Sureselect xt human all exon v5 kit

Manufactured by Agilent Technologies

Sourced in United States

The SureSelect XT Human All Exon V5 kit is a targeted enrichment solution for whole exome sequencing. It is designed to capture all human protein-coding exons, including those in the CCDS, RefSeq, and GENCODE databases. The kit utilizes in-solution hybridization technology to selectively enrich for the targeted regions of the human genome.

Automatically generated - may contain errors

Lab products found in correlation

Hiseq 2500 system, by Illumina (7 mentions) Hiseq 2000, by Illumina (5 mentions) Hiseq 2500, by Illumina (5 mentions) Hiseq 2000 platform, by Illumina (4 mentions) Truseq rapid sbs kit, by Illumina (4 mentions) Real time analysis software sequence pipeline, by Illumina (3 mentions) Truseq rapid pe cluster kit, by Illumina (3 mentions) Qiaamp dna mini kit, by Qiagen (2 mentions) Hiseq 2500 sequencer, by Illumina (2 mentions) Qiaamp dna blood mini kit, by Qiagen (2 mentions) Dna blood mini kit, by Tiangen Biotech (2 mentions) Hiseq x10, by Illumina (2 mentions) Hiseq x10 platform, by Illumina (2 mentions) Sureselect xt reagent, by Agilent Technologies (1 mentions) Nucleospin tissue kit, by Macherey-Nagel (1 mentions) S2 sonicator, by Covaris (1 mentions) Casava software v1, by Illumina (1 mentions) Wizard genomic dna purification kit, by Promega (1 mentions) Hiseq pe cluster kit v4, by Illumina (1 mentions) Hiseq sbs kit v4, by Illumina (1 mentions)

37 protocols using sureselect xt human all exon v5 kit

Whole Exome Sequencing of hiPSC Lines

Cited 2 times

Check if the same lab product or an alternative is used in the 5 most similar protocols

Whole exome sequencing was performed by Takara Bio Inc. Genomic DNA was isolated from hiPSCs using a NucleoSpin Tissue Kit (Macherey-Nagel). DNA (3 μg) was sheared into peak fragment size of 300 bp using a Covaris S2 sonicator (Covaris) and used to conduct end-repair, A-addition, and adaptor ligation with SureSelect XT reagents (Agilent Technologies). Target sequences were enriched with SureSelect XT Human All Exon Kit V5 (Agilent Technologies). Sequencing was performed on a HiSeq 2500 System (Illumina) using a 100 bp paired-end protocol. More than 15 Gbp of read data were generated for each sample of hiPSC line. After trimming the adaptor sequences and quality filtering using Trimmomatic [16 (link)], the reads were mapped to the reference genome (hg 19) using BWA-MEM [17 ], followed by duplicate read removal. Genomic variants, including SNV and short indels, were annotated using SnpEff [18 (link)], Human genetic variation database (HGVD) [19 (link)] and the Exome Aggregation Consortium (ExAC) database [20 (link)], and related to a gene list including the Cancer Gene Census provided in the COSMIC database (S2 Table). The NCBI Sequence Read Archive (SRA) accession number for the whole exome sequencing data is SRP134676.

Yasuda S., Kusakawa S., Kuroda T., Miura T., Tano K., Takada N., Matsuyama S., Matsuyama A., Nasu M., Umezawa A., Hayakawa T., Tsutsumi H, & Sato Y. (2018). Tumorigenicity-associated characteristics of human iPS cell lines. PLoS ONE, 13(10), e0205022.

+ Open protocol

+ Expand

Whole Exome Sequencing from Blood

Check if the same lab product or an alternative is used in the 5 most similar protocols

Blood was drawn in EDTA tubes, and DNA was extracted from blood samples using Wizard Genomic DNA Purification Kit (Promega). WES was carried out by using 1 µg of genomic DNA per sample. Genomic DNA was fragmented into a library of small segments that can be uniformly and accurately sequenced in millions of parallel reactions. Exomes were captured using a commercial enrichment kit (Agilent SureSelectXT Human All Exon KitV5). Uncaptured DNA was washed off. Bounded DNA was clonally amplified and sequenced on Illumina HiSeq2000 to generate paired-end, 100 bp reads. Real-time image analysis and base calling were performed by sequence control software realtime analysis and CASAVA software V. 1.8 (Illumina). We achieved a mean coverage of 61× without duplicates, with 81% of target covered at least 10×.

