Targeted Resequencing

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Background: Researchers in Prof. Hanlee Ji’s laboratory have developed a patented, fast, precise method to capture DNA for targeted resequencing of rare molecular species in a mixed genomic sample. This technology combines a porous matrix (with a large surface area to accelerate chemical reaction rates) and primer extension techniques (to enable sensitive and specific identification of regions of interest in a DNA sample). Furthermore, because the original sample remains tethered to the matrix after the primer extension reaction, it can be reused for replicate or follow-up studies (e.g. analyzing various cancer mutations or infectious pathogens). This basic DNA capture method could be implemented at low cost using commodity reagents and is compatible with any commercially available next-generation sequencing platform for high throughput mutation detection, genotyping, gene expression studies or exome sequencing. Issue date of US Patent No. 9,689,027 is June 27, 2017. Porous phase DNA capture. A DNA sample is tethered to the inside surfaces of a porous matrix (i); targeted primer extension enriches for regions of interest in the DNA sample (ii); extended fragments are eluted(iii) for downstream sequencing (iv).The DNA sample remains stably in the column for follow-up studies.   Applications:   Targeted resequencing - extract rare samples that would otherwise be missed in shotgun sequencing for: end uses such as exome sequencing, mixed organismic population analysis, and gene expression studies sequential analysis for cancer mutation analysis or diagnosis infectious organisms   Advantages:   Fast - high surface area of porous matrix accelerates chemical reaction, reducing DNA capture time from days to ~2 hours Specific - selective capture via primer extension Sensitive - enables precise targeting of rare molecular species Low cost - easy modification of silica membrane columns with commodity reagents to enable mass manufacturing Universal platform - methods can be adapted for any commercially available sequencer Original sample preserved - after the DNA is captured on matrix it can be reused for replicate studies or analysis with different targeting oligonucleotides   Publications:   US Patent Application published May 21, 2015, Publication No. US 2015 0140553 A1