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Sureselect human all exon kit

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The SureSelect Human All Exon Kit is a targeted enrichment system designed for the capture and sequencing of human exonic regions. The kit utilizes biotinylated RNA baits to selectively capture and enrich the protein-coding regions of the human genome, enabling efficient and cost-effective sequencing of the exome.

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Lab products found in correlation

Hiseq 2000, by Illumina (33 mentions) Hiseq 2500, by Illumina (13 mentions) Sureselect human all exon v 2 kit, by Agilent Technologies (4 mentions) Genome analyzer iix, by Illumina (4 mentions) Hiseq 4000, by Illumina (4 mentions) Dneasy blood tissue kit, by Qiagen (3 mentions) Hiseq x ten system, by Illumina (3 mentions) Hiseq platform, by Illumina (3 mentions) Ampure xp system, by Beckman Coulter (3 mentions) Bioanalyzer 2100 system, by Agilent Technologies (3 mentions) S2 ultrasonicator, by Covaris (3 mentions) Paired end sample prep kit v1, by Illumina (3 mentions) Gentra puregene blood kit, by Qiagen (3 mentions) Hiseq 2500 system, by Illumina (3 mentions) Novaseq 6000, by Illumina (3 mentions) Hiseq 2000 sequencer, by Illumina (3 mentions) Qiaamp dna mini kit, by Qiagen (3 mentions) Ultrasonicator, by Covaris (3 mentions) Agilent high sensitivity dna kit, by Agilent Technologies (2 mentions) Maxwell 16 blood dna purification kit, by Promega (2 mentions)

Spelling variants of this product

SureSelect kits (5 citations) SureSelect Human All Exon Kits Version 4 (3 citations) SureSelect Human All Exon Kits Version CRE (2 citations) SureSelect Human All Exon V5/V6 kits (2 citations) Agilent SureSelect Human All Exon V5 and V4 kits (2 citations)

117 protocols using sureselect human all exon kit

1

Exome Sequencing and Variant Analysis

Cited 2 times
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DNA was extracted from EDTA blood using Maxwell 16 Blood DNA Purification Kit (Promega) or PBMC using DNeasy Blood & Tissue Kit (Qiagen). Total of 3 ug of DNA were sheared using E220 focused sonicator (Covaris) and exome libraries were generated using the SureSelect Human All Exon Kits (Agilent) according to manufactures’ protocol. The quality of generated libraries was inspected using Agilent High Sensitivity DNA Kit (Agilent) and quantified using qPCR kit (Agilent). Samples were sequenced on Illumina HiSeq2000 (Illumina) generating 100 bp paired end reads. Sequences were aligned to a human reference genome GRCh37 using bwa v 0.6.1 with default parameters51 (link). Variant calling (Single nucleotide variants and indels) was performed using GATK v.252 (link) and variants were annotated using Annovar53 (link). An in-house custom analysis pipeline was used to filter and prioritize variants based on the likely genetic models and clinical pedigree for patients.
Afzali B., Grönholm J., Vandrovcova J., O’Brien C., Sun H.W., Vanderleyden I., Davis F.P., Khoder A., Zhang Y., Hegazy A.N., Villarino A.V., Palmer I.W., Kaufman J., Watts N.R., Kazemian M., Kamenyeva O., Keith J., Sayed A., Kasperaviciute D., Mueller M., Hughes J.D., Fuss I.J., Sadiyah M.F., Montgomery-Recht K., McElwee J., Restifo N.P., Strober W., Linterman M.A., Wingfield P.T., Uhlig H.H., Roychoudhuri R., Aitman T.J., Kelleher P., Lenardo M.J., O’Shea J.J., Cooper N, & Laurence A.D. (2017). BACH2 immunodeficiency illustrates an association between super-enhancers and haploinsufficiency. Nature immunology, 18(7), 813-823.
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2

