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Kao PY, Chen MH, Chang WA, Pan ML, Shu WD, Jong YJ, Huang HD, Wang CY, Chu HY, Pan CT, Liu YL, Lin YS. A genome-wide association study (GWAS) of the personality constructs in CPAI-2 in Taiwanese Hakka populations. PLoS One 2023; 18:e0281903. [PMID: 36800362 PMCID: PMC9937499 DOI: 10.1371/journal.pone.0281903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 02/02/2023] [Indexed: 02/18/2023] Open
Abstract
Here in this study we adopted genome-wide association studies (GWAS) to investigate the genetic components of the personality constructs in the Chinese Personality Assessment Inventory 2 (CPAI-2) in Taiwanese Hakka populations, who are likely the descendants of a recent admixture between a group of Chinese immigrants with high emigration intention and a group of the Taiwanese aboriginal population generally without it. A total of 279 qualified participants were examined and genotyped by an Illumina array with 547,644 SNPs to perform the GWAS. Although our sample size is small and that unavoidably limits our statistical power (Type 2 error but not Type 1 error), we still found three genomic regions showing strong association with Enterprise, Diversity, and Logical vs. Affective Orientation, respectively. Multiple genes around the identified regions were reported to be nervous system related, which suggests that genetic variants underlying the certain personalities should indeed exist in the nearby areas. It is likely that the recent immigration and admixture history of the Taiwanese Hakka people created strong linkage disequilibrium between the emigration intention-related genetic variants and their neighboring genetic markers, so that we could identify them despite with only limited statistical power.
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Affiliation(s)
- Pei-Ying Kao
- Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Ming-Hui Chen
- Department of Hakka Language and Social Science, National Central University, Taoyuan, Taiwan
| | - Wei-An Chang
- Department of Humanities and Social Sciences, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
- Research Center for Humanities and Social Sciences, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Mei-Lin Pan
- Department of Humanities and Social Sciences, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Wei-Der Shu
- Department of Humanities and Social Sciences, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Yuh-Jyh Jong
- Department of Biological Science and Technology, College of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University (KMU), Kaohsiung, Taiwan
- Departments of Pediatrics and Laboratory Medicine, KMU Hospital, Kaohsiung, Taiwan
| | - Hsien-Da Huang
- Department of Biological Science and Technology, College of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan
| | - Cheng-Yan Wang
- Institute of Education, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Hong-Yan Chu
- Research Center for Humanities and Social Sciences, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Cheng-Tsung Pan
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan
| | - Yih-Lan Liu
- Institute of Education, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
- * E-mail: (YLL); (YSL)
| | - Yeong-Shin Lin
- Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
- Department of Biological Science and Technology, College of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
- * E-mail: (YLL); (YSL)
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2
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Leifsdottir K, Jost K, Siljehav V, Thelin EP, Lassarén P, Nilsson P, Haraldsson Á, Eksborg S, Herlenius E. The cerebrospinal fluid proteome of preterm infants predicts neurodevelopmental outcome. Front Pediatr 2022; 10:921444. [PMID: 35928685 PMCID: PMC9343678 DOI: 10.3389/fped.2022.921444] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 06/29/2022] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Survival rate increases for preterm infants, but long-term neurodevelopmental outcome predictors are lacking. Our primary aim was to determine whether a specific proteomic profile in cerebrospinal fluid (CSF) of preterm infants differs from that of term infants and to identify novel biomarkers of neurodevelopmental outcome in preterm infants. METHODS Twenty-seven preterm infants with median gestational age 27 w + 4 d and ten full-term infants were enrolled prospectively. Protein profiling of CSF were performed utilizing an antibody suspension bead array. The relative levels of 178 unique brain derived proteins and inflammatory mediators, selected from the Human Protein Atlas, were measured. RESULTS The CSF protein profile of preterm infants differed from that of term infants. Increased levels of brain specific proteins that are associated with neurodevelopment and neuroinflammatory pathways made up a distinct protein profile in the preterm infants. The most significant differences were seen in proteins involved in neurodevelopmental regulation and synaptic plasticity, as well as components of the innate immune system. Several proteins correlated with favorable outcome in preterm infants at 18-24 months corrected age. Among the proteins that provided strong predictors of outcome were vascular endothelial growth factor C, Neurocan core protein and seizure protein 6, all highly important in normal brain development. CONCLUSION Our data suggest a vulnerability of the preterm brain to postnatal events and that alterations in protein levels may contribute to unfavorable neurodevelopmental outcome.
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Affiliation(s)
- Kristin Leifsdottir
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden.,Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden.,The Children's Hospital of Iceland, Reykjavik, Iceland
| | - Kerstin Jost
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden.,Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden
| | - Veronica Siljehav
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden.,Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden
| | - Eric P Thelin
- Department of Neurology, Karolinska University Hospital, Stockholm, Sweden.,Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Philipp Lassarén
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Peter Nilsson
- SciLifeLab, Department of Protein Science, KTH Royal Institute of Technology, Solna, Sweden
| | | | - Staffan Eksborg
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden.,Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden
| | - Eric Herlenius
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden.,Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden
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3
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P63 modulates the expression of the WDFY2 gene which is implicated in cancer regulation and limb development. Biosci Rep 2020; 39:221381. [PMID: 31789342 PMCID: PMC6914664 DOI: 10.1042/bsr20192114] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 11/15/2019] [Accepted: 11/29/2019] [Indexed: 12/31/2022] Open
Abstract
TP63 is a member of the TP53 gene family, sharing a common gene structure that produces two groups of mRNAs' encoding proteins with different N-terminal regions (ΔN and TA isoforms); both transcripts are also subjected to alternative splicing mechanisms at C-terminus, generating a variety of isoforms. p63 is a master regulator of epidermal development and homoeostasis as well as an important player in tumorigenesis and cancer progression with both oncogenic and tumour suppressive roles. A number of studies have aimed at the identification of p63 target genes, allowing the dissection of the molecular pathways orchestrated by the different isoforms. In the present study we investigated in more detail the p63 responsiveness of the WDFY2 (WD repeat and FYVE domain containing 2) gene, encoding for an endosomal protein identified as a binding partner of the PI-3K/AKT signalling pathway. We showed that overexpression of different p63 isoforms was able to induce WDFY2 expression in TP53-null cells. The p63-dependent transcriptional activation was associated with specific response elements (REs) that have been identified by a bioinformatics tool and validated by yeast- and mammal-based assays. Interestingly, to confirm that WDFY2 belongs to the p63 network of cancer regulation, we analysed the impact of WDFY2 alterations, by showing its frequent deletion in different types of tumours and suggesting its expression level as a prognostic biomarker. Lastly, we identified a chromosomal translocation involving the WDFY2 locus in a patient affected by a rare congenital limb anomaly, indicating WDFY2 as a possible susceptibility gene placed downstream p63 in the network of limb development.
