588342 DOI: 10.1155/2015/781294] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 04/22/2015] [Indexed: 11/17/2022]
Abstract
Noteworthy heterogeneity exists in the rare diseases associated with childhood glaucoma. Primary congenital glaucoma is mostly sporadic; however, 10% to 40% of cases are familial. CYP1B1 gene mutations seem to account for 87% of familial cases and 27% of sporadic cases. Childhood glaucoma is classified in primary and secondary congenital glaucoma, further divided as glaucoma arising in dysgenesis associated with neural crest anomalies, phakomatoses, metabolic disorders, mitotic diseases, congenital disorders, and acquired conditions. Neural crest alterations lead to the wide spectrum of iridocorneal trabeculodysgenesis. Systemic diseases associated with childhood glaucoma include the heterogenous group of phakomatoses where glaucoma is frequently encountered in the Sturge-Weber syndrome and its variants, in phakomatosis pigmentovascularis associated with oculodermal melanocytosis, and more rarely in neurofibromatosis type 1. Childhood glaucoma is also described in systemic disorders of mitotic and metabolic activity. Acquired secondary glaucoma has been associated with uveitis, trauma, drugs, and neoplastic diseases. A database research revealed reports of childhood glaucoma in rare diseases, which do not include glaucoma in their manifestation. These are otopalatodigital syndrome, complete androgen insensitivity, pseudotrisomy 13, Brachmann-de Lange syndrome, acrofrontofacionasal dysostosis, caudal regression syndrome, and Wolf-Hirschhorn syndrome.
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Affiliation(s)
- Solmaz Abdolrahimzadeh
- Ophthalmology Unit, DAI Head/Neck, Umberto I Policlinic, University of Rome “Sapienza”, Viale del Policlinico 155, 00161 Rome, Italy
| | - Valeria Fameli
- Ophthalmology Unit, Department of Sense Organs, University of Rome “Sapienza”, Viale del Policlinico 155, 00161 Rome, Italy
| | - Roberto Mollo
- Ophthalmology Unit, DAI Head/Neck, Umberto I Policlinic, University of Rome “Sapienza”, Viale del Policlinico 155, 00161 Rome, Italy
| | - Maria Teresa Contestabile
- Ophthalmology Unit, St. Andrea Hospital, NESMOS Department, University of Rome “Sapienza”, via di Grottarossa 1035-1039, 00189 Rome, Italy
| | - Andrea Perdicchi
- Ophthalmology Unit, St. Andrea Hospital, NESMOS Department, University of Rome “Sapienza”, via di Grottarossa 1035-1039, 00189 Rome, Italy
| | - Santi Maria Recupero
- Ophthalmology Unit, St. Andrea Hospital, NESMOS Department, University of Rome “Sapienza”, via di Grottarossa 1035-1039, 00189 Rome, Italy
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9
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Poot M, Haaf T. Mechanisms of Origin, Phenotypic Effects and Diagnostic Implications of Complex Chromosome Rearrangements. Mol Syndromol 2015; 6:110-34. [PMID: 26732513 DOI: 10.1159/000438812] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/23/2015] [Indexed: 01/08/2023] Open
Abstract
Complex chromosome rearrangements (CCRs) are currently defined as structural genome variations that involve more than 2 chromosome breaks and result in exchanges of chromosomal segments. They are thought to be extremely rare, but their detection rate is rising because of improvements in molecular cytogenetic technology. Their population frequency is also underestimated, since many CCRs may not elicit a phenotypic effect. CCRs may be the result of fork stalling and template switching, microhomology-mediated break-induced repair, breakage-fusion-bridge cycles, or chromothripsis. Patients with chromosomal instability syndromes show elevated rates of CCRs due to impaired DNA double-strand break responses during meiosis. Therefore, the putative functions of the proteins encoded by ATM, BLM, WRN, ATR, MRE11, NBS1, and RAD51 in preventing CCRs are discussed. CCRs may exert a pathogenic effect by either (1) gene dosage-dependent mechanisms, e.g. haploinsufficiency, (2) mechanisms based on disruption of the genomic architecture, such that genes, parts of genes or regulatory elements are truncated, fused or relocated and thus their interactions disturbed - these mechanisms will predominantly affect gene expression - or (3) mixed mutation mechanisms in which a CCR on one chromosome is combined with a different type of mutation on the other chromosome. Such inferred mechanisms of pathogenicity need corroboration by mRNA sequencing. Also, future studies with in vitro models, such as inducible pluripotent stem cells from patients with CCRs, and transgenic model organisms should substantiate current inferences regarding putative pathogenic effects of CCRs. The ramifications of the growing body of information on CCRs for clinical and experimental genetics and future treatment modalities are briefly illustrated with 2 cases, one of which suggests KDM4C (JMJD2C) as a novel candidate gene for mental retardation.
