Ten patients with invasive breast carcinoma of no special type were diagnosed and treated in the Cancer Research Institute of Tomsk NRMC (Tomsk, Russia). The histological diagnosis of breast cancer was made according to the WHO criteria [35 (link)]. All tumors were of luminal subtype, T1–3N0–2M0 stage, and the age range of patients was 41–67. DNA was isolated from fresh-frozen tumors (n = 10) and peripheral blood samples (n = 10) using a DNeasy Blood & Tissue kit (Qiagen sciences Inc., Germantown, MD, USA). DNA and library quality was measured using a 2200 TapeStation Instrument (Agilent Technologies, Santa Clara, CA, USA). Whole exome libraries were prepared using SureSelect XT Human All Exon v7 kit (Agilent, USA) and sequenced on a NextSeq 500 instrument (Illumina, San Diego, CA, USA) using paired-end 150 reads. Data were analyzed using the GATK pipeline, and genetic variants were annotated using the ANNOVAR [55 (link),56 (link)]. Mutations that were present in peripheral blood were filtered out. Driver genes were identified based on the IntOGen database. Overall survival was calculated for breast cancer patients depending on PTEN and ZFHX3 mutation status using the cBioPortal tool.
Sureselect xt human all exon v7 kit
Manufactured by Agilent Technologies
Sourced in United States
The SureSelect XT Human All Exon v7 kit is a genomic DNA library preparation kit designed for targeted sequencing of the human exome. The kit includes reagents and protocols for DNA fragmentation, adapter ligation, and hybridization-based target enrichment of coding regions across the human genome.
Automatically generated - may contain errors
Lab products found in correlation
Nextseq 500, by Illumina (1 mentions)
2200 tapestation instrument, by Agilent Technologies (1 mentions)
Dneasy blood tissue kit, by Qiagen (1 mentions)
Novaseq 6000 sequencing system, by Illumina (1 mentions)
Maxwell rsc blood dna kit, by Promega (1 mentions)
Magmax ffpe dna rna ultra kit, by Thermo Fisher Scientific (1 mentions)
E220 focused ultrasonicator, by Agilent Technologies (1 mentions)
Sureselect xt hs and low input library preparation kit for ilm pre pcr, by Agilent Technologies (1 mentions)
2 protocols using sureselect xt human all exon v7 kit
1
Whole Exome Sequencing of Breast Tumors
2
Whole Exome Sequencing of FFPE Tumor Samples
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The tumor samples used for WES analysis were formalin-fixed paraffin-embedded (FFPE). Patient-matched peripheral blood samples were stored in Streck blood collection tubes and used as a normal control for germline filtering. DNA was extracted from the FFPE samples using the MagMAX FFPE DNA/RNA Ultra kit (cat# A31881, ThermoFisher, Waltham, MA, USA) and from the peripheral whole blood samples using the Maxwell RSC blood DNA kit (cat# AS1400, Promega, Madison, WI, USA). The recovered DNA was sheared to approximately ~200 bp using a Covaris E220 Focused-ultrasonicator and then hybridized to whole exome probes from the Agilent SureSelect XT Human All Exon V7 kit (cat# 5991-9039, Agilent, Santa Clara, CA, USA). After enrichment, the captured DNA was amplified, end-repaired, and attached to sequencing adapters and barcodes using the SureSelect XT HS and Low Input Library Preparation Kit for ILM (Pre-PCR) (cat# G9704, Agilent, Santa Clara, CA, USA). The libraries were normalized, pooled, and loaded on the Illumina NovaSeq-6000 Sequencing System to generate 150×150-bp paired-end reads. Raw image analysis and base-calling were carried out using Illumina onboard RTA3 program with default parameters.
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