Genome-wide genotyping arrays
The laboratory work is done by dedicated personnel with more than 12 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 by experienced specialists. 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. 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 received and produced data is stored in a database at FIMM. FIMM guarantees the storage of your data for 5 years.
If you are interested in genotyping with Illumina arrays please contact Päivi Lahermo, paivi.lahermo(at)fimm.fi or Kati Donner, kati.donner(at)fimm.fi or use our Genotyping contact form. A meeting where all project details are discussed can be arrange if needed.
A FIMM Service Agreement must be signed before the project can start in our laboratory. If your project is required by the law to have an ethical permit you need to supply us with a copy of it.
2) Sample information
Provide the sample information using FIMM basic information form. Note! You need to enable the included macros. The filename should be FIMM_Perustietojen_luovutus_v2010.xlsm for the macros to work.
Fill up this sample submission form, print it and bring or send it to the lab together with the samples. Please also remember to submit the form electronically!
The gender information requested for in the FIMM basic information form is optional but central for detection of possible sample mix-ups in our quality control.
3) DNA samples
For the analysis we need good quality DNA in a concentration of 50 ng/µl in a minimum volume of 15-20 µl. Illumina recommends that the samples are diluted 1 x TE (10m mM Tris-HCl, 1 mM EDTA, pH 8.0)).
Note! We recommend that the concentration is measured with two independent methods, e.g. in addition to NanoDrop spectrophotometer with PicoGreen or Qubit fluorometric quantification. If you use only one method it should be PicoGreen, Qubit or other similar method.
For quality control purposes we recommend that there should be one duplicate sample (duplicate pairs preferably be located on different plates and in different positions on the plates) per 96 well plate in <500 sample projects. In projects with more than 500 samples the number of duplicates can be reduced. In case control studies the case and control samples should be evenly distributed / mixed on the plates.
Notice that the arrays are for specific amount of samples and thus the number of samples in a project should be divisible with the number of samples that can be analyzed on one array (all array types) / obtainable in array kits (for other array types than GSA), otherwise also empty slots or unused arrays shall be invoiced.
DNA SHIPPING INSTRUCTIONS
Ship the DNA samples on 96-well plates.
Seal the plates securely using either a removable heat-sealed lid (this is the recommended alternative), an adhesive seal or strip caps. Use Adhesive PCR foil (e.g Cat. # AB-0626, Thermo Fisher Scientific Abgene) only for shipments at room temperature and ground transportation.
Make sure to attach the foil seal properly to each well by rubbing the surface with soft cloth or lab wipe. Pack the plate (or when you stack multiple plates) so that the seals are protected from punctures and opening to prevent accidental spillage and cross contamination by using e.g cardboard, wadding and parafilm for tightly wrapping each individual plate. Pack the plates with adequate padding (e.g. paper, wadding, bubble wrap) to prevent jostiling during shipment.
Note! If you send the plates on dry ice or by air an adhesive foil seal should not be used! To prevent sample leakage use removable heat-seal or strip caps (with plates tightly wrapped with parafilm) instead!
Whenever possible, please avoid shipping on Thursdays and Fridays to avoid the samples arriving over the weekend.
Please inform us before you ship any samples and provide us with e.g the courier tracking numbers of your shipment!
Samples at room temperature
DNA samples can be shipped at room temperature without compromising the results if the samples are free of contaminants, the seals are secure, and the duration of transport is only a few days.
Use adhesive seals only for plates you bring directly to the lab or shipments at room temperature using ground transportation. During air transport such seals may come loose due to changes in air pressure! Make sure to attach the seals properly to each well by rubbing the surface with soft cloth or lab wipe (see instructions above).
Use secondary containment (e.g. cardboard freezer box) when using dry ice as plates may crack when placed directly on dry ice.
Encure there is enough dry ice / gel packs at top, bottom and sides of the container to keep the samples frozen during shipment and any delays that may occur with the courier.
Pack the plates so that they are protected from the possible liquid from melted ice or cracked cold / gel packs if sending your samples on ice.
Please note that if you send the plates on dry ice or by air an adhesive foil seal should not be used! To prevent sample leakage use removable heat-seal or strip caps instead (see instructions above)!
Mark the plate name (the same name as in the FIMM basic information form), sample concentration and date information clearly on the front side of the plate (see the image on left for an example).
University of Helsinki
FIMM Technology Centre