Search results for " Disequilibrium"

Low frequency and rare coding variation contributes to multiple sclerosis risk

2018

AbstractMultiple sclerosis is a common, complex neurological disease, where almost 20% of risk heritability can be attributed to common genetic variants, including >230 identified by genome-wide association studies (Patsopoulos et al., 2017). Multiple strands of evidence suggest that the majority of the remaining heritability is also due to the additive effects of individual variants, rather than epistatic interactions between these variants, or mutations exclusive to individual families. Here, we show in 68,379 cases and controls that as much as 5% of this heritability is explained by low-frequency variation in gene coding sequence. We identify four novel genes driving MS risk independe…

Corrigendum to “Linkage disequilibrium screening for multiple sclerosis implicates JAG1 and POU2AF1 as susceptibility genes in Europeans” [J. Neuroim…

2007

Towards a Physical Map of the HLA Complex

1989

The human major histocompatibility (HLA) complex is located on the short arm of chromosome 6 in the 6p21.31→6p21.33 region (1,2). There are three clusters of genes, the HLA class I, II, and III regions. Whereas the class III loci are only moderately polymorphic (see (3) for review), the class I and II genes which encode cell surface glycoproteins show an extreme degree of polymorphism. There are a minimum of 17 class I loci (4) and at least 15 genes for class II alpha and beta chains (5). In addition, we (6) and others (7) have recently demonstrated that also the loci for tumor necrosis factor (TNFA) and lymphotoxin (TNFB) are part of the HLA complex [see also Ragoussis et al., this volume]…

The TaqIB and −629C>A polymorphisms at the cholesteryl ester transfer protein locus: associations with lipid levels in a multiethnic population. T…

2002

The Singapore population comprises Chinese, Malays and Asian Indians. Within this population, Asian Indians have the highest rates of coronary heart disease, whereas Chinese have the lowest. Conversely, Indians have the lowest high-density lipoprotein cholesterol (HDL-C) concentrations, followed by Malays and Chinese. We studied the TaqIB and -629C>A polymorphisms at the CETP locus in 1300 Chinese, 364 Malay and 282 Asian Indian men, and in 1558 Chinese, 397 Malay and 306 Asian Indian women, to determine whether these polymorphisms are responsible for the ethnic difference in HDL-C concentration. The frequency of the B2 allele in Chinese, Malays and Indians was 0.384, 0.339 and 0.449 in men…

Rapid evolving RNA gene HAR1A and schizophrenia

2008

Genetic variability in environmental isolates of Legionella pneumophila from Comunidad Valenciana (Spain).

2006

Summary Legionella pneumophila is associated to recurrent outbreaks in several Comunidad Valenciana (Spain) localities, especially in Alcoi, where social and climatic conditions seem to provide an excellent environment for bacterial growth. We have analysed the nucleotide sequences of three loci from 25 environmental isolates from Alcoi and nearby locations sampled over 3 years. The analysis of these isolates has revealed a substan- tial level of genetic variation, with consistent patterns of variability across loci, and comparable to that found in a large, European-wide sampling of clinical isolates. Among the tree loci studied, fliC showed the highest level of nucleotide diversity. The an…

Genetic Diversity in Latvian Spring Barley Association Mapping Population

2012

Certified organic crop area is continuously increasing in European Union and in Latvia (Eurostat data), despite somewhat lower yield and higher potential for disease damage in organic farming. It is increasingly recognized that breeding varieties for organic farming requires focus on specific traits that may be less important under conventional agriculture. Molecular markers are becoming essential tools for plant breeding allowing reducing time and cost of development of new varieties by early selection of progeny with desired traits. However, there is lack of information on molecular markers for traits that may be important for organic farming, such as plant morphological traits ensuring c…

Comparing RADseq and microsatellites for estimating genetic diversity and relatedness : Implications for brown trout conservation

2019

The conservation and management of endangered species requires information on their genetic diversity, relatedness and population structure. The main genetic markers applied for these questions are microsatellites and single nucleotide polymorphisms (SNPs), the latter of which remain the more resource demanding approach in most cases. Here, we compare the performance of two approaches, SNPs obtained by restriction-site-associated DNA sequencing (RADseq) and 16 DNA microsatellite loci, for estimating genetic diversity, relatedness and genetic differentiation of three, small, geographically close wild brown trout (Salmo trutta) populations and a regionally used hatchery strain. The genetic di…

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…

TAP-polymorphisms in juvenile onset psoriasis and psoriatic arthritis.

1996

Abstract Juvenile onset psoriasis is strongly associated with the HLA-class I genes Cw6 and B57 whereas patients with psoriatic arthritis show an increased frequency of HLA-B27. It is unclear whether additional major histocompatibility genes also increase disease susceptibility. The TAP genes (transporter associated with antigen processing) encode two membrane-spanning proteins that translocate antigenic peptides from the cytoplasm into the endoplasmic reticulum. Comparison of 60 patients with juvenile onset psoriasis, 63 psoriatic arthritis patients, and 101 caucasoid controls revealed an increase of the TAP1 ∗ 0101 allele in the psoriasis group, that could not be explained by linkage to o…