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Sureselect human all exon v4

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The SureSelect Human All Exon V4 is a targeted enrichment solution designed for whole exome sequencing. It captures the protein-coding regions of the human genome, known as the exome, to enable efficient and cost-effective sequencing of the most biologically relevant portions of the genome.

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Lab products found in correlation

Hiseq 2000, by Illumina (17 mentions) Hiseq 2500, by Illumina (3 mentions) Seqcap ez human exome library v3, by Agilent Technologies (2 mentions) Agilent human exon v3 exon 50mb, by Agilent Technologies (2 mentions) Repli g kit, by Qiagen (2 mentions) Sureselect human all exon 50 m, by Agilent Technologies (2 mentions) Nimblegen seqcap ez exome v2, by Roche (2 mentions) Human all exon v4 utr, by Agilent Technologies (2 mentions) Hiseq platform, by Illumina (2 mentions) Gaiix, by Illumina (1 mentions) Dynabeads myone streptavidin t1, by Thermo Fisher Scientific (1 mentions) Ampure xp reagent, by Agilent Technologies (1 mentions) Agilent 2100 bioanalyzer, by Agilent Technologies (1 mentions) Qiaamp dna mini kit, by Qiagen (1 mentions) Hiseq 2000 platform, by Illumina (1 mentions) Truseq sbs kit v5, by Illumina (1 mentions) Dneasy blood and tissue kit, by Qiagen (1 mentions) Casava 1.6 pipeline, by Illumina (1 mentions) Nextera rapid capture exome, by Illumina (1 mentions) Sure select xt human all exon 50mb, by Agilent Technologies (1 mentions)

35 protocols using sureselect human all exon v4

1

Whole-Exome Sequencing of Metastatic Breast Cancer

Cited 6 times
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DNA from MBC and matched germline of the 35 cases was subjected to whole-exome capture using the SureSelect Human All Exon v4 (Agilent) platform and to massively parallel sequencing on an Illumina GAIIx or HiSeq 2000 at the Institute of Cancer Research, UK (GAIIx) or Memorial Sloan Kettering Cancer Center (MSKCC) Integrated Genomics Operation (IGO, HiSeq 2000) following validated protocols (22 (link)). Paired-end 75/76/101-bp reads were generated (Supplementary Table S1). Sequencing data have been deposited in the NCBI Sequence Read Archive under the accession SRP073692.
Whole-exome sequencing analysis was performed as described (22 (link)) with modifications. CNAs were identified using FACETS (23 (link)) and the cancer cell fraction (CCF) of each mutation using ABSOLUTE (v1.0.6) (24 (link)). Mutations were classified as likely pathogenic, of indeterminate pathogenicity or likely passenger based on mutation function predictors (25 (link)–28 (link)), cancer gene lists (29 (link)–31 (link)), hotspot residues (32 (link)) and loss of heterozygosity status (Supplementary Methods).
Ng C.K., Piscuoglio S., Geyer F.C., Burke K.A., Pareja F., Eberle C.A., Lim R.S., Natrajan R., Riaz N., Mariani O., Norton L., Vincent-Salomon A., Wen Y.H., Weigelt B, & Reis-Filho J.S. (2017). The Landscape of Somatic Genetic Alterations in Metaplastic Breast Carcinomas. Clinical cancer research : an official journal of the American Association for Cancer Research, 23(14), 3859-3870.
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2