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Affiliation(s)
- Martin Poot
- Department of Human Genetics, University of Würzburg, Würzburg, Germany
| | - Thomas Haaf
- Department of Human Genetics, University of Würzburg, Würzburg, Germany
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10
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Abstract
Wolf-Hirschhorn syndrome (WHS) is a rare chromosomal disorder caused by terminal deletion of the short arm of chromosome 4. The clinical picture includes growth retardation, severe mental retardation, characteristic "Greek helmet" like face, seizures and midline defects in the brain, heart, palate and genitalia. Recently-used molecular techniques increase the number of diagnosed cases due to the detection of smaller deletions. The severity of the clinical presentation is variable depending on the haploinsufficiency of genes in a deleted region. We present six children with WHS with variable clinical appearance. The assessment of several elements (facial dysmorphism, mental retardation, additional congenital anomalies) provided classification into minor, mild or severe forms. Three of the children had a visible cytogenetic deletion on chromosome 4p, two had microdeletions detected with fluorescent in situ hybridization (FISH), and one child with a less characteristic clinical picture had a mosaic type of the deletion. Correlation between the clinical presentation and the length of the deleted region was confirmed.
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11
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Czeschik JC, Hehr U, Hartmann B, Lüdecke HJ, Rosenbaum T, Schweiger B, Wieczorek D. 160 kb deletion in ISPD unmasking a recessive mutation in a patient with Walker–Warburg syndrome. Eur J Med Genet 2013; 56:689-94. [DOI: 10.1016/j.ejmg.2013.09.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Accepted: 09/30/2013] [Indexed: 01/03/2023]
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12
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An unusual clinical severity of 16p11.2 deletion syndrome caused by unmasked recessive mutation of CLN3. Eur J Hum Genet 2013; 22:369-73. [PMID: 23860047 DOI: 10.1038/ejhg.2013.141] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2013] [Revised: 05/29/2013] [Accepted: 06/03/2013] [Indexed: 01/09/2023] Open
Abstract
With the introduction of array comparative genomic hybridization (aCGH) techniques in the diagnostic setting of patients with developmental delay and congenital malformations, many new microdeletion syndromes have been recognized. One of these recently recognized microdeletion syndromes is the 16p11.2 deletion syndrome, associated with variable clinical outcomes including developmental delay, autism spectrum disorder, epilepsy, and obesity, but also apparently normal phenotype. We report on a 16-year-old patient with developmental delay, exhibiting retinis pigmentosa with progressive visual failure from the age of 9 years, ataxia, and peripheral neuropathy. Chromosomal microarray analysis identified a 1.7-Mb 16p11.2 deletion encompassing the 593-kb common deletion (∼29.5 to ∼30.1 Mb; Hg18) and the 220-kb distal deletion (∼28.74 to ∼28.95 Mb; Hg18) that partially included the CLN3 gene. As the patient's clinical findings were different from usual 16p11.2 microdeletion phenotypes and showed some features reminiscent of juvenile neuronal ceroid-lipofuscinosis (JNCL, Batten disease, OMIM 204200), we suspected and confirmed a mutation of the remaining CLN3 allele. This case further illustrates that unmasking of hemizygous recessive mutations by chromosomal deletion represents one explanation for the phenotypic variability observed in chromosomal deletion disorders.
