Algorithms for large-scale genotyping microarrays

Liu, Weimin; Di, Xiaojun; Yang, Guang; Matsuzaki, Hajime; Huang, Jing; Mei, Rui; Ryder, Thomas B.; Webster, Teresa A.; Dong, Shoulian; Li, Guoying; Jones, Keith; Kennedy, Giulia C.; Kulp, David

doi:10.1093/bioinformatics/btg332

Cited by 94 publications

(76 citation statements)

References 15 publications

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“…Washing and staining were performed with the Affymetrix Fluidics Station 450 (Affymetrix Inc., Santa Clara, CA, USA) and the signal intensities detected with the GeneChip Scanner 3000 7G (Affymetrix Inc., Santa Clara, CA, USA). The results from the Affymetrix arrays were analysed in GeneChip Genotyping Analysis Software (GTYPE) 10 and GeneChip Operating Software (GCOS). Data handling, Mendelian error control and statistical analyses were done using Progeny Lab software (version 5, Progeny Software, LLC, South Bend, IN, USA), PEDSTATS 11 and MERLIN.…”

Section: Linkage Analysismentioning

confidence: 99%

A mild form of Mucopolysaccharidosis IIIB diagnosed with targeted next-generation sequencing of linked genomic regions

et al. 2011

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Next-generation sequencing (NGS) techniques have already shown their potential in the identification of mutations underlying rare inherited disorders. We report here the application of linkage analysis in combination with targeted DNA capture and NGS to a Norwegian family affected by an undiagnosed mental retardation disorder with an autosomal recessive inheritance pattern. Linkage analysis identified two loci on chromosomes 9 and 17 which were subject to target enrichment by hybridization to a custom microarray. NGS achieved 20-fold or greater sequence coverage of 83% of all protein-coding exons in the target regions. This led to the identification of compound heterozygous mutations in NAGLU, compatible with the diagnosis of Mucopolysaccharidosis IIIB (MPS IIIB or Sanfilippo Syndrome type B). This diagnosis was confirmed by demonstrating elevated levels of heparan sulphate in urine and low activity of a-N-acetyl-glucosaminidase in cultured fibroblasts. Our findings describe a mild form of MPS IIIB and illustrate the diagnostic potential of targeted NGS in Mendelian disease with unknown aetiology.

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Section: Linkage Analysismentioning

confidence: 99%

A mild form of Mucopolysaccharidosis IIIB diagnosed with targeted next-generation sequencing of linked genomic regions

et al. 2011

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“…Several strategies can be used to discriminate between false positives and true findings (for example, more conservative P-levels for significance and corrections for multiple analyses) 320 and specific programmes have been developed for the analyses of array data. 321,322 Several data mining programmes that facilitate the grouping of genes by function or other criteria have been specifically developed for the analyses of large-scale SNP genotyping and are publicly available (http://www.ncbi.nlm.nih.gov/ Tools/#expression). Although these analyses may restrict findings, genome scans have the potential to identify novel genes related to response phenotypes without the need of previous hypothesis, a clear improvement over candidate gene approaches.…”

Section: The Genomic Revolutionmentioning

confidence: 99%

Pharmacogenetics and pharmacogenomics of schizophrenia: a review of last decade of research