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4
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Li X, Chu SG, Shen XN, Hou XH, Xu W, Ou YN, Dong Q, Tan L, Yu JT. Genome-wide association study identifies SIAH3 locus influencing the rate of ventricular enlargement in non-demented elders. Aging (Albany NY) 2019; 11:9862-9874. [PMID: 31711042 PMCID: PMC6874439 DOI: 10.18632/aging.102435] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 10/29/2019] [Indexed: 12/16/2022]
Abstract
Ventricular enlargement occurs in several neurodegenerative and psychiatric diseases. A large genome-wide association study (GWAS) has identified seven loci associated with ventricular volume. The rate of ventricular enlargement increased in the progression of disease from normal cognition to dementia. Here, we aimed to use the rate of ventricular enlargement as an endophenotype for the development and progression of neurodegenerative diseases to discover more common genetic variants. We performed a GWAS of the rate of ventricular enlargement using 507 nondemented non-Hispanic white participants from the Alzheimer’s Disease Neuroimaging Initiative (ADNI) cohort. Linear regression model was used to identify the association of the rate of ventricular enlargement with single nucleotide polymorphisms (SNPs) in PLINK software. The associations of genome-wide significant SNPs with other four phenotypes were further discussed. Two SNPs (rs11620312, P = 4.04×10−8; rs79174114, P = 4.28×10−8) within SIAH3 gene in linkage disequilibrium (LD) reached genome-wide significance for association with increased rate of ventricular enlargement. Some intergenic SNPs and SNPs within NKAIN2, TBC1D2, GALNT18, ABCC1 and SRCIN1 genes were identified as potential candidates. SIAH3 rs11620312-C carriers were associated with poor cognition and brain hypometabolism longitudinally. Our findings indicated that SIAH3 gene may have potential influence on the pathogenesis of neurodegenerative diseases.
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Affiliation(s)
- Xian Li
- Department of Neurology, Qingdao Municipal Hospital, Dalian Medical University, Dalian, China
| | - Shu-Guang Chu
- Department of Radiology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xue-Ning Shen
- Department of Neurology and Institute of Neurology, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xiao-He Hou
- Department of Neurology, Qingdao Municipal Hospital, Qingdao University, Qingdao, China
| | - Wei Xu
- Department of Neurology, Qingdao Municipal Hospital, Qingdao University, Qingdao, China
| | - Ya-Nan Ou
- Department of Neurology, Qingdao Municipal Hospital, Qingdao University, Qingdao, China
| | - Qiang Dong
- Department of Neurology and Institute of Neurology, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Lan Tan
- Department of Neurology, Qingdao Municipal Hospital, Dalian Medical University, Dalian, China
| | - Jin-Tai Yu
- Department of Neurology and Institute of Neurology, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
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5
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Pendleton AL, Shen F, Taravella AM, Emery S, Veeramah KR, Boyko AR, Kidd JM. Comparison of village dog and wolf genomes highlights the role of the neural crest in dog domestication. BMC Biol 2018; 16:64. [PMID: 29950181 PMCID: PMC6022502 DOI: 10.1186/s12915-018-0535-2] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 05/23/2018] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Domesticated from gray wolves between 10 and 40 kya in Eurasia, dogs display a vast array of phenotypes that differ from their ancestors, yet mirror other domesticated animal species, a phenomenon known as the domestication syndrome. Here, we use signatures persisting in dog genomes to identify genes and pathways possibly altered by the selective pressures of domestication. RESULTS Whole-genome SNP analyses of 43 globally distributed village dogs and 10 wolves differentiated signatures resulting from domestication rather than breed formation. We identified 246 candidate domestication regions containing 10.8 Mb of genome sequence and 429 genes. The regions share haplotypes with ancient dogs, suggesting that the detected signals are not the result of recent selection. Gene enrichments highlight numerous genes linked to neural crest and central nervous system development as well as neurological function. Read depth analysis suggests that copy number variation played a minor role in dog domestication. CONCLUSIONS Our results identify genes that act early in embryogenesis and can confer phenotypes distinguishing domesticated dogs from wolves, such as tameness, smaller jaws, floppy ears, and diminished craniofacial development as the targets of selection during domestication. These differences reflect the phenotypes of the domestication syndrome, which can be explained by alterations in the migration or activity of neural crest cells during development. We propose that initial selection during early dog domestication was for behavior, a trait influenced by genes which act in the neural crest, which secondarily gave rise to the phenotypes of modern dogs.
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Affiliation(s)
- Amanda L Pendleton
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Feichen Shen
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Angela M Taravella
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Sarah Emery
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Krishna R Veeramah
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Adam R Boyko
- Department of Biomedical Sciences, Cornell University, Ithaca, New York, 14853, USA
| | - Jeffrey M Kidd
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48109, USA.
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA.
