SNP Array Analysis and Trio Genotyping

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.

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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.

Publication 2019

SNP6.0 arrays HumanCytoSNP-12 BeadChip platform InfiniumCytoSNP-850K BeadChip platform Genome Studio Nexus CopyNumber™

Allele Clinical laboratory Genome Loss of heterozygosity Nexus Parents Patients Trio

Corresponding Organization :

Other organizations : Erasmus MC, University of Helsinki, Helsinki University Hospital, National Institute of Health Dr. Ricardo Jorge, Universidade do Porto, Institute of Child Health, Karolinska University Hospital, University Medical Center Groningen

Top 5 similar protocols

Variable analysis

independent variables

DNA trio analysis platform (Illumina HumanCytoSNP-12 BeadChip, Illumina InfiniumCytoSNP-850K BeadChip)

dependent variables

Copy number analysis
Genotyping
Loss of Heterozygosity (LOH) analysis based on B-allele frequency (BAF)

control variables

Affymetrix SNP6.0 arrays for patients A and B
Standard clinical laboratory procedure for the platforms used

controls

No positive or negative controls were explicitly mentioned

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