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1.
Endometriosis is a complex gynecological condition that affects 6–10% of women in their reproductive years and is defined by the presence of endometrial glands and stroma outside the uterus. Twin, family, and genome-wide association (GWA) studies have confirmed a genetic role, yet only a small part of the genetic risk can be explained by SNP variation. Copy number variants (CNVs) account for a greater portion of human genetic variation than SNPs and include more recent mutations of large effect. CNVs, likely to be prominent in conditions with decreased reproductive fitness, have not previously been examined as a genetic contributor to endometriosis. Here we employ a high-density genotyping microarray in a genome-wide survey of CNVs in a case-control population that includes 2,126 surgically confirmed endometriosis cases and 17,974 population controls of European ancestry. We apply stringent quality filters to reduce the false positive rate common to many CNV-detection algorithms from 77.7% to 7.3% without noticeable reduction in the true positive rate. We detected no differences in the CNV landscape between cases and controls on the global level which showed an average of 1.92 CNVs per individual with an average size of 142.3 kb. On the local level we identify 22 CNV-regions at the nominal significance threshold (P<0.05), which is greater than the 8.15 CNV-regions expected based on permutation analysis (P<0.001). Three CNV''s passed a genome-wide P-value threshold of 9.3×10−4; a deletion at SGCZ on 8p22 (P = 7.3×10−4, OR = 8.5, Cl = 2.3–31.7), a deletion in MALRD1 on 10p12.31 (P = 5.6×10−4, OR = 14.1, Cl = 2.7–90.9), and a deletion at 11q14.1 (P = 5.7×10−4, OR = 33.8, Cl = 3.3–1651). Two SNPs within the 22 CNVRs show significant genotypic association with endometriosis after adjusting for multiple testing; rs758316 in DPP6 on 7q36.2 (P = 0.0045) and rs4837864 in ASTN2 on 9q33.1 (P = 0.0002). Together, the CNV-loci are detected in 6.9% of affected women compared to 2.1% in the general population. 相似文献
2.
Clara Serra-Juhé Benjamín Rodríguez-Santiago Ivon Cuscó Teresa Vendrell Núria Camats Núria Torán Luis A. Pérez-Jurado 《PloS one》2012,7(10)
Background
Congenital malformations are present in approximately 2–3% of liveborn babies and 20% of stillborn fetuses. The mechanisms underlying the majority of sporadic and isolated congenital malformations are poorly understood, although it is hypothesized that the accumulation of rare genetic, genomic and epigenetic variants converge to deregulate developmental networks.Methodology/Principal Findings
We selected samples from 95 fetuses with congenital malformations not ascribed to a specific syndrome (68 with isolated malformations, 27 with multiple malformations). Karyotyping and Multiplex Ligation-dependent Probe Amplification (MLPA) discarded recurrent genomic and cytogenetic rearrangements. DNA extracted from the affected tissue (46%) or from lung or liver (54%) was analyzed by molecular karyotyping. Validations and inheritance were obtained by MLPA. We identified 22 rare copy number variants (CNV) [>100 kb, either absent (n = 7) or very uncommon (n = 15, <1/2,000) in the control population] in 20/95 fetuses with congenital malformations (21%), including 11 deletions and 11 duplications. One of the 9 tested rearrangements was de novo while the remaining were inherited from a healthy parent. The highest frequency was observed in fetuses with heart hypoplasia (8/17, 62.5%), with two events previously related with the phenotype. Double events hitting candidate genes were detected in two samples with brain malformations. Globally, the burden of deletions was significantly higher in fetuses with malformations compared to controls.Conclusions/Significance
Our data reveal a significant contribution of rare deletion-type CNV, mostly inherited but also de novo, to human congenital malformations, especially heart hypoplasia, and reinforce the hypothesis of a multifactorial etiology in most cases. 相似文献3.
