Our unit offers genome-wide genotyping with all currently available Illumina arrays. The laboratory work is done by dedicated personnel with more than 15 years of experience in Illumina analysis methods. Our laboratory uses an electronic lab note-book (ELN) for documentation of the laboratory workflow and an in-house made LIMS system for management of genotype and sample data.
The quality control includes manual checking of markers with GenomeStudio (Illumina) software based on selection criteria such as low call rates, bad cluster separation, low signal intensity, quality scores and heterozygote excess.
The control also includes quality checks done on the samples utilizing Plink 1.9 analysis toolset and in-house developed additional tools. These typically include sex-check, IBD check, duplicate check and Mendel error checks (if family information is available). Genotype data compatible with Plink 1.9 is released together with a report highlighting observations done during our quality control. On request genotype files suitable for imputation (genotypes files in PLUS strand orientation), raw data files and CNV analysis files can also be released. All raw data from the genotyping runs are also provided to our customers.
All received and produced data is stored in a database at FIMM. FIMM guarantees the storage of your data for six months.
Genome-wide methylation profiling is available at our genomics facility with Illumina MethylationEPIC 2.0 array capable of analyzing over 900 000 methylation sites per sample at single-nucleotide resolution.
The laboratory work is done by dedicated personnel with over 15 years of experience in Illumina analysis methods. Our laboratory uses an electronic lab note book (ELN) for documentation of the laboratory workflow and an in-house made LIMS system for management of genotype and sample data.
Projects are managed and quality controlled using Illumina GenomeStudio software. Further analysis and release formats can be discussed with projects. A report of QC and analysis as well as raw data from the runs is included in our data release.
All received and produced data is stored in a database at FIMM. FIMM guarantees the storage of your data for six months.
Human cell line authentication is available at our lab using microsatellite markers. The GenepPrint 24 (linkki) system allows co-amplification and detection of 24 human loci (22 autosomal STR loci and Amelogenin and DYS391 for gender identification). These loci collectively provide a genetic profile with a random match probability of <1 in 2.92 x10 9 (calculated based on the 10 markers shared with GenePrint 10 kit). Identified genetic profile is compared to publicly available data to count allelic identity. Please note, that genetic profile may not be available for your cell line in public databases. The analysis will, however, produce a genetic fingerprint in such cases.
We offer targeted single nucleotide polymorphism (SNP) genotyping with TaqMan chemistry (QuantStudio).
Also available are Illumina’s custom genotyping solution iSelect, as well as genotyping by sequencing with NGS methods or microsatellite analysis.
Targeted genotyping service is available for all organisms with necessary DNA sequence information for assay design.
For additional information on these technologies please contact Päivi Lahermo paivi.lahermo(at)fimm.fi or Kati Donner kati.donner(at)fimm.fi.