title: ISHIKAWA 90% HEC6 10%
design: Approximately 3,000 cells/l (cell lines) were encapsulated with lysis buffer (100mM Tris at pH 8.0, 0.5% IGEPAL, proteinase K 1.0mg/ml) in a Tapestri instrument (Mission Bio), and further lysed on a thermal cycler. The DNA from the encapsulated cell lysate was then primed and barcoded using a custom amplicon panel (Mission Bio), which targets hotspot variants of 64 oncogenes and tumor suppressor genes, including the entire coding sequences of PTEN, PIK3R1 and PIK3CA, for a total of 317 amplicons. PCR products were digested and posteriorly purified using SPRI beads (Beckman Coulter). Sample indices and Illumina adapter sequences (Illumina) were then added and a second SPRI purification was then performed on the completed PCR reactions. Libraries were analyzed on a DNA 1000 assay chip with a Bioanalyzer (Agilent Technologies) and sequenced on a NextSeq 550 instrument (Illumina; 150 bp paired-end reads) at MSKs Integrated Genomics Operation.