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6
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Yasukochi Y, Sakuma J, Takeuchi I, Kato K, Oguri M, Fujimaki T, Horibe H, Yamada Y. Identification of three genetic variants as novel susceptibility loci for body mass index in a Japanese population. Physiol Genomics 2018; 50:179-189. [PMID: 29341862 PMCID: PMC5899233 DOI: 10.1152/physiolgenomics.00117.2017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Recent genome-wide association studies have identified various obesity or metabolic syndrome (MetS) susceptibility loci. However, most studies were conducted in a cross-sectional manner. To address this gap, we performed a longitudinal exome-wide association study to identify susceptibility loci for obesity and MetS in a Japanese population. We traced clinical data of 6,022 Japanese subjects who had annual health check-ups for several years (mean follow-up period, 5 yr) and genotyped ~244,000 genetic variants. The association of single nucleotide polymorphisms (SNPs) with body mass index (BMI) or the prevalence of obesity and MetS was examined in a generalized estimating equation model. Our longitudinal exome-wide association studies detected 21 BMI- and five MetS-associated SNPs (false discovery rate, FDR <0.01). Among these SNPs, 16 have not been previously implicated as determinants of BMI or MetS. Cross-sectional data for obesity- and MetS-related phenotypes in 7,285 Japanese subjects were examined in a replication study. Among the 16 SNPs, three (rs9491140, rs145848316, and rs7863248) were related to BMI in the replication cohort (P < 0.05). In conclusion, three SNPs [rs9491140 of NKAIN2 (FDR = 0.003, P = 1.9 × 10−5), rs145848316 of KMT2C (FDR = 0.007, P = 4.5 × 10−5), and rs7863248 of AGTPBP1 (FDR = 0.006, P = 4.2 × 10−5)] were newly identified as susceptibility loci for BMI.
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Affiliation(s)
- Yoshiki Yasukochi
- Department of Human Functional Genomics, Advanced Science Research Promotion Center, Mie University, Tsu, Mie , Japan.,CREST, Japan Science and Technology Agency, Kawaguchi, Saitama , Japan
| | - Jun Sakuma
- CREST, Japan Science and Technology Agency, Kawaguchi, Saitama , Japan.,Computer Science Department, College of Information Science, University of Tsukuba, Tsukuba, Ibaraki , Japan.,RIKEN Center for Advanced Intelligence Project , Tokyo , Japan
| | - Ichiro Takeuchi
- CREST, Japan Science and Technology Agency, Kawaguchi, Saitama , Japan.,RIKEN Center for Advanced Intelligence Project , Tokyo , Japan.,Department of Computer Science, Nagoya Institute of Technology, Gokiso, Showa, Nagoya, Aichi , Japan
| | - Kimihiko Kato
- Department of Human Functional Genomics, Advanced Science Research Promotion Center, Mie University, Tsu, Mie , Japan.,Department of Internal Medicine, Meitoh Hospital, Nagoya, Aichi , Japan
| | - Mitsutoshi Oguri
- Department of Human Functional Genomics, Advanced Science Research Promotion Center, Mie University, Tsu, Mie , Japan.,Department of Cardiology, Kasugai Municipal Hospital, Kasugai, Aichi , Japan
| | - Tetsuo Fujimaki
- Department of Cardiovascular Medicine, Inabe General Hospital, Inabe, Mie , Japan
| | - Hideki Horibe
- Department of Cardiovascular Medicine, Gifu Prefectural Tajimi Hospital, Tajimi, Gifu , Japan
| | - Yoshiji Yamada
- Department of Human Functional Genomics, Advanced Science Research Promotion Center, Mie University, Tsu, Mie , Japan.,CREST, Japan Science and Technology Agency, Kawaguchi, Saitama , Japan
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7
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Mao X, Luo F, Boyd LK, Zhou B, Zhang Y, Stankiewicz E, Marzec J, Vasiljevic N, Yu Y, Feng N, Xu J, Lorincz A, Jiang Y, Chelala C, Ren G, Berney DM, Zhao SC, Lu YJ. NKAIN2 functions as a novel tumor suppressor in prostate cancer. Oncotarget 2016; 7:63793-63803. [PMID: 27588475 PMCID: PMC5325404 DOI: 10.18632/oncotarget.11690] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 08/22/2016] [Indexed: 11/25/2022] Open
Abstract
Recurrent chromosome breakpoints at 6q22.31, leading to truncation and potential loss-of-function of the NKAIN2 gene, in Chinese prostate cancer patients were previously identified. In this study we investigated genomic, methylation and expression changes of NKAIN2 in a large number of prostate cancer samples and determined its functional role in prostate cancer cells. Fluorescence in situ hybridization analysis confirmed that NKAIN2 truncation is specific to Chinese while deletion of the gene is frequent in both Chinese and UK prostate cancers. Significantly reduced expression of NKAIN2 was also detected at both RNA and protein levels. Somatic mutations of NKAIN2 in prostate cancer samples exist but at very low frequency, suggesting that it is a putative tumor suppressor gene (TSG) with haploid insufficiency. Our functional studies showed that overexpression of NKAIN2 in prostate cancer cells inhibits cellular growth by promoting cell apoptosis, and decreasing cell migration and invasion. Conversely, knockdown of NKAIN2 promotes prostate cancer cell growth by inhibiting cell apoptosis, and increasing cell migration and invasion. These data imply that NKAIN2 is a novel TSG whose activity is commonly reduced in prostate cancer. It may restrain the disease development and progression by inducing apoptosis and suppressing cancer cell growth, migration and invasion. This study provides new insights into prostate carcinogenesis and opportunities for development of novel therapies for prostate cancer.
