Sureselect design tool

Manufactured by Agilent Technologies

The SureSelect design tool is a software application developed by Agilent Technologies to assist users in designing custom target enrichment panels for next-generation sequencing (NGS) applications. The tool allows users to select genomic regions of interest and generate probe sequences that can be used to capture and sequence those regions.

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Lab products found in correlation

Ultra dna library prep kit, by New England Biolabs (1 mentions) Sureselect protocol, by Agilent Technologies (1 mentions) Hiseq 2000, by Illumina (1 mentions) Nebnext ultra dna library prep kit, by New England Biolabs (1 mentions)

2 protocols using sureselect design tool

Targeted Sequencing of Breast Cancer Genes

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The target region for sequencing of the candidate breast cancer susceptibility genes were selected based on coding exons. For established genes, intragenic regions were also included. Baits for solution based hybrid selection capture^{32 (link)} were designed using the Agilent SureSelect design tool (https://earray.chem.agilent.com/suredesign/). 500 nanograms of high molecular weight DNA was fragmented using a Covaris E-220. Fragmentation was verified by bioanalyzer. Library preparation was performed using the NEBNext Ultra DNA Library Prep kit (E7370L), and NEB Dual indexed adapters. Fragmented DNA (mean fragment size 300 ± 20 bp) was end repaired, adapter ligated, and size selected using Ampure XP /SPRI (A63881) and was PCR amplified for eight cycles. A post-PCR clean-up was performed and enrichment for targets was performed using the Agilent SureSelect protocol. Yields were assessed using BioAnalyzer. The mean library size was 300 ± 10 bp. NGS was performed on an Illumina HiSeq 2000 to an estimated 100× mean coverage for the target region to yield paired-end reads of 100 bp per sample, using 24 samples/lane.

Slavin T.P., Maxwell K.N., Lilyquist J., Vijai J., Neuhausen S.L., Hart S.N., Ravichandran V., Thomas T., Maria A., Villano D., Schrader K.A., Moore R., Hu C., Wubbenhorst B., Wenz B.M., D’Andrea K., Robson M.E., Peterlongo P., Bonanni B., Ford J.M., Garber J.E., Domchek S.M., Szabo C., Offit K., Nathanson K.L., Weitzel J.N, & Couch F.J. (2017). The contribution of pathogenic variants in breast cancer susceptibility genes to familial breast cancer risk. NPJ Breast Cancer, 3, 22.

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High-Throughput DNA Repair Gene Sequencing

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Whole blood samples were collected in citrate-phosphate-dextrose- adenine tubes (Sarstedt AG, Numbrecht, Germany) from patients at the time of random assignment. Germline DNA was extracted using the automated magnetic bead-based chemagic MSM I method (PerkinElmer chemagen, Baesweiler, Germany) in accordance with the manufacturer’s instructions. Quality control identified 35 poor-quality DNA samples among 528 samples available for the sequencing study.
The samples were genotyped as part of a multigene panel-based mutation analysis. The target regions included coding sequences and intron/exon boundaries of coding exons from 643 DNA repair genes, including BRCA1 and BRCA2. Baits for solution-based hybrid selection capture were designed using the Agilent SureSelect design tool. Germline DNA was fragmented and subjected to library preparation using the NEBNext Ultra DNA Library Prep kit with NEB Dual indexed adaptors and enriched for target regions by custom capture (Agilent eArray) using the Agilent SureSelect protocol. Products from each capture reaction were sequenced on a HiSEquation 2000 to 100 times mean coverage of target regions. All likely pathogenic mutations were validated using Sanger sequencing.

Fasching P.A., Loibl S., Hu C., Hart S.N., Shimelis H., Moore R., Schem C., Tesch H., Untch M., Hilfrich J., Rezai M., Gerber B., Costa S.D., Blohmer J.U., Fehm T., Huober J., Liedtke C., Weinshilboum R.M., Wang L., Ingle J.N., Müller V., Nekljudova V., Weber K.E., Rack B., Rübner M., von Minckwitz G, & Couch F.J. (2018). BRCA1/2 Mutations and Bevacizumab in the Neoadjuvant Treatment of Breast Cancer: Response and Prognosis Results in Patients With Triple-Negative Breast Cancer From the GeparQuinto Study. Journal of Clinical Oncology, 36(22), 2281-2287.

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