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1.
Background
Studies on the risk of chromosomal abnormalities in early spontaneous abortion after assisted reproductive technology (ART) are relatively controversial and insufficient. Thus, to obtain a more precise evaluation of the risk of embryonic chromosomal abnormalities in first-trimester miscarriage after ART, we performed a meta-analysis of all available case–control studies relating to the cytogenetic analysis of chromosomal abnormalities in first-trimester miscarriage after ART.Methods
Literature search in the electronic databases MEDLINE, EMBASE, and Cochrane Central Register of Controlled Trials (CENTRAL) based on the established strategy. Meta-regression, subgroup analysis, and Galbraith plots were conducted to explore the sources of heterogeneity.Results
A total of 15 studies with 1,896 cases and 1,186 controls relevant to the risk of chromosomal abnormalities in first- trimester miscarriage after ART, and 8 studies with 601 cases and 602 controls evaluating frequency of chromosome anomaly for maternal age≥35 versus <35 were eligible for the meta-analysis. No statistical difference was found in risk of chromosomally abnormal miscarriage compared to natural conception and the different types of ART utilized, whereas the risk of fetal aneuploidy significantly increased with maternal age≥35 (OR 2.88, 95% CI: 1.74–4.77).Conclusions
ART treatment does not present an increased risk for chromosomal abnormalities occurring in a first trimester miscarriage, but incidence of fetal aneuploidy could increase significantly with advancing maternal age. 相似文献2.
Jason M Argyris Aurora Ruiz-Herrera Pablo Madriz-Masis Walter Sanseverino Jordi Morata Marta Pujol Sebastián E Ramos-Onsins Jordi Garcia-Mas 《BMC genomics》2015,16(1)
Background
The genome of the melon (Cucumis melo L.) double-haploid line DHL92 was recently sequenced, with 87.5 and 80.8% of the scaffold assembly anchored and oriented to the 12 linkage groups, respectively. However, insufficient marker coverage and a lack of recombination left several large, gene rich scaffolds unanchored, and some anchored scaffolds unoriented. To improve the anchoring and orientation of the melon genome assembly, we used resequencing data between the parental lines of DHL92 to develop a new set of SNP markers from unanchored scaffolds.Results
A high-resolution genetic map composed of 580 SNPs was used to anchor 354.8 Mb of sequence, contained in 141 scaffolds (average size 2.5 Mb) and corresponding to 98.2% of the scaffold assembly, to the 12 melon chromosomes. Over 325.4 Mb (90%) of the assembly was oriented. The genetic map revealed regions of segregation distortion favoring SC alleles as well as recombination suppression regions coinciding with putative centromere, 45S, and 5S rDNA sites. New chromosome-scale pseudomolecules were created by incorporating to the previous v3.5 version an additional 38.3 Mb of anchored sequence representing 1,837 predicted genes contained in 55 scaffolds. Using fluorescent in situ hybridization (FISH) with BACs that produced chromosome-specific signals, melon chromosomes that correspond to the twelve linkage groups were identified, and a standardized karyotype of melon inbred line T111 was developed.Conclusions
By utilizing resequencing data and targeted SNP selection combined with a large F2 mapping population, we significantly improved the quantity of anchored and oriented melon scaffold genome assembly. Using genome information combined with FISH mapping provided the first cytogenetic map of an inodorus melon type. With these results it was possible to make inferences on melon chromosome structure by relating zones of recombination suppression to centromeres and 45S and 5S heterochromatic regions. This study represents the first steps towards the integration of the high-resolution genetic and cytogenetic maps with the genomic sequence in melon that will provide more information on genome organization and allow for the improvement of the melon genome draft sequence.Electronic supplementary material
The online version of this article (doi:10.1186/s12864-014-1196-3) contains supplementary material, which is available to authorized users. 相似文献3.
