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

Abstract

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.

Interaction of HPA axis genetics and early life stress shapes emotion recognition in healthy adults

“…A locus-specific polymerase chain reaction amplification is followed by a single base extension of the SNP region performed by special primers. Subsequently, SNP alleles are identified with matrix-assisted laser desorption/ionisation time-offlight mass spectrometry (Gabriel and Ziaugra, 2004;Millis, 2011;Weissensteiner et al, 2013).…”

Variation in the corticotropin-releasing hormone receptor 1 (CRHR1) gene modulates age effects on working memory

“…The process begins with a locus-specific PCR amplification followed by a single base extension of the SNP region performed by special primers. Finally SNP alleles are identified with MALDI-TOF mass spectrometry (Gabriel et al, 2009;Millis, 2011;Weissensteiner et al, 2013). Distribution of both SNPs in our sample of N ¼ 517 (24 subjects had to be excluded because of missing genetic data due to technical problems) did not deviate from Hardy-Weinbergequilibrium (see Table 1).…”

Using Pharmacogene Polymorphism Panels to Detect Germline Pharmacodynamic Markers in Oncology

“…These panels return accurate genotype calls (17) with only slightly diminished performance when using whole-genome-amplified DNA (18) or DNA from nonblood sources such as saliva or buccal swab (19). Open source or commercially available software for basic data storage and analysis are available, facilitating the use of these tools by investigators (20,21).…”