Sureselect human all exon v4 kit

Manufactured by Agilent Technologies

Sourced in United States, Canada

The SureSelect Human All Exon V4 kit is a DNA target enrichment solution designed for efficient sequencing of the human exome, which represents the protein-coding regions of the genome. The kit utilizes RNA-based probes to selectively capture and enrich the exonic regions of the human genome, enabling focused and cost-effective sequencing of the most biologically relevant genomic regions.

Automatically generated - may contain errors

Lab products found in correlation

Hiseq 2000, by Illumina (8 mentions) Kapa library prep, by Roche (4 mentions) Hiseq 2000 sequencing system, by Illumina (3 mentions) Hiseq 2000 system, by Illumina (3 mentions) Hiseq 2000 platform, by Illumina (3 mentions) Qiaamp dna ffpe tissue kit, by Qiagen (3 mentions) Qiaamp dna mini kit, by Qiagen (2 mentions) Hiseq 2000 sequencing platform, by Illumina (2 mentions) Hiseq 2500 sequencing platform, by Illumina (2 mentions) Hisequation 2000, by Illumina (1 mentions) Ab library builder system, by Thermo Fisher Scientific (1 mentions) Ez bead system, by Thermo Fisher Scientific (1 mentions) Hiseq 2000 2500 system, by Illumina (1 mentions) Bigdye terminator v1, by Thermo Fisher Scientific (1 mentions) Casava pipeline 1, by Illumina (1 mentions) Agilent 2100 bioanalyzer, by Agilent Technologies (1 mentions) Abi 3730 genetic analyzer, by Thermo Fisher Scientific (1 mentions) Premix taq, by Takara Bio (1 mentions) Metacore, by Thomson Reuters (1 mentions) Dynabead, by Thermo Fisher Scientific (1 mentions)

Spelling variants of this product

SureSelect Human All Exon V4 (35 citations) SureSelect kits (5 citations) Agilent SureSelect Human All Exon V5 and V4 kits (2 citations)

32 protocols using sureselect human all exon v4 kit

Whole-Exome Sequencing of Scrotal Skin Fibroblasts

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

DNA was purified from scrotal skin fibroblasts [5 (link)], and whole-exome sequencing was performed on four affected men (W86, W771/773, W333 and W96/167). Libraries of samples were prepared by using the SureSelect Human All Exon V4 kit (Agilent, Santa Clara, CA). Sequencing was run on an Illumina HiSEquation 2000 with the read length of paired-end 2 × 100 bp by the McDermott Center Sequencing Core at UT Southwestern. Sequences were aligned to the human reference genome hg19, and variants were called by using the Genome Analysis Toolkit HaplotypeCaller and annotated by using snpEff.
We paid special attention to variants in the proximity of the AR gene because linkage studies suggested regions near AR [7 (link)], even though prior efforts with Sanger sequencing of the AR coding region failed to identify any mutations. Of note, the SureSelect Human All Exon V4kit (Agilent) amplified a large region of intron 1 since this region includes exon 1 of an alternative AR transcript NM_001011645.

Ahmad Z., Xing C., Panach K., Kittler R., McPhaul M.J, & Wilson J.D. (2017). Identification of the Underlying Androgen Receptor Defect in the Dallas Reifenstein Family. Journal of the Endocrine Society, 1(7), 836-842.

+ Open protocol

+ Expand

Whole Exome Sequencing for Genetic Disorders

Cited 1 time

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

Whole exome sequencing (WES) was performed on 50 ng of genomic DNA from the two affected brothers as described previously [16 (link)]. In brief, DNA was sheared by sonication with the Covaris S2 instrument (Covaris, Inc.). Fragment libraries were created from the sheared samples using the AB Library Builder System (Life Technologies) and target enrichment was performed according to the manufacturer’s protocols (Agilent SureSelect Human All Exon v4 kit). Exome capture was conducted by hybridizing the DNA libraries with biotinylated RNA baits for 24 h followed by extraction using streptavidin coated magnetic beads. Captured DNA was then amplified followed by emulsion PCR using the EZ Bead System (Life Technologies) and sequenced on the SOLiD5500xl system, generating over 100 million reads of 75 bp length for each of the samples.
Alignment of reads to the human reference sequence (hg19 assembly) and variant detection was performed using v2.1 of the LifeScope Software. SNPs and indel data was stored in an in-house exome database together with variant annotation information obtained from ANNOVAR [17 (link)] and dbSNP135. Custom R scripts were used to identify potentially damaging variants that were shared between the patients while not present in any of the other ~800 exomes in the in-house database.

