Alexander Gonzalez
Alexander Gonzalez
Helios Scholar
School: Columbia University
Hometown: Chandler, Arizona
Mentor: Kamel Lahouel, PhD
PI:  Cristian Tomasetti, PhD

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Investigating motif patterns for early cancer detection in cell free DNA via BestSeq technology

 BestSeq is a cell-free DNA based sequencing technology, currently being developed at TGen that is cheaper and more accessible, compared to existing technologies. BestSeq is an amplicons based technologies targeting repetitive elements of the human genome. Two candidate primer pairs for BestSeq were evaluated, based on a metric score from the GC% bias, a particular instance of motif features, as a low resolution approach to determine which one of these primer pairs separates normal patients from cancer patients the best. Once the best primer pair was identified, refined motif features were utilized to identify which specific patients were more likely to have cancer. These features yielded a cancer detection rate of 50% for one false positive in a preliminary dataset of 13 healthy and 12 cancer individuals. Finally, further investigation of the obtained false positive sample indicates contamination by genomic DNA, pointing to a better specificity of the test when adding a quality control filter based on cfDNA estimated percentage.