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Affiliation(s)
- Xueying Mao
- Centre for Molecular Oncology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Fei Luo
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
- Key Laboratory of Proteomics of Guangdong Province and Key Laboratory of Transcriptomics and Proteomics of Human Diseases Supported by The Ministry of Education of China, Southern Medical University, Guangzhou, 510515, China
| | - Lara K. Boyd
- Centre for Molecular Oncology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Bowei Zhou
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
- Key Laboratory of Proteomics of Guangdong Province and Key Laboratory of Transcriptomics and Proteomics of Human Diseases Supported by The Ministry of Education of China, Southern Medical University, Guangzhou, 510515, China
| | - Yanling Zhang
- Department of Pathology, The First Affiliated Hospital, Zhejiang University Medical College, Hangzhou, 310009, China
- Department of Gynecology and Obstetrics, Sir Run Run Shaw Hospital, Zhejiang University Medical College, Hangzhou, 310009, China
| | - Elzbieta Stankiewicz
- Centre for Molecular Oncology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Jacek Marzec
- Centre for Molecular Oncology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Natasa Vasiljevic
- Centre for Cancer Prevention, Wolfson Institute of Preventive Medicine, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Yongwei Yu
- Department of Pathology, Changhai Hospital, The Second Military Medical University, Shanghai, 200433, China
| | - Ninghan Feng
- Department of Urology, Wuxi Second People's Hospital, Nanjing Medical University, Wuxi, 214002, China
| | - Jia Xu
- Key Laboratory of Proteomics of Guangdong Province and Key Laboratory of Transcriptomics and Proteomics of Human Diseases Supported by The Ministry of Education of China, Southern Medical University, Guangzhou, 510515, China
| | - Attila Lorincz
- Centre for Cancer Prevention, Wolfson Institute of Preventive Medicine, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Yong Jiang
- Key Laboratory of Proteomics of Guangdong Province and Key Laboratory of Transcriptomics and Proteomics of Human Diseases Supported by The Ministry of Education of China, Southern Medical University, Guangzhou, 510515, China
| | - Claude Chelala
- Centre for Molecular Oncology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Guoping Ren
- Department of Pathology, The First Affiliated Hospital, Zhejiang University Medical College, Hangzhou, 310009, China
| | - Daniel M Berney
- Centre for Molecular Oncology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Shan-Chao Zhao
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Yong-Jie Lu
- Centre for Molecular Oncology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
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Desch L, Marle N, Mosca-Boidron AL, Faivre L, Eliade M, Payet M, Ragon C, Thevenon J, Aral B, Ragot S, Ardalan A, Dhouibi N, Bensignor C, Thauvin-Robinet C, El Chehadeh S, Callier P. 6q16.3q23.3 duplication associated with Prader-Willi-like syndrome. Mol Cytogenet 2015; 8:42. [PMID: 26110021 PMCID: PMC4479069 DOI: 10.1186/s13039-015-0151-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 06/10/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Prader-Willi syndrome (PWS) is characterized by hypotonia, delayed neuropsychomotor development, overeating, obesity and mental deficiency. This phenotype is encountered in other conditions, defining Prader-Willi-like syndrome (PWLS). CASE PRESENTATION We report a 14-year-old boy with a complex small supernumerary marker chromosome (sSMC) associated with PWLS. The propositus presents clinical features commonly found in patients with PWLS, including growth hormone deficit. Banding karyotype analysis and fluorescence in situ hybridization (FISH) revealed a marker derived from chromosome 6 and a neocentromere as suspected, but array-CGH enabled us to characterize this marker as a der(10)t(6;10)(6qter → 6q23.3::10p11.1 → 10p11.21)dn. As far as we know, this is the first diagnosed case of PWLS associated with a complex sSMC, involving a 30.9 Mb gain in the 6q16.3q23.3 region and a 3.5 Mb gain in the 10p11.21p11.1 region. Several genes have been mapped to the 6q region including the TCBA1 gene, which is associated with developmental delay and recurrent infections, the ENPP1 gene, associated with insulin resistance and susceptibility to obesity and the BMIQ3 gene, associated with body mass index (BMI). No OMIM gene was found in the smallest 10p11.21p11.1 region. CONCLUSIONS We suggest that the duplicated chromosome segment 6q16.3q23.3 may be responsible for the phenotype of our case and may also be a candidate locus of PWLS.
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Affiliation(s)
- Laurent Desch
- />Laboratoire de Cytogénétique, Plateau Technique de Biologie, CHU de Dijon, Dijon, France
| | - Nathalie Marle
- />Laboratoire de Cytogénétique, Plateau Technique de Biologie, CHU de Dijon, Dijon, France
| | | | - Laurence Faivre
- />Centre de référence maladies rares « anomalies du développement et syndromes malformatifs » de l’Est, Centre de Génétique, CHU de Dijon, Dijon, France
| | - Marie Eliade
- />Laboratoire de Cytogénétique, Plateau Technique de Biologie, CHU de Dijon, Dijon, France
| | - Muriel Payet
- />Laboratoire de Cytogénétique, Plateau Technique de Biologie, CHU de Dijon, Dijon, France
| | - Clemence Ragon
- />Laboratoire de Cytogénétique, Plateau Technique de Biologie, CHU de Dijon, Dijon, France
| | - Julien Thevenon
- />Laboratoire de Cytogénétique, Plateau Technique de Biologie, CHU de Dijon, Dijon, France
| | - Bernard Aral
- />Laboratoire de Cytogénétique, Plateau Technique de Biologie, CHU de Dijon, Dijon, France
| | - Sylviane Ragot
- />Laboratoire de Cytogénétique, Plateau Technique de Biologie, CHU de Dijon, Dijon, France
| | | | | | | | - Christel Thauvin-Robinet
- />Centre de référence maladies rares « anomalies du développement et syndromes malformatifs » de l’Est, Centre de Génétique, CHU de Dijon, Dijon, France
| | - Salima El Chehadeh
- />Centre de référence maladies rares « anomalies du développement et syndromes malformatifs » de l’Est, Centre de Génétique, CHU de Dijon, Dijon, France
| | - Patrick Callier
- />Laboratoire de Cytogénétique, Plateau Technique de Biologie, CHU de Dijon, Dijon, France
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9
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Sheth F, Trivedi S, Andrieux J, Blouin JL, Sheth J. Pure interstitial dup(6)(q22.31q22.31) - a case report. Ital J Pediatr 2015; 41:5. [PMID: 25637059 PMCID: PMC4347966 DOI: 10.1186/s13052-015-0113-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Accepted: 01/17/2015] [Indexed: 11/30/2022] Open
Abstract
‘Pure’ interstitial duplication of chr6q is rare. The varying size of duplication encompassing 6q22.31 is associated with the expressivity of dysmorphism and autism. Here, we report a unique case with facial dysmorphism, developmental delay, complex neurological impairment and spasticity unrelated to autism. Genetic analysis by aCGH exhibited a 627–971 kb dup(6)(q22.31q22.31) encompassing TRDN and NKAIN2 genes. The presence of the duplication was confirmed by quantitative PCR in the proband and phenotypically normal parents. With the current techniques, we cannot exclude presence of a deleterious homozygous point mutation in the proband where each copy would have been inherited from both parents.
