Sureselectxt human all exon v4

Manufactured by Agilent Technologies

Sourced in United States

The SureSelectXT Human All Exon V4 is a targeted sequencing solution designed for comprehensive coverage of protein-coding regions of the human genome. It provides a reliable and efficient method for capturing and sequencing the human exome.

Automatically generated - may contain errors

Lab products found in correlation

Hiseq 2000, by Illumina (3 mentions) Herculase 2, by Agilent Technologies (2 mentions) Agilent sureselectxt humanallexon v4 50 mb, by Agilent Technologies (2 mentions) Streptavidin coated beads, by Thermo Fisher Scientific (2 mentions) Sureselect library preparation kit, by Agilent Technologies (2 mentions) Taqman snp genotyping assay, by Thermo Fisher Scientific (1 mentions) Abi 3730xl dna analyser, by Thermo Fisher Scientific (1 mentions) Truseq exome enrichment kit, by Agilent Technologies (1 mentions) Hiseq 2000 instrument, by Illumina (1 mentions) Miseq sequencing platform, by Illumina (1 mentions) Viia 7 real time pcr system, by Thermo Fisher Scientific (1 mentions) Truseq sbs kit v3, by Illumina (1 mentions) Truseq sbs kit v5, by Illumina (1 mentions) Dneasy blood tissue kit, by Qiagen (1 mentions) 2100 bioanalyzer, by Agilent Technologies (1 mentions) Hiseq 2000 platform, by Illumina (1 mentions) Solid 5500xl system, by Thermo Fisher Scientific (1 mentions)

Close spelling variants of this product

SureSelectXT Human All Exon v4 Capture Library SureSelectXT Human All Exon V4 kit SureSelectXT Human All Exon V4+UTRs Agilent SureSelectXT Human All Exon V4 kit

9 protocols using sureselectxt human all exon v4

Targeted Exome Sequencing and Validation of CCNF Mutations

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

Exomes were captured using TruSeq Exome Enrichment kit or Agilent SureSelectXT Human All Exon V4. Paired-end sequencing was performed using the Illumina HiSeq2000 instrument.
CCNF exons were sequenced using Fluidigm Access Array target enrichment and the MiSeq sequencing platform (Illumina). Amplicon primers were designed using the Fluidigim D3 Design Studio to produce 150 bp amplicons targeting the exons of CCNF.
Validation and analysis of the CCNF mutations was performed by direct DNA sequencing following PCR amplification of coding exons (NM_001761). PCR products were Sanger sequenced using Big-Dye terminator sequencing and an ABI 3730XL DNA analyser (Applied Biosystems).
SNP genotyping in control individuals was performed using a custom TaqMan SNP genotyping assay according to the manufacturer's instructions (Life Technologies) and analysed using a Viia 7 real-time PCR system (Life Technologies).
Control exome data from 967 neurologically healthy individuals of predominantly Western European descent obtained from the Diamantina Institute, University of Queensland (Diamantina Australian Control Collection).

Williams K.L., Topp S., Yang S., Smith B., Fifita J.A., Warraich S.T., Zhang K.Y., Farrawell N., Vance C., Hu X., Chesi A., Leblond C.S., Lee A., Rayner S.L., Sundaramoorthy V., Dobson-Stone C., Molloy M.P., van Blitterswijk M., Dickson D.W., Petersen R.C., Graff-Radford N.R., Boeve B.F., Murray M.E., Pottier C., Don E., Winnick C., McCann E.P., Hogan A., Daoud H., Levert A., Dion P.A., Mitsui J., Ishiura H., Takahashi Y., Goto J., Kost J., Gellera C., Gkazi A.S., Miller J., Stockton J., Brooks W.S., Boundy K., Polak M., Muñoz-Blanco J.L., Esteban-Pérez J., Rábano A., Hardiman O., Morrison K.E., Ticozzi N., Silani V., de Belleroche J., Glass J.D., Kwok J.B., Guillemin G.J., Chung R.S., Tsuji S., Brown RH J.r., García-Redondo A., Rademakers R., Landers J.E., Gitler A.D., Rouleau G.A., Cole N.J., Yerbury J.J., Atkin J.D., Shaw C.E., Nicholson G.A, & Blair I.P. (2016). CCNF mutations in amyotrophic lateral sclerosis and frontotemporal dementia. Nature Communications, 7, 11253.

+ Open protocol

+ Expand

Whole Exome Sequencing Library Prep

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

Genomic DNA (2μg) was captured by hybridization (Agilent SureSelect XT HumanAllExon V4). PCR amplification of the libraries was carried out for 6 cycles (pre-capture) and 10 cycles (post capture). Barcoded samples were run on a Hiseq 2000 in a 75bp/75bp Paired end run (Illumina TruSeq SBS Kit v3). The average number of read pairs per sample was 92 million, the average duplication rate was 4.9%, and 94.2% of the targeted region was covered at 30x.

Jacob L.S., Vanharanta S., Obenauf A.C., Pirun M., Viale A., Socci N.D, & Massagué J. (2015). Metastatic competence can emerge with selection of pre-existing oncogenic alleles without a need of new mutations. Cancer research, 75(18), 3713-3719.