Targeted Sequencing of Tumor Exomes

Cited 1 time
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We constructed sequencing libraries and performed target enrichment using Agilent SureSelect Human All Exon kits designed to target 37.8 Mb regions of all human exons according to the manufacturer's instruction (Agilent, Santa Clara, CA). The PCR-amplified libraries were sequenced on SOLiD™ 4 systems using the 50x35bp paired-end sequencing protocol (Applied Biosystems, Foster City, CA). Sequencing was used to evaluate 120 tumor/normal pairs for coding sequence alterations. An average of 3.3 Gb of non-redundant sequence was mapped on-target per sample to hg19 using BFAST version 0.7.0a(57 ). Duplicates were removed using Picard (http://picard.sourceforge.net/command-line-overview.shtml), normal/tumor bam files were used as input for GATK version 2.1-11 (http://www.broadinstitute.org/gatk/)(58 (link)-60 (link)). Local realignment and base quality recalibration were performed using default parameters. Single nucleotide polymorphisms and indels were called using GATK UnifiedGenotyper (http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_genotyper_UnifiedGenotyper.html). Variants which passed quality score greater than 50, coverage in tumor and normal greater than 10, VAF (Variant Allele Frequency) in the tumor greater than 15% and VAF in normal of 0% were further annotated with ANNOVAR, SIFT, PPH2 and COSMIC.
Shern J.F., Chen L., Chmielecki J., Wei J.S., Patidar R., Rosenberg M., Ambrogio L., Auclair D., Wang J., Song Y.K., Tolman C., Hurd L., Liao H., Zhang S., Bogen D., Brohl A.S., Sindiri S., Catchpoole D., Badgett T., Getz G., Mora J., Anderson J.R., Skapek S.X., Barr F.G., Meyerson M., Hawkins D.S, & Khan J. (2014). Comprehensive genomic analysis of rhabdomyosarcoma reveals a landscape of alterations affecting a common genetic axis in fusion-positive and fusion-negative tumors. Cancer discovery, 4(2), 216-231.
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3

Whole-Genome and Whole-Exome Sequencing of Paired Tumor and Normal Tissues

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A total of 13 paired tumor and adjacent normal tissues underwent either whole-genome or whole-exome sequencing (Supplementary Table 6). Genomic DNA was extracted using a DNeasy blood and tissue kit (Qiagen, Valencia, CA, USA), and the quality of DNA was tested by using an Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA, USA). Whole-genome sequencing for seven of the paired samples was previously reported [13 (link)], and the data were obtained with an average depth of 65× coverage for tumor samples and 42× coverage for control samples. For the remaining six paired samples, sequencing libraries were prepared using a TruSeq DNA HT sample prep kit (Illumina, San Diego, CA, USA), and whole-exome enrichment was performed using SureSelect human all exon kits (Agilent) according to the manufacturer’s instructions. Paired-end sequencing (2 × 150 bp) was performed on a HiSeq 2500 sequencing platform (Illumina), as described in our previous study [13 (link)], acquiring the data with an average depth of 70× coverage for tumor samples and 67× coverage for control samples.
Zhang M., Zhang L., Li Y., Sun F., Fang Y., Zhang R., Wu J., Zhou G., Song H., Xue L., Han B, & Zheng C. (2020). Exome sequencing identifies somatic mutations in novel driver genes in non-small cell lung cancer. Aging (Albany NY), 12(13), 13701-13715.
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4

