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Advancement: Methods development for genome sequencing applications

Speaker Name: 
Balaji Sundararaman
Speaker Title: 
PhD Student (Advisor: Ed Green)
Speaker Organization: 
Biomolecular Engineering & Bioinformatics
Start Time: 
Monday, May 20, 2019 - 2:00pm
End Time: 
Monday, May 20, 2019 - 4:00pm
Biomedical Sciences, Room 200
Ed Green

Abstract:  The human genome contains sequence variations and haplotypes that are collectively inherited variations in a chromosome. Humans are diploids. Therefore, phasing individual chromosomes is needed to understand the function of the variation on each chromosome. Haplotype and genomic diversity are generated by meiotic recombination. Variant detection, haplotype phasing, and identification of meiotic recombination crossover (MR-CO) sites require analysis of DNA sequences over long ranges. Further, sequencing errors require deep sequencing for variant detection. I hypothesis that chromatin cross linking preserves long-range contact information which can be captured by Barcoded-beads. Current synthesis methods for Barcoded-bead and baits for target enrichment are costly. I propose to develop inexpensive and rapid methods for Barcoded-bead and target bait synthesis using rolling circle amplification (RCA). RCA generates multiple copies of circular template as concatemer that can be monomerized into individual copies. I present preliminary results for Barcoded-bead generation using RCA. I discuss method development for phasing using crosslinked chromatin and Barcoded-beads. I will use this method on crosslinked chromatin from sperm samples to map MR-CO. I demonstrate proof-of-concept experiments for inexpensive bait generation. I propose to make baits for cancer genes to use in diagnostics and SNP panel for forensic application.