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Affiliation(s)
- Frenny Sheth
- FRIGE's Institute of Human Genetics, FRIGE House, Jodhpur Gam Road, Satellite, Ahmedabad, 380015, India.
| | - Sunil Trivedi
- FRIGE's Institute of Human Genetics, FRIGE House, Jodhpur Gam Road, Satellite, Ahmedabad, 380015, India.
| | - Joris Andrieux
- Laboratory of Medical Genetics, Jeanne de Flandre Hospital, CHRU, 59000, Lille, France.
| | - Jean-Louis Blouin
- Laboratory of Molecular Diagnostics, Genetic Medicine, University Hospitals of Geneva, CH-1211, Geneva, Switzerland.
| | - Jayesh Sheth
- FRIGE's Institute of Human Genetics, FRIGE House, Jodhpur Gam Road, Satellite, Ahmedabad, 380015, India.
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10
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Poot M. Late breaking chromosomes. Mol Syndromol 2014; 5:1-2. [PMID: 24550758 DOI: 10.1159/000355850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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11
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Functionally enigmatic genes: a case study of the brain ignorome. PLoS One 2014; 9:e88889. [PMID: 24523945 PMCID: PMC3921226 DOI: 10.1371/journal.pone.0088889] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2013] [Accepted: 01/14/2014] [Indexed: 12/26/2022] Open
Abstract
What proportion of genes with intense and selective expression in specific tissues, cells, or systems are still almost completely uncharacterized with respect to biological function? In what ways do these functionally enigmatic genes differ from well-studied genes? To address these two questions, we devised a computational approach that defines so-called ignoromes. As proof of principle, we extracted and analyzed a large subset of genes with intense and selective expression in brain. We find that publications associated with this set are highly skewed--the top 5% of genes absorb 70% of the relevant literature. In contrast, approximately 20% of genes have essentially no neuroscience literature. Analysis of the ignorome over the past decade demonstrates that it is stubbornly persistent, and the rapid expansion of the neuroscience literature has not had the expected effect on numbers of these genes. Surprisingly, ignorome genes do not differ from well-studied genes in terms of connectivity in coexpression networks. Nor do they differ with respect to numbers of orthologs, paralogs, or protein domains. The major distinguishing characteristic between these sets of genes is date of discovery, early discovery being associated with greater research momentum--a genomic bandwagon effect. Finally we ask to what extent massive genomic, imaging, and phenotype data sets can be used to provide high-throughput functional annotation for an entire ignorome. In a majority of cases we have been able to extract and add significant information for these neglected genes. In several cases--ELMOD1, TMEM88B, and DZANK1--we have exploited sequence polymorphisms, large phenome data sets, and reverse genetic methods to evaluate the function of ignorome genes.
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12
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Romania P, Castellano A, Surace C, Citti A, De Ioris MA, Sirleto P, De Mariano M, Longo L, Boldrini R, Angioni A, Locatelli F, Fruci D. High-resolution array CGH profiling identifies Na/K transporting ATPase interacting 2 (NKAIN2) as a predisposing candidate gene in neuroblastoma. PLoS One 2013; 8:e78481. [PMID: 24205241 PMCID: PMC3808344 DOI: 10.1371/journal.pone.0078481] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Accepted: 09/13/2013] [Indexed: 02/06/2023] Open
Abstract
Neuroblastoma (NB), the most common solid cancer in early childhood, usually occurs sporadically but also its familial occurance is known in 1-2% of NB patients. Germline mutations in the ALK and PHOX2B genes have been found in a subset of familial NBs. However, because some individuals harbouring mutations in these genes do not develop this tumor, additional genetic alterations appear to be required for NB pathogenesis. Herein, we studied an Italian family with three NB patients, two siblings and a first cousin, carrying an ALK germline-activating mutation R1192P, that was inherited from their unaffected mothers and with no mutations in the PHOX2B gene. A comparison between somatic and germline DNA copy number changes in the two affected siblings by a high resolution array-based Comparative Genomic Hybridization (CGH) analysis revealed a germline gain at NKAIN2 (Na/K transporting ATPase interacting 2) locus in one of the sibling, that was inherited from the parent who does not carry the ALK mutation. Surprisingly, NKAIN2 was expressed at high levels also in the affected sibling that lacks the genomic gain at this locus, clearly suggesting the existance of other regulatory mechanisms. High levels of NKAIN2 were detected in the MYCN-amplified NB cell lines and in the most aggressive NB lesions as well as in the peripheral blood of a large cohort of NB patients. Consistent with a role of NKAIN2 in NB development, NKAIN2 was down-regulated during all-trans retinoic acid differentiation in two NB cell lines. Taken together, these data indicate a potential role of NKAIN2 gene in NB growth and differentiation.