+ Open protocol

+ Expand

Targeted Genomic Enrichment and Whole Exome Sequencing for NSHL and USH

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

Targeted genomic enrichment with massively parallel sequencing (TGE+MPS) using the OtoSCOPE^® platform (version 7) was performed in one affected person from families L-1644, 51550, Trio-A and Trio-B to screen all known genes implicated in NSHL and USH for pathogenic and likely pathogenic variants as previously described [17 ,18 ]. Whole exome capture was performed with the Agilent SureSelectXT Human All Exon V4 (Agilent Technologies, Santa Clara, CA) on one affected individual from families L-3156 and 661 as previously described [19 –22 ]. Enriched libraries were sequenced on the Illumina HiSeq 2000 (Illumina, Inc., San Diego, CA) using 100bp paired-end reads.

Booth K.T., Kahrizi K., Babanejad M., Daghagh H., Bademci G., Arzhangi S., Zareabdollahi D., Duman D., El-Amraoui A., Tekin M., Najmabadi H., Azaiez H, & Smith R.J. (2018). Variants in CIB2 cause DFNB48 and not USH1J. Clinical genetics, 93(4), 812-821.

+ Open protocol

+ Expand

Exome sequencing for variant identification

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

Exome sequencing was performed on patient and both parents using the Agilent SureSelectXT HumanAllExon V4 (50 Mb) (Agilent Technologies). Briefly, 3 μg of genomic DNA was sheared in 130 μl of low TE buffer to a peak size of 150–200 bp using Covaris E220, and then purified with AmpPure XP beads to remove fragments less than 100 bp. The purified DNA fragments were then subjected to Agilent SureSelect Library preparation Kit, ILM, to be end-repaired, A-tailed, and ligated to indexing-specific paired-end adaptor. The adapter-ligated libraries were amplified for five cycles using Herculase II (Agilent Technologies). Amplified Pre-capture libraries (750 ng) were concentrated in 3 μl and hybridized to the target specific baits (SureSelectXT Human All Exon V4; Agilent Technologies) according to the manufacturer’s recommendations. Hybridized material was captured using streptavidin-coated beads (Invitrogen, Paisley, UK) and amplified for 10 cycles. Captured libraries were pooled in pairs and paired-end sequenced on one lane of the Illumina HiSeq 2000 at the Stanford Center for Genomics and Personalized Medicine.

Kodo K., Ong S.G., Jahanbani F., Termglinchan V., Hirono K., InanlooRahatloo K., Ebert A.D., Shukla P., Abilez O.J., Churko J.M., Karakikes I., Jung G., Ichida F., Wu S.M., Snyder M.P., Bernstein D, & Wu J.C. (2016). iPSC-derived cardiomyocytes reveal abnormal TGFβ signaling in left ventricular non-compaction cardiomyopathy. Nature cell biology, 18(10), 1031-1042.

+ Open protocol

+ Expand

Whole Exome Sequencing of Matched Tumor and Normal Samples

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

Four FFPE and two frozen tumors with matched normal tissue underwent DNA extraction with the DNeasy Blood & Tissue Kit (Qiagen, Valencia, CA) following manufacturer’s instructions. These six samples were subjected to whole exome sequencing. Between 1.5 and 2 μg of genomic DNA was captured by hybridization using the SureSelect XT Human All Exon V4 (Agilent Technologies). Samples were prepared according to the manufacturer’s instructions.
PCR amplification of the libraries was carried out for 6 cycles in the pre-capture step and for 10 cycles post-capture. Samples were barcoded and run on a HiSeq 2500 in 100 bp paired-end runs using the TruSeq SBS Kit v5 (Illumina). The average number of read pairs per sample was 63 million, the average duplication rate was 12%, and 94.4% of the targeted regions were sequenced at 30X or higher coverage. Sequencing data is available on the publicly accessible cBio Portal for Cancer Genomics.^{13 (link)}

Al-Ahmadie H.A., Iyer G., Lee B.H., Scott S.N., Mehra R., Bagrodia A., Jordan E.J., Gao S.P., Ramirez R., Cha E.K., Desai N.B., Zabor E.C., Ostrovnaya I., Gopalan A., Chen Y.B., Fine S.W., Tickoo S.K., Gandhi A., Hreiki J., Viale A., Arcila M.E., Dalbagni G., Rosenberg J.E., Bochner B.H., Bajorin D.F., Berger M.F., Reuter V.E., Taylor B.S, & Solit D.B. (2016). Frequent somatic CDH1 loss-of-function mutations in plasmacytoid-variant bladder cancer. Nature genetics, 48(4), 356-358.

