Idt xgen exome research panel v1

Manufactured by Integrated DNA Technologies

Sourced in United States

The IDT xGen Exome Research Panel V1.0 is a comprehensive genomic enrichment tool designed for targeted sequencing of the human exome. It is a pre-designed panel that captures the coding regions of the human genome.

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Lab products found in correlation

Sureselect target enrichment system, by Agilent Technologies (4 mentions) Novaseq 6000, by Illumina (4 mentions) Nextseq, by Illumina (3 mentions) Seqcap ez vcrome 2, by Roche (3 mentions) Qubit 3.0 fluorometer, by Thermo Fisher Scientific (3 mentions) Qubit 3.0 flurometer, by Thermo Fisher Scientific (2 mentions) Magnetic universal genomic dna kit, by Tiangen Biotech (2 mentions) Nanophotometer, by Implen (2 mentions) Kapa hyper prep kit, by Roche (2 mentions) Nanodrop spectrophotometer, by Thermo Fisher Scientific (2 mentions) Novaseq 6000 platform, by Illumina (1 mentions) Sureselect human all exon v4 50 mb, by Agilent Technologies (1 mentions) Clinical research exome kit, by Agilent Technologies (1 mentions) Hiseq 4000 ngs platforms, by Illumina (1 mentions) Qubit 3.0 with dsdna hs assay kit, by Thermo Fisher Scientific (1 mentions) Xgen lockdown hybridization and wash kit, by Integrated DNA Technologies (1 mentions) Dynabeads m 270, by Thermo Fisher Scientific (1 mentions) Kapa library quantification kit, by Roche (1 mentions) Kapa hifi hotstart readymix, by Roche (1 mentions) 2100 bioanalyzer, by Agilent Technologies (1 mentions)

21 protocols using idt xgen exome research panel v1

Whole-Exome Sequencing of Tumor and Blood

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This study was conducted under an institutional review board–approved protocol at Yale University. The patient's blood and tumor tissue were collected after obtaining written informed consent. Histopathology, including immunohistochemical studies, was evaluated by a board-certified oncologic surgical pathologist.
WES and analysis was performed in accordance with our previously described methods at the Yale Cancer for Genome Analysis (YCGA) (Fomchenko et al. 2019 (link)). Briefly, genomic DNA from the tumor and blood were isolated and exome captured with IDT xGen Exome Research Panel v1 (Integrated DNA Technologies) and then sequenced on the Illumina NovaSeq6000 WES platform with 2 × 100 base pair reads. Downstream analysis of raw reads, including alignment, duplicate marking, realignment, and base quality recalibration was performed according to “GATK Best Practice” recommendations (v.4.1.9, Grch37). Somatic SNVs, indels, and copy-number variations (CNVs) were identified as previously described (Fomchenko et al. 2019 (link)). Mean coverage of 139.4× was achieved for blood and 240× for tumor tissue (Supplemental Table 1).

Hong C.S., Khan M., Sukys J.M., Prasad M., Erson-Omay E.Z., Vining E.M, & Omay S.B. (2022). PIK3CA mutation in a case of CTNNB1-mutant sinonasal glomangiopericytoma. Cold Spring Harbor Molecular Case Studies, 8(1), a006120.

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Genetic Profiling of Rare Fetal Disorders

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Fetal samples of case 1 and case 4 were from amniotic fluid during the invasive prenatal diagnosis. Fetal samples of case 2 and case 3 were from muscle tissue of the aborted fetus. The peripheral blood was collected in EDTA-containing tubes from the four couples. Proband-WES sequencing was performed in family 2, and Trio-WES sequencing was selected in the other three families. WES sequencing was tested by Yin Feng Gene Technology Co., Ltd. (Jinan, China). Briefly, genomic DNA was extracted from peripheral blood for each sample using Magnetic Universal Genomic DNA Kit (TIANGEN, China). The quality and quantity of each DNA sample were detected by 1% agarose gel electrophoresis, NanoPhotometer (IMPLEN, CA, United States) and Qubit^® 3.0 Flurometer (Life Technologies, CA, United States). Then, DNA libraries were prepared using Illumina standard protocol. Based on the manufacturer’s instructions, the exome was captured using IDT xGen Exome Research Panel v1.0 (Integrated DNA Technologies, Coralville, Iowa, United States), and sequenced using Illumina Novaseq 6,000 platform (Illumina Inc., San Diego, CA, United States) with a depth of 100-fold. The data obtained by WES sequencing was then used for mutation hazard prediction, genotype-phenotype correlation analysis and mutation screening.

