Infinium cytosnp 850k beadchip platform

Manufactured by Illumina

Sourced in United States, United Kingdom

The Infinium CytoSNP-850K BeadChip platform is a high-resolution microarray designed for cytogenetic analysis. It provides comprehensive coverage of common cytogenetic regions, including copy number variants and single nucleotide polymorphisms (SNPs), across the human genome.

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Lab products found in correlation

Snp 6.0 array, by Thermo Fisher Scientific (1 mentions) Nexus copy number, by BioDiscovery (1 mentions) Humancytosnp 12 beadchip platform, by Illumina (1 mentions) Genomestudio, by Illumina (1 mentions) Humancytosnp 12 v2.1 beadchip kit, by Illumina (1 mentions)

3 protocols using infinium cytosnp 850k beadchip platform

Genetic Analysis of GAA Gene

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GenBank: NM_001079803.2 and NM_0001079803.2 were used as reference sequences for GAA DNA and mRNA, respectively, where c.1 represents the first nucleotide of the translation start codon ATG. NP000143.2 was used as a reference for GAA protein. We note that in previous annotations, exon 1 comprised 334 nt, whereas in current annotations, this region is divided into two exons (exon 1A and 1B) and a 185-nt intron. All SNP arrays analyses were performed using the Illumina Infinium CytoSNP-850K BeadChip platform. Analysis of genes related to genetic disorders located within specified genomic regions was performed using Genomic Oligoarray and SNP Array Evaluation Tool v3.0.

in ’t Groen S.L., de Faria D.O., Iuliano A., van den Hout J.M., Douben H., Dijkhuizen T., Cassiman D., Witters P., Barba Romero M.Á., de Klein A., Somers-Bolman G.M., Saris J.J., Hoefsloot L.H., van der Ploeg A.T., Bergsma A.J, & Pijnappel W.W. (2020). Novel GAA Variants and Mosaicism in Pompe Disease Identified by Extended Analyses of Patients with an Incomplete DNA Diagnosis. Molecular Therapy. Methods & Clinical Development, 17, 337-348.

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SNP Array Analysis and Trio Genotyping

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For patients A and B, SNP array analysis was performed with Affymetrix SNP6.0 arrays according to the manufacturer’s protocol (Santa Clara, CA, USA) as described [6 (link)]. (Affymetrix is now part of ThermoFisher Scientific, Waltham, MA, USA). DNA trio analysis of patient C and parents was done on the 300 K Illumina (San Diego, CA, USA) HumanCytoSNP-12 BeadChip platform [7 (link), 8 (link)] and trioanalyses of patients D and E and their parents were done on the Illumina InfiniumCytoSNP-850K BeadChip platform [8 (link), 9 (link)]. These platforms had (consecutively) become part of our standard clinical laboratory procedure. A cascade of algorithms was applied for copy number analysis and genotyping, including Genome Studio (Illumina), GTC (Affymetrix) and Nexus CopyNumber™ (Biodiscovery, El Segundo, CA, USA). Analysis of LOH (Loss of Heterozygosity) was based on B-allele frequency calculation (BAF), the B-allele representing the minor non-reference allele. Expected values for BAF are 0 for AA, 0.5 for AB and 1 for BB, meaning ∆BAF represents estimated deviation from the expected AB value.

Labrijn-Marks I., Somers-Bolman G.M., In ’t Groen S.L., Hoogeveen-Westerveld M., Kroos M.A., Ala-Mello S., Amaral O., Miranda C.S., Mavridou I., Michelakakis H., Naess K., Verheijen F.W., Hoefsloot L.H., Dijkhuizen T., Benjamins M., van den Hout H.J., van der Ploeg A.T., Pijnappel W.W., Saris J.J, & Halley D.J. (2019). Segmental and total uniparental isodisomy (UPiD) as a disease mechanism in autosomal recessive lysosomal disorders: evidence from SNP arrays. European Journal of Human Genetics, 27(6), 919-927.

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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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