DNA Chip Research Institute

Yokohama-shi, Japan

DNA Chip Research Institute

Yokohama-shi, Japan
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Sekimoto T.,University of Miyazaki | Ishii M.,University of Miyazaki | Ishii M.,DNA Chip Research Institute | Emi M.,University of Miyazaki | And 8 more authors.
Bone and Joint Research | Year: 2017

Objectives: We have previously investigated an association between the genome copy number variation (CNV) and acetabular dysplasia (AD). Hip osteoarthritis is associated with a genetic polymorphism in the aspartic acid repeat in the N-terminal region of the asporin (ASPN) gene; therefore, the present study aimed to investigate whether the CNV of ASPN is involved in the pathogenesis of AD. Methods: Acetabular coverage of all subjects was evaluated using radiological findings (Sharp angle, centre-edge (CE) angle, acetabular roof obliquity (ARO) angle, and minimum joint space width). Genomic DNA was extracted from peripheral blood leukocytes. Agilent's regiontargeted high-density oligonucleotide tiling microarray was used to analyse 64 female AD patients and 32 female control subjects. All statistical analyses were performed using EZR software (Fisher's exact probability test, Pearson's correlation test, and Student's t-test). Results: CNV analysis of the ASPN gene revealed a copy number loss in significantly more AD patients (9/64) than control subjects (0/32; p = 0.0212). This loss occurred within a 60 kb region on 9q22.31, which harbours the gene for ASPN. The mean radiological parameters of these AD patients were significantly worse than those of the other subjects (Sharp angle, p = 0.0056; CE angle, p = 0.0076; ARO angle, p = 0.0065), and all nine patients required operative therapy such as total hip arthroplasty or pelvic osteotomy. Moreover, six of these nine patients had a history of operative or conservative therapy for developmental dysplasia of the hip. Conclusions: Copy number loss within the region harbouring the ASPN gene on 9q22.31 is associated with severe AD. A copy number loss in the ASPN gene region may play a role in the aetiology of severe AD. © 2017 Cao et al.

Ueno T.,Kyoto University | Emi M.,DNA Chip Research Institute | Sato H.,DNA Chip Research Institute | Ito N.,DNA Chip Research Institute | And 3 more authors.
Expert Opinion on Therapeutic Targets | Year: 2012

Introduction: Carcinogenesis is considered to be a multistep process that may involve cumulative genomic alterations. Loss of chromosomal material would inactivate tumor suppressor genes and gain of chromosomal material has the potential to activate tumor-promoting genes. Areas covered: Recent intensive studies by array comparative genomic hybridization (aCGH) have demonstrated frequent alterations in multiple regions of the genome. This suggests that these regions contain a variety of oncogenes and tumor suppressor genes associated with breast cancer development. The patterns of copy number variations (CNVs) have been suggested to be associated with breast cancer subtypes, indicating the importance of genomic instability in the development of breast cancer. Expert opinion: To further clarify the complexity of gene alterations, one approach is to employ a CNV-targeted platform that harbors a large number of direct CNV markers located in the repeat-rich unstable regions of the human genome. Next generation sequencing is another approach to overcome the limitations of aCGH such as the repeat-rich regions. Genomic analysis should be combined with expression analysis to elucidate individual genes relevant to breast cancer development and progression. The elucidation of the functions of the affected genes would lead to identification of new molecular targets for breast cancer eradication. © 2012 Informa UK, Ltd.

Kudo H.,Tohoku University | Emi M.,DNA Chip Research Institute | Ishigaki Y.,Tohoku University | Tsunoda U.,Tohoku University | And 6 more authors.
Experimental Diabetes Research | Year: 2011

A small portion of Type 2 diabetes mellitus (T2DM) is familial, but the majority occurs as sporadic disease. Although causative genes are found in some rare forms, the genetic basis for sporadic T2DM is largely unknown. We searched for a copy number abnormality in 100 early-onset Japanese T2DM patients (onset age <35 years) by whole-genome screening with a copy number variation BeadChip. Within the 1.3-Mb subtelomeric region on chromosome 4p16.3, we found copy number losses in early-onset T2DM (13 of 100 T2DM versus one of 100 controls). This region surrounds a genome gap, which is rich in multiple low copy repeats. Subsequent region-targeted high-density custom-made oligonucleotide microarray experiments verified the copy number losses and delineated structural changes in the 1.3-Mb region. The results suggested that copy number losses of the genes in the deleted region around the genome gap in 4p16.3 may play significant roles in the etiology of T2DM. Copyright 2011 Hirohito Kudo et al.

