Humancytosnp 12 beadchip platform

Manufactured by Illumina

Sourced in United States

The HumanCytoSNP-12 BeadChip platform is a laboratory equipment designed for genome-wide genotyping. It provides comprehensive coverage of single nucleotide polymorphisms (SNPs) across the human genome.

Automatically generated - may contain errors

Lab products found in correlation

Nexus copy number, by BioDiscovery (2 mentions) Seqscape v2, by Thermo Fisher Scientific (1 mentions) Genemapper v5, by Thermo Fisher Scientific (1 mentions) Abi 3730xl dna analyzer, by Thermo Fisher Scientific (1 mentions) Iscan reader, by Illumina (1 mentions) Genomestudio v2011, by Illumina (1 mentions) Dneasy blood tissue kit, by Qiagen (1 mentions) Snp 6.0 array, by Thermo Fisher Scientific (1 mentions) Infinium cytosnp 850k beadchip platform, by Illumina (1 mentions) Genomestudio, by Illumina (1 mentions) Qbaseplus, by CellCarta (1 mentions) Lightcycler 480, by Roche (1 mentions) Qiacube instrument, by Qiagen (1 mentions) Karyostudio, by Illumina (1 mentions) Pinpoint slide dna isolation system, by Zymo Research (1 mentions) Qiaamp dna mini kit, by Qiagen (1 mentions) Sure select human all exon v5 v6 kit, by Agilent Technologies (1 mentions)

10 protocols using humancytosnp 12 beadchip platform

Genome-Wide Homozygosity Mapping in Siblings

Cited 1 time

Check if the same lab product or an alternative is used in the 5 most similar protocols

This was performed in the two affected siblings by genome-wide single-nucleotide polymorphism chip analysis using the HumanCytoSNP-12 BeadChip platform (Illumina, San Diego, CA). Identity-by-descent regions (>1 Mb) were identified using PLINK software55 (link) integrated in ViVar56 (link). Resulting homozygous regions were ranked according to their length and number of consecutive homozygous single-nucleotide polymorphisms, as described by Coppieters et al57 (link).

Van Schil K., Karlstetter M., Aslanidis A., Dannhausen K., Azam M., Qamar R., Leroy B.P., Depasse F., Langmann T, & De Baere E. (2016). Autosomal recessive retinitis pigmentosa with homozygous rhodopsin mutation E150K and non-coding cis-regulatory variants in CRX-binding regions of SAMD7. Scientific Reports, 6, 21307.

+ Open protocol

+ Expand

Genetic Mapping of CARD9 Mutations

Check if the same lab product or an alternative is used in the 5 most similar protocols

Genomic DNA was isolated from whole blood cells according to standard procedures. Identity-by-descent (IBD) mapping was carried out in two affected individuals (F2 III:2, III:3) from family 2 by genome-wide single-nucleotide polymorphism (SNP) arrays using the HumanCytoSNP-12 BeadChip platform (Illumina, San Diego, CA). Ten IBD regions (>1 Mb) were identified using PLINK software (20 (link)). Starting from the IBD region (3.3 Mb) encompassing CARD9, four microsatellite markers were selected using NCBI Map Viewer (including genetic maps deCODE, Généthon, Marshfield and Rutgers Map v.3). In addition, five tagging SNP markers (UCSC Table Browser) were genotyped to further delineate the common haplotype. Primers were designed with Primer3Plus. Fragment analysis and sequencing were performed on the ABI 3730XL DNA Analyzer (Applied Biosystems). Data analysis of the microsatellite markers was performed with the GeneMapper v5 software (Applied Biosystems) and SNP markers were analyzed with SeqScape v2.5 (Life Technologies). Microsatellite and SNP markers were genotyped for haplotype analysis in ten affected patients and eleven healthy family members of the five families.

De Bruyne M., Hoste L., Bogaert D.J., Van den Bossche L., Tavernier S.J., Parthoens E., Migaud M., Konopnicki D., Yombi J.C., Lambrecht B.N., van Daele S., Alves de Medeiros A.K., Brochez L., Beyaert R., De Baere E., Puel A., Casanova J.L., Goffard J.C., Savvides S.N., Haerynck F., Staal J, & Dullaers M. (2018). A CARD9 Founder Mutation Disrupts NF-κB Signaling by Inhibiting BCL10 and MALT1 Recruitment and Signalosome Formation. Frontiers in Immunology, 9, 2366.

+ Open protocol

+ Expand

Genome-wide SNP Genotyping for Structural Variations

Check if the same lab product or an alternative is used in the 5 most similar protocols

The screening of genomic rearrangements and mapping of the breakpoints were performed with the HumanCytoSNP-12 BeadChip platform (Illumina), comprising 301,232 SNPs. Genomic DNA was prepared from peripheral blood and then extracted using a DNeasy Blood & Tissue Kit (Qiagen) according to manufacturer’s protocol. Genomic DNA samples were adjusted to a final concentration 50 ng/μL. DNA amplification, tagging and hybridization were performed according to the manufacturer's protocol. Array slides were scanned on the iScan Reader (Illumina). The GenomeStudio V2011 software (Illumina) was used to analyse the genotypes (human genome build 37/Hg19 for analysis) and evaluate the experimental quality. The call rates of the samples were greater than 99.5%.

