Sureselect target enrichment

Manufactured by Agilent Technologies

Sourced in United States

The SureSelect Target Enrichment is a laboratory equipment product designed for targeted sequencing. It allows users to selectively capture and sequence specific regions of the genome, enabling focused analysis and efficient data generation.

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Lab products found in correlation

Hiseq 2000, by Illumina (7 mentions) Hiseq 2000 instrument, by Illumina (5 mentions) Sureselect custom kit, by Agilent Technologies (3 mentions) Suredesign, by Agilent Technologies (2 mentions) Suredesign online tool, by Agilent Technologies (2 mentions) Hiseq sequencing, by Illumina (1 mentions) Sureselect human all exon 50 mb kit, by Agilent Technologies (1 mentions) Taq dna polymerase, by Merck Group (1 mentions) Abi prism big dye terminator cycle sequencing v3.1 ready reaction kit, by Thermo Fisher Scientific (1 mentions) Abi prism 3730 dna analyzer, by Thermo Fisher Scientific (1 mentions) Qiaquick purification kit, by Qiagen (1 mentions) Custom capture panel, by Agilent Technologies (1 mentions) Hiseq rapid sbs kit v2, by Illumina (1 mentions) E220 sonicator, by Covaris (1 mentions) Nucleic acid extraction kit, by Qiagen (1 mentions) Truseq, by Illumina (1 mentions)

12 protocols using sureselect target enrichment

Fine-mapping Structural Variation Breakpoints

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We used Agilent SureSelect Target Enrichment to pull down 40-kb regions around breakpoints fine-mapped by custom array CGH. SureSelect followed by Illumina HiSeq sequencing was performed at HudsonAlpha Genomic Services Laboratory, and sequence analysis was performed as described previously (Hermetz et al. 2014 (link)). Custom SureSelect library numbers (ELID) are listed in Supplemental Tables S1 and S2. Arrays and SureSelect libraries were designed using the GRCh37/hg19 genome build, and we kept genomic coordinates in this version so that the design IDs correspond to the coordinates in our tables. Providing genomic coordinates in this genome build does not affect our conclusions.
We performed long-range PCR and Sanger sequencing to confirm breakpoints (Supplemental Table S3). We used the Qiagen LongRange PCR kit (Catalog # 206403), following the manufacturer's protocol. Sanger sequencing was performed by Beckman Coulter Genomics, and the reads were aligned to the human genome reference assembly (GRC37/hg19) using the BLAT tool on the UCSC Genome Browser (http://genome.ucsc.edu/). Junction sequences are provided in Supplemental Table S4.

Weckselblatt B., Hermetz K.E, & Rudd M.K. (2015). Unbalanced translocations arise from diverse mutational mechanisms including chromothripsis. Genome Research, 25(7), 937-947.

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Whole Exome Sequencing Variant Analysis

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Whole blood genomic DNA was fragmented to 150–200 bp by Adaptive Focused Acoustics (Covaris), end-paired, adenylated and ligated to adapters. Exonic sequences were enriched using Agilent SureSelect Target Enrichment (Agilent SureSelect Human All Exon 50 Mb kit). The captured fragments were purified and sequenced on a GAIIx platform using 75 bp paired-end reads. Bioinformatic analysis was performed using an in-house algorithm based on published tools. Sequence was aligned to the human reference genome (UCSC hg19), using NovoAlign (www.novocraft.com). The aligned sequence files were reformatted using SAMtools and duplicate sequence reads were removed using Picard. Single base variants were identified using Varscan (v2.2) and indels were identified using Dindel (v1.01). The raw lists of variants were filtered to include variants within the Sequence Capture target regions (±500 bp). On target variants were annotated using wAnnovar and common variants with a minor allele frequency > 0.02 that were present in the 1000 Genomes (February 2012 data release), the NHLBI-5400 Exome Sequencing Project and 191 unrelated in-house exomes were excluded. Rare, protein altering, homozygous and compound heterozygous variants that fitted the recessive disease model were identified.

Pfeffer G., Gorman G.S., Griffin H., Kurzawa-Akanbi M., Blakely E.L., Wilson I., Sitarz K., Moore D., Murphy J.L., Alston C.L., Pyle A., Coxhead J., Payne B., Gorrie G.H., Longman C., Hadjivassiliou M., McConville J., Dick D., Imam I., Hilton D., Norwood F., Baker M.R., Jaiser S.R., Yu-Wai-Man P., Farrell M., McCarthy A., Lynch T., McFarland R., Schaefer A.M., Turnbull D.M., Horvath R., Taylor R.W, & Chinnery P.F. (2014). Mutations in the SPG7 gene cause chronic progressive external ophthalmoplegia through disordered mitochondrial DNA maintenance. Brain, 137(5), 1323-1336.

