Center for Causal Transcriptional Consequences of Human Genetic Variation (CTCHGV)
The goal of our proposed Center for the Causal
Transcriptional Consequences of Human Genetic Variation (CTCHGV) is to develop methods that will identify and
characterize cause-effect relationships between human genome sequence variation
and transcriptional networks, with specific focus on cis transcription.
Recent genome wide association studies (GWAS)
involving many human cohorts have improved our knowledge of human genetic
variation and its relationship to human physiology and disease. Yet these developments are only early steps
towards the detailed causal understanding of how genetic variation relates to
phenotype needed to translate this knowledge to effective clinical practice.
This is particularly so for variation in non protein coding regions which
comprise 99% of the genome and which obey few known rules. As of this writing (May 2009), 315 GWAS
studies have uncovered 1439 SNPs that associate with ~200 human traits with
p<1e-5, 95% of which are in non coding regions (current information). Most of these are tag SNPs in linkage
disequilibrium with possibly causative SNPs as yet unidentified or even assayed
in their subjects. The tag SNPs are typically common variations and the
contribution to human health and disease of common vs. rarer variations is
still debated. Meanwhile, ongoing
sequencing of diverse populations and the growing number of sequenced
individual human genomes yield an ever-increasing number of previously unseen
and rare point, indel, and rearrangement variations.
To move from association to cause in a manner that is not complicated by variation rarity, population sampling, and sequencing depth, CTCHGV will develop and demonstrate innovative techniques that establish cis variants’ causal status by systematically and precisely varying cis sequences at single-nucleotide resolution using synthetic biology techniques, so that the effects of these variations on cis gene transcriptional level can be observed directly (Aim 1). Data generated by these methods will directly explain many GWAS findings of associations between cis variations and expression, and will enable refinement of hypotheses for disease causation where GWAS finds associations between cis regulatory loci and disease or phenotype. Moreover, to assist such refinement, CTCHGV will extend application of these new methods to human induced Pluripotent Stem cells (iPS) in order to make its methods able to explore the impact of cis variations in diverse human cell types representing different tissues (Aim 2). To achieve scalability in its methods for discerning sequence causality by systematically examining combinations of variations, CTCHGV will develop methods that operate with small samples of cells, including methods that assay many individual cells. Here, to determine causal cis variants requires only that the transcription of one gene—the cis gene—be assayed in small samples and in single cells. To extend beyond this and observe the systematic effects of variations, CTCHGV will therefore also develop new methods for obtaining transcriptome level information in single human cells, including both dispersed cells and in-situ structured tissues (Aim 3). Finally, CTCHGV will develop a number of innovative basic enabling technologies to achieve the scale and control over DNA synthesis and cell handling required to meet the goals above (Aim 4). As these technologies will have great impact and wide utility in biological research, CTCHGV will develop them with general usage in mind, in an open-source manner, and in collaboration with our many academic and business partners.
Last modified: 10/14/2010 11:05 AM by John Aach