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Affiliation(s)
- Paolo Romania
- Paediatric Haematology/Oncology Department, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Aurora Castellano
- Paediatric Haematology/Oncology Department, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Cecilia Surace
- Cytogenetics and Molecular Genetics Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Arianna Citti
- Pathology Department, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | | | - Pietro Sirleto
- Cytogenetics and Molecular Genetics Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Marilena De Mariano
- Immunological Therapy, IRCCS A.O.U. San Martino-IST, Istituto Nazionale per la Ricerca sul Cancro, Genoa, Italy
| | - Luca Longo
- Immunological Therapy, IRCCS A.O.U. San Martino-IST, Istituto Nazionale per la Ricerca sul Cancro, Genoa, Italy
| | - Renata Boldrini
- Pathology Department, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Adriano Angioni
- Cytogenetics and Molecular Genetics Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Franco Locatelli
- Paediatric Haematology/Oncology Department, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
- Pediatrics Department, University of Pavia, Pavia, Italy
| | - Doriana Fruci
- Paediatric Haematology/Oncology Department, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
- * E-mail:
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Marangi G, Orteschi D, Milano V, Mancano G, Zollino M. Interstitial deletion of 3p22.3p22.2 encompassingARPP21andCLASP2is a potential pathogenic factor for a syndromic form of intellectual disability: A co-morbidity model with additional copy number variations in a large family. Am J Med Genet A 2013; 161A:2890-3. [DOI: 10.1002/ajmg.a.36257] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Accepted: 09/05/2013] [Indexed: 11/07/2022]
Affiliation(s)
- Giuseppe Marangi
- Instituto di Genetica Medica; Università Cattolica del Sacro Cuore; Roma Italy
| | - Daniela Orteschi
- Instituto di Genetica Medica; Università Cattolica del Sacro Cuore; Roma Italy
| | - Valentina Milano
- Instituto di Genetica Medica; Università Cattolica del Sacro Cuore; Roma Italy
| | - Giorgia Mancano
- Instituto di Genetica Medica; Università Cattolica del Sacro Cuore; Roma Italy
| | - Marcella Zollino
- Instituto di Genetica Medica; Università Cattolica del Sacro Cuore; Roma Italy
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Zuo L, Wang KS, Zhang XY, Li CSR, Zhang F, Wang X, Chen W, Gao G, Zhang H, Krystal JH, Luo X. Rare SERINC2 variants are specific for alcohol dependence in individuals of European descent. Pharmacogenet Genomics 2013; 23:395-402. [PMID: 23778322 PMCID: PMC4287355 DOI: 10.1097/fpc.0b013e328362f9f2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
OBJECTIVES We have previously reported a top-ranked risk gene [i.e., serine incorporator 2 gene (SERINC2)] for alcohol dependence in individuals of European descent by analyzing the common variants in a genome-wide association study. In the present study, we comprehensively examined the rare variants [minor allele frequency (MAF)<0.05] in the NKAIN1-SERINC2 region to confirm our previous finding. MATERIALS AND METHODS A discovery sample (1409 European-American patients with alcohol dependence and 1518 European-American controls) and a replication sample (6438 European-Australian family participants with 1645 alcohol-dependent probands) were subjected to an association analysis. A total of 39,903 individuals from 19 other cohorts with 11 different neuropsychiatric and neurological disorders served as contrast groups. The entire NKAIN1-SERINC2 region was imputed in all cohorts using the same reference panels of genotypes that included rare variants from the whole-genome sequencing data. We stringently cleaned the phenotype and genotype data, and obtained a total of about 220 single-nucleotide polymorphisms in individuals of European descent and about 450 single-nucleotide polymorphisms in the individuals of African descent with 0 RESULTS Using a weighted regression analysis implemented in the program SCORE-Seq, we found a rare variant constellation across the entire NKAIN1-SERINC2 region that was associated with alcohol dependence in European-Americans (Fp: overall, P=1.8×10(-4); VT: overall, P=1.4×10(-4); Collapsing, P=6.5×10(-5)) and European-Australians (Fp: overall, P=0.028; Collapsing, P=0.025), but not in African-Americans, and not associated with any other disorder examined. Association signals in this region came mainly from SERINC2, a gene that codes for an activity-regulated protein expressed in the brain that incorporates serine into lipids. In addition, 26 individual rare variants were nominally associated with alcohol dependence in European-Americans (P<0.05). The associations of five of these rare variants that lay within SERINC2 showed region-wide significance (P<α=0.0006) and 25 associations survived correction for a false discovery rate (q<0.05). The associations of two rare variants at SERINC2 were replicated in European-Australians (P<0.05). CONCLUSION We concluded that SERINC2 was a replicable and significant risk gene specific for alcohol dependence in individuals of European descent.
