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Affymetrix 500k snp array

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The Affymetrix 500k SNP array is a high-throughput genotyping platform designed to detect single nucleotide polymorphisms (SNPs) across the human genome. It provides comprehensive coverage of genetic variation, enabling researchers to investigate associations between genetic markers and traits or diseases.

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Lab products found in correlation

Snp 6.0 array, by Thermo Fisher Scientific (2 mentions) Snp 6.0 array data, by Thermo Fisher Scientific (2 mentions) Genomic workbench software, by Agilent Technologies (1 mentions) Agilent feature extraction software, by Agilent Technologies (1 mentions)

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500K SNP array (4 citations) 500K array (4 citations) SNP arrays (4 citations)

3 protocols using affymetrix 500k snp array

1

Copy Number Analysis of MLL-R ALL

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Of the 22 infant MLL-R ALL cases from the discovery cohort, 10 had copy number analyses performed using Affymetrix 500k SNP array (Affymetrix) as part of other studies and 12 had copy number data from SNP 6.0 array data (Affymetrix). In this study, we performed copy number analysis using the Affymetrix 6.0 SNP array for all samples in the validation cohort and for the non-infant MLL-R cases.
Andersson A.K., Ma J., Wang J., Chen X., Gedman A.L., Dang J., Nakitandwe J., Holmfeldt L., Parker M., Easton J., Huether R., Kriwacki R., Rusch M., Wu G., Li Y., Mulder H., Raimondi S., Pounds S., Kang G., Shi L., Becksfort J., Gupta P., Payne-Turner D., Vadodaria B., Boggs K., Yergeau D., Manne J., Song G., Edmonson M., Nagahawatte P., Wei L., Cheng C., Pei D., Sutton R., Venn N.C., Chetcuti A., Rush A., Catchpoole D., Heldrup J., Fioretos T., Lu C., Ding L., Pui C.H., Shurtleff S., Mullighan C.G., Mardis E.R., Wilson R.K., Gruber T.A., Zhang J, & Downing J.R. (2015). The landscape of somatic mutations in Infant MLL rearranged acute lymphoblastic leukemias. Nature genetics, 47(4), 330-337.
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2

Copy Number Analysis of MLL-R ALL

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Of the 22 infant MLL-R ALL cases from the discovery cohort, 10 had copy number analyses performed using Affymetrix 500k SNP array (Affymetrix) as part of other studies and 12 had copy number data from SNP 6.0 array data (Affymetrix). In this study, we performed copy number analysis using the Affymetrix 6.0 SNP array for all samples in the validation cohort and for the non-infant MLL-R cases.
Andersson A.K., Ma J., Wang J., Chen X., Gedman A.L., Dang J., Nakitandwe J., Holmfeldt L., Parker M., Easton J., Huether R., Kriwacki R., Rusch M., Wu G., Li Y., Mulder H., Raimondi S., Pounds S., Kang G., Shi L., Becksfort J., Gupta P., Payne-Turner D., Vadodaria B., Boggs K., Yergeau D., Manne J., Song G., Edmonson M., Nagahawatte P., Wei L., Cheng C., Pei D., Sutton R., Venn N.C., Chetcuti A., Rush A., Catchpoole D., Heldrup J., Fioretos T., Lu C., Ding L., Pui C.H., Shurtleff S., Mullighan C.G., Mardis E.R., Wilson R.K., Gruber T.A., Zhang J, & Downing J.R. (2015). The landscape of somatic mutations in Infant MLL rearranged acute lymphoblastic leukemias. Nature genetics, 47(4), 330-337.
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3

Genome-Wide Copy Number Variation Analysis

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The alterations in 10 patients were verified using at least one array platform. The arrays used in this study are the Affymetrix 500 K SNP-array (Affymetrix, Santa Clara, CA, USA), the CytoSure ISCA 180 K oligoarray-CGH (Oxford Gene Technology, Oxford, UK), and a 60 K custom-designed 60-mer oligoarray (Agilent Technologies, Palo Alto, CA, USA). SNP-array testing was performed as previously described [21 (link)]. Oligoarrays were hybridized according to the manufacturer’s’ instructions. Hybridizations were performed in duplicates with dye-reversal method. Scanned images were processed using Agilent Feature Extraction software and analyzed with Genomic Workbench software (both from Agilent Technologies) applying the statistical algorithm ADM-2 with a sensitivity threshold of 6.7. Duplication or deletion was considered when the log2 ratio of the Cy3/Cy5 intensities of a given region encompassing at least three probes was >0.3 or - < 0.3, respectively. Genomic coordinates were converted to UCSC genome browser build February 2009 (GRCh37/hg19).
D’Angelo C.S., Varela M.C., de Castro C.I., Kim C.A., Bertola D.R., Lourenço C.M., Perez A.B, & Koiffmann C.P. (2014). Investigation of selected genomic deletions and duplications in a cohort of 338 patients presenting with syndromic obesity by multiplex ligation-dependent probe amplification using synthetic probes. Molecular Cytogenetics, 7, 75.
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