Diana Zahnleiter Steffen Uebe Arif B. Ekici Juliane Hoyer Antje Wiesener Dagmar Wieczorek Erdmute Kunstmann André Reis Helmuth-Guenther Doerr Anita Rauch Christian T. Thiel 《PLoS genetics》2013,9(3)
Human growth has an estimated heritability of about 80%–90%. Nevertheless, the underlying cause of shortness of stature remains unknown in the majority of individuals. Genome-wide association studies (GWAS) showed that both common single nucleotide polymorphisms and copy number variants (CNVs) contribute to height variation under a polygenic model, although explaining only a small fraction of overall genetic variability in the general population. Under the hypothesis that severe forms of growth retardation might also be caused by major gene effects, we searched for rare CNVs in 200 families, 92 sporadic and 108 familial, with idiopathic short stature compared to 820 control individuals. Although similar in number, patients had overall significantly larger CNVs (p-value<1×10−7). In a gene-based analysis of all non-polymorphic CNVs>50 kb for gene function, tissue expression, and murine knock-out phenotypes, we identified 10 duplications and 10 deletions ranging in size from 109 kb to 14 Mb, of which 7 were de novo (p<0.03) and 13 inherited from the likewise affected parent but absent in controls. Patients with these likely disease causing 20 CNVs were smaller than the remaining group (p<0.01). Eleven (55%) of these CNVs either overlapped with known microaberration syndromes associated with short stature or contained GWAS loci for height. Haploinsufficiency (HI) score and further expression profiling suggested dosage sensitivity of major growth-related genes at these loci. Overall 10% of patients carried a disease-causing CNV indicating that, like in neurodevelopmental disorders, rare CNVs are a frequent cause of severe growth retardation. 相似文献
4.
Li Xie Jin-Lan Chen Wei-Zhi Zhang Shou-Zheng Wang Tian-Li Zhao Can Huang Jian Wang Jin-Fu Yang Yi-Feng Yang Zhi-Ping Tan 《PloS one》2014,9(5)
Background
Ongoing studies using genomic microarrays and next-generation sequencing have demonstrated that the genetic contributions to cardiovascular diseases have been significantly ignored in the past. The aim of this study was to identify rare copy number variants in individuals with congenital pulmonary atresia (PA).Methods and Results
Based on the hypothesis that rare structural variants encompassing key genes play an important role in heart development in PA patients, we performed high-resolution genome-wide microarrays for copy number variations (CNVs) in 82 PA patient-parent trios and 189 controls with an Illumina SNP array platform. CNVs were identified in 17/82 patients (20.7%), and eight of these CNVs (9.8%) are considered potentially pathogenic. Five de novo CNVs occurred at two known congenital heart disease (CHD) loci (16p13.1 and 22q11.2). Two de novo CNVs that may affect folate and vitamin B12 metabolism were identified for the first time. A de novo 1-Mb deletion at 17p13.2 may represent a rare genomic disorder that involves mild intellectual disability and associated facial features.Conclusions
Rare CNVs contribute to the pathogenesis of PA (9.8%), suggesting that the causes of PA are heterogeneous and pleiotropic. Together with previous data from animal models, our results might help identify a link between CHD and folate-mediated one-carbon metabolism (FOCM). With the accumulation of high-resolution SNP array data, these previously undescribed rare CNVs may help reveal critical gene(s) in CHD and may provide novel insights about CHD pathogenesis. 相似文献5.
6.
7.
Pernilla Lindahl Torbj?rn S?ll Anders Bjartell Anna M. Johansson Hans Lilja Christer Halldén 《PloS one》2013,8(7)
The kallikrein gene family (KLK1-KLK15) is the largest contiguous group of protease genes within the human genome and is associated with both risk and outcome of cancer and other diseases. We searched for copy number variants in all KLK genes using quantitative PCR analysis and analysis of inheritance patterns of single nucleotide polymorphisms. Two deletions were identified: one 2235-bp deletion in KLK9 present in 1.2% of alleles, and one 3394-bp deletion in KLK15 present in 4.0% of alleles. Each deletion eliminated one complete exon and created out-of-frame coding that eliminated the catalytic triad of the resulting truncated gene product, which therefore likely is a non-functional protein. Deletion breakpoints identified by DNA sequencing located the KLK9 deletion breakpoint to a long interspersed element (LINE) repeated sequence, while the deletion in KLK15 is located in a single copy sequence. To search for an association between each deletion and risk of prostate cancer (PC), we analyzed a cohort of 667 biopsied men (266 PC cases and 401 men with no evidence of PC at biopsy) using short deletion-specific PCR assays. There was no association between evidence of PC in this cohort and the presence of either gene deletion. Haplotyping revealed a single origin of each deletion, with most recent common ancestor estimates of 3000-8000 and 6000-14 000 years for the deletions in KLK9 and KLK15, respectively. The presence of the deletions on the same haplotypes in 1000 Genomes data of both European and African populations indicate an early origin of both deletions. The old age in combination with homozygous presence of loss-of-function variants suggests that some kallikrein-related peptidases have non-essential functions. 相似文献
8.