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Comprehensive Genetic Screening for Hereditary Hearing Loss

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We have developed a custom capture panel of 180 known and candidate genes associated with sensorineural hearing loss using the Agilent SureDesign online tool (SureDesign/">https://earray.chem.agilent.com/SureDesign/). A SureSelect custom kit (Agilent, Santa Clara, CA, https://www.agilent.com) with a target size of approximately 1.158 Mb encompassing 3494 regions was designed to cover genes associated with both syndromic and nonsyndromic hereditary HL. The target sequencing was processed at the Hussman Institute for Human Genomics (HIHG) Sequencing core, University of Miami. The Agilent's SureSelect Target Enrichment (Agilent, Santa Clara, CA) of coding exons and flanking intronic sequences for each exon by a solution based capture system was used according to the manufacturer's standard protocol [7 (link)]. Adapter sequences for the Illumina HiSeq2000 were ligated and the enriched DNA samples were prepared using the HiSeq2000 instrument (Illumina) following the standard methods. Average insert size was 180 bp and paired-end reads were produced.

Shang H., Yan D., Tayebi N., Saeidi K., Sahebalzamani A., Feng Y., Blanton S, & Liu X. (2018). Targeted Next-Generation Sequencing of a Deafness Gene Panel (MiamiOtoGenes) Analysis in Families Unsuitable for Linkage Analysis. BioMed Research International, 2018, 3103986.

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Targeted Sequencing and Variant Confirmation

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The targeted sequencing was processed at the Hussman Institute for Human Genomics (HIHG) Sequencing core, University of Miami. The Agilent's SureSelect Target Enrichment (Agilent, Santa Clara, CA) of coding exons and flanking intronic sequences in-solutionhybridization capture system was used following the manufacturer's standard protocol. Adapter sequences for the Illumina HiSeq2000 were ligated and the enriched DNA samples were prepared using the standard methods for the HiSeq2000 instrument (Illumina). Paired-end reads of 99 bases length were produced. Conventional capillary sequencing was used to confirm the candidate variants observed in targeted- genes panel. The primers were designed using Primer3, v. 0.4.0 (http://primer3.ut.ee). PCR (polymerase chain reaction) reactions included 40-60 ng of genomic DNA with Taq DNA polymerase (Sigma). PCR products were visualized on agarose gels, purified using Qiagen Qiaquick purification kit according to the manufacturers’ protocols. Sequence analysis was performed with the ABI PRISM Big Dye Terminator Cycle Sequencing V3.1 Ready Reaction Kit and the ABI PRISM 3730 DNA Analyzer (Applied Biosystems). Sequence traces were analyzed using the DNASTAR Lasergene software.

Tekin D., Yan D., Bademci G., Feng Y., Guo S., Foster J I.I., Blanton S., Tekin M, & Liu X. (2016). A NEXT-GENERATION SEQUENCING GENE PANEL (MIAMI OTOGENES) FOR COMPREHENSIVE ANALYSIS OF DEAFNESS GENES. Hearing research, 333, 179-184.

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Capture Hi-C Promoter Enrichment

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Capture Hi-C of promoters was carried out with SureSelect target enrichment, using the custom-designed biotinylated RNA bait library and custom paired-end blockers according to the manufacturer’s instructions (Agilent Technologies). After library enrichment, a post-capture PCR amplification step was carried out using PE PCR 1.0 and PE PCR 2.0 primers with four PCR amplification cycles. CHi-C libraries were sequenced on the Illumina HiSeq 2000 platform for paired-end sequencing.

Villiers W., Kelly A., He X., Kaufman-Cook J., Elbasir A., Bensmail H., Lavender P., Dillon R., Mifsud B, & Osborne C.S. (2023). Multi-omics and machine learning reveal context-specific gene regulatory activities of PML::RARA in acute promyelocytic leukemia. Nature Communications, 14, 724.

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Custom Capture Panel for Deafness Genes

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A custom capture panel (MiamiOtoGenes), with a target size of approximately 1.158 MB encompassing 3494 regions, was designed to include all exons, 5' UTRs and 3' UTRs of 180 known and candidate deafness causing genes using the Agilent SureDesign online tool (SureDesign/">https://earray.chem.agilent.com/SureDesign/). The Agilent's SureSelect Target Enrichment (Agilent, Santa Clara, CA) of coding exons and flanking intronic sequences in-solution hybridization capture system was used following the manufacturer's standard protocol. Adapter sequences for the Illumina HiSeq2000 were ligated and the enriched DNA samples were prepared using the standard methods for the HiSeq2000 instrument (Illumina) (Yan et al. 2016 (link)).

Wang L., Feng Y., Yan D., Qin L., Grati M., Mittal R., Li T., Sundhari A.K., Liu Y., Chapagain P., Blanton S.H., Liao S, & Liu X. (2018). A dominant variant in the PDE1C gene is associated with nonsyndromic hearing loss. Human genetics, 137(6-7), 437-446.