Pan Q., Hu H., Han L., Jing X., Liu H., Yang C., Zhang F., Hu Y., Yue H, & Ning Y. (2016). Mapping Breakpoints of Complex Chromosome Rearrangements Involving a Partial Trisomy 15q23.1-q26.2 Revealed by Next Generation Sequencing and Conventional Techniques. PLoS ONE, 11(5), e0154574.

+ Open protocol

+ Expand

Identifying Shared Regions of Homozygosity

Cited 2 times

Check if the same lab product or an alternative is used in the 5 most similar protocols

In patient 1, ROH were identified using HomozygosityMapper and applying default settings (32 (link)). ROH of less than 3 kb adjacent to each other were merged manually, reducing ROH from 71 to 67. In patient 2, ROH were initially mapped by genome–wide single-nucleotide polymorphism (SNP) chip analysis (HumanCytoSNP-12 BeadChip platform; Illumina). ROH (> 1 Mb) were identified using PLINK software (33 (link)) integrated in ViVar (34 (link)) and ranked according to length and number of consecutive homozygous SNPs. For both patients 1 and 2, ROH were determined with AutoMap (35 (link)) using VCF files from both patients (hg38). After identification of individual ROH, shared ROH (based on coordinates) were determined (Figure 2C and Supplemental Table 1). To define the shared ROH on chromosome 6 and the common haplotype containing the CEP162 variant, all WES variants on chromosome 6 were considered, irrespective of their zygosity (Figure 2C).

Nuzhat N., Van Schil K., Liakopoulos S., Bauwens M., Rey A.D., Käseberg S., Jäger M., Willer J.R., Winter J., Truong H.M., Gruartmoner N., Van Heetvelde M., Wolf J., Merget R., Grasshoff-Derr S., Van Dorpe J., Hoorens A., Stöhr H., Mansard L., Roux A.F., Langmann T., Dannhausen K., Rosenkranz D., Wissing K.M., Van Lint M., Rossmann H., Häuser F., Nürnberg P., Thiele H., Zechner U., Pearring J.N., De Baere E, & Bolz H.J. (2023). CEP162 deficiency causes human retinal degeneration and reveals a dual role in ciliogenesis and neurogenesis. The Journal of Clinical Investigation, 133(8), e161156.

+ Open protocol

+ Expand

SNP Array Analysis and Trio Genotyping

Cited 1 time

Check if the same lab product or an alternative is used in the 5 most similar protocols

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.

+ Open protocol

+ Expand

Genome-wide SNP Genotyping for Autozygous Region

Check if the same lab product or an alternative is used in the 5 most similar protocols

In order to assess the size of the autozygous region and haplotype in which the homozygous FTL 5′UTR mutation is located, genome-wide SNP genotyping was performed using the HumanCytoSNP-12 BeadChip platform (Illumina). Plink software, integrated in ViVar, identified homozygous regions >1 Mb which were ranked according to their length and the number of SNPs, as described^{16 (link)}.

Van de Sompele S., Pécheux L., Couso J., Meunier A., Sanchez M, & De Baere E. (2017). Functional characterization of a novel non-coding mutation “Ghent +49A > G” in the iron-responsive element of L-ferritin causing hereditary hyperferritinaemia-cataract syndrome. Scientific Reports, 7, 18025.

+ Open protocol

+ Expand

Copy Number Variation Screening of CYP4V2

Check if the same lab product or an alternative is used in the 5 most similar protocols

CNV screening on genomic DNA was performed in the families with only one CYP4V2 mutation (probands F, I, and J), using 13 quantitative PCR (qPCR) assays, covering the 11 exons of CYP4V2 and two reference genes (ZNF80 and GPR15) on the LightCycler 480 (Roche, Basel, Switzerland). Four controls were included in each experiment. Conditions and primers can be found in Table S2. Data analysis was performed using qBasePlus (Biogazelle, Zwijnaarde, Belgium).
Genome-wide SNP chip analysis was performed using the HumanCytoSNP-12 BeadChip platform (Illumina, San Diego, CA) (proband F) in order to delineate the deletion.

Astuti G.D., Sun V., Bauwens M., Zobor D., Leroy B.P., Omar A., Jurklies B., Lopez I., Ren H., Yazar V., Hamel C., Kellner U., Wissinger B., Kohl S., De Baere E., Collin R.W, & Koenekoop R.K. (2014). Novel insights into the molecular pathogenesis of CYP4V2-associated Bietti's retinal dystrophy. Molecular Genetics & Genomic Medicine, 3(1), 14-29.