Whole Exome Sequencing for Genetic Diagnosis

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Genomic DNA was extracted from lymphocytes from affected individuals and parents by standard techniques. For whole exome analysis, targeted enrichment and sequencing were performed on 3 μg of DNA extracted from the peripheral blood of three individuals (F102, F163, F259). Enrichment was undertaken using the SureSelect Human All Exon kits following the manufacturer’s protocol (Agilent, Santa Clara, CA, USA) and samples were pair-end sequenced on either an IlluminaHiSeq 2000 or SOLiD platform. Sequence data were mapped using BWA (Burrows-Wheeler Aligner) against hg18 (NCBI36) human genome as a reference. Variants were called using SOAPsnp and SOAPindel (from the Short Oligonucleotide Analysis Package) with medium stringency (Supplementary Table 1).
Rice G.I., del Toro Duany Y., Jenkinson E.M., Forte G.M., Anderson B.H., Ariaudo G., Bader-Meunier B., Baildam E.M., Battini R., Beresford M.W., Casarano M., Chouchane M., Cimaz R., Collins A.E., Cordeiro N.J., Dale R.C., Davidson J.E., De Waele L., Desguerre I., Faivre L., Fazzi E., Isidor B., Lagae L., Latchman A.R., Lebon P., Li C., Livingston J.H., Lourenço C.M., Mancardi M.M., Masurel-Paulet A., McInnes I.B., Menezes M.P., Mignot C., O’Sullivan J., Orcesi S., Picco P.P., Riva E., Robinson R.A., Rodriguez D., Salvatici E., Scott C., Szybowska M., Tolmie J.L., Vanderver A., Vanhulle C., Vieira J.P., Webb K., Whitney R.N., Williams S.G., Wolfe L.A., Zuberi S.M., Hur S, & Crow Y.J. (2014). Gain-of-function mutations in IFIH1 cause a spectrum of human disease phenotypes associated with upregulated type I interferon signaling. Nature genetics, 46(5), 503-509.
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5

Whole Genome Sequencing from Blood and Cell Lines

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Genomic DNA extracted from blood was used except for sample SP-226-003 (Mother), whose DNA was extracted from lymphoblastoid cell line. Whole genome amplification was performed on DNA from SP-198-003 (Mother) and 16(1)-Father using the REPLI-g Mini Kit (Qiagen). Exome capture was conducted using the SureSelect Human ALL Exon kits (Agilent Technologies). High-throughput sequencing was performed on a HiSeq2000 (Illumina). Fastq files were processed by our “in-house” pipeline running on the Vital-IT (http://www.vital-it.ch) Center for high-performance computing of the Swiss Institute of Bioinformatics (SIB) [36] (link).
Guipponi M., Santoni F.A., Setola V., Gehrig C., Rotharmel M., Cuenca M., Guillin O., Dikeos D., Georgantopoulos G., Papadimitriou G., Curtis L., Méary A., Schürhoff F., Jamain S., Avramopoulos D., Leboyer M., Rujescu D., Pulver A., Campion D., Siderovski D.P, & Antonarakis S.E. (2014). Exome Sequencing in 53 Sporadic Cases of Schizophrenia Identifies 18 Putative Candidate Genes. PLoS ONE, 9(11), e112745.
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6

Whole Exome Sequencing for Genetic Diagnosis

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Genomic DNA was extracted from lymphocytes from affected individuals and parents by standard techniques. For whole exome analysis, targeted enrichment and sequencing were performed on 3 μg of DNA extracted from the peripheral blood of three individuals (F102, F163, F259). Enrichment was undertaken using the SureSelect Human All Exon kits following the manufacturer’s protocol (Agilent, Santa Clara, CA, USA) and samples were pair-end sequenced on either an IlluminaHiSeq 2000 or SOLiD platform. Sequence data were mapped using BWA (Burrows-Wheeler Aligner) against hg18 (NCBI36) human genome as a reference. Variants were called using SOAPsnp and SOAPindel (from the Short Oligonucleotide Analysis Package) with medium stringency (Supplementary Table 1).
Rice G.I., del Toro Duany Y., Jenkinson E.M., Forte G.M., Anderson B.H., Ariaudo G., Bader-Meunier B., Baildam E.M., Battini R., Beresford M.W., Casarano M., Chouchane M., Cimaz R., Collins A.E., Cordeiro N.J., Dale R.C., Davidson J.E., De Waele L., Desguerre I., Faivre L., Fazzi E., Isidor B., Lagae L., Latchman A.R., Lebon P., Li C., Livingston J.H., Lourenço C.M., Mancardi M.M., Masurel-Paulet A., McInnes I.B., Menezes M.P., Mignot C., O’Sullivan J., Orcesi S., Picco P.P., Riva E., Robinson R.A., Rodriguez D., Salvatici E., Scott C., Szybowska M., Tolmie J.L., Vanderver A., Vanhulle C., Vieira J.P., Webb K., Whitney R.N., Williams S.G., Wolfe L.A., Zuberi S.M., Hur S, & Crow Y.J. (2014). Gain-of-function mutations in IFIH1 cause a spectrum of human disease phenotypes associated with upregulated type I interferon signaling. Nature genetics, 46(5), 503-509.
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7

