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Basic Cancer Research

At Roychowdhury computational biology lab, we are focused on using Next Generation Sequencing (NGS) technologies to sequence cancer-patients’ samples. Through sequencing, we target cancer-specific genes and look for single-nucleotide variants (SNVs), copy-number variants (CNVs), gene expression changes, gene splicing, and chromosomal translocations. We utilize our own custom-designed computational pipelines for exome sequencing and RNA-sequencing analysis. Information gathered from this analysis should help guide proper treatment courses.

Drug Resistance

We study how cancers with genomic alterations become resistant to novel targeted therapies, including but not limited to inhibitors of BRAF, FGFR, PI3K, CDK, RET, and ALK oncogenes. We do this through pre-clinical models of acquired drug resistance and through acquisition of pretreatment and post-progression tumor samples from patients receiving targeted therapies for their cancer treatment.


Rare Cancers

We study patients with rare cancers that are so poorly characterized that there are no standard of care treatments for these diseases. We consent them to a clinical study that allows molecular characterization of their cancer using genomic sequencing and other approaches. These studies may lead to novel therapies or applications of existing therapies for patients facing these rare cancers.  

Exceptional Responders

During clinical drug development, some trials are considered failures when 20-40% of patients lack obvious benefit from the novel drug. However, selected patients may have an extraordinary response that could be defined by molecular features of their cancer. We seek to evaluate these patients in order to learn what molecular features could predict who might benefit in the future from that therapy.