Recent studies designed to assess the relationship between aortic compliance and heterogeneity of heart electrical activity has shown that hypertrophy aggravates repolarization disturbances in the myocardium. Numerous mechanisms of electrical instability and inhomogeneity associated with left ventricular hypertrophy are now under investigation. Most of the studies have been found to be focused on ventricular Gradient, QT dispersion, amplitudes of isointegral maps during ventricular repolarization, abnormally low-QRST areas, dispersion of the QT interval, and spatial QRS-T angle. These studies point to marked repolarization abnormalities in left ventricular hypertrophy and the dispersion of the QT interval as a valuable index for inhomogeneity of repolarization and the subsequent heart rate variability. The heart rate-corrected QT dispersion and QT apex dispersion seem to be significantly longer in the patients with left ventricular hypertrophy than in normal individuals. The review study has also identified QRST isointegral map as a valuable technique in assessment of the electro-cardiac events in LVH. 相似文献
9.
Lutz Priebe Franziska Degenhardt Jana Strohmaier René Breuer Stefan Herms Stephanie H. Witt Per Hoffmann Rebecca Kulbida Manuel Mattheisen Susanne Moebus Andreas Meyer-Lindenberg Henrik Walter Rainald M?ssner Igor Nenadic Heinrich Sauer Dan Rujescu Wolfgang Maier Marcella Rietschel Markus M. N?then Sven Cichon 《PloS one》2013,8(7)
Large rare copy number variants (CNVs) have been recognized as significant genetic risk factors for the development of schizophrenia (SCZ). However, due to their low frequency (1∶150 to 1∶1000) among patients, large sample sizes are needed to detect an association between specific CNVs and SCZ. So far, the majority of genome-wide CNV analyses have focused on reporting only CNVs that reached a significant P-value within the study cohort and merely confirmed the frequency of already-established risk-carrying CNVs. As a result, CNVs with a very low frequency that might be relevant for SCZ susceptibility are lost for secondary analyses. In this study, we provide a concise collection of high-quality CNVs in a large German sample consisting of 1,637 patients with SCZ or schizoaffective disorder and 1,627 controls. All individuals were genotyped on Illumina''s BeadChips and putative CNVs were identified using QuantiSNP and PennCNV. Only those CNVs that were detected by both programs and spanned ≥30 consecutive SNPs were included in the data collection and downstream analyses (2,366 CNVs, 0.73 CNVs per individual). The genome-wide analysis did not reveal a specific association between a previously unknown CNV and SCZ. However, the group of CNVs previously reported to be associated with SCZ was more frequent in our patients than in the controls. The publication of our dataset will serve as a unique, easily accessible, high-quality CNV data collection for other research groups. The dataset could be useful for the identification of new disease-relevant CNVs that are currently overlooked due to their very low frequency and lack of power for their detection in individual studies. 相似文献
10.
Copy number variation (CNV) contributes in phenotypically relevant ways to the genetic variability of many organisms. Cost-effective genomewide methods for identifying copy number variation are necessary to elucidate the contribution that these structural variants make to the genomes of model organisms. We have developed a novel approach for the identification of copy number variation by next generation sequencing. As a proof of concept our method has been applied to map the deletions of three Drosophila deficiency strains. We demonstrate that low sequence coverage is sufficient for identifying and mapping large deletions at kilobase resolution, suggesting that data generated from high-throughput sequencing experiments are sufficient for simultaneously analyzing many strains. Genomic DNA from two Drosophila deficiency stocks was barcoded and sequenced in multiplex, and the breakpoints associated with each deletion were successfully identified. The approach we describe is immediately applicable to the systematic exploration of copy number variation in model organisms and humans.STRUCTURAL variation is known to contribute extensively to the genetic variability of humans, mammals, and many model organisms. One class of structural variant, termed copy number variation (CNV), includes deletions, duplications, insertions, and genomic rearrangements which affect the number of occurrences of a specific DNA sequence present in the genome (Redon et al. 2006). CNV is known to occur extensively in the Drosophila genome with functionally significant consequences (Bridges 1936; Dopman and Hartl 2007; Tibshirani