Whole Exome Sequencing of Tumor Relapse

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Whole exome capture was performed on DNA isolated from 48-paired diagnosis and relapse patient samples and patient-matched germline samples. Germline DNA (lymphocytes) was subjected to whole genome amplification (repli-g kit; Qiagen) in 25 patients due to limited materials (see Supplementary Table 2). To obtain sufficient quantities of DNA from the remaining samples, T cells were expanded ex vivo (detailed under Sample collection and processing). DNA was extracted using standard techniques. Libraries were prepared per manufacturer’s recommendation using NimbleGen SeqCap EZ Human Exome Library v3.0, Agilent Human Exon V3 (Exon 50Mb), or Agilent SureSelect Human All Exon V4 (51 MB; see Supplementary Table 2 for specification of kit use per patient tumor and germline samples) and sequenced at a minimum of 50bp single-read sequencing on a HiSeq 2000 (Illumina, Inc.) to a mean coverage per base of 73X. See Supplementary Table 4 for sequencing statistics.
Li S., Garrett-Bakelman F.E., Chung S.S., Sanders M.A., Hricik T., Rapaport F., Patel J., Dillon R., Vijay P., Brown A.L., Perl A.E., Cannon J., Bullinger L., Luger S., Becker M., Lewis I.D., To L.B., Delwel R., Löwenberg B., Döhner H., Döhner K., Guzman M.L., Hassane D.C., Roboz G.J., Grimwade D., Valk P.J., D’Andrea R.J., Carroll M., Park C.Y., Neuberg D., Levine R., Melnick A.M, & Mason C.E. (2016). Distinct evolution and dynamics of epigenetic and genetic heterogeneity in acute myeloid leukemia. Nature medicine, 22(7), 792-799.
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3

Transcriptome Analysis of Metastatic Prostate Cancer

Cited 2 times
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The exome-capture RNA-seq data from 47 mCRPC samples in the SU2C cohort was downloaded from dbGaP (dbGaP accession pht004946.v1.p1) [28 (link)]. The cDNA libraries for this RNA-seq dataset were prepared using Agilent SureSelect Human All Exon V4 platform, omitting the polyA selection step [28 (link)]. For VCaP and 22Rv1 cells, the ribodepletion-seq dataset was downloaded from GEO (accession: GSE92574), and the polyA-seq dataset was downloaded from the CCLE–PRAD project in the GDC legacy archive. The raw data for the AGO-PAR-CLIP dataset [38 (link)] was downloaded from the NIH SRA (bioproject accession: SRP075075), and the processed AGO-PAR-CLIP atlas files were downloaded from https://www.synapse.org/#!Synapse:syn5479902. Splicing junction analysis was performed for these datasets as described below.
Cao S., Ma T., Ungerleider N., Roberts C., Kobelski M., Jin L., Concha M., Wang X., Baddoo M., Nguyen H.M., Corey E., Fazli L., Ledet E., Zhang R., Silberstein J.L., Zhang W., Zhang K., Sartor O., Dong X., Flemington E.K, & Dong Y. (2019). Circular RNAs add diversity to androgen receptor isoform repertoire in castration-resistant prostate cancer. Oncogene, 38(45), 7060-7072.
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4

Whole Exome Sequencing of Tumor Samples

Cited 2 times
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DNA extracted from frozen biopsies of the primary tumors, metastases and germline were subjected to exome capture using SureSelect Human All Exon v4 (Agilent) and to massively parallel sequencing on an Illumina HiSeq 2000 following validated protocols (19 (link)) (Supplementary Table S2, Supplementary Methods). WES data have been deposited in the Sequence Read Archive (SRP055001).
WES data processing was performed as previously described (19 (link)). Somatic single nucleotide variants (SNVs) were identified using MuTect (v1.0) (20 (link)) and somatic small insertions and deletions (indels) were identified using GATK (v2.7.4) (21 (link)) and the micro-assembly-based Scalpel (v0.1.1) (22 (link)) (Supplementary Methods).
Ng C.K., Bidard F.C., Piscuoglio S., Geyer F.C., Lim R.S., de Bruijn I., Shen R., Pareja F., Berman S.H., Wang L., Pierga J.Y., Vincent-Salomon A., Viale A., Norton L., Sigal B., Weigelt B., Cottu P, & Reis-Filho J.S. (2017). Genetic Heterogeneity in Therapy-Naïve Synchronous Primary Breast Cancers and Their Metastases. Clinical cancer research : an official journal of the American Association for Cancer Research, 23(15), 4402-4415.
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5