Fang Y., Li S, & Yu D. (2023). Genetic analysis and prenatal diagnosis of short-rib thoracic dysplasia 3 with or without polydactyly caused by compound heterozygous variants of DYNC2H1 gene in four Chinese families. Frontiers in Genetics, 14, 1075187.

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Genetic Diagnostic Workflow for Congenital Skeletal Anomalies

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For fetuses 11–25 (2019.1–2019.6), a special NGS gene panel analysis (including 811 congenital skeletal anomalies genes, Additional file 1: Table S1) was performed by a commercial company (MyGenostics, Inc., Beijing, China). For fetuses 8–10 and 26–55 (2019.7–2021.3), WES was performed and enriched for exonic sequences using the IDT xGen Exome Research Panel V1.0 (Integrated DNA Technologies, San Diego, USA). Sequencing results were mapped to the human genome (GRCh37/hg19). All variants were annotated using databases including the 1000 genomes project (1000G, http://www.internationalgenome.org/), dbSNP (https://www.ncbi.nlm.nih.gov/snp/), the genome aggregation database (GnomAD, https://gnomad.broadinstitute.org/), ClinVar, the Human Genomic Mutation Database (HGMD, http://www.hgmd.cf.ac.uk/ac/index.php) and OMIM. Variants were classified according to the guidelines recommended by the American College of Medical Genetics and Genomics (ACMG).

Bai Y., Sun Y., Liu N., Wang L., Jiao Z., Hou Y., Duan H., Li Q., Zhu X., Meng J, & Kong X. (2022). Genetic analysis of 55 cases with fetal skeletal dysplasia. Orphanet Journal of Rare Diseases, 17, 410.

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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 Identification

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Exome library preparation, sequencing, and bioinformatics were performed as previously described.^{15 (link)} Briefly, samples were prepared using either the SureSelect Target Enrichment System (Agilent Technologies, Santa Clara, CA), SeqCap EZ VCRome 2.0 (Roche NimbleGen, Massion, WI),^{16 (link)} or the IDT xGen Exome Research Panel V1.0 (Integrated DNA Technologies, Coralville, IA) and sequenced using paired-end, 100- or 150-cycle chemistry on the Illumina HiSeq or NextSeq (Illumina, San Diego, CA). Stepwise filtering included the removal of common single-nucleotide polymorphisms, intergenic and 3′/5′ untranslated region variants, intronic variants outside ±2, and synonymous variants (other than potential splice-related synonymous changes at the first and last positions of exons). However, alterations classified as pathogenic or likely pathogenic based on Ambry's variant classification schema as well as alterations with a Human Gene Mutation Database identifier were protected from the aforementioned filtering. Identified candidate alterations were confirmed using automated fluorescence dideoxy sequencing.

Farwell Hagman K.D., Shinde D.N., Mroske C., Smith E., Radtke K., Shahmirzadi L., El-Khechen D., Powis Z., Chao E.C., Alcaraz W.A., Helbig K.L., Sajan S.A., Rossi M., Lu H.M., Huether R., Li S., Wu S., Nuñes M.E, & Tang S. (2016). Candidate-gene criteria for clinical reporting: diagnostic exome sequencing identifies altered candidate genes among 8% of patients with undiagnosed diseases. Genetics in Medicine, 19(2), 224-235.