Ikuko N Motoike Mitsuyo Matsumoto Inaho Danjoh Fumiki Katsuoka Kaname Kojima Naoki Nariai Yukuto Sato Yumi Yamaguchi-Kabata Shin Ito Hisaaki Kudo Ichiko Nishijima Satoshi Nishikawa Xiaoqing Pan Rumiko Saito Sakae Saito Tomo Saito Matsuyuki Shirota Kaoru Tsuda Junji Yokozawa Kazuhiko Igarashi Naoko Minegishi Osamu Tanabe Nobuo Fuse Masao Nagasaki Kengo Kinoshita Jun Yasuda Masayuki Yamamoto 《BMC genomics》2014,15(1)
Background
Validation of single nucleotide variations in whole-genome sequencing is critical for studying disease-related variations in large populations. A combination of different types of next-generation sequencers for analyzing individual genomes may be an efficient means of validating multiple single nucleotide variations calls simultaneously.Results
Here, we analyzed 12 independent Japanese genomes using two next-generation sequencing platforms: the Illumina HiSeq 2500 platform for whole-genome sequencing (average depth 32.4×), and the Ion Proton semiconductor sequencer for whole exome sequencing (average depth 109×). Single nucleotide polymorphism (SNP) calls based on the Illumina Human Omni 2.5-8 SNP chip data were used as the reference. We compared the variant calls for the 12 samples, and found that the concordance between the two next-generation sequencing platforms varied between 83% and 97%.Conclusions
Our results show the versatility and usefulness of the combination of exome sequencing with whole-genome sequencing in studies of human population genetics and demonstrate that combining data from multiple sequencing platforms is an efficient approach to validate and supplement SNP calls.Electronic supplementary material
The online version of this article (doi:10.1186/1471-2164-15-673) contains supplementary material, which is available to authorized users. 相似文献4.
Background
In single-cell human genome analysis using whole-genome amplified product, a strong amplification bias involving allele dropout and preferential amplification hampers the quality of results. Using an oligonucleotide single nucleotide polymorphism (SNP) array, we systematically examined the nature of this amplification bias, including frequency, degree, and preference for genomic location, and we assessed the effects of this amplification bias on subsequent genotype and chromosomal copy number analyses.Methodology/Principal Findings
We found a large variability in amplification bias among the amplified products obtained by multiple displacement amplification (MDA), and this bias had a severe effect on the genotype and chromosomal copy number analyses. We established optimal experimental conditions for pre-screening for high-quality amplified products, processing array data, and analyzing chromosomal structural alterations. Using this optimized protocol, we successfully detected previously unidentified chromosomal structural alterations in single cells from a lymphoblastoid cell line. These alterations were subsequently confirmed by karyotype analysis. In addition, we successfully obtained reproducible chromosomal copy number profiles of single cells from the cell line with a complex karyotype, indicating the applicability and potential of our optimized workflow.Conclusions/Significance
Our results suggest that the quality of amplification products should be critically assessed before using them for genomic analyses. The method of MDA-based whole-genome amplification followed by SNP array analysis described here will be useful for exploring chromosomal alterations in single cells. 相似文献5.
Background and Aims
The sedge genus Carex, the most diversified angiosperm genus of the northern temperate zone, is renowned for its holocentric chromosomes and karyotype variability. The genus exhibits high variation in chromosome numbers both among and within species. Despite the possibility that this chromosome evolution may play a role in the high species diversity of Carex, population-level patterns of molecular and cytogenetic differentiation in the genus have not been extensively studied.Methods
Microsatellite variation (11 loci, 461 individuals) and chromosomal diversity (82 individuals) were investigated in 22 Midwestern populations of the North American sedge Carex scoparia and two Northeastern populations.Key Results
Among Midwestern populations, geographic distance is the most important predictor of genetic differentiation. Within populations, inbreeding is high and chromosome variation explains a significant component of genetic differentiation. Infrequent dispersal among populations separated by >100 km explains an important component of molecular genetic and cytogenetic diversity within populations. However, karyotype variation and correlation between genetic and chromosomal variation persist within populations even when putative migrants based on genetic data are excluded.Conclusions
These findings demonstrate dispersal and genetic connectivity among widespread populations that differ in chromosome numbers, explaining the phenomenon of genetic coherence in this karyotypically diverse sedge species. More generally, the study suggests that traditional sedge taxonomic boundaries demarcate good species even when those species encompass a high range of chromosomal diversity. This finding is important evidence as we work to document the limits and drivers of biodiversity in one of the world''s largest angiosperm genera. 相似文献6.
