SNiPer: Improved SNP genotype calling for Affymetrix 10K GeneChip microarray data
نویسندگان
چکیده
منابع مشابه
SNiPer-HD: improved genotype calling accuracy by an expectation-maximization algorithm for high-density SNP arrays
MOTIVATION The technology to genotype single nucleotide polymorphisms (SNPs) at extremely high densities provides for hypothesis-free genome-wide scans for common polymorphisms associated with complex disease. However, we find that some errors introduced by commonly employed genotyping algorithms may lead to inflation of false associations between markers and phenotype. RESULTS We have develo...
متن کاملA genotype calling algorithm for affymetrix SNP arrays
MOTIVATION A classification algorithm, based on a multi-chip, multi-SNP approach is proposed for Affymetrix SNP arrays. Current procedures for calling genotypes on SNP arrays process all the features associated with one chip and one SNP at a time. Using a large training sample where the genotype labels are known, we develop a supervised learning algorithm to obtain more accurate classification ...
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Affymetrix GeneChip microarrays are the most widely used high-throughput technology to measure gene expression, and a wide variety of preprocessing methods have been developed to transform probe intensities reported by a microarray scanner into gene expression estimates. There have been numerous comparisons of these preprocessing methods, focusing on the most common analyses-detection of differ...
متن کاملSmarter clustering methods for SNP genotype calling
MOTIVATION Most genotyping technologies for single nucleotide polymorphism (SNP) markers use standard clustering methods to 'call' the SNP genotypes. These methods are not always optimal in distinguishing the genotype clusters of a SNP because they do not take advantage of specific features of the genotype calling problem. In particular, when family data are available, pedigree information is i...
متن کاملBRLMM: an Improved Genotype Calling Method for the GeneChip® Human Mapping 500K Array Set
Highly accurate and reliable genotype calling is an essential component of any highthroughput SNP genotyping technology. The Dynamic Model (DM, [1]) which has been extensively used for the GeneChip® Human Mapping 100K Array Set and the GeneChip® Human Mapping 500K Array Set has proven to be very effective, however it is possible to do better. Rabbee & Speed recently developed a model called the...
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ژورنال
عنوان ژورنال: BMC Genomics
سال: 2005
ISSN: 1471-2164
DOI: 10.1186/1471-2164-6-149