Sureselect all exon v5 kit

PicoPure^™ DNA Extraction Kit (Thermofisher,UK) was used to extract genomic DNA from cell lines. Targeted next generation sequencing was investigated for genomic variants in A2780 and A2780cis cells. The SureSelect All Exon V5 kit (Agilent Technologies) was used to enrich for protein coding regions. The sequencing was performed using an Illumina NextSeq500 sequencer with paired end reads (150 bp) and a minimum of 88million reads generated per sample. Raw reads were then fastq formatted. Contaminating adapter sequences and low-quality sequences were later processed using Skewer^{57 (link)}. Quality processed reads were then aligned to the HG19 reference genome using BWA^{58 (link)}. Any duplicate alignments were identified and processed using PicardTools. Realignment was completed using the Abra assembly based realigner^{59 (link)} to allow insertion/deletion variants detection. Variant calling and filtering were performed with Samtools/Bcftools (v1.3.1)^{60 (link)}. Using Vcftools^{61 (link)}, variants, in variant call format (VCF), that associated with Platinum resistance were identified. The functional significance of annotated variants were assessed using the Ensembl Variant Effect Predictor tool^{62 (link)}. Library preparation and sequencing was conducted by Source Biosciences (Nottingham, UK).

Genomic DNA was extracted from patient blood samples using the Gentra Puregene Blood Kit (Qiagen), and tumor DNA was obtained from patients and PDX tumors using the DNeasy Blood & Tissue Kit (Qiagen). Then 250 ng of DNA was sonicated with a Covaris S220 Focused-ultrasonicator, and 101-bp paired-end libraries were constructed with the SureSelect All Exon V5 Kit (Agilent). WES was performed on Illumina HiSeq 2000 instruments, with read lengths of 2 × 101 bp.
RNA extraction from non-tumor tissues and patient and PDX tumors was performed using TRIzol™ (Invitrogen). Samples with an RNA integrity number >5 were further processed. The 101-bp paired-end libraries were constructed with the TruSeq RNA Sample Prep Kit v2 (Illumina), using 1 µg of RNA. Whole-transcriptome sequencing (WTS) was performed on Illumina HiSeq 2000 instruments.