and Wang 2008; Zhou et al. 2008). In one study of 15 Drosophila strains, as many as 10% of genes were observed to harbor CNVs (Emerson et al. 2008). Cryptic CNVs that affect the phenotype observed in a model organism have the potential to confound research on multiple levels. For example, a recent report indicates that terminal deletions on chromosome (chr) 2L are frequent among deficiency kit stocks with mutations on the second chromosome and that the associated deletion of lgl has distorted the results of several previous studies (Roegiers et al. 2009). Despite widespread existence of CNV, the biological consequences of this phenomenon remain largely unexplored due to the lack of efficient tools for detection and characterization.Until recently, comparative genomic hybridization with whole-genome tiling arrays (array-CGH) was the primary method for characterizing CNVs (Carter 2007); however, several limitations for this platform reduce its efficacy and efficiency. First, cross-hybridization and reliance on intensity scores lead to data that are difficult to interpret. Second, custom array design and optimization is labor intensive and costly. Third, array-CGH methods can only detect CNV, not other complex rearrangements such as balanced translocations and inversions. Finally, the overall cost of array-CGH methods is relatively high, particularly when high-resolution, whole-genome tiling arrays are employed.Direct sequencing using next-generation technology has several advantages that make it a potentially powerful alternative to array-CGH for identifying genomic structural variations, including deletions, duplications, and rearrangements (Campbell et al. 2008; Chiang et al. 2009). First, high-throughput sequencing methods overcome the inherent limitations of cross-hybridization and provide a digital count of sequence representation. Second, no prior knowledge or design work is necessary. Third, using paired-end sequencing it is possible to identify complex structural variations. Finally, the current cost of CNV discovery by sequencing is comparable or lower than that of array-CGH and is continuing to decline.In this report, we describe a sequencing-based strategy for high-throughput, cost-effective, genomewide characterization of structural variation at fine resolution by employing the Illumina sequencing platform. Deletions in three deficiency fly stocks were successfully characterized and the associated breakpoints were accurately determined. As we demonstrate, high-throughput sequencing provides an ideal and cost-effective platform for CNV characterization. 相似文献
11.
Nori Matsunami Dexter Hadley Charles H. Hensel G. Bryce Christensen Cecilia Kim Edward Frackelton Kelly Thomas Renata Pellegrino da Silva Jeff Stevens Lisa Baird Brith Otterud Karen Ho Tena Varvil Tami Leppert Christophe G. Lambert Mark Leppert Hakon Hakonarson 《PloS one》2013,8(1)
Structural variation is thought to play a major etiological role in the development of autism spectrum disorders (ASDs), and numerous studies documenting the relevance of copy number variants (CNVs) in ASD have been published since 2006. To determine if large ASD families harbor high-impact CNVs that may have broader impact in the general ASD population, we used the Affymetrix genome-wide human SNP array 6.0 to identify 153 putative autism-specific CNVs present in 55 individuals with ASD from 9 multiplex ASD pedigrees. To evaluate the actual prevalence of these CNVs as well as 185 CNVs reportedly associated with ASD from published studies many of which are insufficiently powered, we designed a custom Illumina array and used it to interrogate these CNVs in 3,000 ASD cases and 6,000 controls. Additional single nucleotide variants (SNVs) on the array identified 25 CNVs that we did not detect in our family studies at the standard SNP array resolution. After molecular validation, our results demonstrated that 15 CNVs identified in high-risk ASD families also were found in two or more ASD cases with odds ratios greater than 2.0, strengthening their support as ASD risk variants. In addition, of the 25 CNVs identified using SNV probes on our custom array, 9 also had odds ratios greater than 2.0, suggesting that these CNVs also are ASD risk variants. Eighteen of the validated CNVs have not been reported previously in individuals with ASD and three have only been observed once. Finally, we confirmed the association of 31 of 185 published ASD-associated CNVs in our dataset with odds ratios greater than 2.0, suggesting they may be of clinical relevance in the evaluation of children with ASDs. Taken together, these data provide strong support for the existence and application of high-impact CNVs in the clinical genetic evaluation of children with ASD. 相似文献
12.
