Search results for "Genome-Wide Association"
showing 10 items of 392 documents
Arabidopsis thalianagenes contributing to differences in the outcome of infection with generalist and specialist strains ofTurnip mosaic virusidentif…
2020
AbstractPathogens can be classified as generalists or specialists depending on their host breadth. While generalists are able to successfully infect a wide variety of host species, the host range of specialists is limited to a few related species. Even though generalists seem to gain an advantage due to their wide host range, they usually pay a cost in terms of fitness within each host species (i.e., the jack-of-all trades, master of none). On the contrary, specialists have high fitness within their own host. A highly relevant yet poorly explored question is whether generalist and specialist viruses differ in the way they interact with their host’s gene expression networks. To identify host…
Successful Replication of GWAS Hits for Multiple Sclerosis in 10,000 Germans Using the Exome Array
2015
Genome-wide association studies (GWAS) successfully identified various chromosomal regions to be associated with multiple sclerosis (MS). The primary aim of this study was to replicate reported associations from GWAS using an exome array in a large German study. German MS cases (n = 4,476) and German controls (n = 5,714) were genotyped using the Illumina HumanExome v1-Chip. Genotype calling was performed with the Illumina Genome Studio(TM) Genotyping Module, followed by zCall. Single-nucleotide polymorphisms (SNPs) in seven regions outside the human leukocyte antigen (HLA) region showed genome-wide significant associations with MS (P values < 5 × 10(-8) ). These associations have been repor…
Class II HLA interactions modulate genetic risk for multiple sclerosis
2015
Association studies have greatly refined the understanding of how variation within the human leukocyte antigen (HLA) genes influences risk of multiple sclerosis. However, the extent to which major effects are modulated by interactions is poorly characterized. We analyzed high-density SNP data on 17,465 cases and 30,385 controls from 11 cohorts of European ancestry, in combination with imputation of classical HLA alleles, to build a high-resolution map of HLA genetic risk and assess the evidence for interactions involving classical HLA alleles. Among new and previously identified class II risk alleles (HLA-DRB1*15:01, HLA-DRB1*13:03, HLA-DRB1*03:01, HLA-DRB1*08:01 and HLA-DQB1*03:02) and cla…
Genome-wide association analysis on normal hearing function identifies PCDH20 and SLC28A3 as candidates for hearing function and loss.
2015
Hearing loss and individual differences in normal hearing both have a substantial genetic basis. Although many new genes contributing to deafness have been identified, very little is known about genes/variants modulating the normal range of hearing ability. To fill this gap, we performed a two-stage meta-analysis on hearing thresholds (tested at 0.25, 0.5, 1, 2, 4, 8 kHz) and on pure-tone averages (low-, medium-and high-frequency thresholds grouped) in several isolated populations from Italy and Central Asia (total N = 2636). Here, we detected two genome-wide significant loci close to PCDH20 and SLC28A3 (top hits: rs78043697, P = 4.71E-10 and rs7032430, P = 2.39E-09, respectively). For both…
Genome-wide association study for milk production traits in an economically important local dairy sheep breed
2021
In this study, we conducted a genome-wide association study (GWAS) for five milk production traits in the Valle del Belice sheep. Repeated measurements for milk yield (MY), fat percentage and yield (F% and FY) and protein percentage and yield (P% and PY) on 481 ewes, were available for the analysis. The animals were genotyped using the Illumina Ovine 50k BeadChip. Weighted deregressed breeding values (DEBVw) were used as phenotypes for GWAS analysis. A total of 23 genome-wide significant SNPs were identified: 3 associated with MY, 9 with FY, and 11 with P%. Several SNPs mapped within known candidate genes or previously reported QTL for milk production traits in livestock species. Additional…
Genome-wide scan for selection signatures reveals novel insights into the adaptive capacity in local North African cattle
2020
International audience; Natural-driven selection is supposed to have left detectable signatures on the genome of North African cattle which are often characterized by the fixation of genetic variants associated with traits under selection pressure and/or an outstanding genetic differentiation with other populations at particular loci. Here, we investigate the population genetic structure and we provide a first outline of potential selection signatures in North African cattle using single nucleotide polymorphism genotyping data. After comparing our data to African, European and indicine cattle populations, we identified 36 genomic regions using three extended haplotype homozygosity statistic…
Developing the "next generation" of genetic association databases for complex diseases
2012
Tens of thousands of genetic association studies investigating the influence of common polymorphisms on disease susceptibility have been published to date. These include similar to 1,000 genome-wide association studies (GWAS). This vast amount of data in the field of complex genetics is becoming increasingly difficult to follow and interpret. It can be expected that the situation will become even more complex with the advent of association projects using next-generation technologies. One of the aims of the Human Variome Project is to concatenate such data in meaningful ways, for example, within the context of publicly available field synopses. Here, we present various examples of online gen…
openSNP–A Crowdsourced Web Resource for Personal Genomics
2014
Genome-Wide Association Studies are widely used to correlate phenotypic traits with genetic variants. These studies usually compare the genetic variation between two groups to single out certain Single Nucleotide Polymorphisms (SNPs) that are linked to a phenotypic variation in one of the groups. However, it is necessary to have a large enough sample size to find statistically significant correlations. Direct-To-Consumer (DTC) genetic testing can supply additional data: DTC-companies offer the analysis of a large amount of SNPs for an individual at low cost without the need to consult a physician or geneticist. Over 100,000 people have already been genotyped through Direct-To-Consumer genet…
Identification and characterization of novel associations in the CASP8/ALS2CR12 region on chromosome 2 with breast cancer risk.
2014
Previous studies have suggested that polymorphisms in CASP8 on chromosome 2 are associated with breast cancer risk. To clarify the role of CASP8 in breast cancer susceptibility, we carried out dense genotyping of this region in the Breast Cancer Association Consortium (BCAC). Single-nucleotide polymorphisms (SNPs) spanning a 1 Mb region around CASP8 were genotyped in 46 450 breast cancer cases and 42 600 controls of European origin from 41 studies participating in the BCAC as part of a custom genotyping array experiment (iCOGS). Missing genotypes and SNPs were imputed and, after quality exclusions, 501 typed and 1232 imputed SNPs were included in logistic regressionmodels adjusting for stud…
Testing for goodness rather than lack of fit of an X–chromosomal SNP to the Hardy-Weinberg model
2019
The problem of checking the genotype distribution obtained for some diallelic marker for compatibility with the Hardy-Weinberg equilibrium (HWE) condition arises also for loci on the X chromosome. The possible genotypes depend on the sex of the individual in this case: for females, the genotype distribution is trinomial, as in the case of an autosomal locus, whereas a binomial proportion is observed for males. Like in genetic association studies with autosomal SNPs, interest is typically in establishing approximate compatibility of the observed genotype frequencies with HWE. This requires to replace traditional methods tailored for detecting lack of fit to the model with an equivalence test…