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

PLoS ONE

Volumn 8, Issue 3, 2013, Pages

  Weissensteiner, Hansi ^a,b   Haun, Margot ^a   Schönherr, Sebastian ^a,b   Neuner, Mathias ^b   Forer, Lukas ^a,b   Specht, Günther ^b   Kloss Brandstätter, Anita ^a   Kronenberg, Florian ^a   Coassin, Stefan ^a  

^a INNSBRUCK MEDICAL UNIVERSITY   (Austria)

^b UNIVERSITY OF INNSBRUCK   (Austria)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; AUTOANALYSIS; COMPUTER INTERFACE; COMPUTER PROGRAM; CONTROLLED STUDY; DATA ANALYSIS SOFTWARE; DNA DETERMINATION; FLUORESCENCE RESONANCE ENERGY TRANSFER; GENE CONVERSION; GENE FREQUENCY; GENETIC VARIABILITY; QUALITY CONTROL; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SENSITIVITY ANALYSIS; SEX DETERMINATION; SINGLE NUCLEOTIDE POLYMORPHISM; WORKFLOW;

COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; GENOTYPE; POLYMORPHISM, SINGLE NUCLEOTIDE; SOFTWARE;

EID: 84875096541     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0059508     Document Type: Article

References (45)

1. Manolio TA, Brooks LD, Collins FS, (2008) A HapMap harvest of insights into the genetics of common disease. J Clin Invest 118: 1590-1605.
2. Hindorff LA, Sethupathy P, Junkins HA, Ramos EM, Mehta JP, et al. (2009) Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc Natl Acad Sci U S A 106: 9362-9367.
3. Livak KJ, Flood SJ, Marmaro J, Giusti W, Deetz K, (1995) Oligonucleotides with fluorescent dyes at opposite ends provide a quenched probe system useful for detecting PCR product and nucleic acid hybridization. PCR Methods Appl 4: 357-362.
4. Jurinke C, van den Boom D, Cantor CR, Koster H, (2002) The use of MassARRAY technology for high throughput genotyping. Adv Biochem Eng Biotechnol 77: 57-74.
5. Millis MP, (2011) Medium-throughput SNP genotyping using mass spectrometry: multiplex SNP genotyping using the iPLEX(R) Gold assay. Methods Mol Biol 700: 61-76.
6. Tyagi S, Kramer FR, (1996) Molecular beacons: probes that fluoresce upon hybridization. Nat Biotechnol 14: 303-308.
7. Syvänen AC, Aalto-Setälä K, Harju L, Kontula K, Söderlund H, (1990) A primer-guided nucleotide incorporation assay in the genotyping of apolipoprotein E. Genomics. 8: 684-692.
8. The International HapMap Consortium, (2005) A haplotype map of the human genome. Nature 437: 1299-1320.
9. The 1000 Genomes Project Consortium, Abecasis GR, Altshuler D, Auton A, Brooks LD, et al (2010) A map of human genome variation from population-scale sequencing. Nature 467: 1061-1073.
10. Döring A, Gieger C, Mehta D, Gohlke H, Prokisch H, et al. (2008) SLC2A9 influences uric acid concentrations with pronounced sex-specific effects. Nat Genet 40: 430-436.
11. Heid IM, Boes E, Müller M, Kollerits B, Lamina C, et al. (2008) Genome-Wide Association Analysis of High-Density Lipoprotein Cholesterol in the Population-Based KORA Study Sheds New Light on Intergenic Regions. Circ Cardiovasc Genet 1: 10-20.
12. Kollerits B, Coassin S, Beckmann ND, Teumer A, Kiechl S, et al. (2009) Genetic evidence for a role of adiponutrin in the metabolism of apolipoprotein B-containing lipoproteins. Hum Mol Genet 18: 4669-4676.
13. Kollerits B, Coassin S, Kiechl S, Hunt SC, Paulweber B, et al. (2010) A common variant in the adiponutrin gene influences liver enzyme levels. J Med Genet 47: 116-119.
14. Murabito JM, White CC, Kavousi M, Sun YV, Feitosa MF, et al. (2012) Association between chromosome 9p21 variants and the ankle-brachial index identified by a meta-analysis of 21 genome-wide association studies. Circ Cardiovasc Genet 5: 100-112.
15. Böger CA, Chen MH, Tin A, Olden M, Kottgen A, et al. (2011) CUBN Is a Gene Locus for Albuminuria. J Am Soc Nephrol 22: 555-570.
16. Wassel CL, Lamina C, Nambi V, Coassin S, Mukamal KJ, et al. (2012) Genetic determinants of the ankle-brachial index: A meta-analysis of a cardiovascular candidate gene 50K SNP panel in the candidate gene association resource (CARe) consortium. Atherosclerosis, in press.
17. Coassin S, Schweiger M, Kloss-Brandstätter A, Lamina C, Haun M, et al. (2010) Investigation and Functional Characterization of Rare Genetic Variants in the Adipose Triglyceride Lipase in a Large Healthy Working Population. PLoS Genet 6: e1001239.
18. Smedley D, Haider S, Ballester B, Holland R, London D, et al. (2009) BioMart- biological queries made easy. BMC Genomics 10: 22.
19. Smith AV, (2008) Retrieving HapMap Data Using HapMart. CSH Protoc 2008: pdb.prot5026 doi:10.1101/pdb.prot5026.
20. Flicek P, Amode MR, Barrell D, Beal K, Brent S, et al. (2012) Ensembl 2012. Nucleic Acids Res 40: D84-D90.