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Comprehensive Genomic DNA Extraction and Sequencing

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Genomic DNAs from FFPE samples and the whole blood control samples were extracted using Qiagen QIAamp DNA FFPE Tissue Kit and DNeasy Blood and tissue kits (Qiagen, USA)), respectively, and quantified using Qubit 3.0 with dsDNA HS Assay Kit (ThermoFisher Scientific, USA). Sequencing library preparation was performed with KAPA Hyper Prep Kit (KAPA Biosystems, USA). DNA libraries were pooled and captured with a custom 425 cancer-gene panel. The capture reaction was performed with Dynabeads M- 270 (Life Technologies, CA, USA) and xGen Lockdown hybridization and wash kit (Integrated DNA Technologies) according to manufacturers’ protocols. Captured libraries were PCR amplified with KAPA HiFi HotStartReadyMix (KAPA Biosystems), followed by purification using AgencourtAMPure XP beads. Libraries were quantified by qPCR using KAPA Library Quantification kit (KAPA Biosystems). Library fragment size was determined by Bioanalyzer 2100 (Agilent Technologies). The target-enriched library was then sequenced on HiSeq4000 NGS platforms (Illumina) to a minimum coverage depth of 100X and 600X for blood and FFPE, respectively. Exome capture was performed using the IDT xGen Exome Research Panel V1.0 (Integrated DNA Technologies) and sequenced using HiSeq4000 to a mean coverage depth of ~60X for the normal control (white blood cells samples) and ~150X for the tumor FFPE samples.

Gao B., Yang F., Han M., Bao H., Shen Y., Cao R., Wu X., Shao Y., Liu C, & Zhang Z. (2021). Genomic landscape and evolution of arm aneuploidy in lung adenocarcinoma. Neoplasia (New York, N.Y.), 23(9), 870-878.

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Genomic DNA Analysis of Proband and Parents

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Genomic DNA analysis was performed on cells sampled from proband and both parents by buccal swab technique.
11 (link)
Exomes and flanking splice junctions were captured using the IDT xGen Exome Research Panel v1.0 (Integrated DNA Technologies, Coralville, Iowa, United States). Massively parallel NextGen sequencing was done on an Illumina platform with ≥100bp paired-end reads. These were aligned to human genome build GRCh37/UCSC hg19, and analyzed for sequence variants using a custom-developed analysis tool.
12 (link)
Additional sequencing and variant interpretation were applied as described previously.
13 (link)
Variant classification criteria are available at GeneDx ClinVar page (
http://www.ncbi.nlm.nih.gov/clinvar/submitters/26957/).

Sills E.S, & Wood S.H. (2022). Phenotype from SAMD9 Mutation at 7p21.2 Appears Attenuated by Novel Compound Heterozygous Variants at RUNX2 and SALL1. Global Medical Genetics, 9(2), 124-128.

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Exome Sequencing and SNP Genotyping from Blood/Saliva

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Genomic DNA (gDNA) was extracted from blood (or rarely, saliva) samples of consenting study participants using Gentra Puregene kit (Qiagen, MD). DNA concentration was measured in a NanoDrop spectrophotometer or by fluorescence using Qubit (Thermo Fisher Scientific, MA). gDNA from study participants were sent to our collaborator, Regeneron Genetics Center LLC (Tarrytown, NY), for exome sequencing and SNP genotyping. Due to poor DNA quality, or sex discrepancy, or contamination, 55 samples were excluded from the analysis. Exons in the remaining samples were captured using the IDT xGen Exome Research Panel v1.0 (Integrated DNA Technologies, Coralville, IA) and sequenced at >30X coverage on the Illumina HiSeq2500 platform (Illumina, San Diego, CA). Raw reads were mapped to GRCh38 using Burrows-Wheeler Alignment Tool (BWA) [54 (link)] and variants were called using the Genome Annotation Toolkit (GATK) Best Practices pipeline (https://software.broadinstitute.org/gatk/best-practices/). GATK’s Variant Quality Score Recalibration (VQSR) procedure was performed to extract superior quality variants. All Mendelian errors, genotypes with GQ < 20, DP < 10 and AB < 0.25/ > 0.75, and variants with >2% missing calls were excluded.

