Machine learning approaches for phenotype-genotype mapping: predicting heterozygous mutations in the CYP21B gene from steroid profiles.
OBJECTIVE
Non-linear relations between multiple biochemical parameters are the basis for the diagnosis of many diseases. Traditional linear analytical methods are not reliable predictors. Novel nonlinear techniques are increasingly used to improve the diagnostic accuracy of automated data interpretation. This has been exemplified in particular for the classification and diagnostic prediction of cancers based on expression profiling data. Our objective was to predict the genotype from complex biochemical data by comparing the performance of experienced clinicians to traditional linear analysis, and to novel non-linear analytical methods.


METHODS
As a model, we used a well-defined set of interconnected data consisting of unstimulated serum levels of steroid intermediates assessed in 54 subjects heterozygous for a mutation of the 21-hydroxylase gene (CYP21B) and in 43 healthy controls.


RESULTS
The genetic alteration was predicted from the pattern of steroid levels with an accuracy of 39% by clinicians and of 64% by linear analysis. In contrast, non-linear analysis, such as self-organizing artificial neural networks, support vector machines, and nearest neighbour classifiers, allowed for higher accuracy up to 83%.


CONCLUSIONS
The successful application of these non-linear adaptive methods to capture specific biochemical problems may have generalized implications for biochemical testing in many areas. Nonlinear analytical techniques such as neural networks, support vector machines, and nearest neighbour classifiers may serve as an important adjunct to the decision process of a human investigator not 'trained' in a specific complex clinical or laboratory setting and may aid them to classify the problem more directly.
Prank
Klaus
K
International NRW Graduate School in Bioinformatics and Genome Research Center of Biotechnology (CeBiTec), Bielefeld University, Germany. klaus.prank@cebitec.uni-bielefeld.de
Schulze
Egbert
E
Eckert
Olaf
O
Nattkemper
Tim W
TW
Bettendorf
Markus
M
Maser-Gluth
Christiane
C
Sejnowski
Terrence J
TJ
Grote
Arno
A
Penner
Erika
E
von Zur Mühlen
Alexander
A
Brabant
Georg
G
D000328:Adult; D001185:Artificial Intelligence; D002874:Chromosome Mapping / Q000379:methods*; D005838:Genotype; D006579:Heterozygote; D006801:Humans; D016014:Linear Models; D008875:Middle Aged; D008957:Models, Genetic; D009154:Mutation; D017711:Nonlinear Dynamics; D010641:Phenotype; D011237:Predictive Value of Tests; D013255:Steroid 21-Hydroxylase / Q000235:genetics*; D013256:Steroids / Q000097:blood*
D013256:Steroids; D013255:Steroid 21-Hydroxylase