Nakayama M.,National Center for Child Health and Development | Nakayama M.,Tohoku University | Nozu K.,Kobe University | Goto Y.,National Center for Child Health and Development | And 8 more authors.
Pediatric Nephrology | Year: 2010

Hepatocyte nuclear factor 1β (HNF1β) abnormalities have been recognized to cause congenital anomalies of the kidney and urinary tract (CAKUT), predominantly affecting bilateral renal malformations. To further understand the spectrum of HNF1β related phenotypes, we performed HNF1B gene mutation and deletion analyses in Japanese patients with renal hypodysplasia (n=31), unilateral multicystic dysplastic kidney (MCDK; n=14) and others (n=5). We identified HNF1B alterations in 5 out of 50 patients (10%). De novo heterozygous complete deletions of HNF1B were found in 3 patients with unilateral MCDK. Two of the patients showed contralateral hypodysplasia, whereas the other patient showed a radiologically normal contralateral kidney with normal renal function. Copy number variation analyses showed 1.4 Mb microdeletions involving the whole HNF1B gene with breakpoints in flanking segmental duplications. We also identified 1 novel truncated mutation (1007insC) and another missense mutation (226G>T) in patients with bilateral hypodysplasia. HNF1B alterations leading to haploinsufficiency affect a diverse spectrum of CAKUT. The existence of a patient with unilateral MCDK with normal renal function might provide genetic insight into the etiology of these substantial populations of only unilateral MCDK. The recurrent microdeletions encompassing HNF1B could have a significant impact on the mechanism of HNF1B deletions. © 2010 IPNA.

Oyazato Y.,Kobe University | Iijima K.,Kobe University | Emi M.,DNA Chip Research Institute | Sekine T.,Toho University | And 6 more authors.
Kobe Journal of Medical Sciences | Year: 2011

Background: Tuberous sclerosis complex (TSC) is an autosomal dominant disorder caused by mutations in either of two genes, TSC1 and TSC2. Autosomal dominant polycystic kidney disease (ADPKD) is caused by mutations in either PKD1 or PKD2. TSC2 lies immediately adjacent to PKD1 and large heterozygous deletions can result in the TSC2/PKD1 contiguous gene syndrome (PKDTS). PKDTS has been identified in patients with TSC and early-onset severe ADPKD. However, genetic diagnosis with conventional methods proved to be difficult because its genetic aberrations are large monoallelic mutations. Methods: In the study presented here, we used both multiplex ligation-dependent probe amplification (MLPA) and array comparative genomic hybridization (array-CGH) for four PKDTS patients. Results: We were able to detect large heterozygous deletions including TSC2 and PKD1 by both of MLPA and array-CGH in all four patients. And in two patients, array-CGH identified relatively large genomic aberrations (RAB26, NTHL1, etc.), that extended outside of TSC2 or PKD1. Conclusion: The identical results obtained with these two completely different methods show that both constitute highly reliable strategies. Only a few studies have determined the breakpoints of large deletions in this disease and ours is the first to have identified the breakpoints by using array-CGH. We suggest that these methods are not only useful for the diagnosis of PKDTS but also for elucidation of its molecular mechanism.

Kato T.,Yamagata University | Emi M.,Yamagata University | Emi M.,DNA Chip Research Institute | Sato H.,Yamagata University | And 10 more authors.
Biochemical and Biophysical Research Communications | Year: 2010

Aims: Sporadic amyotrophic lateral sclerosis (SALS) seems to be a multifactorial disease, the pathogenesis of which may involve both genetic and environmental factors. The present study aims at identifying a possible genetic change that confers risk for SALS. Methods: We performed whole-genome screening of a copy-number variation (CNV) using a CNV beadchip, followed by real-time quantitative polymerase chain reaction (qPCR) and region-targeted high-density oligonucleotide tiling microarray. Results: Within the 40-kb region on 10p15.3 subtelomere, which harbours two genes encoding isopentenyl diphosphate isomerase 1 (IDI1) and IDI2, we found a segmental copy-number gain in a large proportion of SALS patients. qPCR analysis demonstrated the copy-number gain in 46 out of 83 SALS patients, as compared with 10 out of 99 controls (p=4.86×10-11, Odds Ratio 10.8); subsequent tiling microarray validated qPCR results and elucidated the fine structure of segmental gains. Conclusions: A segmental copy-number gain in the IDI1/IDI2 gene region may play a significant role in the pathogenesis of SALS. © 2010 Elsevier Inc.

Yanagimachi M.,Yokohama City University | Naruto T.,Yokohama City University | Miyamae T.,Yokohama City University | Hara T.,Yokohama City University | And 7 more authors.
Journal of Rheumatology | Year: 2011

Objective. Systemic-onset juvenile idiopathic arthritis (systemic JIA) and macrophage activation syndrome (MAS), the most devastating complication of systemic JIA, are characterized by abnormal levels of proinflammatory cytokines. Interferon regulatory factor 5 (IRF5) is a member of the IRF family of transcription factors, and acts as a master transcription factor in the activation of genes encoding proinflammatory cytokines. Polymorphisms in the IRF5 gene have been associated with susceptibility to autoimmune diseases such as systemic lupus erythematosus (SLE) and rheumatoid arthritis. Our aim was to assess associations of IRF5 gene polymorphisms with susceptibility to systemic JIA and MAS. Methods. Three IRF5 single-nucleotide polymorphisms (rs729302, rs2004640, and rs2280714) were genotyped using TaqMan assays in 81 patients with systemic JIA (33 with MAS, 48 without) and 190 controls. Results. There were no associations of the IRF5 gene polymorphisms or haplotypes under study with susceptibility to systemic JIA. There was a significant association of the rs2004640 T allele with MAS susceptibility (OR 4.11; 95% CI 1.84, 9.16; p = 0.001). The IRF5 haplotype (rs729302 A, rs2004640 T, and rs2280714 T), which was reported as conferring an increased risk of SLE, was significantly associated with MAS susceptibility in patients with systemic JIA (OR 4.61; 95% CI 1.73, 12.3; p < 0.001). Conclusion. IRF5 gene polymorphism is a genetic factor influencing susceptibility to MAS in patients with systemic JIA, and IRF5 contributes to the pathogenesis of MAS in these patients. The Journal of Rheumatology Copyright © 2011. All rights reserved.