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Affiliation(s)
- Lingjun Zuo
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - Ke-Sheng Wang
- Department of Biostatistics and Epidemiology, College of Public Health, East Tennessee State University, Johnson City, TN, USA
| | - Xiang-Yang Zhang
- Menninger Department of Psychiatry and Behavioral Sciences, Baylor College of Medicine, Houston, Texas, USA
| | - Chiang-Shan R. Li
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - Fengyu Zhang
- Lieber Institute for Brain Development, Johns Hopkins University Medical Campus, Baltimore, MD, USA
| | - Xiaoping Wang
- Department of Neurology, First People's Hospital, Shanghai Jiaotong University, Shanghai, China
| | - Wenan Chen
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA, USA
| | - Guimin Gao
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA, USA
| | - Heping Zhang
- Department of Biostatistics, Yale University School of Epidemiology and Public Health, New Haven, CT, USA
| | - John H. Krystal
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
- Psychiatry Services, Yale-New Haven Hospital, New Haven, CT
- VA Alcohol Research Center, VA Connecticut Healthcare System, West Haven, CT
| | - Xingguang Luo
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
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Kim HN, Roh SJ, Sung YA, Chung HW, Lee JY, Cho J, Shin H, Kim HL. Genome-wide association study of the five-factor model of personality in young Korean women. J Hum Genet 2013; 58:667-74. [PMID: 23903073 DOI: 10.1038/jhg.2013.75] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2013] [Revised: 05/30/2013] [Accepted: 06/07/2013] [Indexed: 12/30/2022]
Abstract
Personality is a determinant of behavior and lifestyle associated with health and human diseases. Although personality is known to be a heritable trait, its polygenic nature has made the identification of genetic variants elusive. We performed a genome-wide association study on 1089 Korean women aged 18-40 years whose personality traits were measured with the Revised NEO Personality Inventory for the five-factor model of personality. To reduce environmental factors that may influence personality traits, this study was restricted to young adult women. In the discovery phase, we identified variants of PTPRD (protein tyrosine phosphatase, receptor type D) that associated this gene with the Openness domain. Other genes that were previously reported to be associated with neurological phenotypes were also associated with personality traits. In particular, DRD1 and OR1A2 were linked to Neuroticism, NKAIN2 with Extraversion, HTR5A with Openness and DRD3 with Agreeableness. Data from our replication study of 2090 subjects confirmed the association between OR1A2 and Neuroticism. We first identified and confirmed a novel region on OR1A2 associated with Neuroticism [corrected]. Candidate genes for psychiatric disorders were also enriched. These findings contribute to our understanding of the genetic architecture of personality traits and provide critical clues to the neurobiological mechanisms that influence them.
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Affiliation(s)
- Han-Na Kim
- Department of Biochemistry, School of Medicine, Ewha Womans University, Seoul, Korea
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16
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Newbury DF, Mari F, Sadighi Akha E, Macdermot KD, Canitano R, Monaco AP, Taylor JC, Renieri A, Fisher SE, Knight SJL. Dual copy number variants involving 16p11 and 6q22 in a case of childhood apraxia of speech and pervasive developmental disorder. Eur J Hum Genet 2012; 21:361-5. [PMID: 22909776 PMCID: PMC3598310 DOI: 10.1038/ejhg.2012.166] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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17
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Filges I, Suda L, Weber P, Datta AN, Fischer D, Dill P, Glanzmann R, Benzing J, Hegi L, Wenzel F, Huber AR, Mori AC, Miny P, Röthlisberger B. High resolution array in the clinical approach to chromosomal phenotypes. Gene 2012; 495:163-9. [PMID: 22240311 DOI: 10.1016/j.gene.2011.12.042] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2011] [Revised: 12/19/2011] [Accepted: 12/23/2011] [Indexed: 12/11/2022]
Abstract
Array genomic hybridization (AGH) has recently been implemented as a diagnostic tool for the detection of submicroscopic copy number variants (CNVs) in patients with developmental disorders. However, there is no consensus regarding the choice of the platform, the minimal resolution needed and systematic interpretation of CNVs. We report our experience in the clinical diagnostic use of high resolution AGH up to 100 kb on 131 patients with chromosomal phenotypes but previously normal karyotype. We evaluated the usefulness in our clinics and laboratories by the detection rate of causal CNVs and CNVs of unknown clinical significance and to what extent their interpretation would challenge the systematic use of high-resolution arrays in clinical application. Prioritizing phenotype-genotype correlation in our interpretation strategy to criteria previously described, we identified 33 (25.2%) potentially pathogenic aberrations. 16 aberrations were confirmed pathogenic (16.4% syndromic, 8.5% non-syndromic patients); 9 were new and individual aberrations, 3 of them were pathogenic although inherited and one is as small as approx 200 kb. 13 of 16 further CNVs of unknown significance were classified likely benign, for 3 the significance remained unclear. High resolution array allows the detection of up to 12.2% of pathogenic aberrations in a diagnostic clinical setting. Although the majority of aberrations are larger, the detection of small causal aberrations may be relevant for family counseling. The number of remaining unclear CNVs is limited. Careful phenotype-genotype correlations of the individual CNVs and clinical features are challenging but remain a hallmark for CNV interpretation.
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18
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Calboli FCF, Tozzi F, Galwey NW, Antoniades A, Mooser V, Preisig M, Vollenweider P, Waterworth D, Waeber G, Johnson MR, Muglia P, Balding DJ. A genome-wide association study of neuroticism in a population-based sample. PLoS One 2010; 5:e11504. [PMID: 20634892 PMCID: PMC2901337 DOI: 10.1371/journal.pone.0011504] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2009] [Accepted: 05/17/2010] [Indexed: 11/22/2022] Open
Abstract
Neuroticism is a moderately heritable personality trait considered to be a risk factor for developing major depression, anxiety disorders and dementia. We performed a genome-wide association study in 2,235 participants drawn from a population-based study of neuroticism, making this the largest association study for neuroticism to date. Neuroticism was measured by the Eysenck Personality Questionnaire. After Quality Control, we analysed 430,000 autosomal SNPs together with an additional 1.2 million SNPs imputed with high quality from the Hap Map CEU samples. We found a very small effect of population stratification, corrected using one principal component, and some cryptic kinship that required no correction. NKAIN2 showed suggestive evidence of association with neuroticism as a main effect (p<10−6) and GPC6 showed suggestive evidence for interaction with age (p≈10−7). We found support for one previously-reported association (PDE4D), but failed to replicate other recent reports. These results suggest common SNP variation does not strongly influence neuroticism. Our study was powered to detect almost all SNPs explaining at least 2% of heritability, and so our results effectively exclude the existence of loci having a major effect on neuroticism.
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Affiliation(s)
- Federico C F Calboli
- Department of Epidemiology and Biostatistics, Imperial College London, London, United Kingdom.
