Genome-Wide Association Study Software - Isis Project No 7376

Available to license: GenoSNP - Genotyping without a reference population.

Understanding and preventing disease

Genetic make-up affects the way in which humans develop diseases, and respond to medical treatment, from drugs to vaccines. Genotyping, a process for identifying genetic make-up and DNA sequencing, plays an essential role in understanding genetic based diseases and the control of pandemic outbreaks.  The technology is therefore extremely important for the future study of personalised medicine and prevention of disease.

Genotype calling is practiced using a variety of biological assays but current genotyping algorithms typically require the availability of a large number of control samples that have been sampled on the same array and platform. Oxford have now developed GenoSNP, an algorithm which is entirely independent of such control samples, enabling the study of individual samples.

Existing Methods

Existing genotype calling methods typically assume that the user has generated data for a large number (100-1000s) of samples, or that a reference panel of data is available. Genotype calling then proceeds by examining data at each genetic location across a number of samples. These approaches are commonly known as “population” methods due to the requirement for a population of samples for genotyping to proceed.

Our Approach

Our genotype calling approach, GenoSNP, differs from this standard paradigm by working on one sample at a time. Originally designed for the Illumina Infinium SNP genotyping arrays, GenoSNP takes advantage of microarray technologies where the probe-specific variation is small, relative to the overall signal separation between genotype classes. GenoSNP is able to achieve genotyping accuracies of greater than 99% when tested on the Illumina SNP genotyping platform. It is also immune to many potential biases that are commonly observed in genome-wide association studies and introduced by factors such as DNA batch effects and laboratory or machine-specific calibration effects.

Rare Variants

Investigations of rare variants are a further important part of modern genome-wide association studies and accurate genotype calling of these variants is crucial. GenoSNP is highly suited for calling rare variants with high accuracy by using the information from other probes on the same array as a reference. In contrast, an equivalent population-based genotype calling approach would typically require 10,000s of samples for correct functionality.

Custom Arrays

GenoSNP per-sample functionally is also beneficial for users of customisable genotyping arrays where suitable reference panels may not exist, or may have to be produced at considerable additional cost to the user.

If you would like further information, please contact the Isis Project Manager.

Request Further Information: Project Number 7376 - Genome-Wide Association Study Software