Objective
The present study sought to establish an animal model to study the feasibility and safety of rapid retraction of maxillary anterior teeth en masse aided by alveolar surgery in order to reduce orthodontic treatment time.Method
Extraction of the maxillary canine and alveolar surgery were performed on twelve adult beagle dogs. After that, the custom-made tooth-borne distraction devices were placed on beagles'' teeth. Nine of the dogs were applied compression at 0.5 mm/d for 12 days continuously. The other three received no force as the control group. The animals were killed in 1, 14, and 28 days after the end of the application of compression.Results
The tissue responses were assessed by craniometric measurement as well as histological examination. Gross alterations were evident in the experimental group, characterized by anterior teeth crossbite. The average total movements of incisors within 12 days were 4.63±0.10 mm and the average anchorage losses were 1.25±0.12 mm. Considerable root resorption extending into the dentine could be observed 1 and 14 days after the compression. But after consolidation of 28 days, there were regenerated cementum on the dentine. There was no apparent change in the control group. No obvious tooth loosening, gingival necrosis, pulp degeneration, or other adverse complications appeared in any of the dogs.Conclusions
This is the first experimental study for testing the technique of rapid anterior teeth retraction en masse aided by modified alveolar surgery. Despite a preliminary animal model study, the current findings pave the way for the potential clinical application that can accelerate orthodontic tooth movement without many adverse complications.Clinical Relevance
It may become a novel method to shorten the clinical orthodontic treatment time in the future. 相似文献7.
GL Huang BK Li MY Zhang RR Wei YF Yuan M Shi XQ Chen L Huang HZ Zhang W Liu BJ Huang H Li XF Zheng XR Luo HY Wang 《PloS one》2012,7(8):e44061
Objectives
The role of heparanase (HPSE) gene in cancers including hepatocellular carcinoma (HCC) is currently controversial. This study was aimed at investigating the impact of genetic alteration and expression change of HPSE on the progression and prognosis of HCC.Methods
The HPSE gene was studied in three different aspects: (1) loss of heterozygosity (LOH) by a custom SNP microarray and DNA copy number by real-time PCR; (2) mRNA level by qRT-PCR; and (3) protein expression by immunohistochemistry. The clinical significances of allele loss and expression change of HPSE were analyzed.Results
Microarray analysis showed that the average LOH frequency for 10 SNPs located within HPSE gene was 31.6%, three of which were significantly correlated with tumor grade, serum HBV-DNA level, and AFP concentration. In agreement with SNP LOH data, DNA copy number loss of HPSE was observed in 38.74% (43/111) of HCC cases. HPSE mRNA level was notably reduced in 74.1% (83/112) of tumor tissues compared with non-tumor liver tissues, which was significantly associated with DNA copy number loss, increased tumor size, and post-operative metastasis. HPSE protein level was also remarkably reduced in 66.3% (53/80) of tumor tissues, which was correlated with tumor grade. Patients with lower expression level of HPSE mRNA or protein had a significantly lower survival rate than those with higher expression. Cox regression analysis suggested that HPSE protein was an independent predictor of overall survival in HCC patients.Conclusions
The results in this study demonstrate that genetic alteration and reduction of HPSE expression are associated with tumor progression and poor prognosis of HCCs, suggesting that HPSE behaves like a tumor suppressor gene and is a potential prognostic marker for HCC patients. 相似文献8.