Detera-Wadleigh S.D., Kassem L., Besancon E., Lopes F., Akula N., Sung H., Blattner M., Sheridan L., Lacbawan L.N., Garcia J., Gordovez F., Hosey K., Donner C., Salvini C., Schulze T., Chen D.T., England B., Cross J., Jiang X., Corona W., Russ J., Mallon B., Dutra A., Pak E., Steiner J., Malik N., de Guzman T., Horato N., Mallmann M.B., Mendes V., Dűck A.L., Nardi A.E, & McMahon F.J. (2023). A resource of induced pluripotent stem cell (iPSC) lines including clinical, genomic, and cellular data from genetically isolated families with mood and psychotic disorders. Translational Psychiatry, 13, 397.

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Exome Sequencing and Bioinformatics Processing

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Exome sequencing and bioinformatics processing were performed as previously described [Farwell et al., 2015]. Briefly, patient samples were prepared using either the SureSelect Target Enrichment System (Agilent Technologies, Santa Clara, CA), SeqCap EZ VCRome 2.0 (Roche NimbleGen, Mason, WI), or the IDT xGen Exome Research Panel V1.0 (Integrated DNA Technologies, Coralville, IA). Sequencing was performed using paired‐end, 100 or 150‐cycle chemistry on the Illumina HiSeq or NextSeq (Illumina, San Diego, CA). Bioinformatics filtering removed common benign variants, intergenic and 3′/5′ UTR variants, intronic variants outside ±2, and nonsplice‐related synonymous variants. Alterations that were previously classified as pathogenic or likely pathogenic and those that have an HGMD [Stenson et al., 2014] accession number were protected from filtering. Family history‐based filtering and inheritance models were applied to the data, and identified candidate alterations were subsequently confirmed using automated fluorescence dideoxy sequencing.

Smith E.D., Radtke K., Rossi M., Shinde D.N., Darabi S., El‐Khechen D., Powis Z., Helbig K., Waller K., Grange D.K., Tang S, & Farwell Hagman K.D. (2017). Classification of Genes: Standardized Clinical Validity Assessment of Gene–Disease Associations Aids Diagnostic Exome Analysis and Reclassifications. Human Mutation, 38(5), 600-608.

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Whole Exome Sequencing Using Illumina NovaSeq6000

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Whole exome sequencing was performed on an Illumina NovaSeq6000 device (Illumina, San Diego, CA, USA). The library construction was done using the IDT xGen^® Exome Research Panel v1.0 (Integrated DNA Technologies, Inc., Carolville, IA, USA) according to the manufacturer’s recommendations by pooling the DNA in batches of 8 samples for library capture. Due to the inadequate DNA integrity number (DIN), we had to adjust the DNA input for each sample. Instead of using 200 ng, we used the total available DNA for each sample. So, we ended up generating 11 pools with a starting amount ranging from 510–39 ng. The resulting 8 sample library pools were paired-end sequenced.
Whole exome sequencing quality control: An in-house developed pipline, called “megSAP” was used for data analysis (https://github.com/imgag/megSAP, vers. 0.1-484-g9ad29f4 and 0.1-614-g21d6cfe). In brief, sequencing reads were aligned to the human genome reference sequence (GRCh37) using BWA (vers. 0.7.15) [29 (link)]. Quality control parameters, like sample or data swaps as well as all meta data were collected during all analysis steps [30 (link)].

Forschner A., Hilke F.J., Bonzheim I., Gschwind A., Demidov G., Amaral T., Ossowski S., Riess O., Schroeder C., Martus P., Klumpp B., Gonzalez-Menendez I., Garbe C., Niessner H, & Sinnberg T. (2020). MDM2, MDM4 and EGFR Amplifications and Hyperprogression in Metastatic Acral and Mucosal Melanoma. Cancers, 12(3), 540.

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