21. Kinsella RJ, Kahari A, Haider S, Zamora J, Proctor G, et al. (2011) Ensembl BioMarts: a hub for data retrieval across taxonomic space. Database (Oxford) 2011: bar030.
22. The International HapMap Consortium, (2007) A second generation human haplotype map of over 3.1 million SNPs. Nature 449: 851-861.
23. The International HapMap 3 Consortium, Altshuler DM, Gibbs RA, Peltonen L, Altshuler DM, et al (2010) Integrating common and rare genetic variation in diverse human populations. Nature 467: 52-58.
24. Kim JJ, Han BG, Lee HI, Yoo HW, Lee JK, (2010) Development of SNP-based human identification system. Int J Legal Med 124: 125-131.
25. Holzapfel C, Siegrist M, Rank M, Langhof H, Grallert H, et al. (2011) Association of a MTNR1B gene variant with fasting glucose and HOMA-B in children and adolescents with high BMI-SDS. Eur J Endocrinol 164: 205-212.
26. Truong CV, Groeneveld LF, Morgenstern B, Groeneveld E, (2011) MolabIS- An integrated information system for storing and managing molecular genetics data. BMC Bioinformatics 12: 425.
27. Teo YY, (2008) Common statistical issues in genome-wide association studies: a review on power, data quality control, genotype calling and population structure. Curr Opin Lipidol 19: 133-143.
28. Orro A, Guffanti G, Salvi E, Macciardi F, Milanesi L, (2008) SNPLims: a data management system for genome wide association studies. BMC Bioinformatics 9Suppl 2: S13.
29. Jayashree B, Reddy PT, Leeladevi Y, Crouch JH, Mahalakshmi V, et al. (2006) Laboratory Information Management Software for genotyping workflows: applications in high throughput crop genotyping. BMC Bioinformatics 7: 383.
30. Monnier S, Cox DG, Albion T, Canzian F, (2005) T.I.M.S: TaqMan Information Management System, tools to organize data flow in a genotyping laboratory. BMC Bioinformatics 6: 246.
31. Zhao LJ, Li MX, Guo YF, Xu FH, Li JL, et al. (2005) SNPP: automating large-scale SNP genotype data management. Bioinformatics 21: 266-268.
32. Hampe J, Wollstein A, Lu T, Frevel HJ, Will M, et al. (2001) An integrated system for high throughput TaqMan based SNP genotyping. Bioinformatics 17: 654-655.
33. Li JL, Deng H, Lai DB, Xu F, Chen J, et al. (2001) Toward high-throughput genotyping: dynamic and automatic software for manipulating large-scale genotype data using fluorescently labeled dinucleotide markers. Genome Res 11: 1304-1314.
34. Morcillo-Suarez C, Alegre J, Sangros R, Gazave E, de CR, et al. (2008) SNP analysis to results (SNPator): a web-based environment oriented to statistical genomics analyses upon SNP data. Bioinformatics 24: 1643-1644.
35. Yoo J, Lee Y, Kim Y, Rha SY, Kim Y, (2008) SNPAnalyzer 2.0: a web-based integrated workbench for linkage disequilibrium analysis and association analysis. BMC Bioinformatics 9: 290.
36. Wendl MC, Smith S, Pohl CS, Dooling DJ, Chinwalla AT, et al. (2007) Design and implementation of a generalized laboratory data model. BMC Bioinformatics 8: 362.
37. Fiddy S, Cattermole D, Xie D, Duan XY, Mott R, (2006) An integrated system for genetic analysis. BMC Bioinformatics 7: 210.
38. Atallah MJ, Li J, (2005) Secure outsourcing of sequence comparisons. International Journal of Information Security 4: 277-287.
39. Schoenherr S, Weissensteiner H, Coassin S, Specht G, Kronenberg F, et al. (2009) eCOMPAGT- efficient Combination and Management of Phenotypes and Genotypes for Genetic Epidemiology. BMC Bioinformatics 10: 139.
40. Weissensteiner H, Schonherr S, Specht G, Kronenberg F, Brandstatter A, (2010) eCOMPAGT integrates mtDNA: import, validation and export of mitochondrial DNA profiles for population genetics, tumour dynamics and genotype-phenotype association studies. BMC Bioinformatics 11: 122.
41. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, et al. (2007) PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 81: 559-575.
42. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, et al. (2010) The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 20: 1297-1303.
43. Heid IM, Jackson AU, Randall JC, Winkler TW, Qi L, et al. (2010) Meta-analysis identifies 13 new loci associated with waist-hip ratio and reveals sexual dimorphism in the genetic basis of fat distribution. Nat Genet 42: 949-960.
44. Speliotes EK, Willer CJ, Berndt SI, Monda KL, Thorleifsson G, et al. (2010) Association analyses of 249,796 individuals reveal 18 new loci associated with body mass index. Nat Genet 42: 937-948.
45. Voight BF, Scott LJ, Steinthorsdottir V, Morris AP, Dina C, et al. (2010) Twelve type 2 diabetes susceptibility loci identified through large-scale association analysis. Nat Genet 42: 579-589.