Background
Recent molecular genetics studies showed significant associations between dopamine-related genes (including genes for dopamine receptors, transporters, and degradation) and working memory, but little is known about the role of genes for dopamine modulation, such as those related to neurotensin (NT), in working memory. A recent animal study has suggested that NT antagonist administration impaired working memory in a learning task. The current study examined associations between NT genes and working memory among humans.Methods
Four hundred and sixty healthy undergraduate students were assessed with a 2-back working memory paradigm. 5 SNPs in the NTSR1 gene were genotyped. 5 ANOVA tests were conducted to examine whether and how working memory differed by NTSR1 genotype, with each SNP variant as the independent variable and the average accuracy on the working memory task as the dependent variable.Results
ANOVA results suggested that two SNPs in the NTSR1 gene (rs4334545 and rs6090453) were significantly associated with working memory. These results survived corrections for multiple comparisons.Conclusions
Our results demonstrated that NTSR1 SNP polymorphisms were significantly associated with variance in working memory performance among healthy adults. This result extended previous rodent studies showing that the NT deficiency impairs the working memory function. Future research should replicate our findings and extend to an examination of other dopamine modulators. 相似文献9.
Christopher G Jacob John C Tan Becky A Miller Asako Tan Shannon Takala-Harrison Michael T Ferdig Christopher V Plowe 《BMC genomics》2014,15(1)
Background
Analysis of single nucleotide polymorphisms (SNPs) derived from whole-genome studies allows for rapid evaluation of genome-wide diversity, and genomic epidemiology studies of Plasmodium falciparum provide insights into parasite population structure, gene flow, drug resistance and vaccine development. In areas with adequate cold chain facilities, large volumes of leukocyte-depleted patient blood can be frozen for use in parasite genomic analyses. In more remote endemic areas smaller volumes of infected blood are taken by finger prick, and dried and stored on filter paper. These dried blood spots do not generally yield enough concentrated parasite DNA for whole-genome sequencing.Results
A DNA microarray was designed for use on field samples to type a genome-wide set of SNPs which prior sequencing had shown to be variable in Africa, Southeast Asia, and Papua New Guinea. An algorithm was designed to call SNPs in samples with low parasite DNA. With this new algorithm SNP-calling accuracy of 98% was measured by hybridizing purified DNA from malaria lab strains and comparing calls with SNPs called from full genome sequences. An average accuracy of >98% was likewise obtained for DNA extracted from malaria field samples collected in studies in Southeast Asia, with an average call rate of > 82%.Conclusion
This new high-density microarray provided high quality SNP calls from a wide range of parasite DNA quantities, and represents a robust tool for genome-wide analysis of malaria parasites in diverse settings. 相似文献10.
11.
Joseph Andrews Wendy Kennette Jenna Pilon Alexandra Hodgson Alan B. Tuck Ann F. Chambers David I. Rodenhiser 《PloS one》2010,5(1)
Background
We have previously identified genome-wide DNA methylation changes in a cell line model of breast cancer metastasis. These complex epigenetic changes that we observed, along with concurrent karyotype analyses, have led us to hypothesize that complex genomic alterations in cancer cells (deletions, translocations and ploidy) are superimposed over promoter-specific methylation events that are responsible for gene-specific expression changes observed in breast cancer metastasis.Methodology/Principal Findings
We undertook simultaneous high-resolution, whole-genome analyses of MDA-MB-468GFP and MDA-MB-468GFP-LN human breast cancer cell lines (an isogenic, paired lymphatic metastasis cell line model) using Affymetrix gene expression (U133), promoter (1.0R), and SNP/CNV (SNP 6.0) microarray platforms to correlate data from gene expression, epigenetic (DNA methylation), and combination copy number variant/single nucleotide polymorphism microarrays. Using Partek Software and Ingenuity Pathway Analysis we integrated datasets from these three platforms and detected multiple hypomethylation and hypermethylation events. Many of these epigenetic alterations correlated with gene expression changes. In addition, gene dosage events correlated with the karyotypic differences observed between the cell lines and were reflected in specific promoter methylation patterns. Gene subsets were identified that correlated hyper (and hypo) methylation with the loss (or gain) of gene expression and in parallel, with gene dosage losses and gains, respectively. Individual gene targets from these subsets were also validated for their methylation, expression and copy number status, and susceptible gene pathways were identified that may indicate how selective advantage drives the processes of tumourigenesis and metastasis.Conclusions/Significance
Our approach allows more precisely profiling of functionally relevant epigenetic signatures that are associated with cancer progression and metastasis. 相似文献12.