Basha M., Demeer B., Revencu N., Helaers R., Theys S., Bou Saba S., Boute O., Devauchelle B., Francois G., Bayet B, & Vikkula M. (2018). Whole exome sequencing identifies mutations in 10% of patients with familial non-syndromic cleft lip and/or palate in genes mutated in well-known syndromes. Journal of medical genetics, 55(7).

+ Open protocol

+ Expand

Whole-Exome Sequencing of Lung Tumors

Check if the same lab product or an alternative is used in the 5 most similar protocols

Exomes of 11 formalin-fixed and paraffin-embedded lung tumor tissues and paired blood samples were captured using the SureSelectXT Human All Exon V5 kit (5190-6208, Agilent, Santa Clara, CA, USA). Sequencing libraries were constructed for the HiSeq2500 system (Illumina, San Diego, CA, USA) and sequenced using the 100-bp paired-end mode of the Hiseq PE Cluster kit v4 (PE-401-4001, Illumina, San Diego, CA, USA), and the Hiseq SBS kit v4 (PE-401-4003, Illumina, San Diego, CA, USA). Exome-sequencing reads were aligned to the hg38 reference genome using BWA-0.7.17. Putative duplications were marked by Picard (version picard-tools-2.18.2-SNAPSHOT). Sites potentially harboring small insertions or deletions were realigned, and recalibrated by employing GATK (v4.0.5.1) modules with known variant sites identified from phase 3 of the 1000 Genomes Project and dbSNP-151. GATK4 Mutect2 was used to call somatic mutations. The whole-exome sequencing (WES) coverage used was 100× for the tumors and 50× for the paired blood samples.

Kim N., Kim H.K., Lee K., Hong Y., Cho J.H., Choi J.W., Lee J.I., Suh Y.L., Ku B.M., Eum H.H., Choi S., Choi Y.L., Joung J.G., Park W.Y., Jung H.A., Sun J.M., Lee S.H., Ahn J.S., Park K., Ahn M.J, & Lee H.O. (2020). Single-cell RNA sequencing demonstrates the molecular and cellular reprogramming of metastatic lung adenocarcinoma. Nature Communications, 11, 2285.

+ Open protocol

+ Expand

Whole-Exome Sequencing of Bulk Tumor and Blood

Cited 4 times

Check if the same lab product or an alternative is used in the 5 most similar protocols

WES and data processing were performed as previously described [16 (link)]. Briefly, genomic DNA was extracted from the bulk tumor and whole blood using the QIAamp® DNA mini kit (Qiagen, Germantown, MD, USA) and QIAamp DNA blood maxi kit (Qiagen), respectively. Exome sequences were enriched using the SureSelect XT Human All Exon V5 kit (Agilent, Santa Clara, CA, USA) and sequenced in the 100-bp paired-end mode on the HiSeq 2500 system (Illumina, San Diego, CA, USA). The tumor and matched blood DNA were sequenced to 100× and 50× coverages, respectively. The sequencing reads were mapped to the human genome build hg19/GRCh37 with BWA-0.7.10 [27 (link)]. Aligned reads were realigned for known insertions or deletions, and their base-quality scores were recalibrated using GATK-3.2 modules with known variant sites identified from phase I of the 1000 Genomes Project (http://www.1000genomes.org/) and dbSNP-137 (http://www.ncbi.nlm.nih.gov/SNP/). MuTect-1.1.5 was used with default parameters to detect somatic SNVs, and mutations were annotated using Oncotator [28 (link)]. Additionally, the Control-FREEC package [29 (link)] was used to detect copy-number variations (CNVs), and CNVs with a P < 0.05 (Wilcoxon rank-sum test) were obtained. Druggable targeting genetic alterations were annotated from the OncoKB database (http://oncokb.org).

Lee H.W., Chung W., Lee H.O., Jeong D.E., Jo A., Lim J.E., Hong J.H., Nam D.H., Jeong B.C., Park S.H., Joo K.M, & Park W.Y. (2020). Single-cell RNA sequencing reveals the tumor microenvironment and facilitates strategic choices to circumvent treatment failure in a chemorefractory bladder cancer patient. Genome Medicine, 12, 47.

+ Open protocol

+ Expand

Whole Exome Sequencing and CNV Detection

Cited 2 times

Check if the same lab product or an alternative is used in the 5 most similar protocols

Genomic DNA fragments were enriched using the Agilent SureSelect XT Human All Exon V5 kit. After enrichment, DNA libraries were sequenced with the HiSeq 2000 platform according to the manufacturer’s instructions (Illumina, San Diego, CA) with an average on-target sequencing depth of 120 × . More information about sequencing and data analysis, particularly of single nucleotide variations, can be found in a previous study [14 (link)]. The pipeline for clinical NGS-involved CNV detection (PICNIC) was used to detect CNVs from whole-exome sequencing (WES) data. PICNIC filters out high-frequency gene deletions/duplications. The detailed process for CNV analysis was presented in published studies [15 , 16 (link)]. CNVs were further verified by performing comparative genomic hybridization (CGH) or multiplex ligation-dependent probe amplification (MLPA).

