NordicDB: a Nordic pool and portal for genome-wide control data

Leu, Monica; Humphreys, Keith; Surakka, Ida; Rehnberg, Emil; Muilu, Juha; Rosenström, Päivi; Almgren, Peter; Jääskeläinen, Juha E.; Lifton, Richard P.; Kyvik, Kirsten Ohm; Kaprio, Jaakko; Pedersen, Nancy L.; Palotie, Aarno; Hall, Per; Grönberg, Henrik; Groop, Leif; Peltonen, Leena; Palmgren, Juni; Ripatti, Samuli

doi:10.1038/ejhg.2010.112

Cited by 11 publications

(8 citation statements)

References 20 publications

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“…• NordicDB: the database of high-density genome-wide SNP information from 5,000 controls originating from Finnish, Swedish and Danish studies [ 13 ]. See http://www.nordicdb.org…”

Section: Resultsmentioning

confidence: 99%

The MOLGENIS toolkit: rapid prototyping of biosoftware at the push of a button

et al. 2010

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BackgroundThere is a huge demand on bioinformaticians to provide their biologists with user friendly and scalable software infrastructures to capture, exchange, and exploit the unprecedented amounts of new *omics data. We here present MOLGENIS, a generic, open source, software toolkit to quickly produce the bespoke MOLecular GENetics Information Systems needed.MethodsThe MOLGENIS toolkit provides bioinformaticians with a simple language to model biological data structures and user interfaces. At the push of a button, MOLGENIS’ generator suite automatically translates these models into a feature-rich, ready-to-use web application including database, user interfaces, exchange formats, and scriptable interfaces. Each generator is a template of SQL, JAVA, R, or HTML code that would require much effort to write by hand. This ‘model-driven’ method ensures reuse of best practices and improves quality because the modeling language and generators are shared between all MOLGENIS applications, so that errors are found quickly and improvements are shared easily by a re-generation. A plug-in mechanism ensures that both the generator suite and generated product can be customized just as much as hand-written software.ResultsIn recent years we have successfully evaluated the MOLGENIS toolkit for the rapid prototyping of many types of biomedical applications, including next-generation sequencing, GWAS, QTL, proteomics and biobanking. Writing 500 lines of model XML typically replaces 15,000 lines of hand-written programming code, which allows for quick adaptation if the information system is not yet to the biologist’s satisfaction. Each application generated with MOLGENIS comes with an optimized database back-end, user interfaces for biologists to manage and exploit their data, programming interfaces for bioinformaticians to script analysis tools in R, Java, SOAP, REST/JSON and RDF, a tab-delimited file format to ease upload and exchange of data, and detailed technical documentation. Existing databases can be quickly enhanced with MOLGENIS generated interfaces using the ‘ExtractModel’ procedure.ConclusionsThe MOLGENIS toolkit provides bioinformaticians with a simple model to quickly generate flexible web platforms for all possible genomic, molecular and phenotypic experiments with a richness of interfaces not provided by other tools. All the software and manuals are available free as LGPLv3 open source at http://www.molgenis.org.

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“…• NordicDB: the database of high-density genome-wide SNP information from 5,000 controls originating from Finnish, Swedish and Danish studies [ 13 ]. See http://www.nordicdb.org…”

Section: Resultsmentioning

confidence: 99%

The MOLGENIS toolkit: rapid prototyping of biosoftware at the push of a button

et al. 2010

Self Cite

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“…The populations are further described in the Supplementary Material . Briefly, the Finnish individuals ( n = 936) in the GWAS discovery population originated from Kuopio (64 cases, 64 controls), Tampere (124 cases), and Helsinki/Kuopio (684 controls) regions 33 34 35 36 . A subset of the GWAS population was collected in Gothenburg, Sweden (29 cases, 30 controls) 37 .…”

Section: Methodsmentioning

confidence: 99%

Genome-Wide Association Study of Polymorphisms Predisposing to Bronchiolitis

Pasanen

Karjalainen

Bont

et al. 2017

Sci Rep

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Bronchiolitis is a major cause of hospitalization among infants. Severe bronchiolitis is associated with later asthma, suggesting a common genetic predisposition. Genetic background of bronchiolitis is not well characterized. To identify polymorphisms associated with bronchiolitis, we conducted a genome-wide association study (GWAS) in which 5,300,000 single nucleotide polymorphisms (SNPs) were tested for association in a Finnish–Swedish population of 217 children hospitalized for bronchiolitis and 778 controls. The most promising SNPs (n = 77) were genotyped in a Dutch replication population of 416 cases and 432 controls. Finally, we used a set of 202 Finnish bronchiolitis cases to further investigate candidate SNPs. We did not detect genome-wide significant associations, but several suggestive association signals (p < 10−5) were observed in the GWAS. In the replication population, three SNPs were nominally associated (p < 0.05). Of them, rs269094 was an expression quantitative trait locus (eQTL) for KCND3, previously shown to be associated with occupational asthma. In the additional set of Finnish cases, the association for another SNP (rs9591920) within a noncoding RNA locus was further strengthened. Our results provide a first genome-wide examination of the genetics underlying bronchiolitis. These preliminary findings require further validation in a larger sample size.

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“…GWAS data for public controls were generated using the following arrays: Illumina 660-Quad (QIMR), Illumina 550(v1) (CGEMS), Illumina 550 (KORA), and Illumina 1.2M (WTCCC). For HEBCS, population allele and genotype frequencies on 221 healthy population controls genotyped on Illumina HumanHap 370CNV in the NordicDB, a Nordic pool and portal for genome-wide control data, were obtained from the Finnish Genome Center (25). These GWAS data were independently evaluated by an iterative QC process with the following exclusion criteria: minor allele frequency (MAF) <0.01, call rate <95%, HWE p-value <1×10 -7 among controls and sample call rate <98%.…”

Section: Methodsmentioning

confidence: 99%

Common Breast Cancer Susceptibility Loci Are Associated with Triple-Negative Breast Cancer

et al. 2011

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Triple negative breast cancers are an aggressive subtype of breast cancer with poor survival, but there remains little known about the etiological factors which promote its initiation and development. Commonly inherited breast cancer risk factors identified through genome wide association studies (GWAS) display heterogeneity of effect among breast cancer subtypes as defined by estrogen receptor (ER) and progesterone receptor (PR) status. In the Triple Negative Breast Cancer Consortium (TNBCC), 22 common breast cancer susceptibility variants were investigated in 2,980 Caucasian women with triple negative breast cancer and 4,978 healthy controls. We identified six single nucleotide polymorphisms (SNPs) significantly associated with risk of triple negative breast cancer, including rs2046210 (ESR1), rs12662670 (ESR1), rs3803662 (TOX3), rs999737 (RAD51L1), rs8170 (19p13.11) and rs8100241 (19p13.11). Together, our results provide convincing evidence of genetic susceptibility for triple negative breast cancer.

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NordicDB: a Nordic pool and portal for genome-wide control data

Cited by 11 publications

References 20 publications

The MOLGENIS toolkit: rapid prototyping of biosoftware at the push of a button

The MOLGENIS toolkit: rapid prototyping of biosoftware at the push of a button

Genome-Wide Association Study of Polymorphisms Predisposing to Bronchiolitis

Common Breast Cancer Susceptibility Loci Are Associated with Triple-Negative Breast Cancer

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