Customizable Exon-centric Target Enrichment Strategy for Copy Number and SNP Analysis
Poster Apr 12, 2016
Arjun Vadapalli*, Kyeong Soo Jeong*, Ashutosh Ashutosh, Devendra Joshi , Eric Lin, Carlos Pabon, Gilbert Amparo, Jayati Ghosh, Douglas Roberts *Equally contributed
Structural variations in the genome can be determined from NGS data with either whole genome sequencing (WGS) or targeted enrichment using exome or gene panels. Copy number variation (CNV) of genomic segments is a large category of structural variation and has been implicated in many Mendelian diseases and complex traits. The impact of CNVs on gene expression is not limited to only the coding regions of genes localized within the CNV but also their flanking regions, an effect that could even extend over the entire length of the chromosome. Genomic coverage of coding regions and their upstream and downstream regions can vary between different platforms that are currently being used to study CNVs. DNA sequencing technologies which allow human genomes to be re-sequenced rapidly and inexpensively, are being used increasingly to detect a comprehensive list of variants relative to the reference genome. Combining DNA sequencing with the ability to selectively capture DNA targets provides additional cost benefits and lower amounts of DNA input per experiment. WGS has the potential to provide a single platform solution for detecting copy number variations (CNVs). However, it is prohibitively expensive in identifying mutations such as single nucleotide polymorphisms (SNPs), and insertions and deletions (INDELs) that require high sequencing read depths.
Characterization of a Type 2 diabetes-associated islet-specific enhancer cluster in STARD10 by genome editing of EndoC-βH1 cellsPoster
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
P450 Induction in Cryopreserved Hepatocytes from PXR and CAR Nuclear Receptor Knock-out RatsPoster
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
Psychiatric Risk Gene Cacna1c and Early Life Stress: Potential Gene-Environment interactions?Poster
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.
International Conference on Neurooncology and Neurosurgery
Sep 17 - Sep 18, 2018