Lien Tembuyser Véronique Tack Karen Zwaenepoel Patrick Pauwels Keith Miller Lukas Bubendorf Keith Kerr Ed Schuuring Erik Thunnissen Elisabeth M. C. Dequeker 《PloS one》2014,9(11)
Background and Purpose
Molecular profiling should be performed on all advanced non-small cell lung cancer with non-squamous histology to allow treatment selection. Currently, this should include EGFR mutation testing and testing for ALK rearrangements. ROS1 is another emerging target. ALK rearrangement status is a critical biomarker to predict response to tyrosine kinase inhibitors such as crizotinib. To promote high quality testing in non-small cell lung cancer, the European Society of Pathology has introduced an external quality assessment scheme. This article summarizes the results of the first two pilot rounds organized in 2012–2013.Materials and Methods
Tissue microarray slides consisting of cell-lines and resection specimens were distributed with the request for routine ALK testing using IHC or FISH. Participation in ALK FISH testing included the interpretation of four digital FISH images.Results
Data from 173 different laboratories was obtained. Results demonstrate decreased error rates in the second round for both ALK FISH and ALK IHC, although the error rates were still high and the need for external quality assessment in laboratories performing ALK testing is evident. Error rates obtained by FISH were lower than by IHC. The lowest error rates were observed for the interpretation of digital FISH images.Conclusion
There was a large variety in FISH enumeration practices. Based on the results from this study, recommendations for the methodology, analysis, interpretation and result reporting were issued. External quality assessment is a crucial element to improve the quality of molecular testing. 相似文献13.
Aliakbar Rahbarimanesh Pupak Derakhshandeh-Peykar Amirhassan Barkhordari Reza Ebrahimzadeh-Vesal Soja Shamizadeh Kalkhoran 《Reports of Biochemistry & Molecular Biology》2013,1(2):87-90
Background:
Here we describe a new case of partial distal 10q trisomy in a 6-year-old Iranian girl from healthy parents with mental, growth, and psychomotor retardations.Methods:
Additional clinical features include dysmorphic craniofacial features, microcephaly, bilateral hydronephrosis without heart problems, small and rotated low-set ears, bow-shaped mouth, abnormal teeth, short neck, and as a first case reported, fingers with camptodactly (i.e., without any furrows or ridges in the palms and fingers).Results:
Cytogenetic analysis (GTG-banding) revealed an unbalanced female karyotype with additional bands at the end of the long arm of chromosome 10, karyotype: 46,XX,dup(10)(q25q26).Conclusion:
According to the banding pattern it is most likely that a duplication of the distal part of the long arm of chromosome 10 occurred.Key Words: Trisomy, 10q, Distal, de novo 相似文献14.