Priit Palta Lauris Kaplinski Liina Nagirnaja Andres Veidenberg M?rt M?ls Mari Nelis T?nu Esko Andres Metspalu Maris Laan Maido Remm 《PloS one》2015,10(4)
DNA copy number variants (CNVs) that alter the copy number of a particular DNA segment in the genome play an important role in human phenotypic variability and disease susceptibility. A number of CNVs overlapping with genes have been shown to confer risk to a variety of human diseases thus highlighting the relevance of addressing the variability of CNVs at a higher resolution. So far, it has not been possible to deterministically infer the allelic composition of different haplotypes present within the CNV regions. We have developed a novel computational method, called PiCNV, which enables to resolve the haplotype sequence composition within CNV regions in nuclear families based on SNP genotyping microarray data. The algorithm allows to i) phase normal and CNV-carrying haplotypes in the copy number variable regions, ii) resolve the allelic copies of rearranged DNA sequence within the haplotypes and iii) infer the heritability of identified haplotypes in trios or larger nuclear families. To our knowledge this is the first program available that can deterministically phase null, mono-, di-, tri- and tetraploid genotypes in CNV loci. We applied our method to study the composition and inheritance of haplotypes in CNV regions of 30 HapMap Yoruban trios and 34 Estonian families. For 93.6% of the CNV loci, PiCNV enabled to unambiguously phase normal and CNV-carrying haplotypes and follow their transmission in the corresponding families. Furthermore, allelic composition analysis identified the co-occurrence of alternative allelic copies within 66.7% of haplotypes carrying copy number gains. We also observed less frequent transmission of CNV-carrying haplotypes from parents to children compared to normal haplotypes and identified an emergence of several de novo deletions and duplications in the offspring. 相似文献
13.
Background
Adiponectin directly protects against cardiac remodeling. Despite this beneficial effect, most epidemiological studies have reported a negative relationship between adiponectin level and left ventricular mass index (LVMI). However, a positive relationship has also been reported in subjects at high risk of left ventricular hypertrophy (LVH). Based on these conflicting results, we hypothesized that the relationship between serum adiponectin level and LVMI varies with the risk of LVH.Methods
A community-based, cross-sectional study was performed on 1414 subjects. LVMI was measured by echocardiography. Log-transformed adiponectin levels (Log-ADPN) were used for the analysis.Results
Serum adiponectin level had a biphasic distribution (an increase after a decrease) with increasing LVMI. Although Log-ADPN did not correlate with LVMI, Log-ADPN was modestly associated with LVMI in the multivariate analysis (β = 0.079, p = 0.001). The relationship between adiponectin level and LVMI was bidirectional according to the risk of LVH. In normotensive subjects younger than 50 years, Log-ADPN negatively correlated with LVMI (r = −0.204, p = 0.005); however, Log-ADPN positively correlated with LVMI in ≥50-year-old obese subjects with high arterial stiffness (r = 0.189, p = 0.030). The correlation coefficient between Log-ADPN and LVMI gradually changed from negative to positive with increasing risk factors for LVH. The risk of LVH significantly interacted with the relationship between Log-ADPN and LVMI. In the multivariate analysis, Log-ADPN was associated with LVMI in the subjects at risk of LVH; however, Log-ADPN was either not associated or negatively associated with LVMI in subjects at low risk of LVH.Conclusion
Adiponectin level and LVMI are negatively associated in subjects at low risk of LVH and are positively associated in subjects at high risk of LVH. Therefore, the relationship between adiponectin and LVMI varies with the risk of LVH. 相似文献14.
15.
Siddharth Prakash Shao-Qing Kuang GenTAC Registry Investigators Ellen Regalado Dongchuan Guo Dianna Milewicz 《PloS one》2016,11(4)
Thoracic Aortic Aneurysms and Dissections (TAAD) are a major cause of death in the United States. The spectrum of TAAD ranges from genetic disorders, such as Marfan syndrome, to sporadic isolated disease of unknown cause. We hypothesized that genomic copy number variants (CNVs) contribute causally to early onset TAAD (ETAAD). We conducted a genome-wide SNP array analysis of ETAAD patients of European descent who were enrolled in the National Registry of Genetically Triggered Thoracic Aortic Aneurysms and Cardiovascular Conditions (GenTAC). Genotyping was performed on the Illumina Omni-Express platform, using PennCNV, Nexus and CNVPartition for CNV detection. ETAAD patients (n = 108, 100% European American, 28% female, average age 20 years, 55% with bicuspid aortic valves) were compared to 7013 dbGAP controls without a history of vascular disease using downsampled Omni 2.5 data. For comparison, 805 sporadic TAAD patients with late onset aortic disease (STAAD cohort) and 192 affected probands from families with at least two affected relatives (FTAAD cohort) from our institution were screened for additional CNVs at these loci with SNP arrays. We identified 47 recurrent CNV regions in the ETAAD, FTAAD and STAAD groups that were absent or extremely rare in controls. Nine rare CNVs that were either very large (>1 Mb) or shared by ETAAD and STAAD or FTAAD patients were also identified. Four rare CNVs involved genes that cause arterial aneurysms when mutated. The largest and most prevalent of the recurrent CNVs were at Xq28 (two duplications and two deletions) and 17q25.1 (three duplications). The percentage of individuals harboring rare CNVs was significantly greater in the ETAAD cohort (32%) than in the FTAAD (23%) or STAAD (17%) cohorts. We identified multiple loci affected by rare CNVs in one-third of ETAAD patients, confirming the genetic heterogeneity of TAAD. Alterations of candidate genes at these loci may contribute to the pathogenesis of TAAD. 相似文献
16.