Whole Exome Sequencing and Variant Analysis

Cited 3 times
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Exon enrichment was performed using Agilent SureSelect Human All Exon V4. Paired-end sequencing was performed on the Illumina HiSeq2000 platform using TruSeq v3 chemistry. Read files (Fastq) were generated from the sequencing platform via the manufacturer’s proprietary software. Reads were mapped using the Burrows-Wheeler Aligner48 (link) and local realignment of the mapped reads around potential insertion/deletion (indel) sites was carried out with the GATK version 1.649 (link). Duplicate reads were marked using Picard version 1.62 (http://picard.sourceforge.net). Additional BAM file manipulations were performed with Samtools (0.1.18)50 (link). SNP and indel variants were called using the GATK Unified Genotyper for each sample. SNP novelty was determined against dbSNP138. Novel variants were analyzed by a range of web-based bioinformatics tools using the EnsEMBL SNP Effect Predictor (http://www.ensembl.org/homosapiens/userdata/uploadvariations). All variants were screened manually against the Human Gene Mutation Database Professional Biobase (http://www.biobase-international.com/product/hgmd). In silico analysis was performed to determine the potential pathogenicity of the variants. Potentially pathogenic mutations were verified using classic Sanger sequencing
Murphy M.W., Lee J.K., Rojo S., Gearhart M.D., Kurahashi K., Banerjee S., Loeuille G.A., Bashamboo A., McElreavey K., Zarkower D., Aihara H, & Bardwell V.J. (2015). An ancient protein-DNA interaction underlying metazoan sex determination. Nature structural & molecular biology, 22(6), 442-451.
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6

Whole Exome Sequencing Data Analysis

Cited 2 times
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WES libraries were prepared using the Agilent SureSelect Human All Exon V4 (Agilent Technologies, Los Angeles, CA) capture kit and sequenced using an Illumina HiSeq2000 platform (100 base pair paired-end sequencing). Reads were aligned to the hg19 human reference genome using the Burrows-Wheeler Aligner tool.6 (link) Variant calling was performed using the HaplotypeCaller tool from the Genome Analysis Toolkit v.3.5.7 (link),8 (link) Finally, variants were annotated for predicted protein alterations and population frequencies using annotate variation (ANNOVAR).9 (link)
Akçimen F., Spiegelman D., Dionne-Laporte A., Gan-Or Z., Dion P.A, & Rouleau G.A. (2018). Screening of novel restless legs syndrome–associated genes in French-Canadian families. Neurology: Genetics, 4(6), e296.
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7

Exome Sequencing Library Preparation

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A total of 1.5 μg of high-quality genomic DNA per sample was used in the Agilent SureSelect Human All Exon v4 kit capture process. Randomly fragmented DNA was end-repaired, extended with an ‘A’ nucleotide at the 3’end, ligated with the indexing-specific paired-end adapter and amplified according to the manufacturer’s protocol (SureSelect Target Enrichment for Illumina Multiplexed Sequencing version 1.5; Agilent Technologies, Los Angeles, CA). Exome-containing adapter-ligated libraries were hybridized with RNA baits for 24 h at 65 °C, and enriched with streptavidin-conjugated magnetic beads (Dynabeads MyOne Streptavidin T1; Invitrogen). Captured libraries were amplified, and then purified with the Agencourt AMPure XP reagent, then analysed with the Agilent Bioanalyzer 2100 to evaluate the library quality. The qualified exome-captured libraries were sequenced using HiSeq 2000 with the TruSeq PE Cluster kit v3 and TruSeq SBS kit v3 according to the manufacturer’s protocol.
Zhang G., Wang J., Yang J., Li W., Deng Y., Li J., Huang J., Hu S, & Zhang B. (2015). Comparison and evaluation of two exome capture kits and sequencing platforms for variant calling. BMC Genomics, 16(1), 581.
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8

Whole Exome Sequencing of Tumor Relapse

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Whole exome capture was performed on DNA isolated from 48-paired diagnosis and relapse patient samples and patient-matched germline samples. Germline DNA (lymphocytes) was subjected to whole genome amplification (repli-g kit; Qiagen) in 25 patients due to limited materials (see Supplementary Table 2). To obtain sufficient quantities of DNA from the remaining samples, T cells were expanded ex vivo (detailed under Sample collection and processing). DNA was extracted using standard techniques. Libraries were prepared per manufacturer’s recommendation using NimbleGen SeqCap EZ Human Exome Library v3.0, Agilent Human Exon V3 (Exon 50Mb), or Agilent SureSelect Human All Exon V4 (51 MB; see Supplementary Table 2 for specification of kit use per patient tumor and germline samples) and sequenced at a minimum of 50bp single-read sequencing on a HiSeq 2000 (Illumina, Inc.) to a mean coverage per base of 73X. See Supplementary Table 4 for sequencing statistics.
Li S., Garrett-Bakelman F.E., Chung S.S., Sanders M.A., Hricik T., Rapaport F., Patel J., Dillon R., Vijay P., Brown A.L., Perl A.E., Cannon J., Bullinger L., Luger S., Becker M., Lewis I.D., To L.B., Delwel R., Löwenberg B., Döhner H., Döhner K., Guzman M.L., Hassane D.C., Roboz G.J., Grimwade D., Valk P.J., D’Andrea R.J., Carroll M., Park C.Y., Neuberg D., Levine R., Melnick A.M, & Mason C.E. (2016). Distinct evolution and dynamics of epigenetic and genetic heterogeneity in acute myeloid leukemia. Nature medicine, 22(7), 792-799.
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9

