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Copy Number Variants (copy + number_variants)

Distribution by Scientific Domains

Life Sciences	60%

Selected Abstracts

From age correction to genome-wide association

ACTA PSYCHIATRICA SCANDINAVICA, Issue 5 2009
S. Cohen-Woods
Objective:, Eric Strömgren was one of the pioneers of psychiatric genetics and family studies. There has now been an explosion of interest in this field and research progress, including linkage and association studies, whole genome genotyping, copy number variants and epigenetics is reviewed here. Method:, An overview of this area of psychiatric research is presented and discussed based on the relevant literature aiming at giving a recent status of the progress. Results:, Broadly speaking linkage and association are complementary approaches used to locate genes contributing to the genetic aetiology of psychopathology. Linkage can be detected over comparatively large distances, however power is problematic when searching for quantitative trait loci with small effect sizes. In contrast, association studies can detect small effects but only over very small distances. Therefore, while several genome-wide linkage studies in psychiatric disorders have been performed, the majority of association studies have investigated specific functional candidate genes. Conclusion:, Due to very recent technological advancements, genome-wide association studies have now become possible and have identified some completely novel susceptibility loci. Other recent advances include the discovery of epigenetic phenomena and copy number variants. [source]

A locus for an auditory processing deficit and language impairment in an extended pedigree maps to 12p13.31-q14.3

GENES, BRAIN AND BEHAVIOR, Issue 6 2010
L. Addis
Despite the apparent robustness of language learning in humans, a large number of children still fail to develop appropriate language skills despite adequate means and opportunity. Most cases of language impairment have a complex etiology, with genetic and environmental influences. In contrast, we describe a three-generation German family who present with an apparently simple segregation of language impairment. Investigations of the family indicate auditory processing difficulties as a core deficit. Affected members performed poorly on a nonword repetition task and present with communication impairments. The brain activation pattern for syllable duration as measured by event-related brain potentials showed clear differences between affected family members and controls, with only affected members displaying a late discrimination negativity. In conjunction with psychoacoustic data showing deficiencies in auditory duration discrimination, the present results indicate increased processing demands in discriminating syllables of different duration. This, we argue, forms the cognitive basis of the observed language impairment in this family. Genome-wide linkage analysis showed a haplotype in the central region of chromosome 12 which reaches the maximum possible logarithm of odds ratio (LOD) score and fully co-segregates with the language impairment, consistent with an autosomal dominant, fully penetrant mode of inheritance. Whole genome analysis yielded no novel inherited copy number variants strengthening the case for a simple inheritance pattern. Several genes in this region of chromosome 12 which are potentially implicated in language impairment did not contain polymorphisms likely to be the causative mutation, which is as yet unknown. [source]

Clinical Genetics & Human Genome Variation: The 2008 Human Genome Variation Society Scientific Meeting

HUMAN MUTATION, Issue 5 2009
William S. Oetting
Abstract The annual scientific meeting of the Human Genome Variation Society (HGVS) was held on 11 November 2008, in Philadelphia, PA. The major theme of this meeting was "Clinical Genetics & Human Genome Variation." For complex diseases, it is becoming evident that the contribution of most associated genetic variants to the disease process is small and, most likely, multiple variants are required to explain the predisposition and variation that is observed. As genome-wide association studies (GWASs) identify variants that are associated with a disease, there is a need to determine if the associated variants are causative, or simply in genetic disequilibrium with the true functional variant. New methods are being devised to help classify these genetic variants as either functional or nonfunctional. As study populations increase in size, there is also a need for better-constructed databases that can bring together the different genetic variants being identified, including SNPs, copy number variants (CNVs), and methylation differences, environmental risk factors, and the clinical information needed to construct useful phenotypes. These topics and others were discussed in this year's meeting. Hum Mutat 30, 852,856, 2009. © 2009 Wiley-Liss, Inc. [source]

Segmentation and Estimation for SNP Microarrays: A Bayesian Multiple Change-Point Approach

BIOMETRICS, Issue 3 2010
Yu Chuan Tai
Summary High-density single-nucleotide polymorphism (SNP) microarrays provide a useful tool for the detection of copy number variants (CNVs). The analysis of such large amounts of data is complicated, especially with regard to determining where copy numbers change and their corresponding values. In this article, we propose a Bayesian multiple change-point model (BMCP) for segmentation and estimation of SNP microarray data. Segmentation concerns separating a chromosome into regions of equal copy number differences between the sample of interest and some reference, and involves the detection of locations of copy number difference changes. Estimation concerns determining true copy number for each segment. Our approach not only gives posterior estimates for the parameters of interest, namely locations for copy number difference changes and true copy number estimates, but also useful confidence measures. In addition, our algorithm can segment multiple samples simultaneously, and infer both common and rare CNVs across individuals. Finally, for studies of CNVs in tumors, we incorporate an adjustment factor for signal attenuation due to tumor heterogeneity or normal contamination that can improve copy number estimates. [source]

Carbohydrate metabolic pathway genes associated with quantitative trait loci (QTL) for obesity and type 2 diabetes: Identification by data mining

BIOTECHNOLOGY JOURNAL, Issue 9 2010
Dr. Vijayalakshmi Varma
Abstract Increasing consumption of refined carbohydrates is now being recognized as a primary contributor to the development of nutritionally related chronic diseases such as obesity and type 2 diabetes mellitus (T2DM). A data mining approach was used to evaluate the role of carbohydrate metabolic pathway genes in the development of obesity and T2DM. Data from public databases were used to map the position of the carbohydrate metabolic pathway genes to known quantitative trait loci (QTL) for obesity and T2DM and for examining the pathway genes for the presence of sequence and structural genetic variants such as single nucleotide polymorphisms (SNPs) and copy number variants (CNS), respectively. The results demonstrated that a majority of the genes of the carbohydrate metabolic pathways are associated with QTL for obesity and many for T2DM. In addition, some key genes of the pathways also encode non-synonymous SNPs that exhibit significant differences in population frequencies. This study emphasizes the significance of the metabolic pathways genes in the development of disease phenotypes, its differential occurrence across populations and between individuals, and a strategy for interpreting an individuals' risk for disease. [source]