Samin A. Sajan Liliana Fernandez Sahar Esmaeeli Nieh Eric Rider Polina Bukshpun Mari Wakahiro Susan L. Christian Jean-Baptiste Rivière Christopher T. Sullivan Jyotsna Sudi Michael J. Herriges Alexander R. Paciorkowski A. James Barkovich Joseph T. Glessner Kathleen J. Millen Hakon Hakonarson William B. Dobyns Elliott H. Sherr 《PLoS genetics》2013,9(10)
Agenesis of the corpus callosum (ACC), cerebellar hypoplasia (CBLH), and polymicrogyria (PMG) are severe congenital brain malformations with largely undiscovered causes. We conducted a large-scale chromosomal copy number variation (CNV) discovery effort in 255 ACC, 220 CBLH, and 147 PMG patients, and 2,349 controls. Compared to controls, significantly more ACC, but unexpectedly not CBLH or PMG patients, had rare genic CNVs over one megabase (p = 1.48×10−3; odds ratio [OR] = 3.19; 95% confidence interval [CI] = 1.89–5.39). Rare genic CNVs were those that impacted at least one gene in less than 1% of the combined population of patients and controls. Compared to controls, significantly more ACC but not CBLH or PMG patients had rare CNVs impacting over 20 genes (p = 0.01; OR = 2.95; 95% CI = 1.69–5.18). Independent qPCR confirmation showed that 9.4% of ACC patients had de novo CNVs. These, in comparison to inherited CNVs, preferentially overlapped de novo CNVs previously observed in patients with autism spectrum disorders (p = 3.06×10−4; OR = 7.55; 95% CI = 2.40–23.72). Interestingly, numerous reports have shown a reduced corpus callosum area in autistic patients, and diminished social and executive function in many ACC patients. We also confirmed and refined previously known CNVs, including significantly narrowing the 8p23.1-p11.1 duplication present in 2% of our current ACC cohort. We found six novel CNVs, each in a single patient, that are likely deleterious: deletions of 1p31.3-p31.1, 1q31.2-q31.3, 5q23.1, and 15q11.2-q13.1; and duplications of 2q11.2-q13 and 11p14.3-p14.2. One ACC patient with microcephaly had a paternally inherited deletion of 16p13.11 that included NDE1. Exome sequencing identified a recessive maternally inherited nonsense mutation in the non-deleted allele of NDE1, revealing the complexity of ACC genetics. This is the first systematic study of CNVs in congenital brain malformations, and shows a much higher prevalence of large gene-rich CNVs in ACC than in CBLH and PMG. 相似文献
17.