Background
It is well known that genetic components play an important role in the etiology of mandibular prognathism, but few susceptibility loci have been mapped.Methodology
In order to identify linkage regions for mandibular prognathism, we analyzed two Chinese pedigrees with 6,090 genome-wide single-nucleotide polymorphism (SNP) markers from Illumina Linkage-12 DNA Analysis Kit (average spacing 0.58 cM). Multipoint parametric and non-parametric (model-free) linkage analyses were used for the pedigrees.Principal Finding
The most statistically significant linkage results were with markers on chromosome 4 (LOD = 3.166 and NPL = 3.65 with rs 875864, 4p16.1, 8.38 cM). Candidate genes within the 4p16.1 include EVC, EVC2.Conclusion
We detected a novel suggestive linkage locus for mandibular prognathism in two Chinese pedigrees, and this linkage region provides target for susceptibility gene identification, a process that will provide important insights into the molecular and cellular basis of mandibular prognathism. 相似文献15.
Anatoly L. Mayburd 《PloS one》2009,4(6)
Background
Stochastic fluctuations in the protein turnover underlie the random emergence of neural precursor cells from initially homogenous cell population. If stochastic alteration of the levels in signal transduction networks is sufficient to spontaneously alter a phenotype, can it cause a sporadic chronic disease as well – including cancer?Methods
Expression in >80 disease-free tissue environments was measured using Affymetrix microarray platform comprising 54675 probe-sets. Steps were taken to suppress the technical noise inherent to microarray experiment. Next, the integrated expression and expression variability data were aligned with the mechanistic data covering major human chronic diseases.Results
Measured as class average, variability of expression of disease associated genes measured in health was higher than variability of random genes for all chronic pathologies. Anti-cancer FDA approved targets were displaying much higher variability as a class compared to random genes. Same held for magnitude of gene expression. The genes known to participate in multiple chronic disorders demonstrated the highest variability. Disease-related gene categories displayed on average more intricate regulation of biological function vs random reference, were enriched in adaptive and transient functions as well as positive feedback relationships.Conclusions
A possible causative link can be suggested between normal (healthy) state gene expression variation and inception of major human pathologies, including cancer. Study of variability profiles may lead to novel diagnostic methods, therapies and better drug target prioritization. The results of the study suggest the need to advance personalized therapy development. 相似文献16.
Background
Mannose-binding Lectin protein (MBL) has been suggested to be relevant in the defence against infections in immunosuppressed individuals. In a Swedish adult cohort immunosuppressed from both the underlying disease and from iatrogenic treatments for their underlying disease we investigated the role of MBL in susceptibility to infection.Methods
In this cross sectional, prospective study, blood samples obtained from 96 neutropaenic febrile episodes, representing 82 individuals were analysed for single nucleotide polymorphism (SNP) in the MBL2 gene. Concurrent measurement of plasma MBL protein concentrations was also performed for observation of acute response during febrile episodes.Findings
No association was observed between MBL2 genotype or plasma MBL concentrations, and the type or frequency of infection. Adding to the literature, we found no evidence that viral infections or co-infections with virus and bacteria would be predisposed by MBL deficiency. We further saw no correlation between MBL2 genotype and the risk of fever. However, fever duration in febrile neutropaenic episodes was negatively associated with MBL2 SNP mutations (p<0.05). Patients with MBL2 SNP mutations presented a median febrile duration of 1.8 days compared with 3 days amongst patients with wildtype MBL2 genotype.Interpretation
We found no clear association between infection, or infection type to MBL2 genotypes or plasma MBL concentration, and add to the reports casting doubts on the benefit of recombinant MBL replacement therapy use during iatrogenic neutropaenia. 相似文献17.
