Agilent haloplex target enrichment kit

NGS analysis was performed on the same samples used for FISH and cytogenetic analyses. In all samples, the percentage of CLL cells was over 90 % as assessed by flow cytometry analysis. Agilent HaloPlex Target Enrichment kit (Agilent Technologies, Santa Clara, CA, USA) was used to produce libraries of exonic regions from 20 genes (ATM, BIRC3, BRAF, CDKN2A, PTEN, CDH2, DDX3X, FBXW7, KIT, KLHL6, KRAS, MYD88, NOTCH1, NRAS, PIK3CA, POT1, SF3B1, TP53, XPO1, ZMYM3) starting from genomic DNA from PB samples, according to HaloPlex Target Enrichment System (Agilent Technologies, Santa Clara, CA, USA). Diluted libraries were linked to Ion Sphere Particles, clonally amplified in an emulsion PCR and enriched using Ion OneTouch emulsion PCR System (Life technologies, Foster City, CA, USA). Exon-enriched DNA was precipitated with magnetic beads coated with streptavidin. Enriched, template-positive Ion Sphere Particles were loaded in one ion chip and sequenced using Ion Torrent PGM (Life technologies, Foster City, CA, USA). Sequencing data were aligned to the human reference genome (GRCh37). Data analysis and variant identification were performed using Torrent Suite 3.4 and Variant Caller plugin 3.4.4 (Life technologies, Foster City, CA, USA) [37 (link)].