An integrated system for genetic analysis

Fiddy, Simon; Cattermole, D.M.; Xie, Dong; Duan, Xiao Yuan; Mott, Richard

doi:10.1186/1471-2105-7-210

Cited by 18 publications

(16 citation statements)

References 6 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…The phenotype data were uploaded to a database (Integrated Genotyping System 41 ) in batches over the three years of data collection. All relevant covariates were evaluated for their effect on each measure.…”

Section: Methodsmentioning

confidence: 99%

Combined sequence-based and genetic mapping analysis of complex traits in outbred rats

2013

Nat Genet

178

200

View full text Add to dashboard Cite

Genetic mapping on fully sequenced individuals is transforming our understanding of the relationship between molecular variation and variation in complex traits. Here we report a combined sequence and genetic mapping analysis in outbred rats that maps 355 quantitative trait loci for 122 phenotypes. We identify 35 causal genes involved in 31 phenotypes, implicating novel genes in models of anxiety, heart disease and multiple sclerosis. The relation between sequence and genetic variation is unexpectedly complex: at approximately 40% of quantitative trait loci a single sequence variant cannot account for the phenotypic effect. Using comparable sequence and mapping data from mice, we show the extent and spatial pattern of variation in inbred rats differ significantly from those of inbred mice, and that the genetic variants in orthologous genes rarely contribute to the same phenotype in both species.

show abstract

Section: Methodsmentioning

confidence: 99%

Combined sequence-based and genetic mapping analysis of complex traits in outbred rats

2013

Nat Genet

178

200

View full text Add to dashboard Cite

show abstract

“…Some other groups have developed bioinformatic solutions addressing at least some of the issues mentioned in the Introduction section [26]–[37]. These range from customary Visual Basic scripts for the reformatting of Microsoft Excel files (T.I.M.S.…”

Section: Discussionmentioning

confidence: 99%

“…These range from customary Visual Basic scripts for the reformatting of Microsoft Excel files (T.I.M.S. [30]) to comprehensive laboratory information management systems (LIMS) (SNPator [34], IGS [37]). We would like to briefly discuss here four solutions, which we regard to be partially comparable to SNPflow: Genotool [32], T.I.M.S.…”

Section: Discussionmentioning

confidence: 99%

“…We would like to briefly discuss here four solutions, which we regard to be partially comparable to SNPflow: Genotool [32], T.I.M.S. [30], SNPator [34] and IGS [37]. Table 1 summarizes all relevant features compared to SNPflow.…”

Section: Discussionmentioning

confidence: 99%

“…Similarly, IGS is the LIMS system of the Wellcome Trust Centre for Human Genetics (Oxford, UK) [37] and provides features for the administration of sample IDs, phenotypic data, microplates, marker-related information and genotyping data. The processing of raw data from genotyping systems is only a minor feature of the whole application.…”

Section: Discussionmentioning

confidence: 99%

See 2 more Smart Citations

SNPflow: A Lightweight Application for the Processing, Storing and Automatic Quality Checking of Genotyping Assays

et al. 2013

View full text Add to dashboard Cite

Single nucleotide polymorphisms (SNPs) play a prominent role in modern genetics. Current genotyping technologies such as Sequenom iPLEX, ABI TaqMan and KBioscience KASPar made the genotyping of huge SNP sets in large populations straightforward and allow the generation of hundreds of thousands of genotypes even in medium sized labs. While data generation is straightforward, the subsequent data conversion, storage and quality control steps are time-consuming, error-prone and require extensive bioinformatic support. In order to ease this tedious process, we developed SNPflow. SNPflow is a lightweight, intuitive and easily deployable application, which processes genotype data from Sequenom MassARRAY (iPLEX) and ABI 7900HT (TaqMan, KASPar) systems and is extendible to other genotyping methods as well. SNPflow automatically converts the raw output files to ready-to-use genotype lists, calculates all standard quality control values such as call rate, expected and real amount of replicates, minor allele frequency, absolute number of discordant replicates, discordance rate and the p-value of the HWE test, checks the plausibility of the observed genotype frequencies by comparing them to HapMap/1000-Genomes, provides a module for the processing of SNPs, which allow sex determination for DNA quality control purposes and, finally, stores all data in a relational database. SNPflow runs on all common operating systems and comes as both stand-alone version and multi-user version for laboratory-wide use. The software, a user manual, screenshots and a screencast illustrating the main features are available at http://genepi-snpflow.i-med.ac.at.

show abstract

MET and autism susceptibility: family and case–control studies

et al. 2008

View full text Add to dashboard Cite

Autism is a common, severe and highly heritable neurodevelopmental disorder. The International Molecular Genetic Study of Autism Consortium (IMGSAC) genome screen for linkage in affected sib-pair families identified a chromosome 7q susceptibility locus (AUTS1), that has subsequently shown evidence of increased sharing in several independent multiplex samples and in two meta-analyses. Taking into account the location of the MET gene under this linkage peak, and the fact that it has recently been reported to be associated with autism, the gene was further analyzed as a promising autism candidate. The gene encodes a transmembrane receptor tyrosine kinase of the hepatocyte growth factor/scatter factor (HGF/SF). MET is best known as an oncogene, but its signalling also participates in immune function, peripheral organ development and repair, and the development of the cerebral cortex and cerebellum (all of which have been observed earlier as being disregulated in individuals with autism). Here we present a family-based association analysis covering the entire MET locus. Significant results were obtained in both single locus and haplotype approaches with a single nucleotide polymorphism in intron 1 (rs38845, Po0.004) and with one intronic haplotype (AAGTG, Po0.009) in 325 multiplex IMGSAC families and 10 IMGSAC trios. Although these results failed to replicate in an independent sample of 82 Italian trios, the association itself was confirmed by a case-control analysis performed using the Italian cohort (Po0.02). The previously reported positive association of rs1858830 failed to replicate in this study. Overall, our findings provide further evidence that MET may play a role in autism susceptibility.

show abstract

An integrated system for genetic analysis

Abstract: Background: Large-scale genetic mapping projects require data management systems that can handle complex phenotypes and detect and correct high-throughput genotyping errors, yet are easy to use.

Cited by 18 publications

References 6 publications

Combined sequence-based and genetic mapping analysis of complex traits in outbred rats

Combined sequence-based and genetic mapping analysis of complex traits in outbred rats

SNPflow: A Lightweight Application for the Processing, Storing and Automatic Quality Checking of Genotyping Assays

MET and autism susceptibility: family and case–control studies

Contact Info

Product

Resources

About