Agilent sureselect human all exon v4 kit

Manufactured by Agilent Technologies

Sourced in Canada, United States

The Agilent SureSelect Human All Exon V4 kit is a targeted sequencing solution that captures the protein-coding regions of the human genome, known as the exome. It is designed to enable efficient and cost-effective sequencing of the human exome.

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Lab products found in correlation

Solid 5500xl platform, by Thermo Fisher Scientific (1 mentions) Ribo spia technology, by Tecan (1 mentions) Hiseq 2000, by Illumina (1 mentions) Kapa library prep, by Roche (1 mentions) Hiseq 2000 sequencing platform, by Illumina (1 mentions) Qiaamp dna ffpe tissue kit, by Qiagen (1 mentions)

3 protocols using agilent sureselect human all exon v4 kit

Whole Exome Sequencing for Variant Analysis

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Whole exome sequencing was performed in the patient sample by The Centre for Applied
Genomics, The Hospital for Sick Children (Toronto, Canada) using the Agilent
SureSelect Human All Exon V4 Kit (Agilent Technologies) and SOLiD 5500xl platform
(Applied Biosystems). All data were aligned to the hg19/GRCh37 reference genome build
via BFAST and BWA aligner. Variants were quality trimmed using the Genome Analysis Toolkit (GATK 1.1.28) and they
were annotated for functional effect by SnpEff
2.0.5. SnpEff also provided a simple assessment of the putative impact of the variant
(e.g. High, Moderate, or Low impact). Alignment, calling and annotation of the
variants against databases such as 1000 Genomes (April 2012 release), NHLBI Exome Sequencing Project (ESP6500) and
Single Nucleotide Polymorphism database (dbSNP137) were done using a software
developed in-house called Mendel,MD (Cardenas et al., 2015 ). The prediction software SIFT (Sorting Intolerant From Tolerant) was used
in order to estimate whether a given amino acid substitution affected protein
function. SIFT prediction is based on the degree of conservation of amino acid
residues in sequence alignments derived from closely related sequences and on the
physical properties of amino acids.

Linhares N.D., Freire M.C., Cardenas R.G., Pena H.B., Lachlan K., Dallapiccola B., Bacino C., Delobel B., James P., Thuresson A.C., Annerén G, & Pena S.D. (2016). 1p13.2 deletion displays clinical features overlapping Noonan syndrome, likely related to NRAS gene haploinsufficiency. Genetics and Molecular Biology, 39(3), 349-357.

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Transcriptome and Exome Sequencing of NSCLC

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Twelve primary tumor samples were collected from four patients with non-small cell lung cancer (3 regions per tumor) including Adenocarcinoma (n=3) and Squamous Cell Carcinoma (n=1). Matched normal samples were collected from white blood cells (n=3) or adjacent lung tissue (n=1). Informed consent was obtained from all patients. No compensation was provided for the patients. Collection and use of patient samples were approved by the Institutional Review Board of The University of Texas MD Anderson Cancer Center (MDACC). Detailed cohort characteristics including age, gender, and smoking status are given in Sup. Table 3.
Using the Ribo-SPIA Technology (NuGen, San Carlos, CA, USA), we converted the extracted RNA to cDNA libraries, which were then sequenced as 76 bp paired-end reads on the Illumina HiSeq 2000 platform (Illumina, Inc., San Diego, CA, USA). Genomic DNA was extracted and utilized for library preparation for sequencing with the Agilent SureSelect Human All Exon V4 kit, according to the manufacturer’s instructions (Agilent Technologies, Inc., Santa Clara, CA, USA). 76-bp paired-end whole exome sequencing was performed on the Illumina HiSeq 2000 platform with mean target sequencing coverage of 200x (Illumina, Inc., San Diego, CA, USA).

Lu T., Park S., Han Y., Wang Y., Hubert S.M., Futreal P.A., Wistuba I., Heymach J.V., Reuben A., Zhang J, & Wang T. (2022). Netie: Inferring the evolution of neoantigen-T cell interactions in tumors. Nature methods, 19(11), 1480-1489.

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Whole-Exome Sequencing of FFPE Samples

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DNA was extracted using the QIAamp DNA FFPE Tissue Kit (QIAGEN) and the resulting genomic DNA was sheared into 300-400 bp segments and subjected to library preparation for whole-exome sequencing using KAPA library prep (Kapa Biosystems) with the Agilent SureSelect Human All Exon V4 kit according to the manufacturer's instructions. Paired-end multiplex sequencing of DNA samples was performed on the Illumina HiSeq 2000 sequencing platform.

Tang M., Abbas H.A., Negrão M.V., Ramineni M., Hu X., Fujimoto J., Reuben A., Varghese S., Zhang J., Li J., Chow C., Mao X., Song X., Lee W., Wu J., Little L., Gumbs C., Behrens C., Moran C.A., Weissferdt A., Lee J., Sepesi B., Swisher S.G., Heymach J.V., Wistuba I.I., Futreal P.A., Kalhor N., & Zhang J. (2021). The histologic phenotype of lung cancers may be driven by transcriptomic features rather than genomic characteristics.

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