LOHA Comprehensive Assay for Single Nucleotide Polymorphism, Copy Number Variants and Loss of Heterozygosity Using SureSelect Target Enrichment
Poster Apr 09, 2015
Kyeong Soo Jeong, Arjun Vadapalli, Ashutosh Ashutosh, Paula Costa, Brian Peter, Stephanie Fulmer-Smentek, Magnus Isaksson, Jayati Ghosh, Douglas Roberts, Holly Hogrefe
Genetic variation in the mammalian genome spans a size extreme that includes cytogenetically recognizable elements and single-nucleotide polymorphisms. Copy number variations (CNVs) are an important intermediate size class of structural variations that involve unbalanced arrangements that increase or decrease the DNA content in mammalian genomes. CNVs are responsible for a continuous spectrum of phenotypic effects ranging from adaptive traits to embryonic lethality. The technology platforms available to identify CNVs include fluorescence in situ hybridization (FISH), array comparative genomic hybridization (aCGH) and more recently next generation sequencing. More mature platforms such as FISH and aCGH suffer from low resolution of genomic regions. The rapid development of low cost short-read sequencing technologies has paved the way to detect mutations and high resolution structural variation detection in a single experiment. Here we describe a comprehensive assay that enables researchers to identify SNP, INDEL, CNV, and LOH using SureSelect target enrichment. This design can be employed as a standalone entity or in concert with other bait designs for SNP and INDEL detection. We also describe methods for data analysis and visualization.
Genome-wide association studies (GWAS) have identified more than 100 genetic loci associated with type 2 diabetes. The majority of these are located in the intergenic or intragenic regions suggesting that the implicated variants may alter chromatin conformation. This, in turn, is likely to influence the expression of nearby or more remotely located genes to alter beta cell function. At present, however, detailed molecular and functional analyses are still lacking for most of these variants. We recently analysed one of these loci and mapped five causal variants in an islet-specific enhancer cluster within the STARD10 gene locus. Here, we aimed to understand how these causal variants influence b-cell function by alteration of the chromatin structure of enhancer clusterREAD MORE
The nuclear receptors pregnane X receptor (PXR) and constitutive androstane receptor (CAR) are closely related transcription factors that regulate the expression of phase I (cytochrome P450s), phase II metabolizing enzymes and transporter genes in response to xenobiotics, including prescription drugs.READ MORE
Early life stress (ELS) is highly associated with development of psychopathology
and mood disorders in adulthood. Genetic studies have identified variation in the gene calcium voltage-gated channel subunit alpha1C (CACNA1C) to increase risk for several psychiatric disorders. This poster assessed the expression of Cacna1c following prepubertal stress.