Laeyendecker O Latimore A Eshleman SH Summerton J Oliver AE Gamiel J Dobbs T Mei J Murphy G Parry JV Owen SM Quinn TC 《PloS one》2011,6(10):e25899
Objective(s)
To determine if mishandling prior to testing would make a sample from a chronically infected subject appear recently infected when tested by cross-sectional HIV incidence assays.Methods
Serum samples from 31 subjects with chronic HIV infection were tested. Samples were subjected to different handling conditions, including incubation at 4°C, 25°C and 37°C, for 1, 3, 7 or 15 days prior to testing. Samples were also subjected to 1,3, 7 and 15 freeze-thaw cycles prior to testing. Samples were tested using the BED capture enzyme immuno assay (BED-CEIA), Vironostika-less sensitive (V-LS), and an avidity assay using the Genetic Systems HIV-1/HIV-2 plus O EIA (avidity assay).Results
Compared to the sample that was not subjected to any mishandling conditions, for the BED-CEIA, V-LS and avidity assay, there was no significant change in test results for samples incubated at 4°C or 25°C prior to testing. No impact on test results occurred after 15 freeze-thaw cycles. A decrease in assay results was observed when samples were held for 3 days or longer at 37°C prior to testing.Conclusions
Samples can be subjected up to 15 freeze-thaw cycles without affecting the results the BED-CEIA, Vironostika-LS, or avidity assays. Storing samples at 4°C or 25°C for up to fifteen days prior to testing had no impact on test results. However, storing samples at 37°C for three or more days did affect results obtained with these assays. 相似文献18.
Background
Gene set testing has become an important analysis technique in high throughput microarray and next generation sequencing studies for uncovering patterns of differential expression of various biological processes. Often, the large number of gene sets that are tested simultaneously require some sort of multiplicity correction to account for the multiplicity effect. This work provides a substantial computational improvement to an existing familywise error rate controlling multiplicity approach (the Focus Level method) for gene set testing in high throughput microarray and next generation sequencing studies using Gene Ontology graphs, which we call the Short Focus Level.Results
The Short Focus Level procedure, which performs a shortcut of the full Focus Level procedure, is achieved by extending the reach of graphical weighted Bonferroni testing to closed testing situations where restricted hypotheses are present, such as in the Gene Ontology graphs. The Short Focus Level multiplicity adjustment can perform the full top-down approach of the original Focus Level procedure, overcoming a significant disadvantage of the otherwise powerful Focus Level multiplicity adjustment. The computational and power differences of the Short Focus Level procedure as compared to the original Focus Level procedure are demonstrated both through simulation and using real data.Conclusions
The Short Focus Level procedure shows a significant increase in computation speed over the original Focus Level procedure (as much as ∼15,000 times faster). The Short Focus Level should be used in place of the Focus Level procedure whenever the logical assumptions of the Gene Ontology graph structure are appropriate for the study objectives and when either no a priori focus level of interest can be specified or the focus level is selected at a higher level of the graph, where the Focus Level procedure is computationally intractable.Electronic supplementary material
The online version of this article (doi:10.1186/s12859-014-0349-3) contains supplementary material, which is available to authorized users. 相似文献19.
Background
Single nucleotide polymorphisms (SNPs) have been used extensively in genetics and epidemiology studies. Traditionally, SNPs that did not pass the Hardy-Weinberg equilibrium (HWE) test were excluded from these analyses. Many investigators have addressed possible causes for departure from HWE, including genotyping errors, population admixture and segmental duplication. Recent large-scale surveys have revealed abundant structural variations in the human genome, including copy number variations (CNVs). This suggests that a significant number of SNPs must be within these regions, which may cause deviation from HWE.Results
We performed a Bayesian analysis on the potential effect of copy number variation, segmental duplication and genotyping errors on the behavior of SNPs. Our results suggest that copy number variation is a major factor of HWE violation for SNPs with a small minor allele frequency, when the sample size is large and the genotyping error rate is 0∼1%.Conclusions
Our study provides the posterior probability that a SNP falls in a CNV or a segmental duplication, given the observed allele frequency of the SNP, sample size and the significance level of HWE testing. 相似文献20.
Eriko Asano Takeshi Ebara Chisato Yamada-Namikawa Tamao Kitaori Nobuhiro Suzumori Kinue Katano Yasuhiko Ozaki Makoto Nakanishi Mayumi Sugiura-Ogasawara 《PloS one》2014,9(12)