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Dai Y, Yang J, Chen Y, Bao L, Cheng Q. Microarray analysis of unbalanced translocation in Wolf-Hirschhorn syndrome. Pediatr Int 2013; 55:368-70. [PMID: 23782367 DOI: 10.1111/j.1442-200x.2012.03684.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/28/2012] [Revised: 05/28/2012] [Accepted: 06/06/2012] [Indexed: 12/01/2022]
Abstract
Wolf-Hirschhorn syndrome (WHS) is caused by deletions involving chromosome region 4p16.3, which is characterized by growth delay, mild-to-severe mental retardation, hypotonia, facial dysmorphisms and shows extensive phenotypic variability include feeding difficulties, epilepsy and congenital anomalies. Variation in the size of the deletion involving chromosome region 4p16.3 may explain the clinical variation. However, previous studies indicate that duplication for another chromosome region due to an unbalanced translocation elucidate approximately 40-45% WHS patients. Therefore, we used whole genomic cytogenetics array to analyze the entire genome at a significantly higher resolution over conventional cytogenetics to characterize the exact subtelomeric aberration region of one patient with developmental delay and several facial characteristics reminiscent Wolf-Hirschhorn syndrome. Here we report that our patient had 3.7 Mb deletion at the 4p16.2 and 6.8 Mb duplication at 8p23.1 resulted from the unbalanced translocations der(4)t(4;8)(p16.2;p23.1). We confirmed that our patient with monosomy 4p16.2 which is consistent with Wolf-Hirschhorn syndrome and trisomy 8p23.1. The combination of the 4p deletion with 8p partial trisomy explains the complex phenotype presented by our patient.
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Affiliation(s)
- Ying Dai
- Department of Primary Child Health Care, Children's Hospital of Chongqing Medical University, Chongqing, China
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14
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Shimada S, Miya K, Oda N, Watanabe Y, Kumada T, Sugawara M, Shimojima K, Yamamoto T. An unmasked mutation of EIF2B2 due to submicroscopic deletion of 14q24.3 in a patient with vanishing white matter disease. Am J Med Genet A 2012; 158A:1771-7. [PMID: 22678813 DOI: 10.1002/ajmg.a.35431] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Accepted: 03/29/2012] [Indexed: 12/21/2022]
Abstract
Leukodystrophy with vanishing white matter (VWM) is a neurodegenerative disorder with autosomal recessive traits that is caused by alteration of the eukaryotic translation initiation factor-2B (EIF2B). An 11-month-old patient with distinctive features began to exhibit progressive developmental deterioration associated with intractable epilepsy, which was triggered by recurrent acute infectious diseases. Brain magnetic resonance imaging (MRI) revealed abnormal white matter intensity. Chromosomal microarray testing identified a submicroscopic deletion at 14q24.3 that included EIF2B2, the gene encoding one of the subunits of EIF2B. Because the patient's clinical findings were distinctive for VWM, compound heterozygous mutations of EIF2B2 were suspected, and subsequent sequencing analysis of the remaining allele unmasked the existence of a novel missense mutation of EIF2B2 (V85W). Some distinctive features including small palpebral fissures, bushy eyebrows, ear abnormalities, small upturned nose, downturned corners of the mouth, and micrognathia may be the common features of the patients with 14q24.3 deletions.
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Affiliation(s)
- Shino Shimada
- Tokyo Women's Medical University Institute of Integrated Medical Sciences, Tokyo, Japan
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Holt R, Sykes NH, Conceição IC, Cazier JB, Anney RJL, Oliveira G, Gallagher L, Vicente A, Monaco AP, Pagnamenta AT. CNVs leading to fusion transcripts in individuals with autism spectrum disorder. Eur J Hum Genet 2012; 20:1141-7. [PMID: 22549408 PMCID: PMC3476715 DOI: 10.1038/ejhg.2012.73] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
There is strong evidence that rare copy number variants (CNVs) have a role in susceptibility to autism spectrum disorders (ASDs). Much research has focused on how CNVs mediate a phenotypic effect by altering gene expression levels. We investigated an alternative mechanism whereby CNVs combine the 5′ and 3′ ends of two genes, creating a ‘fusion gene'. Any resulting mRNA with an open reading frame could potentially alter the phenotype via a gain-of-function mechanism. We examined 2382 and 3096 rare CNVs from 996 individuals with ASD and 1287 controls, respectively, for potential to generate fusion transcripts. There was no increased burden in individuals with ASD; 122/996 cases harbored at least one rare CNV of this type, compared with 179/1287 controls (P=0.89). There was also no difference in the overall frequency distribution between cases and controls. We examined specific examples of such CNVs nominated by case–control analysis and a candidate approach. Accordingly, a duplication involving REEP1-POLR1A (found in 3/996 cases and 0/1287 controls) and a single occurrence CNV involving KIAA0319-TDP2 were tested. However, no fusion transcripts were detected by RT-PCR. Analysis of additional samples based on cell line availability resulted in validation of a MAPKAPK5-ACAD10 fusion transcript in two probands. However, this variant was present in controls at a similar rate and is unlikely to influence ASD susceptibility. In summary, although we find no evidence that fusion-gene generating CNVs lead to ASD susceptibility, discovery of a MAPKAPK5-ACAD10 transcript with an estimated frequency of ∼1/200 suggests that gain-of-function mechanisms should be considered in future CNVs studies.
