Whole Genome Sequencing (WGS) is a method to comprehensively consider the DNA base pairs of a sample and evaluate variants that arise in the sequence.  The role of genomic variants in disease phenotypes and outcomes can be further investigated with expression, molecular modeling and epigenetic regulation studies.  The flexible method allows for sequencing of any species of interest including, but not limited to human, model organisms (mice, rat, etc.), plants, microbes and more.

Whole Exome Sequencing (WES) allows for the enrichment of ~2% of the human genome and focuses on the protein-coding regions that contain a large percentage of the known disease variants.  Focusing on a smaller sequencing region allows for greater depth and maintains a concentrated approach to understanding the role of variants in disease phenotypes.  Beyond categorization of variants with curated databases, research analysis can further investigate protein structure, dynamics, and function of the variant. 

Transcriptomic Sequencing (RNA-Seq) provides scientists with an understanding of how a sample system responds to changes in conditions, treatments, gene variants, and a wide variety of other study designs.  Measuring gene expression changes (differential expression, DE) can provide understanding of cellular and molecular mechanisms that underly disease initiation, progression, response to environmental or therapeutic interventions and substantially more conditions. Sequencing the gene transcripts also produces information and insight into the expression of protein variants, transcript isoforms and novel fusion genes. 

MicroRNA (miRNA) plays an important role in controlling cellular gene expression and often create inhibitory feedback loops and act as negative regulators.  To reveal the miRNAs present in cellular systems, investigators can hybridize samples with an expression panel that identifies levels of up to 800 biologically relevant miRNA molecules (available as human, mouse or rat panels). 

Reduced Representation Bisulfide Sequence (RRBS) seeks to understand the level of DNA methylation on cytosines as this an epigenetic mechanism for regulation of gene expression.  Through identification of methylation in regions of the genome with high CpG content (~1% of the genome), further understanding of the differential regulation of gene expression can be discovered in a variety of diseases, cancer, aging and many other experimental models.

Chromatin Immunoprecipitation Sequencing (ChIP-Seq) is a method to further understand the intersection of proteins (transcription factors or histones) with various regions of the human genome.  Understanding and mapping these interactions can reveal common binding sites and overall structural changes that can regulate the ultimate ability of the cell to express various genes. 

The Bioinformatics Analysis Shared Resource is dedicated to providing comprehensive solutions to a wide variety of research areas and experience levels. We deliver broad bioinformatic analysis for DNA, epigenetic, and RNA-based sequencing.  Our interactive web-based reports include technology-specific quality control metrics, multi-sample comparisons, and advanced analyses beyond current national core standards.  As your trusted partner, we consistently develop and apply custom analyses to meet your program's research and publication needs.