Annotation of genetic variants

Tools such as ANNOVAR, Variant Effect Predictor (VEP) or SnpEff annotate genetic variants (SNPs, INDELS, CNVs etc) present in VCF file. These tools integrate the annotations within the INFO column of the original VCF file. >>>
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A multi-tiered RNA-seq analyses approach to clinical diagnosis of a genetic disease

A novel three-tiered approach of targeted RNA-seq analysis for molecular diagnosis of a genetic disease (ex. neuromuscular disease; NMD) was proposed. Analysis will be stopped if molecular diagnosis is achieved in any of the Tiers and the results will be clinically correlated to reclassify variants of uncertain significance (VUSs), identify pathogenic events at the mRNA
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Genomic variants from RNA-seq data

RNA-Seq allows the detection and quantification of known and rare RNA transcripts within a sample. In addition to differential expression and detection of novel transcripts, RNA-seq also supports the detection of genomic variation in expressed regions. >>>
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eQTL analysis of RNA-seq data

Genetic locus that affects gene expression is often referred to as expression quantitative trait locus (eQTL). eQTL mapping studies assesses the association of SNPs with genome-wide expression levels. >>>
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Quality control for GWAS studies

An important step in the analysis of genome-wide association studies (GWAS) is to identify problematic subjects and markers. Quality control (QC) in GWAS removes markers and individuals, and greatly increases the accuracy of findings. >>>
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