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Affiliation(s)
- Richard Holt
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
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Abstract
Array-based genome-wide segmental aneuploidy screening detects both de novo and inherited copy number variations (CNVs). In sporadic patients de novo CNVs are interpreted as potentially pathogenic. However, a deletion, transmitted from a healthy parent, may be pathogenic if it overlaps with a mutated second allele inherited from the other healthy parent. To detect such events, we performed multiplex enrichment and next-generation sequencing of the entire coding sequence of all genes within unique hemizygous deletion regions in 20 patients (1.53 Mb capture footprint). Out of the detected 703 non-synonymous single-nucleotide variants (SNVs), 8 represented variants being unmasked by a hemizygous deletion. Although evaluation of inheritance patterns, Grantham matrix scores, evolutionary conservation and bioinformatic predictions did not consistently indicate pathogenicity of these variants, no definitive conclusions can be drawn without functional validation. However, in one patient with severe mental retardation, lack of speech, microcephaly, cheilognathopalatoschisis and bilateral hearing loss, we discovered a second smaller deletion, inherited from the other healthy parent, resulting in loss of both alleles of the highly conserved heat shock factor binding protein 1 (HSBP1) gene. Conceivably, inherited deletions may unmask rare pathogenic variants that may exert a phenotypic impact through a recessive mode of gene action.
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News Briefs. Genet Med 2012. [DOI: 10.1038/gim.2011.74] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
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Gijsbers ACJ, Schoumans J, Ruivenkamp CAL. Interpretation of array comparative genome hybridization data: a major challenge. Cytogenet Genome Res 2011; 135:222-7. [PMID: 22086107 DOI: 10.1159/000334066] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The advent and application of high-resolution array-based comparative genome hybridization (array CGH) has led to the detection of large numbers of copy number variants (CNVs) in patients with developmental delay and/or multiple congenital anomalies as well as in healthy individuals. The notion that CNVs are also abundantly present in the normal population challenges the interpretation of the clinical significance of detected CNVs in patients. In this review we will illustrate a general clinical workflow based on our own experience that can be used in routine diagnostics for the interpretation of CNVs.
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Affiliation(s)
- A C J Gijsbers
- Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
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Array comparative genomic hybridization analysis in patients with anophthalmia, microphthalmia, and coloboma. Genet Med 2011; 13:437-42. [PMID: 21285886 DOI: 10.1097/gim.0b013e318204cfd2] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
PURPOSE The goal of our study was to determine whether genomic copy number abnormalities (deletions and duplications) affecting genes involved in eye development contributed to the etiology of anophthalmia, microphthalmia, and coloboma. METHODS The affected individuals were evaluated for the presence of deletions and duplications in genomic DNA by a very high-resolution array comparative genomic hybridization. RESULTS Array analysis of 32 patients detected one case with a deletion encompassing the renal-coloboma syndrome associated gene PAX2. Nonpolymorphic copy number changes were also observed at several candidate chromosomal regions, including 6p12.3, 8q23.1q23.2, 13q31.3, 15q11.2q13.1, 16p13.13, and 20q13.13. CONCLUSIONS This study identified the first patient with the typical phenotype of the renal-coloboma syndrome caused by a submicroscopic deletion of the coding region of the PAX2 gene. The finding suggests that PAX2 deletion testing should be performed in addition to gene sequencing as a part of molecular evaluation for the renal-coloboma syndrome. Array comparative genomic hybridization testing of 32 affected individuals showed that genomic deletions and duplications are not a common cause of nonsyndromic anophthalmia, microphthalmia, or coloboma but undoubtedly contribute to the etiology of these eye anomalies. Therefore, array comparative genomic hybridization testing represents an important and valuable addition to candidate gene sequencing in research and diagnostics of ocular birth defects.