Whole Exome Sequencing of Blood and Nail Samples

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A total of 13 blood samples and paired normal fingernail samples were subjected to WES. In order to enrich the coding regions as much as possible, Sure Select Human All Exon 50M (Agilent Technologies, Inc.) was used for blood samples and Sure Select Human All Exon V4 (Agilent Technologies, Inc.) for nail samples. High-throughput sequencing of blood and nail samples was performed using an Illumina HiSeq2500 instrument (Illumina, Inc.). The average sequencing depths for blood and nail samples were 100× (range, 47–107×) and 102× (range, 96–106×), respectively. The sequencing depth of the above genes is presented in Fig. 1A. Broadband Wireless Access (BWA) was used to perform the alignment with the default parameters and human genome 19/the Genome Reference Consortium Human Genome Build 37 (hg19/GRCh37; ftp://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens) served as the reference genome. The relevant details were as follows: Genome version number, hg19/GRCh37; genome size, 3095677412 bp; capture chip, SeqCap EZ Human Exome Library NimbleGen v2.0; exon sequencing genes >20,000 genes; and capture target area size, 44.1 Mb. The associated 1000G database was utilized to annotate and report mutations in MAF (https://www.ncbi.nlm.nih.gov/variation/tools/1000genomes/).
Li L., Liu H., Wang H., Liu Z., Chen Y., Li L., Song J., Wang G, & Fu R. (2019). Abnormal expression and mutation of the RBPJ gene may be involved in CD59− clonal proliferation in paroxysmal nocturnal hemoglobinuria. Experimental and Therapeutic Medicine, 17(6), 4536-4546.
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10

Exome Sequencing Data Processing Protocol

Cited 4 times
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CASAVA v1.8.2 performed demultiplexing and conversion, while the custom script, Pulse_conversion.py [13 ], extracted raw sequence reads during the sequence run at the predefined SBS cycles: 35, 50, 75 and 100.
Sequence and alignment quality metrics for each patient and PE pulse are available in Additional file 1: Table S2-S3. Variant quality metrics for 2 SE pulses are available in Additional file 1: Table S4. Briefly, the sequence reads were aligned to the whole human genome reference GRCH37 using BWA v0.7.5a [14 (link)], while selecting only aligned reads mapping to the exome, as defined by SureSelect Human All Exon V4 (Agilent), for downstream analysis using SAMtools [15 (link)], BEDTools [16 (link)] and Picard [17 ]. All coverage metrics were calculated using Chanjo v0.4 [11 ]. GATK [18 (link), 19 (link)] v2.7-2 performed realignment, base recalibration, variant identification, recalibration and genotyping. Annovar [20 (link)] v2012-10-23 annotated the variants and MIPs custom scripts ranked them according to pathogenic potential. A summary of annotations and score parameters are available in Additional file 1: Table S5. All variants overlapping dbCMMS v.1.0 were loaded into Scout v1.0 hosted at SciLifeLab for clinical evaluation.
Stranneheim H., Engvall M., Naess K., Lesko N., Larsson P., Dahlberg M., Andeer R., Wredenberg A., Freyer C., Barbaro M., Bruhn H., Emahazion T., Magnusson M., Wibom R., Zetterström R.H., Wirta V., von Döbeln U, & Wedell A. (2014). Rapid pulsed whole genome sequencing for comprehensive acute diagnostics of inborn errors of metabolism. BMC Genomics, 15(1), 1090.
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