Exome sequencing pipeline was extensively described in a previous work [22 (link)]. Briefly, Genomic DNA from the set of 42 adjacent-tumor paired samples was sequenced in the National Center of Genomic Analysis, Barcelona, Spain (CNAG) using the Illumina HiSeq-2000 platform. Exome capture was performed with the commercial kit Sure Select XT Human All Exon 50MB (Agilent). After data alignment and processing, high quality single nucleotide variants (SNVs) were identified using GATK software and germline variants were filtered. Finally, somatic SNVs were annotated using the SeattleSeq Variant Annotation web tool. Only potentially functional single nucleotide variants (SNVs) were taken into account in this work. Those include variants annotated as: coding-synonymous-near-splice, missense, missense-near-splice, splice-3, splice-5, stop-gained, stop-gained-near-splice, stop-lost, utr-3 and utr-5.
Sure select xt human all exon 50mb
Manufactured by Agilent Technologies
Sourced in United States
SureSelect XT Human All Exon 50MB is a targeted sequencing solution designed to capture and sequence the protein-coding regions of the human genome. It provides comprehensive coverage of the exonic regions, enabling focused and efficient analysis of the most biologically relevant genomic areas.
Automatically generated - may contain errors
Lab products found in correlation
Hiseq 2000, by Illumina (1 mentions)
Nextera rapid capture exome, by Illumina (1 mentions)
Sureselect human all exon v4, by Agilent Technologies (1 mentions)
Sureselectxt automated target enrichment for paired end multiplexed sequencing version a, by Illumina (1 mentions)
S2 instrument, by Covaris (1 mentions)
3 protocols using sure select xt human all exon 50mb
1
Exome Sequencing for Tumor-Adjacent Samples
2
Whole Exome Sequencing Protocol
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WES was carried out on either SOLiD or Illumina platforms. SOLiD libraries were prepared either with Sure Select XT Human All Exon 50 MB (Agilent Technologies, 5190-0407) or with SureSelect Human All Exon V4 (Agilent Technologies, 5190-4631). Sequencing was carried out either on SOLiD 5500 in Frag75/ECC mode or on SOLiD Wildfire in Frag50/ECC runs using single-end mode. For Illumina, libraries were prepared with Nextera Rapid Capture Exome and Expanded Exome Kits (Illumina, FC-140-1006). Paired-end libraries (2 × 51 bp) were sequenced on HiSeq 2000/2500 instruments with v3 chemistry.
3
Exome Sequencing Library Preparation
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Exome sequencing was performed at the Science for Life laboratory, Stockholm, Sweden. Each DNA library was prepared from 3 µg of pooled genomic DNA sheared to 300 bp using a Covaris S2 instrument (Covaris, MA, USA) and enriched using the SureSelectXT Human All Exon 50 Mb (Agilent technologies, CA, USA) and an Agilent NGS workstation according to the manufacturer's instructions (SureSelectXT Automated Target Enrichment for Illumina Paired-End Multiplexed Sequencing, version A; Agilent technologies, CA, USA).
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