Sun B., Yang M., Hou J., Wang W., Ying W., Hui X., Zhou Q., Yao H., Sun J, & Wang X. (2022). Chromosomal abnormalities related to fever of unknown origin in a Chinese pediatric cohort and literature review. Orphanet Journal of Rare Diseases, 17, 292.

+ Open protocol

+ Expand

Exome Sequencing of PDOs and Blood

Check if the same lab product or an alternative is used in the 5 most similar protocols

Sequencing libraries were prepared from > = 500 ng DNA from PDOs and matched blood using the Agilent SureSelectXT Human All Exon v5 kit according to the manufacturer’s protocol. Paired-end sequencing was performed on an Illumina HiSeq2500 with a target depth of 100x.

Newey A., Griffiths B., Michaux J., Pak H.S., Stevenson B.J., Woolston A., Semiannikova M., Spain G., Barber L.J., Matthews N., Rao S., Watkins D., Chau I., Coukos G., Racle J., Gfeller D., Starling N., Cunningham D., Bassani-Sternberg M, & Gerlinger M. (2019). Immunopeptidomics of colorectal cancer organoids reveals a sparse HLA class I neoantigen landscape and no increase in neoantigens with interferon or MEK-inhibitor treatment. Journal for Immunotherapy of Cancer, 7, 309.

+ Open protocol

+ Expand

Whole-exome sequencing of brain and fibroblasts

Check if the same lab product or an alternative is used in the 5 most similar protocols

Pulverized brain cortex (0.98 g) and fibroblasts were provided by the Lieber Institute for Brain Development, (Baltimore, MD). Fibroblasts were cultured in fibroblast culture media containing MEM (Gibco), 20% FBS (Gibco), and 1× Pen/Strep (Gibco). Confluent fibroblasts were harvested and gDNA was extracted from pulverized brain and fibroblast samples using Qiagen Maxiprep kits according to the protocols provided by the manufacturer. Genomic DNA samples were prepared for whole-exome sequencing using the Agilent SureSelect XT Human All Exon v.5 kit. Then, 125 bp paired-end reads (median insert size ~ 210 bp) were generated using the Illumina HiSeq X 2500 platform. The sequencing experiments were designed to yield three datasets of ~ 100× coverage on each sample, sequencing completed at the New York Genome Center, NY.

Wang Y., Bae T., Thorpe J., Sherman M.A., Jones A.G., Cho S., Daily K., Dou Y., Ganz J., Galor A., Lobon I., Pattni R., Rosenbluh C., Tomasi S., Tomasini L., Yang X., Zhou B., Akbarian S., Ball L.L., Bizzotto S., Emery S.B., Doan R., Fasching L., Jang Y., Juan D., Lizano E., Luquette L.J., Moldovan J.B., Narurkar R., Oetjens M.T., Rodin R.E., Sekar S., Shin J.H., Soriano E., Straub R.E., Zhou W., Chess A., Gleeson J.G., Marquès-Bonet T., Park P.J., Peters M.A., Pevsner J., Walsh C.A., Weinberger D.R., Vaccarino F.M., Moran J.V., Urban A.E., Kidd J.M., Mills R.E, & Abyzov A. (2021). Comprehensive identification of somatic nucleotide variants in human brain tissue. Genome Biology, 22, 92.

+ Open protocol

+ Expand

Whole-Exome Sequencing of Classical Hodgkin Lymphoma

Cited 2 times

Check if the same lab product or an alternative is used in the 5 most similar protocols

