Delila Tandefelt

Androgen receptor (AR) gene aberrations are rare in prostate cancer before primary hormone treatment but emerge with castration resistance. To determine AR gene status using a minimally invasive assay that could have broad clinical utility, we developed a targeted next-generation sequencing approach amenable to plasma DNA, covering all AR coding bases and genomic regions that are highly informative in prostate cancer. We sequenced 274 plasma samples from 97 castration-resistant prostate cancer patients treated with abiraterone at two institutions. We controlled for normal DNA in patients' circulation and detected a sufficiently high tumor DNA fraction to quantify AR copy number state in 217 samples (80 patients). Detection of AR copy number gain and point mutations in plasma were inversely correlated, supported further by the enrichment of nonsynonymous versus synonymous mutations in AR copy number normal as opposed to AR gain samples. Whereas AR copy number was unchanged from b...

We evaluated whether next generation sequencing (NGS) of cfDNA could be used for patient selection and as a tumor clone response biomarker in patients with advanced cancers participating in early phase clinical trials of targeted drugs. Plasma samples from patients with known tumor mutations who completed at least 2 courses of investigational targeted therapy were collected monthly, until disease progression. NGS was performed sequentially on the Ion Torrent PGM platform. cfDNA was extracted from 39 patients with various tumor types. Treatments administered targeted mailnly the PI3K-AKT-mTOR pathway (n=28) or MEK (n=7). Overall 159 plasma samples were sequenced with a mean sequencing coverage achieved of 1,685X across experiments. At trial initiation (C1D1), 23 of 39 (59%) patients had at least one mutation identified in cfDNA (mean 2, range 1-5). TP53, PIK3CA and KRAS were the top 3 mutated genes identified, with 16 (39%), 9 (22%) and 8 (17%) different mutations, respectively. Out ...