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Human cytosnp 12 array

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The Human CytoSNP-12 array is a high-density single nucleotide polymorphism (SNP) genotyping array designed for cytogenetic analysis. The array contains probes targeting over 300,000 SNP loci across the human genome.

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Lab products found in correlation

Beadstudio software, by Illumina (3 mentions) 1m array, by Illumina (2 mentions) Snp arrays, by Illumina (2 mentions) Quantisnp70, by BioDiscovery (2 mentions) Nexus copy number version 7, by BioDiscovery (2 mentions) Iscan control, by Illumina (1 mentions) Genomestudio software, by Illumina (1 mentions)

Close spelling variants of this product

CytoSNP-12 (5 citations) Human CytoSNP array (2 citations)

9 protocols using human cytosnp 12 array

1

Validating Genotyping and Familial Relationships

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Illumina SNP arrays were run on some WGS500 samples and other relatives. This was to check the genotyping accuracy of our sequencing pipeline, to refine linkage regions, to confirm familial relationships, and, in two cases, to investigate whether large stretches of homozygosity were likely due to uniparental disomy or unreported consanguinity. We ran 200 ng of DNA on the Illumina Human CytoSNP12 array or on the 1M array (Illumina Inc.), following the manufacturer’s guidelines. Concordance between the CytoSNP12 genotypes and the WGS data is shown in Supplementary Tables 1 and 2, and the dependence on coverage in Supplementary Figure 2. In most cases, array-CGH had already been performed prior to submission of samples, but we also used QuantiSNP70 to check for CNVs, as well as Nexus Copy Number version 7 (BioDiscovery, Hawthorn, CA). We used MERLIN71 in familial studies to identify regions identical-by-descent.
Taylor J.C., Martin H.C., Lise S., Broxholme J., Cazier J.B., Rimmer A., Kanapin A., Lunter G., Fiddy S., Allan C., Aricescu A.R., Attar M., Babbs C., Becq J., Beeson D., Bento C., Bignell P., Blair E., Buckle V.J., Bull K., Cais O., Cario H., Chapel H., Copley R.R., Cornall R., Craft J., Dahan K., Davenport E.E., Dendrou C., Devuyst O., Fenwick A.L., Flint J., Fugger L., Gilbert R.D., Goriely A., Green A., Greger I.H., Grocock R., Gruszczyk A.V., Hastings R., Hatton E., Higgs D., Hill A., Holmes C., Howard M., Hughes L., Humburg P., Johnson D., Karpe F., Kingsbury Z., Kini U., Knight J.C., Krohn J., Lamble S., Langman C., Lonie L., Luck J., McCarthy D., McGowan S.J., McMullin M.F., Miller K.A., Murray L., Németh A.H., Nesbit M.A., Nutt D., Ormondroyd E., Oturai A.B., Pagnamenta A., Patel S.Y., Percy M., Petousi N., Piazza P., Piret S.E., Polanco-Echeverry G., Popitsch N., Powrie F., Pugh C., Quek L., Robbins P.A., Robson K., Russo A., Sahgal N., van Schouwenburg P.A., Schuh A., Silverman E., Simmons A., Sørensen P.S., Sweeney E., Taylor J., Thakker R.V., Tomlinson I., Trebes A., Twigg S.R., Uhlig H.H., Vyas P., Vyse T., Wall S.A., Watkins H., Whyte M.P., Witty L., Wright B., Yau C., Buck D., Humphray S., Ratcliffe P.J., Bell J.I., Wilkie A.O., Bentley D., Donnelly P, & McVean G. (2015). Factors influencing success of clinical genome sequencing across a broad spectrum of disorders. Nature genetics, 47(7), 717-726.
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2

Genomic DNA Profiling via SNP Array

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Genomic DNA was extracted from peripheral blood and hybridized to a Human CytoSNP-12 array (Illumina, San Diego, CA, USA) as reported before [21 (link)]. The array was scanned with the Illumina iScan Control. Data were processed using Genome Studio v2.1 software and analyzed with Nexus Copy Number software v5.0 (Biodiscovery, El Segundo, CA, USA).
Pellikaan K., van Woerden G.M., Kleinendorst L., Rosenberg A.G., Horsthemke B., Grosser C., van Zutven L.J., van Rossum E.F., van der Lely A.J., Resnick J.L., Brüggenwirth H.T., van Haelst M.M, & de Graaff L.C. (2021). The Diagnostic Journey of a Patient with Prader–Willi-Like Syndrome and a Unique Homozygous SNURF-SNRPN Variant; Bio-Molecular Analysis and Review of the Literature. Genes, 12(6), 875.
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3

Chromosomal Microarray Analysis for Mosaic Abnormalities

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DNA was extracted from villi, amniotic fluid, or cord blood. Chromosomal microarray analysis was performed using the Illumina Human CytoSNP-12 array, according to the manufacturer’s instructions. The results were analyzed with Illumina BeadStudio software.
Mosaic changes were detected by assessing for aberrations in probe intensities (log R ratios) along with shifts in genotype frequencies of the SNP probes (B allele frequencies) [26 (link)]. Mosaic trisomy is diagnosed when the log R ratio shows an increase in copy number, with between two and three copies; in addition, the B allele frequency must appear to be altered. In the case of mosaic monosomy, the log R ratio indicates a decrease in copy number, between one and two copies.
Zhou L., Li H., Xu C., Xu X., Zheng Z, & Tang S. (2023). Characteristics and mechanisms of mosaicism in prenatal diagnosis cases by application of SNP array. Molecular Cytogenetics, 16, 13.
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4

