Cnvpartition v3

Manufactured by Illumina

Sourced in United States

CNVPartition v3.2 is a software tool developed by Illumina for the detection and analysis of copy number variations (CNVs) in genomic data. The core function of this product is to identify and characterize CNVs from Next Generation Sequencing (NGS) data.

Automatically generated - may contain errors

Lab products found in correlation

Humanomniexpressexome beadchip, by Illumina (2 mentions) Nexus copy number v7, by BioDiscovery (2 mentions) Genomestudio v2011, by Illumina (2 mentions) Omniexpressexome beadchip, by Illumina (2 mentions) Omniexpress beadchip, by Illumina (2 mentions) Humanexome beadchip, by Illumina (1 mentions) Genomestudio, by Illumina (1 mentions) Genomestudio v2, by Illumina (1 mentions) Genomestudio software, by Illumina (1 mentions)

6 protocols using cnvpartition v3

Twin Genotyping and Copy Number Variation Analysis

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Fifteen twin pairs were genotyped using the HumanOmniExpressExome BeadChip platform (964,193 SNPs), following the Illumina Infinium Assay protocol. The data were scanned by iScan and processed with the genotype module in GenomeStudio v2011.1 (Illumina, San Diego, CA). Samples with a call rate of <0.99 and SNPs with a GenTrain score of <0.7 were excluded from analysis. Copy number analysis was performed on the remaining 941,932 SNPs using CNVPartition v3.2 (Illumina, San Diego, CA) and Nexus Copy Number v7 (Biodiscovery, Inc, El Segundo, CA). Details of CNV definition are given in Supplementary Methods 11. We focused on CNVs that recurred across either affected or unaffected twins.

Chen Y.C., Sudre G., Sharp W., Donovan F., Chandrasekharappa S.C., Hansen N., Elnitski L, & Shaw P. (2017). Neuroanatomic, epigenetic, and genetic differences in monozygotic twins discordant for Attention Deficit Hyperactivity Disorder. Molecular psychiatry, 23(3), 683-690.

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DNA Variant Detection Using Exome Chip

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The patient DNA samples were run on the Illumina HumanExome Bead Chip, containing ~250,000 SNPs. The data were processed using GenomeStudio (Illumina, Inc.), and CNVs were detected using cnvPartition v3.2 (Illumina, Inc.) and Nexus v7.5 (BioDiscovery, Inc.).

Chandrasekharappa S.C., Chinn S.B., Donovan F.X., Chowdhury N.I., Kamat A., Adeyemo A.A., Thomas J.W., Vemulapalli M., Hussey C.S., Reid H.H., Mullikin J.C., Wei Q, & Sturgis E.M. (2017). Assessing the Spectrum of Germline Variation in Fanconi Anemia Genes among Patients with Head and Neck Carcinoma before Age 50. Cancer, 123(20), 3943-3954.

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Molecular Karyotyping and Identity Analysis of iPSCs

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Molecular karyotyping and identity analysis was performed on the iPS clones at Life&Brain GmBH (Bonn, Germany) using the Illumina BeadArray HumanOmni2.5Exome-8 BeadChip v1.3 on the Illumina iScan (Serial Number: N263) scanner (Illumina Inc. San Diego, CA, USA). A genotype analysis was performed using GenomeStudio V2.0.2 with a copy number analysis undertaken using the CNV-Partition V3.2 (Illumina Inc. San Diego, CA, USA). Copy number events were reported if larger than 350,000 base pairs. The method overviewing the high-resolution whole sequence genomic profiling technology that was used in this study has been previously described [32 (link)]. The molecular karyotyping report for each iPS clone analyzed are available with the authors and can be made available upon reasonable request.

Barbuti P., Antony P., Santos B., Massart F., Cruciani G., Dording C., Arias J., Schwamborn J, & Krüger R. (2020). Using High-Content Screening to Generate Single-Cell Gene-Corrected Patient-Derived iPS Clones Reveals Excess Alpha-Synuclein with Familial Parkinson’s Disease Point Mutation A30P. Cells, 9(9), 2065.

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Twin Genotyping and Copy Number Variation Analysis

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Genotyping of Genomic Variants

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Genotyping was performed at John P. Hussman Institute for Human Genomics, University of Miami using Illumina (San Diego, CA) OmniExpress BeadChip or Illumina OmniExpressExome BeadChip. Genotype calls were generated with Illumina GenomeStudio software. Overlapping markers from 2 genotyping platforms were combined for data quality control (QC); single nucleotide polymorphisms (SNPs) were excluded if they had call rate < 95%, were monomorphic, or deviated from Hardy-Weinberg equilibrium (p < 0.00001). Samples were excluded if they showed call rate < 95%, had sex mismatch, had unconfirmed relatedness, or did not carry the classic 1.5 Mb duplication on chromosome 17p. Copy number variation (CNV) was checked using Illumina cnvPartition v3.2.1. Population stratification was assessed using EigenStrat.^{15 (link)} All other QC procedures were performed with PLINK v1.07.^{16 (link)} The combined dataset after QC included 699,650 markers and 903 samples.

Tao F., Beecham G.W., Rebelo A.P., Blanton S.H., Moran J.J., Lopez-Anido C., Svaren J., Morrow J.M., Abreu L., Rizzo D., Kirk C.A., Wu X., Feely S., Verhamme C., Saporta M.A., Herrmann D.N., Day J.W., Sumner C.J., Lloyd T.E., Li J., Yum S.W., Taroni F., Baas F., Choi B.O., Pareyson D., Scherer S.S., Reilly M.M., Shy M.E, & Züchner S. (2019). Variation in SIPA1L2 Is Correlated with Phenotype Modification in Charcot– Marie– Tooth Disease Type 1A. Annals of neurology, 85(3), 316-330.

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Genotyping and Quality Control for GWAS

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Genotyping and data QC have been described previously in [32, 33 ]. Patient DNA samples were genotyped using Illumina OmniExpress beadchip or Illumina OmniExpress Exome beadchip. Standard GWAS QC was performed using PLINK v1.07 [10 (link)] to remove monomorphic SNPs and SNPs with low call rate (<95%) or deviating from Hardy-Weinberg equilibrium (HWE P < 0.00001). Samples were checked for the classic 1.5 Mb duplication on chromosome 17p using Illumina cnvPartition v3.2.1. Population stratification was assessed by principal component analysis (PCA) using EigenStrat [11 (link)].

Tao F., Beecham G.W., Rebelo A.P., Blanton S.H., Moran J.J., Lopez-Anido C., Svaren J., Abreu L., Rizzo D., Kirk C.A., Wu X., Feely S., Verhamme C., Saporta M.A., Herrmann D.N., Day J.W., Sumner C.J., Lloyd T.E., Li J., Yum S.W., Taroni F., Baas F., Choi B.O., Pareyson D., Scherer S.S., Reilly M.M., Shy M.E, & Züchner S. (2019). Modifier Gene Candidates in Charcot-Marie-Tooth Disease Type 1A: A Case-Only Genome-Wide Association Study. Journal of Neuromuscular Diseases, 6(2), 201-211.

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