Humancytosnp 12 v2.1 beadchip kit

Manufactured by Illumina

Sourced in United States

The HumanCytoSNP-12 v2.1 BeadChip kit is a microarray-based genome-wide genotyping product designed by Illumina. It is used to detect genetic variations, specifically single nucleotide polymorphisms (SNPs), across the human genome. The kit provides comprehensive coverage of the genome for cytogenetic research applications.

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Lab products found in correlation

Genomestudio 2011, by Illumina (1 mentions) Iscan system, by Illumina (1 mentions) Cytoscan 750k array, by Thermo Fisher Scientific (1 mentions) Infinium cytosnp 850k beadchip platform, by Illumina (1 mentions)

4 protocols using humancytosnp 12 v2.1 beadchip kit

Genotyping and Linkage Analysis of HM1 Family

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Eighteen samples from the HM1 family were genotyped using Illumina iScan system (Illumina, USA) and Illumina HumanCytoSNP-12 V.2.1 BeadChip kit. Genotypes were called and quality controlled using Illumina GenomeStudio 2011. Genome-wide linkage disequilibrium of HM1 family was tested by merlin V.1.1.226 (link) under multiple-parameter analysis with ‘High_myopia 0.001 0.001,0.9,0.99 rare_dominant’ settings. The ‘merlin’ or ‘minx’ prompt was used to analyse the autosomal or X linked linkage disequilibrium separately. Merlin V.1.1.2 drew the haplotype of HM1 and HM2 families with the ‘best’ option.

Tian Q., Tong P., Chen G., Deng M., Cai T., Tian R., Zhang Z., Xia K, & Hu Z. (2022). GLRA2 gene mutations cause high myopia in humans and mice. Journal of Medical Genetics, 60(2), 193-203.

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Karyotyping of SOD1 iPSC Clones

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SOD1 iPSC and control cell lines were karyotyped using the HumanCytoSNP-12 v2.1 BeadChip Kit (Illumina Inc., San Diego, CA, USA). All clones showing pathological SNPs were excluded prior to the study.

Günther R., Pal A., Williams C., Zimyanin V.L., Liehr M., von Neubeck C., Krause M., Parab M.G., Petri S., Kalmbach N., Marklund S.L., Sterneckert J., Munch Andersen P., Wegner F., Gilthorpe J.D, & Hermann A. (2022). Alteration of Mitochondrial Integrity as Upstream Event in the Pathophysiology of SOD1-ALS. Cells, 11(7), 1246.

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Maternal and Fetal CNV Confirmation Techniques

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Maternal CNVs were con rmed on DNA extracted from maternal white blood cells, obtained from the stored buffy coats of the NIPS blood samples or from additional maternal blood samples. Fetal CNVs were con rmed on DNA extracted from amniotic uid. The CNV con rmation was performed using the Agilent ISCA 60 K or 44 K array (Agilent, Santa Clara, CA, USA), Cytoscan 750 K array (Affymetrix, Santa Clara, CA, USA), HumanCytoSNP-12 v2.1 BeadChip kit (Illumina) or by shallow genome sequencing (CNVSeq). Fluorescent in situ hybridization (FISH) and conventional karyotyping were performed according to standard procedures. To determine maternal or paternal inheritance of the duplication, the methylation status of the CNVs was investigated by Methylation-Speci c Multiplex Ligation-Dependent Probe Ampli cation using the SALSA MLPA kit P140 probe mix HBA (MRC-Holland, Amsterdam, the Netherlands) or by an alternative methylation speci c method in which bisul te treatment was used following a speci c PCR and migration on the ABI 3130 genetics analyzer.

Parijs I., Brison N., Vancoillie L., Baetens M., Blaumeiser B., Boulanger S., Désir J., Dimitrov B., Fieremans N., Janssens K., Janssens S., Marichal A., Menten B., Meunier C., Van Berkel K., Van Den Bogaert A., Devriendt K., Van Den Bogaert K, & Vermeesch J.R. (2024). Population screening for 15q11-q13 duplications: corroboration of the difference in impact between maternally and paternally inherited alleles. European journal of human genetics : EJHG, 32(1).

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Genome-wide SNP Analysis for Copy Number

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Genome-wide SNPs were investigated on the HumanCytoSNP-12 v2.1 BeadChip kit (n Z 11) or the Infinium CytoSNP-850K BeadChip platform (n Z 2) (Illumina Inc., UK) and for every SNP the log2 (ratio) was called with GenomeStudio 2.0 according to the manufacturer's instructions (samples from Motol Hospital). Afterwards, these individual positions were converted to GRCh38 and grouped into regions of 200 kb with bedtools [29] (link) v2.27.1 by taking the mean of each individual SNP. The CBS algorithm (DNA copy R package [30] ) was then applied to group these bins into segments with equal copy numbers.

Van Paemel R., Vandeputte C., Raman L., Van Thorre J., Willems L., Van Dorpe J., Van Der Linden M., De Wilde J., De Koker A., Menten B., Devalck C., Vicha A., Grega M., Schleiermacher G., Iddir Y., Chicard M., van Zogchel L., Stutterheim J., Lak N.S.M., Tytgat G.A.M., Laureys G., Speleman F., De Wilde B., Lammens T., De Preter K, & Van Roy N. (2022). The feasibility of using liquid biopsies as a complementary assay for copy number aberration profiling in routinely collected paediatric cancer patient samples. European journal of cancer (Oxford, England : 1990), 160.

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