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Description

Abstract: Precision medicine continues to be a driving force for utilizing complex genomic data at the bedside, and analyses of these high-density data requires high-performance computing workflows. Advancements in DNA sequencing technology and computing capabilities have propelled the use of genetic and genomic data in precision medicine efforts. The first part of this tutorial will review computational pipelines for processing Illumina pair-end whole exome sequencing data. Specifically, attendees will be provided access to biomix, a high performance cluster hosted by University of Delaware, as instructors review a pipeline for processing fastq files (raw) into variant call files (VCF): bwa, samtools, picards, GATK, SnpEff / ClinEff. The NGS data are simulated for a clinically relevant autosomal recessive disorder with co-occurring common drug metabolizing variant alleles. The second part of this tutorial will involve an overview of web-based bioinformatics resources, combining data mining, text mining, network analysis and visualization tools for translating variant data into biological knowledge.

Learning Objective 1: Prepare a computational pipeline for analyzing whole exome sequencing data

Learning Objective 2 (Optional): Evaluate benefits and limitations of clinical NGS data

Learning Objective 3 (Optional): Develop the skill sets (basic and advance) for utilizing a high-performance cluster

Learning Objective 4 (Optional): Evaluate systems for translating variant data into knowledge

Authors:

Erin Crowgey (Presenter)
Nemours Alfred I. duPont Hospital for Children

Jeffrey Myers (Presenter)
Nemours Alfred I. duPont Hospital for Children

Joseph Romano (Presenter)
Columbia University

Shawn Polson (Presenter)
University of Delaware

Presentation Materials:

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