Breast Neoplasms study with SNP Genotypes (NGS), WXS data on dbGaP (12 participants)

phs003165 — Phase I Study and Cell-Free DNA Analysis of T-DM1 and Metronomic    Temozolomide for Secondary Prevention of HER2-Positive Breast Cancer    Brain Metastases

<p>This study is a phase I trial combining ado-trastuzumab emtansine (T-DM1) with Temozolomide (TMZ) for the prevention of additional brain metastases after previous occurrence and local treatment in HER2+ breast cancer patients. Twelve patients were enrolled in this study. Data includes whole exome sequencing (WES) from patients' cerebrospinal fluid (CSF) and plasma samples. The CSF was collected from each patient at trial entry and after the initial two treatment cycles of TMZ and T-DM1 treatment. Blood was collected through a standard peripheral venipuncture at the following four time points: 1) upon trial entry, 2) after two treatment cycles, 3) the treatment cycle prior to the last follow-up, and 4) most recent follow-up. Whole exome libraries were captured by the <a href="https://www.agilent.com/en/product/next-generation-sequencing/hybridization-based-next-generation-sequencing-ngs/exome-probes/sureselect-human-all-exon-232866">SureSelect Human All Exon V8 Kit</a> (Agilent, Santa Clara, CA, USA) and sequenced by <a href="https://www.illumina.com/systems/sequencing-platforms/novaseq.html">NovaSeq 6000</a> S2 Sequencer in paired-end sequencing mode (Illumina, San Diego, CA, USA). Gene mutations in <a href="https://www.ncbi.nlm.nih.gov/gene/1788">DNMT3A</a>, <a href="https://www.ncbi.nlm.nih.gov/gene/8518">ELP1</a>, <a href="https://www.ncbi.nlm.nih.gov/gene/4855">NOTCH4</a>, <a href="https://www.ncbi.nlm.nih.gov/gene/9757">KMT2B</a>, <a href="https://www.ncbi.nlm.nih.gov/gene/64109">CRLF2</a><i>, </i>and <a href="https://www.ncbi.nlm.nih.gov/gene/100134444">KCNJ18</a> were observed in patients' CSF.</p>

Phase I Study and Cell-Free DNA Analysis of T-DM1 and Metronomic    Temozolomide for Secondary Prevention of HER2-Positive Breast Cancer    Brain Metastases