Comprehensive Cancer Gene Mutation Profiling

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The mutation status of key cancer genes was assessed in all samples using mass array sequencing panels from Sequenom, Inc. (OncoCarta panels I, II and III) and then confirmed by Sanger sequencing of individual exons or whole exome sequencing. Moreover, 64/79 PDX samples were profiled by whole exome sequencing. Exonic regions from Oncotest DNA samples were targeted using Agilent SureSelect Human All Exon kits 38 MB (60 samples) or 51 MB (4 samples). Enriched genomic DNA was sequenced using an Illumina HiSeq-2000 platform in 100 bp paired-end (PE) reads and an expected coverage of ~80×. To remove the mouse stroma content, PE reads that mapped better on the mouse (mm10) than on the human (hg19) genome were discarded from the human mapped read dataset (based on the Burrows-Wheeler Alignment mapping score) using PicardTools. Variants were detected by independently using 3 different variant callers: the GATK’s UnifiedGenotyper, the combination of Samtools mpileup and bcftools caller, and the Freebayes caller. Only variants identified with all 3 tools, showing a minimum number of variant-supporting reads of 3 and a minimum variant frequency of 5 %, were further analyzed.
Maier A., Peille A.L., Vuaroqueaux V, & Lahn M. (2015). Anti-tumor activity of the TGF-β receptor kinase inhibitor galunisertib (LY2157299 monohydrate) in patient-derived tumor xenografts. Cellular Oncology (Dordrecht), 38(2), 131-144.
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8

Exome Sequencing and Variant Analysis

Cited 2 times
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DNA was extracted from EDTA blood using Maxwell 16 Blood DNA Purification Kit (Promega) or PBMC using DNeasy Blood & Tissue Kit (Qiagen). Total of 3 ug of DNA were sheared using E220 focused sonicator (Covaris) and exome libraries were generated using the SureSelect Human All Exon Kits (Agilent) according to manufactures’ protocol. The quality of generated libraries was inspected using Agilent High Sensitivity DNA Kit (Agilent) and quantified using qPCR kit (Agilent). Samples were sequenced on Illumina HiSeq2000 (Illumina) generating 100 bp paired end reads. Sequences were aligned to a human reference genome GRCh37 using bwa v 0.6.1 with default parameters51 (link). Variant calling (Single nucleotide variants and indels) was performed using GATK v.252 (link) and variants were annotated using Annovar53 (link). An in-house custom analysis pipeline was used to filter and prioritize variants based on the likely genetic models and clinical pedigree for patients.
Afzali B., Grönholm J., Vandrovcova J., O’Brien C., Sun H.W., Vanderleyden I., Davis F.P., Khoder A., Zhang Y., Hegazy A.N., Villarino A.V., Palmer I.W., Kaufman J., Watts N.R., Kazemian M., Kamenyeva O., Keith J., Sayed A., Kasperaviciute D., Mueller M., Hughes J.D., Fuss I.J., Sadiyah M.F., Montgomery-Recht K., McElwee J., Restifo N.P., Strober W., Linterman M.A., Wingfield P.T., Uhlig H.H., Roychoudhuri R., Aitman T.J., Kelleher P., Lenardo M.J., O’Shea J.J., Cooper N, & Laurence A.D. (2017). BACH2 immunodeficiency illustrates an association between super-enhancers and haploinsufficiency. Nature immunology, 18(7), 813-823.
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9

