New Method Identifies Genes Affecting Health In Fraction Of A Second

July 11, 2008

A new tool which makes it possible to extract information about an

individual's health from genotypes in a fraction of a second, has

been developed by an academic at the University of Southampton.

Professor Joao Marques-Silva, at the University's School of

Electronics and Computer Science and collaborators have developed a

new approach to the process of inferring haplotype information from

genotype data.

A haplotype can be defined as a group of alleles of one or more genes

on a single chromosome that are closely enough linked to be inherited

usually as a unit and a genotype refers to the combination of alleles

inherited from both parents.

According to Professor Marques-Silva, the current method of

extracting haplotypes from genotype data is based on statistical

approaches, which can take a long time to compute.

Professor Marques-Silva and collaborators approached this scenario by

taking the Haplotype Inference by Pure Parsimony (HIPP), a solution

that minimises the total number of distinct haplotypes used, and

developed new algorithms which they applied to achieve faster results.

'Biologists have been using these statistical approaches for a long

time and may not be open to change,' he said. 'However, these methods

can take days, even months to terminate, whereas our approach

produces an almost instant result.'

Further research is being carried out currently by Professor Marques-

Silva and collaborators to validate this new method and to prove that

it could replace statistical methods in a number of settings.

'This is the biggest development that we have made in this field so

far,' said Professor Marques-Silva. 'It remains to be seen whether

biologists will use this instead of existing techniques.'

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