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Colnaghi R, Carpenter G, Volker M, O'Driscoll M. The consequences of structural genomic alterations in humans: genomic disorders, genomic instability and cancer. Semin Cell Dev Biol 2011; 22:875-85. [PMID: 21802523 DOI: 10.1016/j.semcdb.2011.07.010] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2011] [Revised: 07/11/2011] [Accepted: 07/14/2011] [Indexed: 12/20/2022]
Abstract
Over the last decade or so, sophisticated technological advances in array-based genomics have firmly established the contribution of structural alterations in the human genome to a variety of complex developmental disorders, and also to diseases such as cancer. In fact, multiple 'novel' disorders have been identified as a direct consequence of these advances. Our understanding of the molecular events leading to the generation of these structural alterations is also expanding. Many of the models proposed to explain these complex rearrangements involve DNA breakage and the coordinated action of DNA replication, repair and recombination machinery. Here, and within the context of Genomic Disorders, we will briefly overview the principal models currently invoked to explain these chromosomal rearrangements, including Non-Allelic Homologous Recombination (NAHR), Fork Stalling Template Switching (FoSTeS), Microhomology Mediated Break-Induced Repair (MMBIR) and Breakage-fusion-bridge cycle (BFB). We will also discuss an unanticipated consequence of certain copy number variations (CNVs) whereby the CNVs potentially compromise fundamental processes controlling genomic stability including DNA replication and the DNA damage response. We will illustrate these using specific examples including Genomic Disorders (DiGeorge/Veleocardiofacial syndrome, HSA21 segmental aneuploidy and rec (3) syndrome) and cell-based model systems. Finally, we will review some of the recent exciting developments surrounding specific CNVs and their contribution to cancer development as well as the latest model for cancer genome rearrangement; 'chromothripsis'.
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Affiliation(s)
- Rita Colnaghi
- Human DNA Damage Response Disorders Group, Genome Damage and Stability Centre, University of Sussex, Brighton, United Kingdom
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Poot M, van der Smagt J, Brilstra E, Bourgeron T. Disentangling the Myriad Genomics of Complex Disorders, Specifically Focusing on Autism, Epilepsy, and Schizophrenia. Cytogenet Genome Res 2011; 135:228-40. [DOI: 10.1159/000334064] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
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A three-step workflow procedure for the interpretation of array-based comparative genome hybridization results in patients with idiopathic mental retardation and congenital anomalies. Genet Med 2010; 12:478-85. [PMID: 20734469 DOI: 10.1097/gim.0b013e3181e3914a] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
One of the aims of clinical genetics is to identify gene mutations or genomic rearrangements that may underlie complex presentations of phenotypic features, such as multiple congenital malformations and mental retardation. During the decade after publication of the first article on array-based comparative genome hybridization, this technique has supplemented karyotyping as the prime genome-wide screening method in patients with idiopathic multiple congenital malformations and mental retardation. The use of this novel, discovery-based, approach has dramatically increased the detection rate of genomic imbalances. Array-based comparative genome hybridization detects copy number changes in the genome of patients and healthy subjects, some of which may represent phenotypically neutral copy number variations. This prompts the need for properly distinguishing between those copy number changes that may contribute to the clinical phenotype amid a pool of neutral copy number variations. We briefly review the characteristics of copy number changes in relation to their clinical relevance. Second, we discuss several published workflow schemes to identify copy number changes putatively contributing to the phenotype, and third, we propose a three-step procedure aiming to rapidly evaluate copy number changes on a case-by-case basis as to their potential contribution to the phenotype of patients with idiopathic multiple congenital malformations and mental retardation. This workflow is gene-centered and should aid in identification of disease-related candidate genes and in estimating the recurrence risk for the disorder in the family.