Jameel M., Klar J., Tariq M., Moawia A., Altaf Malik N., Seema Waseem S., Abdullah U., Naeem Khan T., Raininko R., Baig S.M, & Dahl N. (2014). A novel AP4M1 mutation in autosomal recessive cerebral palsy syndrome and clinical expansion of AP-4 deficiency. BMC Medical Genetics, 15, 133.

+ Open protocol

+ Expand

Whole Exome Sequencing and Variant Analysis

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

DNA extraction was performed using the QIAamp DNA Mini Kit (Qiagen, Hilden, Germany). The SureSelect Human All Exon V4 Kit (Agilent Technologies, Santa Clara, CA) was used for whole exome capture, and the HiSeq 2000 Sequencing System (Illumina Inc., San Diego, CA) was used for massive parallel sequencing. The sequence reads were mapped against the University of California, Santa Cruz hg19 Genome Browser (http://hgdownload.cse.ucsc.edu/goldenPath/hg19/chromosomes/). Sequence variations, including single nucleotide polymorphisms and insertion/deletions were detected using the Genome Analysis Toolkit software (GATK; Broad Institute, Cambridge, MA). All of the whole exome sequencing and analysis was performed at Riken Genesis (Riken Genesis, Tokyo, Japan). To predict the effect of nonsynonymous single nucleotide substitutions on protein structure, function, and phenotype, we used tools available online, such as SIFT (http://sift.jcvi.org/) [22 (link)] and Polyphen2 (http://genetics.bwh.harvard.edu/pph2/) [23 (link)].

Hayashi T., Yamashita T., Okada H., Nio K., Hara Y., Nomura Y., Hayashi T., Asahina Y., Yoshida M., Oishi N., Sunagozaka H., Takatori H., Honda M, & Kaneko S. (2017). Sporadic PCDH18 somatic mutations in EpCAM-positive hepatocellular carcinoma. Cancer Cell International, 17, 94.

+ Open protocol

+ Expand

Genetic Screening for Hereditary Spastic Paraplegia

Cited 2 times

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

Genomic DNA was extracted from the peripheral blood according to standard procedures.^{9 (link)} For a subset of the cohort from the province of Ontario (37 patients), all exons and flanking intron sequences of a panel of 51 genes known to cause HSP were sequenced both in forward and reverse directions at the Hospital for Sick Children using next-generation sequencing techniques. Sanger validation was performed according to standard protocols using BigDye terminator v1.1 (Life Technologies, Carlsbad, CA), and sequencing products were separated on an Applied Biosystems model 3730 Capillary Sequencer (Life Technologies) and analyzed using SeqPilot software (JSI Medical Systems, Kippenheim, Germany). Whole-exome sequencing was performed on 108 samples from 51 families without a genetic diagnosis, using the Agilent SureSelect Human All Exon v4 kit for capture and targeted enrichment of the exome. The captured samples were sequenced in the Illumina HiSeq 2000/2500 system (Genome Québec Innovation Centre, Montreal, QC, Canada). The reads were then aligned against the human genome (GRCh37 assembly) using Burrows-Wheeler Aligner.^{10 (link)} Variant calling and annotation were performed using Genome Analysis ToolKit^{11 (link)} and Annotate Variation.^{12 (link)} The exome data were then screened for all known HSP-causing genes and mutations.^{13 (link),14 (link)}

Chrestian N., Dupré N., Gan-Or Z., Szuto A., Chen S., Venkitachalam A., Brisson J.D., Warman-Chardon J., Ahmed S., Ashtiani S., MacDonald H., Mohsin N., Mourabit-Amari K., Provencher P., Boycott K.M., Stavropoulos D.J., Dion P.A., Ray P.N., Suchowersky O., Rouleau G.A, & Yoon G. (2016). Clinical and genetic study of hereditary spastic paraplegia in Canada. Neurology: Genetics, 3(1), e122.