Two EBV-negative classical Hodgkin lymphoma cases were examined by whole-exome sequencing. Whole-exome libraries were prepared from genomic DNAs of FACS-purified Hodgkin/Reed–Sternberg cells (CD3− CD19− CD30+ CD40+), from two classical Hodgkin lymphoma patients, and matched T cells (CD19− CD3+ CD4+ CD8+) as normal controls, using SureSelectXT Human All Exon V5 kit (Agilent Technologies, Santa Clara, CA). The prepared whole-exome libraries were sequenced by 100-bp paired-end reads on HiSeq2500 Sequencer (Illumina, San Diego, CA). Sequence alignment and mutation calling were performed using our in-house pipelines described previously [16 (link)]. Briefly, the sequence reads were mapped to the human reference genome GRCh37/hg19 using Burrows–Wheeler Aligner (v0.7.10) [17 (link)]. Possible PCR duplicates were removed using Picard tool (http://broadinstitute.github.io/picard/), and reads with a mapping quality of <30 and with mismatches of more than 5% of sequence reads were also excluded. Somatic variants (single-nucleotide variations, and insertion/deletions) were called with the following parameters, (i) base quality of ≥15, (ii) sequence depth of ≥10, (iii) variant depth of ≥2, (iv) variant frequency in tumor of ≥10%, (v) variant frequency in normal of <2%, and (vi) Fisher P value of <0.05. SNVs and indels were annotated based on RefGene using ANNOVAR [18 (link)].

Van Slambrouck C., Huh J., Suh C., Song J.Y., Menon M.P., Sohani A.R., Duffield A.S., Goldberg R.C., Dama P., Kiyotani K., Godfrey J., Fitzpatrick C., Kline J., Smith S.M., Jaffe E.S., Hartmann S, & Venkataraman G. (2019). Diagnostic utility of STAT6YE361 expression in classical Hodgkin lymphoma and related entities. Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc, 33(5), 834-845.

+ Open protocol

+ Expand

Whole Exome Sequencing Data Analysis

Cited 2 times

Check if the same lab product or an alternative is used in the 5 most similar protocols

Germline WES data were available from previous studies [12 (link),21 (link),31 (link)]. WES was performed in tumor samples of selected patients using the HiSeq2000 platform (Illumina, San Diego, CA, USA) and SureSelectXT Human All Exon v5 kit (Agilent, Santa Clara, CA, USA) for exon enrichment. Indexed libraries were pooled and massively parallel-sequenced using a paired-end 2 × 75 bp read length protocol.
The quality control of sequencing data was made in all samples previous to their analysis using the Real-Time Analysis software sequence pipeline (Illumina). Additionally, the proportion of all shared exome regions sequenced with a coverage ≥ 10× was evaluated for tumor samples. A good ratio of shared regions with high coverage (≥ 70%) was expected in good-quality samples, whereas low-quality ones were characterized by a significant drop in this percentage.
WES data analysis was performed in accordance with the workflow displayed in Figure 2. The Burrows–Wheeler Aligner (BWA-MEM algorithm) was used for read mapping to the human reference genome (build hs37d5, based on NCBI GRCh37) [43 (link)]. PCR duplicates were discarded using the MarkDuplicates tool from Picard, and then indel realignment and base quality score recalibration were performed with the Genome Analysis Toolkit (GATK, Broad Institute, Cambridge, USA) [44 (link)].

Díaz-Gay M., Franch-Expósito S., Arnau-Collell C., Park S., Supek F., Muñoz J., Bonjoch L., Gratacós-Mulleras A., Sánchez-Rojas P.A., Esteban-Jurado C., Ocaña T., Cuatrecasas M., Vila-Casadesús M., Lozano J.J., Parra G., Laurie S., Beltran S., Castells A., Bujanda L., Cubiella J., Balaguer F, & Castellví-Bel S. (2019). Integrated Analysis of Germline and Tumor DNA Identifies New Candidate Genes Involved in Familial Colorectal Cancer. Cancers, 11(3), 362.

+ Open protocol

+ Expand

Whole Exome Sequencing for ABCB11 Disorders

Check if the same lab product or an alternative is used in the 5 most similar protocols

Whole exome sequencing was performed on patients with ABCB11 spectrum liver disorders to analyze multiple candidate genes simultaneously. Targeted exonic regions were captured with the Agilent SureSelect XT Human All Exon v5 kit (Agilent Technologies, Santa Clara, CA, USA). Exome sequencing was performed on an Illumina HiSeq-2000 (Illumina, San Diego, CA, USA) platform with 100-bp paired-end runs at an average mean target depth of 100× coverage. Rare or novel mutations were prioritized.

Lee S.J., Kim J.E., Choe B.H., Seo A.N., Bae H.I, & Hwang S.K. (2017). Early Diagnosis of ABCB11 Spectrum Liver Disorders by Next Generation Sequencing. Pediatric Gastroenterology, Hepatology & Nutrition, 20(2), 114-123.

+ Open protocol

+ Expand

About PubCompare

Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.

We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.

However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.

Ready to get started?

Revolutionizing how scientists
search and build protocols!