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Girirajan S, Eichler EE. Phenotypic variability and genetic susceptibility to genomic disorders. Hum Mol Genet 2010; 19:R176-87. [PMID: 20807775 PMCID: PMC2953748 DOI: 10.1093/hmg/ddq366] [Citation(s) in RCA: 201] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2010] [Revised: 07/28/2010] [Accepted: 08/24/2010] [Indexed: 11/13/2022] Open
Abstract
The duplication architecture of the human genome predisposes our species to recurrent copy number variation and disease. Emerging data suggest that this mechanism of mutation contributes to both common and rare diseases. Two features regarding this form of mutation have emerged. First, common structural polymorphisms create susceptible and protective chromosomal architectures. These structural polymorphisms occur at varying frequencies in populations, leading to different susceptibility and ethnic predilection. Second, a subset of rearrangements shows extreme variability in expressivity. We propose that two types of genomic disorders may be distinguished: syndromic forms where the phenotypic features are largely invariant and those where the same molecular lesion associates with a diverse set of diagnoses including epilepsy, schizophrenia, autism, intellectual disability and congenital malformations. Copy number variation analyses of patient genomes reveal that disease type and severity may be explained by the occurrence of additional rare events and their inheritance within families. We propose that the overall burden of copy number variants creates differing sensitized backgrounds during development leading to different thresholds and disease outcomes. We suggest that the accumulation of multiple high-penetrant alleles of low frequency may serve as a more general model for complex genetic diseases, posing a significant challenge for diagnostics and disease management.
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Affiliation(s)
| | - Evan E. Eichler
- Department of Genome Sciences, Howard Hughes Medical Institute,University of Washington School of Medicine, PO Box 355065, Foege S413C, 3720 15th Avenue NE, Seattle, WA 98195, USA
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Four patients with speech delay, seizures and variable corpus callosum thickness sharing a 0.440 Mb deletion in region 1q44 containing the HNRPU gene. Eur J Med Genet 2010; 53:179-85. [PMID: 20382278 DOI: 10.1016/j.ejmg.2010.04.001] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2009] [Accepted: 04/02/2010] [Indexed: 01/26/2023]
Abstract
Structural genome aberrations are frequently associated with highly variable congenital phenotypes involving mental retardation and developmental delay. Although some of these aberrations may result in recognizable phenotypes, a high degree of phenotypic variability often complicates a comprehensive clinical and genetic diagnosis. We describe four patients with overlapping deletions in chromosomal region 1q44, who show developmental delay, in particular of expressive speech, seizures, hypotonia, CNS anomalies, including variable thickness of the abnormal corpus callosum in three of them. High resolution oligonucleotide and SNP array-based segmental aneuploidy profiling showed that these three patients share a 0.440 Mb interstitial deletion, which does not overlap with previously published consensus regions of 1q44 deletions. Two copies of AKT3 and ZNF238, two previously proposed dosage sensitive candidate genes for microcephaly and agenesis of the corpus callosum, were retained in two of our patients. The deletion shared by our patients encompassed the FAM36A, HNRPU, EFCAB2 and KIF26B genes. Since HNRPU is involved in the regulation of embryonic brain development, this represents a novel plausible candidate gene for the combination of developmental delay, speech delay, hypotonia, hypo- or agenesis of the corpus callosum, and seizures in patients with 1q44 deletions. Since only one of the two patients with deletions including the ZNF124 gene showed a vermis hypoplasia, mere hemizygosity for this gene is not sufficient to cause this anomaly. Moreover, to reconcile the variability in the corpus callosum thickness, additional mechanisms, such as unmasking of hemizygous mutations, position effects and possible interactions with other loci need consideration.
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Poot M, Eleveld MJ, van 't Slot R, Ploos van Amstel HK, Hochstenbach R. Recurrent copy number changes in mentally retarded children harbour genes involved in cellular localization and the glutamate receptor complex. Eur J Hum Genet 2010; 18:39-46. [PMID: 19623214 DOI: 10.1038/ejhg.2009.120] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
To determine the phenotypic significance of copy number changes (CNCs) in the human genome, we performed genome-wide segmental aneuploidy profiling by BAC-based array-CGH of 278 unrelated patients with multiple congenital abnormalities and mental retardation (MCAMR) and in 48 unaffected family members. In 20 patients, we found de novo CNCs composed of multiple consecutive probes. Of the 125 probes making up these probably pathogenic CNCs, 14 were also found as single CNCs in other patients and 5 in healthy individuals. Thus, these CNCs are not by themselves pathogenic. Almost one out of five patients and almost one out of six healthy individuals in our study cohort carried a gain or a loss for any one of the recently discovered microdeletion/microduplication loci, whereas seven patients and one healthy individual showed losses or gains for at least two different loci. The pathogenic burden resulting from these CNCs may be limited as they were found with similar frequencies among patients and healthy individuals (P=0.165; Fischer's exact test), and several individuals showed CNCs at multiple loci. CNCs occurring specifically in our study cohort were enriched for components of the glutamate receptor family (GRIA2, GRIA4, GRIK2 and GRIK4) and genes encoding proteins involved in guiding cell localization during development (ATP1A2, GIRK3, GRIA2, KCNJ3, KCNJ10, KCNK17 and KCNK5). This indicates that disease cohort-specific compilations of CNCs may aid in identifying loci, genes and biological processes that contribute to the phenotype of patients.