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Griseri P, Vos Y, Giorda R, Gimelli S, Beri S, Santamaria G, Mognato G, Hofstra RMW, Gimelli G, Ceccherini I. Complex pathogenesis of Hirschsprung's disease in a patient with hydrocephalus, vesico-ureteral reflux and a balanced translocation t(3;17)(p12;q11). Eur J Hum Genet 2008; 17:483-90. [PMID: 19300444 DOI: 10.1038/ejhg.2008.191] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Hirschsprung's disease (HSCR), a congenital complex disorder of intestinal innervation, is often associated with other inherited syndromes. Identifying genes involved in syndromic HSCR cases will not only help understanding the specific underlying diseases, but it will also give an insight into the development of the most frequent isolated HSCR. The association between hydrocephalus and HSCR is not surprising as a large number of patients have been reported to show the same clinical association, most of them showing mutations in the L1CAM gene, encoding a neural adhesion molecule often involved in isolated X-linked hydrocephalus. L1 defects are believed to be necessary but not sufficient for the occurrence of the intestinal phenotype in syndromic cases. In this paper, we have carried out the molecular characterization of a patient affected with Hirschsprung's disease and X-linked hydrocephalus, with a de novo reciprocal balanced translocation t(3;17)(p12;q21). In particular, we have taken advantage of this chromosomal defect to gain access to the predisposing background possibly leading to Hirschsprung's disease. Detailed analysis of the RET and L1CAM genes, and molecular characterization of MYO18A and TIAF1, the genes involved in the balanced translocation, allowed us to identify, besides the L1 mutation c.2265delC, different additional factors related to RET-dependent and -independent pathways which may have contributed to the genesis of enteric phenotype in the present patient.
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Affiliation(s)
- Paola Griseri
- Laboratory Molecular Genetics and Cytogenetics, Genova, Italy
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Shann YJ, Cheng C, Chiao CH, Chen DT, Li PH, Hsu MT. Genome-wide mapping and characterization of hypomethylated sites in human tissues and breast cancer cell lines. Genome Res 2008; 18:791-801. [PMID: 18256232 DOI: 10.1101/gr.070961.107] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
We have developed a method for mapping unmethylated sites in the human genome based on the resistance of TspRI-digested ends to ExoIII nuclease degradation. Digestion with TspRI and methylation-sensitive restriction endonuclease HpaII, followed by ExoIII and single-strand DNA nuclease allowed removal of DNA fragments containing unmethylated HpaII sites. We then used array comparative genomic hybridization (CGH) to map the sequences depleted by these procedures in human genomes derived from five human tissues, a primary breast tumor, and two breast tumor cell lines. Analysis of methylation patterns of the normal tissue genomes indicates that the hypomethylated sites are enriched in the 5' end of widely expressed genes, including promoter, first exon, and first intron. In contrast, genomes of the MCF-7 and MDA-MB-231 cell lines show extensive hypomethylation in the intragenic and intergenic regions whereas the primary tumor exhibits a pattern between those of the normal tissue and the cell lines. A striking characteristic of tumor cell lines is the presence of megabase-sized hypomethylated zones. These hypomethylated zones are associated with large genes, fragile sites, evolutionary breakpoints, chromosomal rearrangement breakpoints, tumor suppressor genes, and with regions containing tissue-specific gene clusters or with gene-poor regions containing novel tissue-specific genes. Correlation with microarray analysis shows that genes with a hypomethylated sequence 2 kb up- or downstream of the transcription start site are highly expressed, whereas genes with extensive intragenic and 3' untranslated region (UTR) hypomethylation are silenced. The method described herein can be used for large-scale screening of changes in the methylation pattern in the genome of interest.
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Affiliation(s)
- Yih-Jyh Shann
- Institute of Biochemistry and Molecular Biology, School of Life Science, National Yang-Ming University, Taipei, Taiwan, Republic of China
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Gorokhova S, Bibert S, Geering K, Heintz N. A novel family of transmembrane proteins interacting with beta subunits of the Na,K-ATPase. Hum Mol Genet 2007; 16:2394-410. [PMID: 17606467 DOI: 10.1093/hmg/ddm167] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We characterized a family consisting of four mammalian proteins of unknown function (NKAIN1, 2, 3 and 4) and a single Drosophila ortholog dNKAIN. Aside from highly conserved transmembrane domains, NKAIN proteins contain no characterized functional domains. Striking amino acid conservation in the first two transmembrane domains suggests that these proteins are likely to function within the membrane bilayer. NKAIN family members are neuronally expressed in multiple regions of the mouse brain, although their expression is not ubiquitous. We demonstrate that mouse NKAIN1 interacts with the beta1 subunit of the Na,K-ATPase, whereas Drosophila ortholog dNKAIN interacts with Nrv2.2, a Drosophila homolog of the Na,K-ATPase beta subunits. We also show that NKAIN1 can form a complex with another beta subunit-binding protein, MONaKA, when binding to the beta1 subunit of the Na,K-ATPase. Our results suggest that a complex between mammalian NKAIN1 and MONaKA is required for NKAIN function, which is carried out by a single protein, dNKAIN, in Drosophila. This hypothesis is supported by the fact that dNKAIN, but not NKAIN1, induces voltage-independent amiloride-insensitive Na(+)-specific conductance that can be blocked by lanthanum. Drosophila mutants with decreased dNKAIN expression due to a P-element insertion in the dNKAIN gene exhibit temperature-sensitive paralysis, a phenotype also caused by mutations in the Na,K-ATPase alpha subunit and several ion channels. The neuronal expression of NKAIN proteins, their membrane localization and the temperature-sensitive paralysis of NKAIN Drosophila mutants strongly suggest that this novel protein family may be critical for neuronal function.
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Affiliation(s)
- Svetlana Gorokhova
- Laboratory of Molecular Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10021, USA
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