Clinical research exome kit

Manufactured by Agilent Technologies

The Clinical Research Exome kit is a comprehensive genomic profiling solution designed for clinical research applications. The kit targets the protein-coding regions of the human genome, known as the exome, providing a focused and cost-effective approach to genomic analysis. The kit is intended to be used by researchers in the clinical setting for the identification and analysis of genetic variants associated with various diseases and conditions.

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Lab products found in correlation

Sureselect human all exon v4 50 mb, by Agilent Technologies (3 mentions) Abi 3730, by Thermo Fisher Scientific (2 mentions) Hiseq 2000 or 2500 sequencing system with 100 bp paired end reads, by Illumina (2 mentions) Xgen exome research panel v1, by Illumina (2 mentions) Hiseq 2000, by Illumina (1 mentions) Idt xgen exome research panel v1, by Integrated DNA Technologies (1 mentions) Hiseq sequencing system, by Illumina (1 mentions) Hiseq 2500, by Illumina (1 mentions) Hiseq 4000, by Illumina (1 mentions)

Spelling variants of this product

SureSelectXT Clinical Research Exome kit (13 citations) SureSelect Clinical Research Exome kit (13 citations) Agilent Clinical Research Exome kit (7 citations) SureSelect Clinical Research Exome V2 kit (6 citations) Agilent SureSelect Clinical Research Exome kit (3 citations) Agilent SureSelect XT Clinical Research Exome kit (2 citations)

16 protocols using clinical research exome kit

Whole Exome Sequencing for Disease Identification

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Genomic DNA was extracted from whole blood from the affected children and their parents. Exome sequencing at GeneDx was performed on exon targets captured using the Agilent SureSelect Human All Exon V4 (50 Mb) or the Clinical Research Exome kit (Agilent Technologies) according to the manufacturer's instructions. Libraries were sequenced using the Illumina HiSeq 2000 or 2500 sequencing system with 100-bp paired-end reads (Illumina). Whole-exome sequence data for all sequenced family members was analyzed using GeneDx's XomeAnalyzer (a variant annotation, filtering, and viewing interface for WES data) as described previously (Table 3; Tanaka et al. 2016 (link)). Identified sequence variants of interest were confirmed in each proband and both parents by conventional di-deoxy DNA sequence analysis using an ABI3730 (Life Technologies).

Tanaka A.J., Cho M.T., Willaert R., Retterer K., Zarate Y.A., Bosanko K., Stefans V., Oishi K., Williamson A., Wilson G.N., Basinger A., Barbaro-Dieber T., Ortega L., Sorrentino S., Gabriel M.K., Anderson I.J., Sacoto M.J., Schnur R.E, & Chung W.K. (2017). De novo variants in EBF3 are associated with hypotonia, developmental delay, intellectual disability, and autism. Cold Spring Harbor Molecular Case Studies, 3(6), a002097.

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Trio Whole Exome Sequencing Analysis

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A trio of WES analyses of the proband and both her parents was performed at a GeneDx-certified clinical diagnostic laboratory (Galthersburg, USA, https://www.genedx.com). The sequencing methodology and variant interpretation protocol have been previously described^{25 (link)}. Briefly, the Agilent Clinical Research Exome kit was used to target the exonic regions and flanking splice junctions of the genome. These targeted regions were sequenced simultaneously on an Illumina HiSeq 2000 sequencing system with 100-bp paired-end reads. Bidirectional sequences were assembled and aligned to reference gene sequences based on the human genome build GRCh37/UCSC hg19 (http://genome.uscs.edu/).

Alhamoudi K.M., Barhoumi T., Al-Eidi H., Asiri A., Nashabat M., Alaamery M., Alharbi M., Alhaidan Y., Tabarki B., Umair M, & Alfadhel M. (2021). A homozygous nonsense mutation in DCBLD2 is a candidate cause of developmental delay, dysmorphic features and restrictive cardiomyopathy. Scientific Reports, 11, 12861.