+ Open protocol

+ Expand

FFPE DNA Extraction and SNP Microarray

Check if the same lab product or an alternative is used in the 5 most similar protocols

DNA was extracted using 4–10 unstained slides of FFPE tissue using the Pinpoint Slide DNA Isolation system (Zymo Research, Orange, CA). In brief, unstained slides were deparaffinized with xylene followed by tissue dissection and Proteinase K digestion. DNA cleanup was performed using the QIAamp DNA mini kit with the QIAcube instrument (QIAGEN, Valencia, CA). SNP-microarray using the HumanCytoSNP12 BeadChip platform (Illumina, San Diego, CA), which assesses ~300,000 polymorphic loci, was performed per manufacturer’s protocol. Analysis was completed using KaryoStudio (Illumina, San Diego, CA) and Nexus Copy Number (BioDiscovery, Hawthorne, CA). SNP and gene annotations were compared against the National Center for Biotechnology Information (NCBI) genome build 37 (GRCh37/hg19). CNVs were determined by independent and consensus review by R.R.X and C.D.G. Detailed interpretive criteria can be found in Supplementary Information.

Xian R.R., Xie Y., Haley L.M., Yonescu R., Pallavajjala A., Pittaluga S., Jaffe E.S., Duffield A.S., McCall C.M., Gheith S.M, & Gocke C.D. (2020). CREBBP and STAT6 co-mutation and 16p13 and 1p36 loss define the t(14;18)-negative diffuse variant of follicular lymphoma. Blood Cancer Journal, 10(6), 69.

+ Open protocol

+ Expand

Identifying Runs of Homozygosity Using Genotyping and Exome Sequencing

Cited 1 time

Check if the same lab product or an alternative is used in the 5 most similar protocols

DNA from F3:II-1 and F3:II-2 of family 3 were genotyped with the HumanCytoSNP-12 BeadChip platform (Illumina). The genotypes were evaluated for runs of homozygosity (ROH) >1 Mb via PLINK software¹⁴ (link) integrated in in-house software ViVar.¹⁵ (link) Resulting ROH were ranked according to their length and number of consecutive homozygous single-nucleotide polymorphisms (SNPs).¹⁶ (link) For ES, exome enrichment and sequencing were performed with the Agilent SureSelect Human All exon V5/V6 kit followed by paired-end sequencing on a HiSeq2000 (2 × 100 cycles). The CLC Genomics Workbench version 9.0.1 (CLCBio) was used for read-mapping against the human genome reference (NCBI build37/hg19 version), post-mapping duplicate read removal, coverage analysis, and quality-based variant calling via Alamut (visual version 2.7.2; interactive biosoftware).

Mechaussier S., Almoallem B., Zeitz C., Van Schil K., Jeddawi L., Van Dorpe J., Dueñas Rey A., Condroyer C., Pelle O., Polak M., Boddaert N., Bahi-Buisson N., Cavallin M., Bacquet J.L., Mouallem-Bézière A., Zambrowski O., Sahel J.A., Audo I., Kaplan J., Rozet J.M., De Baere E, & Perrault I. (2020). Loss of Function of RIMS2 Causes a Syndromic Congenital Cone-Rod Synaptic Disease with Neurodevelopmental and Pancreatic Involvement. American Journal of Human Genetics, 106(6), 859-871.

+ Open protocol

+ Expand

Homozygosity Mapping for DSD Genes

Check if the same lab product or an alternative is used in the 5 most similar protocols

Homozygosity mapping was performed by genome-wide single-nucleotide polymorphism (SNP) genotyping in case 1 and in two unaffected siblings using the HumanCytoSNP-12 BeadChip platform (Illumina, San Diego, CA). Plink software, integrated in ViVar, identified homozygous regions of > 1 Mb, which were ranked according to their length and the number of SNPs, as described. 14 Only homozygous regions unique to the index case were selected. The presence of relevant known DSD genes was excluded using BioMart filtering. Next, different gene prioritization tools (Endeavour, GeneDistiller, GeneWanderer, PosMed, SUSPECTS, and ToppGene) were used to identify candidate genes in the selected regions. 15 For this purpose, known DSD genes were used as training genes (Supplementary Data and Supplementary Table S1 online).

Baetens D., Güran T., Mendonca B.B., Gomes N.L., De Cauwer L., Peelman F., Verdin H., Vuylsteke M., Van der Linden M., Atay Z., Bereket A., de Krijger R.R., Preter K., Domenice S., Turan S., Stoop H., Looijenga L.H., De Bosscher K., Cools M, & De Baere E. (2018). Biallelic and monoallelic ESR2 variants associated with 46,XY disorders of sex development. Genetics in medicine : official journal of the American College of Medical Genetics, 20(7).

+ Open protocol

+ Expand

About PubCompare

Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.

We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.

However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.

Ready to get started?

Revolutionizing how scientists
search and build protocols!