Location

Targeted genotyping

We offer targeted single nucleotide polymorphism (SNP) genotyping with Agena Bioscience (Sequenom) MassARRAY System and Real-time PCR (Roche LightCycler). 

Also available are Illumina’s custom genotyping solution iSelect, as well as genotyping by sequencing with NGS methods (for additional information on these technologies or any others you are interested in please contact Päivi Lahermo or Kati Donner.

Targeted genotyping service is available for all organisms with necessary DNA sequence information for assay design.

Pricing

Examples of prices per sample run for the Agena MassARRAY platform:

Number of samples per run,

including controls

University of Helsinki

(includes 0% VAT)

Other academic

(includes 24% VAT)

193-384  1900 € 2473.80 €
<192 950  € 1236.90 €

 

 

 

 

 

 

One run can include up to ~32 SNPs.

In addition to the sums mentioned above the project invoicing include also purchase price of the oligos and DNA plating costs. SNP design and optimizing costs depend on project plan agreed with the group.

If you are a non-academic user, or are interested in the other targeted genotyping methods, please contact us for pricing.

 

Service description

The laboratory work is done by dedicated personnel with nearly 15 years of experience in Agena Biosciences/Sequenom 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 AgenaBiosciences MassARRAY analysis software, or other applicable system specific software, and with in-house developed tools. These include typically success rates, duplicate checks, sex-check and mendel error check (where applicable). Genotype data is released in linkage files together with possible family structures and map information. Different genome builds can be used upon request. A report highlighting observations done during quality control is included in data release. 

All received and produced data is stored in a database at FIMM. FIMM guarantees the storage of your data for 5 years.

How to get started 

If you are interested in targeted genotyping please contact Päivi Lahermo or Kati Donner. A meeting can be organized, where all project details can be discussed.

Customer provides

1) Documentation

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) Sequence or SNP information

You must provide us with information of the SNPs for assay design. This can be rs-numbers or DNA sequences. You may also design the assays yourself with Agena Assay Design Tools or with DesignStudio for Illumina iSelect arrays. For detailed instructions please contact us.

4) DNA samples

For the analysis with AgenaBiosciences MassARRAY platform or Real-time PCR we need good quality DNA in concentration of 10 ng / µl in nuclease-free water. For MassARRAY the total amount is a minimum of 12 µl per one multiplex and 2 µl for each additional multiplex. Real-time PCR requires 12 µl per reaction. iSelect and NGS genotyping projects need a minimum of 250 ng in 50 ng/ µl concentration (1xTE).

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 for Agena targeted genotyping we recommend that there should be two water controls, 2 duplicated samples and 2 internal controls (CEPH DNA) in different positions one each 96-well plate. 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 in projects where sex specific markers are used.

DNA shipping instructions

Ship the DNA samples on 96-well plates.

Seal the plates securely using either an adhesive seal, strip caps or a removable heat-sealed lid. Use Adhesive PCR foil (e.g Cat. # AB-0626, Thermo Fisher Scientific Abgene) only for shipments at room temperature. Make sure to attach the foil seal properly to each well by rubbing the surface with soft cloth or lab wipe. Make sure to protect the seals from punches. If you stack multiple plates, put cardboard or wadding layer between the plates. 

Note! If you send the plates on dry ice an adhesive foil seal should not be used. Use strip caps instead! 

Whenever possible, please avoid shipping on Thursdays and Fridays to avoid the samples arriving over the weekend. Pack the samples so that the plates or seals are not damaged during shipment. If you stack multiple plates put cardboard or wadding layer between the plates.

Please ask us for instructions before sending the samples via air courier!

Plate naming:

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 below for an example).

Frozen samples:

Frozen plates should be placed in the shipping container with enough dry ice/blocks to keep the samples frozen during shipment and any delays that may occur with the courier.

Shipping address:

FIMM Genotyping Lab
FIMM Technology Centre
Room: F215a
Biomedicum 2U
Tukholmankatu 8
00290 HELSINKI
FINLAND

Last updated: 16.04.2018 - 13:53