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Trio Exome Sequencing for Genetic Diagnosis

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Peripheral blood samples from the patient and both biological parents were collected and shipped to the laboratory. In cases in which mitochondrial DNA sequencing was required and the patient had undergone recent red blood cell transfusion, a buccal swab was collected. The laboratory also received a pedigree and the consultant geneticist’s notes.
Trio ES was performed by a send out laboratory (GeneDX) that provides a verbal preliminary result within 10 calendar days of receipt of samples. Sequencing was done using the Agilent Clinical Research Exome kit. Targeted regions were sequenced simultaneously on an Illumina HiSeq with 100bp paired end reads. The bidirectional sequence was assembled and aligned to human reference genome build GRCh37/UCSC hg19 and analyzed for sequence variants using a custom developed analysis tool (Xome Analyzer).^{22 (link)}

Freed A.S., Candadai S.V., Sikes M.C., Thies J., Byers H.M., Dines J.N., Ndugga-Kabuye M.K., Smith M.B., Fogus K., Mefford H.C., Lam C., Adam M.P., Sun A., McGuire J.K., DiGeronimo R., Dipple K.M., Deutsch G.H., Billimoria Z.C, & Bennett J.T. (2020). The Impact of Rapid Exome Sequencing on Medical Management of Critically Ill Children. The Journal of pediatrics, 226, 202-212.e1.

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Exome Sequencing Variant Analysis

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Exome sequencing was carried out by GeneDx. Using genomic DNA from the proband and parents, the exonic regions and flanking splice junctions of the genome were captured using the SureSelect Human All Exon V4 (50 Mb), the Clinical Research Exome kit (Agilent Technologies, Santa Clara, CA) or the IDT xGen Exome Research Panel v1.0 (Integrated DNA Technologies, Coralville, IA). Massively parallel (NextGen) sequencing was done on an Illumina system with 100 bp or greater paired-end reads. Reads were aligned to human genome build GRCh37/UCSC hg19 and analyzed for sequence variants using a custom-developed analysis tool. A prediction tool, PROVEAN, (https://www.jcvi.org/research/provean), was used to assist in interpretation. Additional sequencing technology and the variant interpretation protocol has been previously described (Retterer et al., 2016 (link)). The general assertion criteria for variant classification are publicly available on the GeneDx ClinVar submission page (http://www.ncbi.nlm.nih.gov/clinvar/submitters/26957/).

Veale E.L., Golluscio A., Grand K., Graham JM J.r, & Mathie A. (2022). A KCNB1 gain of function variant causes developmental delay and speech apraxia but not seizures. Frontiers in Pharmacology, 13, 1093313.

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Exome Sequencing Variant Analysis

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Exome sequencing at GeneDx was performed on exon targets isolated by capture with the Clinical Research Exome kit (Agilent Technologies) using Illumina HiSeq 2500 2×100 bp. The other sequencing technology and variant interpretation protocol has been previously described (Tanaka et al. 2015 (link)). The general assertion criteria for variant classification are publicly available on the GeneDx ClinVar submission page (http://www.ncbi.nlm.nih.gov/clinvar/submitters/26957/).

Rohanizadegan M., Abdo S.M., O'Donnell-Luria A., Mihalek I., Chen P., Sanders M., Leeman K., Cho M., Hung C, & Bodamer O. (2017). Utility of rapid whole-exome sequencing in the diagnosis of Niemann–Pick disease type C presenting with fetal hydrops and acute liver failure. Cold Spring Harbor Molecular Case Studies, 3(6), a002147.

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Exome sequencing for genetic diagnosis

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Genomic DNA from the proband and parents were processed using the Agilent Clinical Research Exome kit. The targeted regions (exonic regions and flanking splicing junctions) were sequenced simultaneously by massively parallel (NextGen) sequencing on an Illumina HiSeq sequencing system with 100-bp paired-end reads with a mean depth of coverage of 104× (quality threshold 95.3%) (Supplemental Table 1). Bidirectional sequences were assembled, aligned to reference gene sequences based on GRCh37/UCSC hg19, and analyzed for sequence variants using XomeDx software (GeneDx). Variants were filtered based on predicted loss-of-function or missense mutation, presence of gene or variant in the Human Gene Mutation Database, and MAF of <0.01 (Stenson et al. 2014 (link)). MAFs were obtained from the 1000 Genomes Project using the Ensembl Variant Effect Predictor (VEP) tool. The remaining variants were analyzed by SIFT and PolyPhen-2 (Supplemental Table 4; Sim et al. 2012 (link); Adzhubei et al. 2013 (link)). Capillary sequencing was used to confirm all potentially pathogenic variants identified in the proband and parent samples. The identified variant was submitted to ClinVar (ID 279987) (Landrum et al. 2014 (link)).