Sasaki H.,Hokkaido University | Emi M.,DNA Chip Research Institute | Iijima H.,DNA Chip Research Institute | Ito N.,DNA Chip Research Institute | And 6 more authors.
Molecular Brain | Year: 2011

Abstract. Background: Multiple system atrophy (MSA) is a sporadic disease. Its pathogenesis may involve multiple genetic and nongenetic factors, but its etiology remains largely unknown. We hypothesized that the genome of a patient with MSA would demonstrate copy number variations (CNVs) in the genes or genomic regions of interest. To identify genomic alterations increasing the risk for MSA, we examined a pair of monozygotic (MZ) twins discordant for the MSA phenotype and 32 patients with MSA. Results: By whole-genome CNV analysis using a combination of CNV beadchip and comparative genomic hybridization (CGH)-based CNV microarrays followed by region-targeting, high-density, custom-made oligonucleotide tiling microarray analysis, we identified disease-specific copy number loss of the (Src homology 2 domain containing)-transforming protein 2 (SHC2) gene in the distal 350-kb subtelomeric region of 19p13.3 in the affected MZ twin and 10 of the 31 patients with MSA but not in 2 independent control populations (p = 1.04 × 10-8, odds ratio = 89.8, Pearson's chi-square test). Conclusions: Copy number loss of SHC2 strongly indicates a causal link to MSA. CNV analysis of phenotypically discordant MZ twins is a powerful tool for identifying disease-predisposing loci. Our results would enable the identification of novel diagnostic measure, therapeutic targets and better understanding of the etiology of MSA. © 2011 Sasaki et al; licensee BioMed Central Ltd.

Kato T.,Yamagata University | Sato H.,Yamagata University | Sato H.,DNA Chip Research Institute | Emi M.,Yamagata University | And 7 more authors.
Internal Medicine | Year: 2011

Objective Idiopathic normal pressure hydrocephalus (iNPH) is clinically important as a treatable gait disturbance or preventable dementia by shunt operation. We have recently reported that approximately 1.5% of the elderly living in a Japanese community showed ventriculomegaly with features of iNPH on MRI (VIM), which may represent a preclinical stage of iNPH. The purpose of the present study was to identify a possible genetic change in VIM subjects. Methods Eight subjects with VIM and 10 healthy individuals were examined for copy number variations (CNV) with a CNV-targeted whole-genome oligonucleotide microarray (Agilent 400 K CNV array). Another panel of 100 healthy Japanese individuals was screened for CNV by whole-genome using the deCODE-Illumina CNV 370 K chip. Immunohistochemical examination of the human brain was performed using an avidin-biotin-peroxidase complex method. Results Among several genetic changes observed, a copy number loss within the SFMBT1 gene was seen in half of the VIM cases (4 of 8 cases), that was rare among the Japanese control subjects (0/10 by Agilent 400 K CNV array or 1/100 by deCODE/Illumina CNV 370 K chip). Immunohistochemical examination of the human brain revealed that the SFMBT1 protein was localized mainly in the arterial walls, the ependymal cells, and the epithelium of the choroid plexus, all of which play a crucial role in the CSF circulation. Conclusion A segmental copy number loss of the SFMBT1 gene may be involved in the pathological process in some individuals with VIM/iNPH. © 2011 The Japanese Society of Internal Medicine.

Sekimoto T.,University of Miyazaki | Ishii M.,DNA Chip Research Institute | Emi M.,University of Hawaii at Manoa | Kurogi S.,University of Miyazaki | And 3 more authors.
Journal of Orthopaedic Research | Year: 2013

Acetabular dysplasia (AD) appears to be a multi-factorial disease, which may involve both genetic and environmental factors and whose pathogenesis remains obscure. The present study aims to identify a genetic variation that might confer risk of AD. We performed whole-genome screening of a copy number variation (CNV) using a deCODE-Illumina CNV beadchip with 20 female AD patients and 131 control subjects. Subsequently, Agilent's region-targeted high-density oligonucleotide tiling microarray was used to analyze 64 female AD patients and 32 female control subjects. By sequential analyses, we found a copy number loss in 18 of 64 AD patients, but none in the 32 controls. The loss occurred within a 472 kb region on 9q22.2, which harbors the gene for Semaphorin 4D (Sema4D; 18/64 vs. 0/32, p = 4.81 × 10-4, OR = 25.86). We suggest that a copy number loss of the Sema4D gene region may play a role in the etiology of AD. © 2013 Orthopaedic Research Society. Published by Wiley Periodicals, Inc.

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