Chromosomal Microarray Analysis of Supernumerary Marker Chromosomes

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Chromosomal microarray analysis was performed on the 15 cases of sSMC using the Affymetrix CytoScan 750 k Array or the Illumina Human CytoSNP-12 array according to the manufacturer’s instructions. The results were analysed with Chromosome Analysis Suite software or Illumina’s BeadStudio software. All detected CNVs were compared with known CNVs in the scientific literature and with those in the following publicly available databases: Database of Genomic Variants (http://dgv.tcag.ca/dgv/app/home), DECIPHER database (http://decipher.sanger.ac.uk/), International Standards for Cytogenomic Array (ISCA; https://www.iscaconsortium.org/), Online Mendelian Inheritance in Man (OMIM; http://www.omim.org) and ClinGen Dosage Sensitivity Map (https://www.ncbi.nlm.nih.gov/projects/dbvar/clingen).
Based on the American College of Medical Genetics Standards and Guidelines, the CNVs were classified as pathogenic (P), likely pathogenic (LP), likely benign (LB), variant of unknown significance (VOUS) or benign (B). All reported CNVs were based on the National Center for Biotechnology Information human genome build 37 (hg 19).
Zhou L., Zheng Z., Wu L., Xu C., Wu H., Xu X, & Tang S. (2020). Molecular delineation of small supernumerary marker chromosomes using a single nucleotide polymorphism array. Molecular Cytogenetics, 13, 19.
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5

Validating Genotyping and Familial Relationships

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Illumina SNP arrays were run on some WGS500 samples and other relatives. This was to check the genotyping accuracy of our sequencing pipeline, to refine linkage regions, to confirm familial relationships, and, in two cases, to investigate whether large stretches of homozygosity were likely due to uniparental disomy or unreported consanguinity. We ran 200 ng of DNA on the Illumina Human CytoSNP12 array or on the 1M array (Illumina Inc.), following the manufacturer’s guidelines. Concordance between the CytoSNP12 genotypes and the WGS data is shown in Supplementary Tables 1 and 2, and the dependence on coverage in Supplementary Figure 2. In most cases, array-CGH had already been performed prior to submission of samples, but we also used QuantiSNP70 to check for CNVs, as well as Nexus Copy Number version 7 (BioDiscovery, Hawthorn, CA). We used MERLIN71 in familial studies to identify regions identical-by-descent.
Taylor J.C., Martin H.C., Lise S., Broxholme J., Cazier J.B., Rimmer A., Kanapin A., Lunter G., Fiddy S., Allan C., Aricescu A.R., Attar M., Babbs C., Becq J., Beeson D., Bento C., Bignell P., Blair E., Buckle V.J., Bull K., Cais O., Cario H., Chapel H., Copley R.R., Cornall R., Craft J., Dahan K., Davenport E.E., Dendrou C., Devuyst O., Fenwick A.L., Flint J., Fugger L., Gilbert R.D., Goriely A., Green A., Greger I.H., Grocock R., Gruszczyk A.V., Hastings R., Hatton E., Higgs D., Hill A., Holmes C., Howard M., Hughes L., Humburg P., Johnson D., Karpe F., Kingsbury Z., Kini U., Knight J.C., Krohn J., Lamble S., Langman C., Lonie L., Luck J., McCarthy D., McGowan S.J., McMullin M.F., Miller K.A., Murray L., Németh A.H., Nesbit M.A., Nutt D., Ormondroyd E., Oturai A.B., Pagnamenta A., Patel S.Y., Percy M., Petousi N., Piazza P., Piret S.E., Polanco-Echeverry G., Popitsch N., Powrie F., Pugh C., Quek L., Robbins P.A., Robson K., Russo A., Sahgal N., van Schouwenburg P.A., Schuh A., Silverman E., Simmons A., Sørensen P.S., Sweeney E., Taylor J., Thakker R.V., Tomlinson I., Trebes A., Twigg S.R., Uhlig H.H., Vyas P., Vyse T., Wall S.A., Watkins H., Whyte M.P., Witty L., Wright B., Yau C., Buck D., Humphray S., Ratcliffe P.J., Bell J.I., Wilkie A.O., Bentley D., Donnelly P, & McVean G. (2015). Factors influencing success of clinical genome sequencing across a broad spectrum of disorders. Nature genetics, 47(7), 717-726.
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6