2007

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The last decade of research into the pharmacogenetics of antipsychotics has seen the development of genetic tests to determine the patients' metabolic status and the first attempts at personalization of antipsychotic treatment. The most significant results are the association between drug metabolic polymorphisms, mainly in cytochrome P450 genes, with variations in drug metabolic rates and side effects. Patients with genetically determined CYP2D6 poor metabolizer (PMs) status may require lower doses of antipsychotic. Alternatively, CYP2D6 ultrarapid matabolizers (UMs) will need increased drug dosage to obtain therapeutic response. Additionally, polymorphisms in dopamine and serotonin receptor genes are repeatedly found associated with response phenotypes, probably reflecting the strong affinities that most antipsychotics display for these receptors. In particular, there is important evidence suggesting association between dopamine 2 receptor (D2) polymorphisms (Taq I and À141-C Ins/Del) and a dopamine 3 receptor (D3) polymorphism (Ser9Gly) with antipsychotic response and drug-induced tardive dyskinesia. Additionally, there is accumulating evidence indicating the influence of a 5-HT2C polymorphism (À759ÀT/C) in antipsychotic-induced weight gain. Application of this knowledge to clinical practice is slowly gathering pace, with pretreatment determination of individual's drug metabolic rates, via CYP genotyping, leading the field. Genetic determination of patients' metabolic status is expected to bring clinical benefits by helping to adjust therapeutic doses and reduce adverse reactions. Genetic tests for the pretreatment prediction of antipsychotic response, although still in its infancy, have obvious implications for the selection and improvement of antipsychotic treatment. These developments can be considered as successes, but the objectives of bringing pharmacogenetic and pharmacogenomic research in psychiatric clinical practice are far from being realized. Further development of genetic tests is required before the concept of tailored treatment can be applied to psychopharmatherapy. This review aims to summarize the key findings from the last decade of research in the field. Current knowledge on genetic prediction of drug metabolic status, general response and drug-induced side effects will be reviewed and future pharmacogenomic and epigenetic research will be discussed.

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“…2B). A genotype-calling algorithm, described by Liu et al (2003), clusters RAS points from a training set of 133 ethnically diverse individuals into three classes corresponding to the genotypes. For each SNP, the clustering aggregates the 133 points into three median points, each representing a group of individuals from the training set who share the same genotype.…”

Section: Oligonucleotide Array Design and Snp Contentmentioning

confidence: 99%

“…Scan images were processed to get hybridization signal intensity values using either Micro Array Suite (MAS) v5 software (Affymetrix) or GCOS v1 software (Affymetrix). The genotype-calling algorithm as described in Liu et al (2003) was implemented in GenoTyping Tools (GTT; Affymetrix) and GDAS v2 (Affymetrix) analysis software. Default algorithm parameters, that is, a discrimination score cutoff of 0.08 and call zones of 0.8, were used to make all of the genotype calls.…”

Section: Genotyping By Allele-specific Hybridizationmentioning

confidence: 99%

Parallel Genotyping of Over 10,000 SNPs Using a One-Primer Assay on a High-Density Oligonucleotide Array

Matsuzaki¹,

Loi²,

Dong³

et al. 2004

Genome Res.

282

220

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The analysis of single nucleotide polymorphisms (SNPs) is increasingly utilizedto investigate the genetic causes of complex human diseases. Here we present a high-throughput genotyping platform that uses a one-primer assay to genotype over 10,000 SNPs per individual on a single oligonucleotide array. This approach uses restriction digestion to fractionate the genome, followed by amplification of a specific fractionated subset of the genome. The resulting reduction in genome complexity enables allele-specific hybridization to the array. The selection of SNPs was primarily determined by computer-predicted lengths of restriction fragments containing the SNPs, andwas further driven by strict empirical measurements of accuracy, reproducibility, andaverage call rate, which we estimate to be >9.5%, >99.9%, and>95%, respectively. With average heterozygosity of 0.38 andgenome scan resolution of 0.31 cM, the SNP array is a viable alternative to panels of microsatellites (STRs). As a demonstration of the utility of the genotyping platform in whole-genome scans, we have replicated and refined a linkage region on chromosome 2p for chronic mucocutaneous candidiasis and thyroid disease, previously identified using a panel of microsatellite (STR) markers

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Algorithms for large-scale genotyping microarrays

Abstract: The algorithms will be available commercially in the Affymetrix software package.

Cited by 94 publications

References 15 publications

A mild form of Mucopolysaccharidosis IIIB diagnosed with targeted next-generation sequencing of linked genomic regions

A mild form of Mucopolysaccharidosis IIIB diagnosed with targeted next-generation sequencing of linked genomic regions

Pharmacogenetics and pharmacogenomics of schizophrenia: a review of last decade of research

Parallel Genotyping of Over 10,000 SNPs Using a One-Primer Assay on a High-Density Oligonucleotide Array

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