Velez G., Bassuk A.G., Schaefer K.A., Brooks B., Gakhar L., Mahajan M., Kahn P., Tsang S.H., Ferguson P.J, & Mahajan V.B. (2018). A novel de novo CAPN5 mutation in a patient with inflammatory vitreoretinopathy, hearing loss, and developmental delay. Cold Spring Harbor Molecular Case Studies, 4(3), a002519.

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Exome Sequencing for Genetic Diagnosis

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Using genomic DNA from the proband, parents, and siblings, when available, the exonic regions and flanking splice junctions of the genome were captured using the Clinical Research Exome kit (Agilent Technologies, Santa Clara, CA) or the IDT xGen Exome Research Panel v1.0. Massively parallel (NextGen) sequencing was done on an Illumina system with 100bp or greater paired-end reads. Reads were aligned to human genome build GRCh37/UCSC hg19, and analyzed for sequence variants using a custom-developed analysis tool. Additional sequencing technology and variant interpretation protocol has been previously described.^{8 (link)} The general assertion criteria for variant classification are publicly available on the GeneDx ClinVar submission page (http://www.ncbi.nlm.nih.gov/clinvar/submitters/26957/).

Gracie S., Sengupta N., Ferreira C., Pemberton J., Anderson I., Wang X., Rhodes L., Brown K., Balla T, & Larson A. (2022). De novo loss-of-function variant in PTDSS1 is associated with developmental delay. American journal of medical genetics. Part A, 188(6), 1739-1745.

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Molecular Analysis of Neurodevelopmental Disorders

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Patients were enrolled in the Developmental Brain Disorders Research Program at Seattle Children’s Research Institute, with IRB approval. The investigators reviewed all clinical, neuroimaging and molecular data. Molecular analysis was performed through clinically available targeted next generation commercial panels consisting of >1000 genes associated with epilepsy, intellectual disability and autism using the Agilent Clinical Research Exome kit. Sequencing was performed using the Illumina sequencing system with 2×100 bp paired-end reads.

Michels S., Foss K., Park K., Golden-Grant K., Saneto R., Lopez J, & Mirzaa G.M. (2017). Mutations of KIF5C cause a neurodevelopmental disorder of infantile-onset epilepsy, absent language, and distinctive malformations of cortical development. American journal of medical genetics. Part A, 173(12), 3127-3131.

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Exome Sequencing and Variant Detection

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Exome sequencing was performed at GeneDx following targeted exon capture with the Clinical Research Exome kit (Agilent Technologies) on an Illumina HiSeq 2500 2 × 100 bp. Both the sequencing technology and variant interpretation protocols have previously been described (Tanaka et al. 2015 (link)). The general assertion criteria for variant classification are publicly available on the GeneDx ClinVar submission page (http://www.ncbi.nlm.nih.gov/clinvar/submitters/26957/). The GeneDx pipeline also detects exon-level copy-number changes with single-exon resolution for deletions (Retterer et al. 2015 (link)).

Rohanizadegan M., Siddharath A., Retterer K., Hung C, & Bodamer O. (2020). The tale of two genes: from next-generation sequencing to phenotype. Cold Spring Harbor Molecular Case Studies, 6(2), a004846.

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Whole Exome Sequencing for Genetic Diagnosis

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WES was carried out at GeneDx, Inc. subsequent to informed consent of the parents and assent of the affected individuals. Using genomic DNA from the ID cases and their parents, the exonic regions and flanking splice junctions of the genome were captured using the Clinical Research Exome kit (Agilent Technologies, Santa Clara, CA). Massively parallel (NextGen) sequencing was done on an Illumina system with 100 bp paired-end reads. The percent coverage at 10X or greater in the two brothers and their two parents ranged from 97.14 to 97.49%; the younger brother had 97.18% coverage that was at least 10X and the older brother had 97.49% coverage at least at 10X. The mean coverage in the younger brother was 132X and in the older brother 197X. The mean coverage in the father and the mother was 134.29X and 222.05X, respectively.

Kellaris G., Khan K., Baig S.M., Tsai I.C., Zamora F.M., Ruggieri P., Natowicz M.R, & Katsanis N. (2018). A hypomorphic inherited pathogenic variant in DDX3X causes male intellectual disability with additional neurodevelopmental and neurodegenerative features. Human Genomics, 12, 11.

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