Efficient Identification of Null-Allele Single Nucleotide Polymorphism Markers.
Hum Hered
; 80(2): 79-89, 2015.
Article
em En
| MEDLINE
| ID: mdl-26613255
ABSTRACT
OBJECTIVES:
At the beginning of a genome-wide association study, many markers are discarded because they fail to meet standard quality control criteria. Some of these markers are out of Hardy-Weinberg equilibrium (HWE) because they have 'null alleles' (which may be deletions or third alleles that do not hybridize to standard probes). It may be useful to identify null-allele markers so that they can be analyzed under different models or in order to explore regions of copy number variation.METHODS:
We present a model for the chip-based genotype data that are produced when a null-allele single nucleotide polymorphism (SNP) is genotyped under standard (2-allele) assumptions. We show that this model can be combined with the standard HWE model to develop classification procedures based on the supervised learning algorithms Support Vector Machines (SVM), Classification and Regression Trees (CART) or Random Forests for identifying null-allele SNPs.RESULTS:
We report a list of null-allele SNPs we identified on the Illumina 660W-Quad chip and provide suggestions for applying our CART model to other SNP sets.CONCLUSIONS:
Properly identified null-allele SNPs can be used to test for genotype-phenotype associations or to identify regions which may contain copy number variants.
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Marcadores Genéticos
/
Polimorfismo de Nucleotídeo Único
/
Modelos Genéticos
Tipo de estudo:
Diagnostic_studies
/
Prognostic_studies
/
Risk_factors_studies
Limite:
Humans
Idioma:
En
Ano de publicação:
2015
Tipo de documento:
Article