Genome Capture and Sequencing to Comprehensively Map Chromatin Structure in Complex Genomes

This invention brings significant improvement to our ability to query the chromatin structure of select important regions of the entire human genome. Utilizing a unique sequencing strategy, the invention offers a solution-based sequence capture method enabling the enrichment of the 2000 bp surrounding the transcription start site of 25,464 human open reading frames. This enrichment reduces the sequence space of the human genome from 3.4 Gb in total to 50 Mb of transcription start sites, a 98.5% reduction. Additionally, the enrichment is analogous to that achieved for well-documented exome sequencing experiments. This sequence capture approach will allow researchers to multiplex chromatin structure analyses in Illumina HiSeq2500 lanes, thereby opening this strategy for a wide range of diagnostic and prognostic indicators in human disease.

Applications:

• Identify stages in the progression of cancer
• Identify host response in viral infection (HIV and KSHV)
• Define cryptic effects of drugs of abuse (amphetamines, cocaine, and nicotine)

Advantages:

• Allows for the targeted analysis of specific areas of interest in complex genomes
• Provides a cost effective strategy for querying multiple samples in a single reaction
• Provides an extremely cost effective way to screen patient samples
• Opens a new field of biomarker development: distribution of nucleosomes
• Nucleosome distribution mapping is independent of genotype and gene expression