Genotype-Based Parametric Linkage Analysis

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Genomic DNAs from 8 individuals (100290, 100471, 100475, 100481, 100487, 100784, 100889, 100913) were genotyped using the Illumina HumanCytoSNP-12 array. A total of 299,671 markers were called for each individual. SNP pruning was then performed using PLINK (http://pngu.mgh.harvard.edu/~purcell/plink/index.shtml). The genotype calls were filtered for the following criteria, in sequential order: genotype missingness, with a cutoff of 30% (289,305 SNPs remaining); Mendelian errors (289,305 SNPs remaining); and absence of linkage disequilibrium using pairwise genotypic correlation, with r2 cutoff of 0.1, and a sliding window of 50 SNPs (4,782 SNPs remaining). The filtered set of SNPs was used to calculate linkage, using the parametric linkage capabilities of the software package MERLIN (http://www.sph.umich.edu/csg/abecasis/Merlin/index.html). Map positions of each marker were calculated using interpolation of the Rutgers Combined Linkage-Physical Map Build 36/37. The parametric model assumed an autosomal dominant mode of inheritance with 90% penetrance.
Shi G., Xing L., Wu D., Bhattacharyya B.J., Jones C.R., McMahon T., Chong S.Y., Chen J.A., Coppola G., Geschwind D., Krystal A., Ptáček L.J, & Fu Y.H. (2019). A rare mutation of β1-adrenergic receptor affects sleep/wake behaviors. Neuron, 103(6), 1044-1055.e7.
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7

Chromosomal Microarray Analysis for CNV and UPD

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Chromosomal microarray analysis was performed using the Illumina Human CytoSNP-12 array (Illumina, USA) according to the manufacturer’s instructions. The results were analyzed with Illumina BeadStudio software. All detected CNVs were compared with known CNVs in the scientific literature and publicly available databases: Database of Genomic Variants, DECIPHER database, International Standards for Cytogenomic Array, Online Mendelian Inheritance in Man and ClinGen Dosage Sensitivity Map. All reported copy number variants (CNVs) were based on the National Center for Biotechnology Information human genome build 37 (hg 19).
UPD changes were detected by assessing for aberrations in probe intensities (log R ratios) along with shifts in genotype frequencies of the SNP probes (B allele frequencies) [8 (link)]. UPD is diagnosed when the log R ratio is zero, which equates to two copies. Meanwhile, in UPD, the B allele frequency is 0% and 100%, and only two haplotypes can be seen. When UPD is visible near the telomeres, but not the centromere, meiosis I non-disjunction is indicated. When UPD is present at the centromeres, meiosis II non-disjunction is indicated. When UPD is present at the whole chromosome, mitosis non-disjunction is indicated.
Zhou L., Zheng Z., Xu Y., Lv X., Xu C, & Xu X. (2021). Prenatal diagnosis of 7 cases with uniparental disomy by utilization of single nucleotide polymorphism array. Molecular Cytogenetics, 14, 19.
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8

Identifying Pathogenic Variant through Genome-wide Genotyping and Exome Sequencing

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In order to map the chromosomal location of the pathogenic variant, samples from the family were genotyped using an Illumina Human CytoSNP-12 array incorporating ~330,000 genetic markers, according to the manufacturer’s protocol.
In order to identify the disease associated gene, whole-exome sequencing was performed on a single affected individual in this family (subject III:12, Fig. 1) to generate a profile of variants not present in publically available databases and rare sequence variants. Coding regions were captured by HiSeq2000 using paired-end (2 x 100) protocol at a mean coverage depth of 30X at Otogenetics Corporation (Norcross, GA, USA). The Agilent SureSelect Human All ExonV4 (51 Mb) enrichment kit was used for exome enrichment. Sequence reads were aligned to the human genome reference sequence [hg19] and read alignment, variant calling, and annotation were performed by DNAnexus (DNAnexus Inc., Mountain View, CA; https://dnanexus.com)
Aharoni S., Barwick K.E., Straussberg R., Harlalka G.V., Nevo Y., Chioza B.A., McEntagart M.M., Mimouni-Bloch A., Weedon M, & Crosby A.H. (2016). Novel homozygous missense mutation in GAN associated with Charcot-Marie-Tooth disease type 2 in a large consanguineous family from Israel. BMC Medical Genetics, 17, 82.
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9

iPSC Clone Characterization Protocol

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DNA sample was collected from fibroblasts or blood cells and iPSC clones (p16-BBANTWi006-A, p10-BBANTWi007-A). DNA was extracted using an automatic DNA extraction system Maxwell® RSC with Maxwell® RSC Cultured Cells DNA Kit (Promega), following manufacturer’s protocol and DNA samples were stored at + 4 °C after extraction. HumanCytoSNP-12 array (Illumina) was run according to the manufacturer’s protocol for the automated Infinium HD Assay Ultra on an iScan instrument. Results were visualized using Genome Studio software (Illumina) and identity between the iPSC clones and original cell line confirmed. Results were further analysed with CNV-WebStore, an in-house developed online available CNV Analysis tool (http://cnv-webstore.ua.ac.be).
Simons E., Nijak A., Loeys B, & Alaerts M. (2022). Generation of two induced pluripotent stem cell (iPSC) lines (BBANTWi006-A, BBANTWi007-A) from Brugada syndrome patients carrying an SCN5A mutation. Stem Cell Research, 60, 102719.
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