Whole-exome Sequencing of Affected Individuals

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Genomic DNA was extracted from lymphocytes from affected individuals by standard techniques. For whole-exome analysis, targeted enrichment and sequencing were performed on DNA extracted from peripheral blood from 19 patients F281, F330, F331 (2 affected individuals), F343, F344, F362 (2 affected individuals), F426 (2 affected individuals), F433, F446, F451, F454 (2 affected individuals), F521 (2 affected individuals), F551 and F564. Enrichment was undertaken using the SureSelect Human All Exon kits following the manufacturer’s protocol (Agilent Technologies), and samples were paired-end sequenced on either an Illumina HiSeq 2000 or SOLiD platform. Sequence data were mapped using BWA (Burrows-Wheeler Aligner) and the hg18 (NCBI36) human genome as a reference. Variants were called using SOAPsnp and SOAPindel (from the Short Oligonucleotide Analysis Package) with medium stringency.
Jenkinson E.M., Rodero M.P., Kasher P.R., Uggenti C., Oojageer A., Goosey L.C., Rose Y., Kershaw C.J., Urquhart J.E., Williams S.G., Bhaskar S.S., O’Sullivan J., Baerlocher G.M., Haubitz M., Aubert G., Barañano K.W., Barnicoat A.J., Battini R., Berger A., Blair E.M., Brunstrom-Hernandez J.E., Buckard J.A., Cassiman D.M., Caumes R., Cordelli D.M., De Waele L.M., Fay A.J., Ferreira P., Fletcher N.A., Fryer A.E., Goel H., Hemingway C.A., Henneke M., Hughes I., Jefferson R.J., Kumar R., Lagae L., Landrieu P.G., Lourenço C.M., Malpas T.J., Mehta S.G., Metz I., Naidu S., Õunap K., Panzer A., Prabhakar P., Quaghebeur G., Schiffmann R., Sherr E.H., Sinnathuray K.R., Soh C., Stewart H.S., Stone J., Van Esch H., Van Mol C.E., Vanderver A., Wakeling E.L., Whitney A., Pavitt G.D., Griffiths-Jones S., Rice G.I., Revy P., van der Knaap M.S., Livingston J.H., O’Keefe R.T, & Crow Y.J. (2016). Mutations in SNORD118 cause the cerebral microangiopathy leukoencephalopathy with calcifications and cysts. Nature genetics, 48(10), 1185-1192.
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10

Trio Whole Exome Sequencing for Genetic Disorders

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Trio whole Exome Sequencing (WES) was performed on trio for individuals 7.10, 7.11, 9.1, 9.2, 9.3, 17.1, 17.2, 17.3, 17.4, 18.3, 18.8, 18.10, and 24.2 by Integragen (Evry, France, 2014). Exons of DNA samples were captured using in-solution enrichment methodology (SureSelect Human All Exon Kits, Agilent, Massy, France) with the company’s biotinylated oligonucleotide probe library (Agilent Human All Exon v5+UTR 75 Mb Kit) and sequenced with an Illumina HISEQ 2000 (Illumina, San Diego, United States) as paired-end 75 bp reads, resulting in an average coverage of 80X.
Bloch-Zupan A., Rey T., Jimenez-Armijo A., Kawczynski M., Kharouf N., Dure-Molla M.D., Noirrit E., Hernandez M., Joseph-Beaudin C., Lopez S., Tardieu C., Thivichon-Prince B., Dostalova T., Macek M J.r., Alloussi M.E., Qebibo L., Morkmued S., Pungchanchaikul P., Orellana B.U., Manière M.C., Gérard B., Bugueno I.M, & Laugel-Haushalter V. (2023). Amelogenesis imperfecta: Next-generation sequencing sheds light on Witkop’s classification. Frontiers in Physiology, 14, 1130175.
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