+ Open protocol

+ Expand

Exome Sequencing Reveals Genetic Variants

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

DNA from the affected individuals (IV-14, IV-19, V-4 and V-6) was enriched for the human exome using Sure Select Human All Exon V4 kit according to the manufacturer’s protocol (Agilent Technologies, Santa Clara, CA, USA). The enriched DNAs were sequenced on the HiSeq 2000 system (Illumina, San Diego, CA, USA) with 100-bp paired-end runs. The reads were aligned to the UCSC human reference genome (version hg19) with BWA (Burrows-Wheeler Aligner). Variants, including single nucleotide variations (SNVs), insertions and deletions (indels) were labeled using SAM tools (Sequence Alignment/Map Tools) and GATK (The Genome Analysis Toolkit). SNPs deposited in the 1000 Genomes project data or in the dbSNP (build 132) were removed. We searched for heterozygous SNVs and indels shared by the four patients, but not shared by our in-house disease control SNV database (exome sequencing data from 166 Japanese samples, unpublished data). The indels that were not described as pathogenic in the dbSNP (build 137) were excluded. Afterwards, we focused on the SNVs and indels that were located within the linkage regions. Sanger sequencing confirmed the presence of the two most likely candidates after the aforementioned filtering, which resided in the MYH7 and HSPA6 genes.

Oda T., Xiong H., Kobayashi K., Wang S., Satake W., Jiao H., Yang Y., Cha P.C., Hayashi Y.K., Nishino I., Suzuki Y., Sugano S., Wu X, & Toda T. (2015). A de novo mutation of the MYH7 gene in a large Chinese family with autosomal dominant myopathy. Human Genome Variation, 2, 15022-.

+ Open protocol

+ Expand

Sequencing Tumor DNA Exomes

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

For comparative purposes, sequence capture of unamplified tumor DNA material was achieved according to the protocol provided with the SureSelect Human All Exon V4 kit (Agilent, Santa Clara, CA, USA). Library preparation and sequencing were performed using the HiSeq2000 instrument as described above.

Hasmats J., Gréen H., Orear C., Validire P., Huss M., Käller M, & Lundeberg J. (2014). Assessment of Whole Genome Amplification for Sequence Capture and Massively Parallel Sequencing. PLoS ONE, 9(1), e84785.

+ Open protocol

+ Expand

Whole Exome Sequencing for ASD and ID

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 on the proband with ASD (II:2) using the SureSelect Human All Exon V4 Kit (Agilent Technologies, Santa Clara, CA, United States) and sequenced on an HiSeq2000 (Illumina) with 101-bp paired-end reads. Exome sequencing data processing, base calling and primary data analysis were performed using the Illumina Real-Time Analysis (RTA) version 1.12.4 and Illumina’s CASAVA pipeline 1.8.2 with default parameters. The paired-end reads were aligned to the reference human genome (hg19/GRCh37) using the Burrows-Wheeler Aligner (BWA). Variant calling was performed using SAMtools (Li et al., 2009 (link)) and sequence variants were annotated using ANNOVAR (Wang et al., 2010 (link)). The remaining variants were then filtered against our candidate ASD gene set (762 genes) from AutDB, SFARI, and TruSight Autism genes. Subsequently, to search more widely for the cause of disease in the patient, the variants were also filtered against a candidate ID gene set (1,912 genes) from literature reviews. Sanger sequencing was then performed to confirm sequence variants and to assess segregation in the family. The details and simplified diagram of WES analysis and variants filtering are shown in Supplementary Figure S1.

Hnoonual A., Graidist P., Kritsaneepaiboon S, & Limprasert P. (2019). Novel Compound Heterozygous Mutations in the TRAPPC9 Gene in Two Siblings With Autism and Intellectual Disability. Frontiers in Genetics, 10, 61.