Manuela Zanda Suna Onengut-Gumuscu Neil Walker Corina Shtir Daniel Gallo Chris Wallace Deborah Smyth John A. Todd Matthew E. Hurles Vincent Plagnol Stephen S. Rich 《PLoS genetics》2014,10(5)
Genome-wide association studies (GWAS) for type 1 diabetes (T1D) have successfully identified more than 40 independent T1D associated tagging single nucleotide polymorphisms (SNPs). However, owing to technical limitations of copy number variants (CNVs) genotyping assays, the assessment of the role of CNVs has been limited to the subset of these in high linkage disequilibrium with tag SNPs. The contribution of untagged CNVs, often multi-allelic and difficult to genotype using existing assays, to the heritability of T1D remains an open question. To investigate this issue, we designed a custom comparative genetic hybridization array (aCGH) specifically designed to assay untagged CNV loci identified from a variety of sources. To overcome the technical limitations of the case control design for this class of CNVs, we genotyped the Type 1 Diabetes Genetics Consortium (T1DGC) family resource (representing 3,903 transmissions from parents to affected offspring) and used an association testing strategy that does not necessitate obtaining discrete genotypes. Our design targeted 4,309 CNVs, of which 3,410 passed stringent quality control filters. As a positive control, the scan confirmed the known T1D association at the INS locus by direct typing of the 5′ variable number of tandem repeat (VNTR) locus. Our results clarify the fact that the disease association is indistinguishable from the two main polymorphic allele classes of the INS VNTR, class I-and class III. We also identified novel technical artifacts resulting into spurious associations at the somatically rearranging loci, T cell receptor, TCRA/TCRD and TCRB, and Immunoglobulin heavy chain, IGH, loci on chromosomes 14q11.2, 7q34 and 14q32.33, respectively. However, our data did not identify novel T1D loci. Our results do not support a major role of untagged CNVs in T1D heritability. 相似文献
18.
Hajime Yokota Yasuko Imai Yusuke Tsuboko Aya M. Tokumaru Hajime Fujimoto Kazumasa Harada 《PloS one》2013,8(6)
Background
Left ventricular hypertrophy (LVH) is an independent predictor of cardiac mortality, regardless of its etiology. Previous studies have shown that high nocturnal blood pressure (BP) affects LV geometry in hypertensive patients. It has been suggested that continuous pressure overload affects the development of LVH, but it is unknown whether persistent pressure influences myocardial fibrosis or whether the etiology of LVH is associated with myocardial fibrosis. Comprehensive cardiac magnetic resonance (CMR) including the late gadolinium enhancement (LGE) technique can evaluate both the severity of changes in LV geometry and myocardial fibrosis. We tested the hypothesis that the nocturnal non-dipper BP pattern causes LV remodeling and fibrosis in patients with hypertension and LVH.Methods
Forty-seven hypertensive patients with LVH evaluated by echocardiography (29 men, age 73.0±10.4 years) were examined by comprehensive CMR and 24-h ambulatory blood pressure monitoring (ABPM).Results and Conclusions
Among the 47 patients, twenty-four had nocturnal non-dipper BP patterns. Patients with nocturnal non-dipper BP patterns had larger LV masses and scar volumes independent of etiologies than those in patients with dipper BP patterns (p = 0.035 and p = 0.015, respectively). There was no significant difference in mean 24-h systolic BP between patients with and without nocturnal dipper BP patterns (p = 0.367). Among hypertensive patients with LVH, the nocturnal non-dipper blood pressure pattern is associated with both LV remodeling and myocardial fibrosis independent of LVH etiology. 相似文献19.
20.
Makeeva O. A. Puzyrev K. V. Pavlyukova E. N. Koshelskaya O. A. Golubenko M. V. Efimova E. V. Kucher A. N. Tsimbalyuk I. V. Karpov R. S. Puzyrev V. P. 《Molecular Biology》2004,38(6):844-849
The A2350G polymorphism of exon 17 of the angiotensin I-converting enzyme gene (ACE) and the A1166C polymorphism of the 3-untranslated region (3-UTR) of the angiotensin II type 1 receptor gene (AGTR1) were tested for association with left ventricular hypertrophy (LVH) in patients with essential hypertension (EH) or arterial hypertension (AH) combined with diabetes mellitus type 2 (DM2). The patients with EH or AH + DM2 did not differ significantly in ACE or AGTR1 allele or genotype frequencies from healthy subjects. Both polymorphisms were associated with LVH in EH. AGTR1 allele 1166C was more frequent in patients with LVH than without (33.6 vs. 20.7%) and affected the left ventricular mass index (LVMI) in patients with EH (p = 0.007). The frequency of ACE allele 2350G in EH patients with LVH was 1.5 times higher, and that of genotype GG was 3.5 times higher, than in patients without LVH. LVMI differed significantly (p = 0.002) between patients with different ACE genotypes, being maximum in homozygotes GG and minimum in homozygotes AA. Thus, AGTR1 allele 1166C and ACE allele 2350G were identified as predisposing to LVH in EH. The two polymorphisms were not associated with the incidence or severity of LVH in patients with AH and DM2. 相似文献