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Affiliation(s)
- Martin Poot
- Department of Medical Genetics, University Medical Center Utrecht, PO Box 85090, Mail stop: KC.04.084.2, Utrecht, 3508 AB, The Netherlands.
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Sharp AJ. Emerging themes and new challenges in defining the role of structural variation in human disease. Hum Mutat 2009; 30:135-44. [DOI: 10.1002/humu.20843] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Abstract
Wolfram syndrome (WS), an infrequent cause of diabetes mellitus, derives its name from the physician who first reported the combination of juvenile-onset diabetes mellitus and optic atrophy. Also referred to as DIDMOAD (diabetes insipidus, diabetes mellitus, optic atrophy and deafness), it is an autosomal recessive neurodegenerative disease characterized by various clinical manifestations, such as diabetes mellitus, optic atrophy, diabetes insipidus, deafness, neurological symptoms, renal tract abnormalities, psychiatric manifestations and gonadal disorders. The condition is very rare with an estimated prevalence of one in 770,000 of the normal population, one out of 150 cases of juvenile-onset insulin-dependent diabetes mellitus, and with a carrier frequency of one in 354. This progressive neurodegenerative disease usually results in death before the age of 50 years and many patients lead a morbid life. The pathogenesis of the disorder although unknown is ascribed to mutation of a gene on chromosome 4p encoding a transmembrane protein of undetermined function called wolframin. This review summarizes the variable presentation of the disorder, its widespread complications, poor quality of life in affected individuals, and the problems in diagnosis and treatment of the syndrome.
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Affiliation(s)
- Mohd Ashraf Ganie
- Department of Endocrinology, Sheri-Kashmir Institute of Medical Sciences, Post Box 930, GPO Srinagar, J&K, India 190010.
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Poot M, Eleveld MJ, van 't Slot R, van Genderen MM, Verrijn Stuart AA, Hochstenbach R, Beemer FA. Proportional growth failure and oculocutaneous albinism in a girl with a 6.87 Mb deletion of region 15q26.2-->qter. Eur J Med Genet 2007; 50:432-40. [PMID: 17931990 DOI: 10.1016/j.ejmg.2007.08.003] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2007] [Accepted: 08/30/2007] [Indexed: 01/16/2023]
Abstract
We report on an 8(1)/(2)-year-old girl with severe pre- and postnatal growth retardation, congenital heart malformation, facial asymmetry, oculocutaneous albinism without misrouting and subluxation of the radial heads. Her intelligence was in the low normal range. By GTG-banding a deletion of band 15q26 was found. Array-CGH, using a 3783 BAC array, revealed a segmental monosomy of the 15(q26.2-->qter) region, which was narrowed down to a 6.87Mb deletion by using the Illumina Infinium 317 K SNP array system, and subsequently confirmed by fluorescence in situ hybridisation (FISH) analysis. The deletion appeared to have arisen de novo. The IGF1R (insulin-like growth factor 1 receptor) and the NR2F2 genes were situated within, but the OCA2 (oculocutaneous albinism II) gene (formerly called the P gene) was located outside the deleted region. Clinical findings in our patient were compared with previously reported cases carrying terminal deletions of 15q26.2. This allowed us to expand the clinical phenotype of terminal 15q26.2 deletions and to indicate candidate genes for several phenotypic features.
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Affiliation(s)
- Martin Poot
- Department of Medical Genetics, University Medical Center Utrecht, Mail stop: KC.04.084.2, P.O. Box 85090, 3508 AB Utrecht, The Netherlands.
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