+ Open protocol

+ Expand

Whole Exome Sequencing Workflow

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

Quality control was applied to DNA samples (3–5 µg needed per reaction at a concentration of 50–300 ng/µl measured by PicoGreen, A260/280 = 1.7–2, integrity check by agarose electrophoresis). The whole exome was characterized by using the HiSeq2000 platform (Illumina, San Diego, CA) and SureSelectXT Human All Exon V4 for exon enrichment (Agilent, Santa Clara, CA). Initial DNA shearing was performed using the Covaris S2 equipment, achieving an optimal range in the size distribution of fragments. Library size and concentration were checked by capillary electrophoresis (Bioanalyzer 2100; Agilent). Adapters with different indexes for each sample were incorporated during enrichment, allowing samples to be multiplexed before sequencing. After enrichment, the indexed libraries were pooled and massively parallel sequenced using a paired-end 2 × 75–base pair (bp) read length protocol.

Esteban-Jurado C., Vila-Casadesús M., Garre P., Lozano J.J., Pristoupilova A., Beltran S., Muñoz J., Ocaña T., Balaguer F., López-Cerón M., Cuatrecasas M., Franch-Expósito S., Piqué J.M., Castells A., Carracedo A., Ruiz-Ponte C., Abulí A., Bessa X., Andreu M., Bujanda L., Caldés T, & Castellví-Bel S. (2014). Whole-exome sequencing identifies rare pathogenic variants in new predisposition genes for familial colorectal cancer. Genetics in Medicine, 17(2), 131-142.

+ Open protocol

+ Expand

Exome Sequencing for Genetic Diagnosis

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

Sequencing of the exome was performed after the participants were counseled by a clinical geneticist at one of the medical university centers located in the Netherlands. DNA was extracted from peripheral blood using standard procedures. In all 266 cases, exome enrichment was performed using Agilent's SureSelect XT Human All Exon V4 (Agilent Technologies, Santa Clara, CA, USA). For 48 cases, next-generation sequencing was performed using a 5500xl SOLiD System (Life Technologies) and data analysis was performed as described previously.^{17 (link)} For 218 cases, next-generation sequencing was performed using a Illumina HiSeq2000TM sequencer at BGI-Europe (Copenhagen, Denmark). Read alignment to the human reference genome (GrCH37/hg19) and variant calling was performed at BGI using BWA and GATK software, respectively. For all cases, variant annotation was performed using a custom designed in-house annotation and variant prioritization pipeline. Copy number analysis was performed in all cases using CoNIFER 0.2.0 software and annotation was performed using an in-house strategy.

Haer-Wigman L., van Zelst-Stams W.A., Pfundt R., van den Born L.I., Klaver C.C., Verheij J.B., Hoyng C.B., Breuning M.H., Boon C.J., Kievit A.J., Verhoeven V.J., Pott J.W., Sallevelt S.C., van Hagen J.M., Plomp A.S., Kroes H.Y., Lelieveld S.H., Hehir-Kwa J.Y., Castelein S., Nelen M., Scheffer H., Lugtenberg D., Cremers F.P., Hoefsloot L, & Yntema H.G. (2017). Diagnostic exome sequencing in 266 Dutch patients with visual impairment. European Journal of Human Genetics, 25(5), 591-599.

+ Open protocol

+ Expand

Exome sequencing for variant identification

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

+ Open protocol

+ Expand

Whole Exome Sequencing of Tumor Samples

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

gDNA isolated from each sample were normalized to 1-3 μg. Libraries were prepared from using the Agilent SureSelectXT Target Enrichment Library protocol and Agilent SureSelectXT Human All Exon v4 enrichment capture library. The libraries were prepared using 6 pre-capture and 12 post-capture PCR cycles. Captured Whole Exome final libraries passing the final QC step were normalised to 2nM and pooled for sequencing on the HiSeq 2500 instrument. Dual HiSeq SBS v4 runs at 101bp paired-end reads generated the data for analysis. Target coverage was 400-500x for the tumour regions and 100-200x for the associated normal.

Turajlic S., Xu H., Litchfield K., Rowan A., Horswell S., Chambers T., O’Brien T., Lopez J.I., Watkins T.B., Nicol D., Stares M., Challacombe B., Hazell S., Chandra A., Mitchell T.J., Au L., Eichler-Jonsson C., Jabbar F., Soultati A., Chowdhury S., Rudman S., Lynch J., Fernando A., Stamp G., Nye E., Stewart A., Xing W., Smith J.C., Escudero M., Huffman A., Matthews N., Elgar G., Phillimore B., Costa M., Begum S., Ward S., Salm M., Boeing S., Fisher R., Spain L., Navas C., Grönroos E., Hobor S., Sharma S., Aurangzeb I., Lall S., Polson A., Varia M., Horsfield C., Fotiadis N., Pickering L., Schwarz R.F., Silva B., Herrero J., Luscombe N.M., Jamal-Hanjani M., Rosenthal R., Birkbak N.J., Wilson G.A., Pipek O., Ribli D., Krzystanek M., Csabai I., Szallasi Z., Gore M., McGranahan N., Van Loo P., Campbell P., Larkin J, & Swanton C. (2018). Deterministic Evolutionary Trajectories Influence Primary Tumor Growth: TRACERx Renal. Cell, 173(3), 595-610.e11.

+ 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!