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Validation of Genetic Variants via Targeted Enrichment and Sequencing

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Mutations were validated by Agilent Sure Select Target Enrichment as described (non-peer reviewed study)²³. Bait design was successful for 2261 of the 2728 putative variants (Supplementary Data 1). After enrichment, all variants were multiplexed and sequenced to ~ > 300x coverage using Illumina sequencing. Duplicates were removed and in-house scripts were used to quantify read counts at each candidate site to determine if the variant was a true de novo, inherited, or a false positive based on parental and child VAFs (Supplementary Fig. 3). The Integrative Genomics Viewer^{46 (link)} was used to manually inspect all confirmed mutations. Further filtering was applied to eliminate mosaic mutations (mutations called in siblings) and mutations that occurred during embryogenesis (VAF in offspring <39%; Supplementary Fig. 4).

Beal M.A., Meier M.J., Williams A., Rowan-Carroll A., Gagné R., Lindsay S.J., Fitzgerald T., Hurles M.E., Marchetti F, & Yauk C.L. (2019). Paternal exposure to benzo(a)pyrene induces genome-wide mutations in mouse offspring. Communications Biology, 2, 228.

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Genomic DNA Shearing and Enrichment

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The Covaris E220 sonicator was used for the shearing of genomic DNA. The SureSelectCT library system (Agilent Technologies) was used to perform the end repair, A tailing and ligation of adaptors. SureSelect target enrichment (Agilent Technologies) performed target enrichment using custom in house designed probes. Sequencing was performed on the Illumina HiSeq using the HiSeq Rapid SBS Kit v2 performing 2 × 108 base pair paired end reads.

Campanini E.H., Baker D., Arundel P., Bishop N.J., Offiah A.C., Keigwin S., Cadden S., Dall'Ara E., Nicolaou N., Giles S., Fernandes J.A, & Balasubramanian M. (2021). High bone mass phenotype in a cohort of patients with Osteogenesis Imperfecta caused due to BMP1 and C-propeptide cleavage variants in COL1A1. Bone Reports, 15, 101102.

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Targeted Sequencing of Deafness Genes

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Using the Agilent SureDesign online tool (https://earray.chem.agilent.com/suredesign/), a SureSelect custom kit (Agilent, Santa Clara, CA, https://www.agilent.com) was designed to include all exons, 5′ UTRs and 3′ UTRs of 180 known and candidate deafness causing genes (Supplementary Table S1) (Tekin et al. 2016 (link)). This custom capture panel (MiamiOtoGenes), with a target size of approximately 1.158 MB encompassing 3494 regions, covers genes associated with both syndromic and non-syndromic forms of HL. The targeted sequencing was processed at the Hussman Institute for Human Genomics (HIHG) Sequencing core, University of Miami. The Agilent’s SureSelect Target Enrichment (Agilent, Santa Clara, CA) of coding exons and flanking intronic sequences in-solution hybridization capture system was used following the manufacturer’s standard protocol. Adapter sequences for the Illumina HiSeq2000 were ligated and the enriched DNA samples were prepared using the standard methods for the HiSeq2000 instrument (Illumina). Through the sample preparation average insert size was 180 bp and paired end reads were used. Regions with lower coverage were not subjected to additional sequencing.

Yan D., Tekin D., Bademci G., Foster J I.I., Cengiz F.B., Kannan-Sundhari A., Guo S., Mittal R., Zou B., Grati M., Kabahuma R.I., Kameswaran M., Lasisi T.J., Adedeji W.A., Lasisi A.O., Menendez I., Herrera M., Carranza C., Maroofian R., Crosby A.H., Bensaid M., Masmoudi S., Behnam M., Mojarrad M., Feng Y., Duman D., Mawla A.M., Nord A.S., Blanton S.H., Liu X, & Tekin M. (2016). Spectrum of DNA variants for nonsyndromic deafness in a large cohort from multiple continents. Human genetics, 135(8), 953-961.

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Targeted Cancer Gene Sequencing from Biopsies

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DNA was extracted from biopsied tissue and cytology specimens (and patient-matched normal tissue) using Qiagen nucleic acid extraction kits. Using our MSK-IMPACT assay (Integrated Mutation Profiling of Actionable Cancer Targets), bar-coded sequence libraries were prepared (Illumina TruSeq), and exon capture was performed on bar-coded pools by hybridization (Agilent SureSelect Target Enrichment) using custom oligonucleotides to capture all exons and select introns of 279 cancer genes. DNA was sequenced on an Illumina HiSeq 2000 to maximize sensitivity for detecting mutations. This strategy enables the identification of mutations, indels, and copy number alterations involving these 279 genes.

Varghese A.M., Zakowski M.F., Yu H.A., Won H.H., Riely G.J., Krug L.M., Kris M.G., Rekhtman N., Ladanyi M., Wang L., Berger M.F, & Pietanza M.C. (2014). BRIEF REPORT: SMALL CELL LUNG CANCERS IN PATIENTS WHO NEVER SMOKED CIGARETTES. Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer, 9(6), 892-896.

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