+ Open protocol

+ Expand

Exome Sequencing of Human Blood Samples

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

Genomic DNA was extracted from peripheral blood lymphocytes and analyzed by gel electrophoresis to confirm its high-molecular weight. Exome capture and library preparation were performed using the Agilent SureSelect Human All Exon V4 kit according to the manufacturer's protocols. In brief, 3 μg of DNA from each of the three individuals was sheared to about 200 bp using adaptive focused acoustic technology. Then the sheared samples were end repaired, A-tailed, and ligated with the SureSelect Adaptor Oligo Mix. After ligation, the adaptor-ligated libraries were amplified by PCR and validated with an Agilent 2100 Bioanalyzer before capture. In-solution hybridization was performed at 65°C for 24 hours by combining the precapture DNA library with hybridization buffers, blocking reagents, and the SureSelect biotinylated capture library, according to Agilent's standard protocol. Then, the captured targets were isolated with streptavidin-coated beads and multiplexed by posthybridization amplification. The final enriched libraries were analyzed on the HiSeq 2000 platform (Illumina) by sequencing of paired-end 100 bp reads.

Zhao M., Hou L., Teng H., Li J., Wang J., Zhang K, & Yang L. (2019). Whole-Exome Sequencing Identified a Novel Compound Heterozygous Genotype in ASL in a Chinese Han Patient with Argininosuccinate Lyase Deficiency. BioMed Research International, 2019, 3530198.

+ Open protocol

+ Expand

Exome Sequencing and Copy Number Analysis

Cited 3 times

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

The sequencing libraries were prepared and captured using SureSelect Human All Exon V4 kit (Agilent Technologies) following the manufacturer’s instructions. The sequencing was performed using the Illumina HiSeq 2000 system, generating 100 bp paired-end reads. All raw 100 bp paired-end reads were aligned to the human genome reference sequence (hg19) using BWA^{37 (link)} and further jointly realigned around indels sites using GATK’s^{38 (link)} IndelRealigner. Duplicate reads were removed using Picard Tools MarkDuplicates³⁹. Supplementary Table 4 presents the summary statistics of the sequencing. The variants were called using Freebayes⁴⁰ and filtered for high quality (QUAL/AO > 10). We annotated the variants with ANNOVAR^{41 (link)}, removed non-coding and synonymous variants, variants in dbSNP147, or shared between all samples, leading to a total of 93 variants across all 8 samples (Supplementary Table 2). The copy number changes were called independently on each chromosome using CODEX^{42 (link)} with default settings (Supplementary Table 1), limited to the expected exonic target from the SureSelect capture kits and expecting fractional copy number from aneuploidy. Segments smaller than 100 kb, supported by less than 3 exons, or with copy number between 1.5 and 2.5 were excluded.

Wenzel A.T., Champa D., Venkatesh H., Sun S., Tsai C.Y., Mesirov J.P., Bui J.D., Howell S.B, & Harismendy O. (2022). Single-cell characterization of step-wise acquisition of carboplatin resistance in ovarian cancer. NPJ Systems Biology and Applications, 8, 20.

+ Open protocol

+ Expand

Whole Exome Sequencing Identifies Pathogenic Variants

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

Whole exome sequencing (WES) was performed on genomic DNA of three affected individuals (III8, III12, and IV2). Exome libraries were prepared using the SureSelect Human All Exon V4 kit (Agilent, Santa Clara, CA, USA) and sequenced using the HiSeq2000 system (Illumina, San Diego, CA, USA). The quality-control metrics (QC) were set to only retain variants in the positions with read depth ≥10, genotype quality ≥20, and alternate allele read ratio ≥0.25. Variations were annotated using UCSC hg19 refGene.txt.gz (http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/). Genome Analysis Toolkit (Broad Institute, Harvard and MIT, MA, USA) was used for data quality assurance as well as variant discovery. After removing the variants with an allele frequency more than 1%, the variants shared by three affected individuals were selected. The candidate pathogenic variants were confirmed using Sanger sequencing in all family members. Primers were designed using Oligo Primer Analysis Software Version 7 (Molecular Biology Insight, Inc., Cascade, CO, USA). Polymerase chain reaction (PCR) was performed according to the Takara protocol for Premix Taq™ (Takara Bio., Dalian, China) and purified products were run on an ABI 3730 Genetic Analyzer (Applied Biosystems, Foster City, CA, USA).

Huang J., Liu H.Y., Wang R.R., Xiao H., Wu D., Li T., Jiang Y.H, & Zhang X. (2019). A 3.06-Mb interstitial deletion on 12p11.22-12.1 caused brachydactyly type E combined with pectus carinatum. Chinese Medical Journal, 132(14), 1681-1688.

+ 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!