Related Experiment Video
Updated: May 21, 2026

Infinium Assay for Large-scale SNP Genotyping Applications
Published on: November 19, 2013
Clinical utility of sequence-based genotype compared with that derivable from genotyping arrays
Alexander A Morgan1, Rong Chen, Atul Janardhan Butte
1Department of Biochemistry, Stanford Genome Technology Center, Stanford University, Stanford, California, USA. alexmo@stanford.edu
Objective:
We investigated the common-disease relevant information obtained from sequencing compared with that reported from genotyping arrays.
Materials And Methods:
Using 187 publicly available individual human genomes, we constructed genomic disease risk summaries based on 55 common diseases with reported gene-disease associations in the research literature using two different risk models, one based on the product of likelihood ratios and the other on the allelic variant with the maximum associated disease risk. We also constructed risk profiles based on the single nucleotide polymorphisms (SNPs) of these individuals that could be measured or imputed from two common genotyping array platforms.
Results:
We show that the model risk predictions derived from sequencing differ substantially from those obtained from the SNPs measured on commercially available genotyping arrays for several different non-monogenic diseases, although high density genotyping arrays give identical results for many diseases.
Conclusions:
Our approach may be used to compare the ability of different platforms to probe known genetic risks disease by disease.
Related Concept Videos
Modern Molecular Taxonomy
Next-generation Sequencing
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features.
Evolutionary Relationships through Genome Comparisons
DNA Microarrays
Comparing Copy Number Variations and SNPs
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
Sanger Sequencing

