FAQ

Frequently asked questions from our customers

Genetic Background Testing

Scientific Questions

Why is it necessary to determine the genetic background?

A clearly defined genetic background is essential for the reproducibility of studies with genetically modified lines. Inbred strains have accumulated different mutations that can have a strong influence on the phenotype of the test animals. Substrains of C57BL/6 with identical designation, but provided by different breeders, differ genetically significantly. Knowing which inbred strain is specifically used is necessary so that the correct reference strain can be used in a study.

When generating a genetically modified mouse line, different strains are often included. By appropriate breeding measures, they must subsequently be backcrossed to a defined genetic background. The identity of the inbred strain and the degree of admixture of foreign DNA can be checked by determining the genetic background.

Genetic quality assurance and genetic monitoring of laboratory mice and rats:
FELASA Working Group Report (Laboratory Animals, vol. 2 2020):

Verify authenticity and uniformity of inbred strains and substrains
Describe precise genetic composition of genetically modified lines including Y chromosomal origin
Detect potential genetic contamination
Monitor genetic drift
Obtain qualified breeding advice to speed up congenic backcrossing projects
Quantify and control genetic diversity of outbred strains

From which inbred strains can you determine the genetic background?

Our standard set of STR markers works equally well for all mouse inbred strains of mice such as C57BL/6, 129, C3H, CBA, DBA, A/J, BALB/c etc. There are a large number of substrains of each inbred strain, which are available from different breeders and differ genetically from each other. The STR genotypes of the most commonly used inbred strains are already deposited with us for reference. This list is continuously expanded.

A separate STR genotyping set is also available for inbred strains of rat.

Why is knowing the presence of the correct Y chromosome so important?

The mice Y chromosome of the father has a significant influence on the phenotype via epigenetic effects, also in female offspring (see Nelson et. al (2010), Case and Teuscher (2015) - a review), which may have a stronger effect than the actual gene of interest (GOI) of the scientific study. Therefore, it is important to make sure that the Y chromosome typical for the specific inbred strain is present. Our genotyping data indicate that it is not the case in about 40% of all genetically modified mouse lines!

What are the advantages of genotyping with STR markers compared to SNPs?

STR’s are polymorphic and, therefore, much more informative than SNP‘s. We can apply the one set of markers to differentiate between all mouse (or rat) strains and substrains with a large number of discriminating markers which allows us to carry out speed congenics projects or genetic background differentiation even between very closely related substrains.

Y chromosomal haplotyping can be performed with STR markers only, but not with SNPs.

STR’s form a dynamic set of markers. Compared to SNPs STR markers have significantly higher mutation rates, leading to the occurence and detection of new STR alleles. Due to the resulting accumulation of newly occurred alleles after “n” generations of breeding, STRs can be used to monitor genetic drift. SNP’s, on the other hand, form a very stable, but static set of markers, and for this reason cannot be employed to monitor genetic drifts.

With an identical set of a limited number of STR markers (1 STR per chromosome), the genetic diversity of outbred strains can be described perfectly, the reduction of genetic diversity of a particular outbred strain over time/generations can be monitored and documented. Different outbred strains can be compared with each other

You are strongly recommending genotyping of at least three samples per mouse line. Why is analysis of one sample not sufficient?

From our point of view, the "minimum variant" of genotyping three samples per mouse line is the lower limit to be able to estimate the real situation within a mouse line. As a typical result of the determination of BL6-specific mutations, for example, we regularly get within a line the findings consisting of wt/wt, wt/mut and mut/mut in one of the three samples each. Therefore, one should not rely on the finding of only one sample, because a single result can lead to a completely wrong conclusion.

When is 3x complete genotyping (Large panel) or Mixed panel the better option?

The Mixed panel (1 x complete genotyping with 250 STR markers, 3 x.BL6-specific mutations, 3 x Y chromosomal haplotype) can be used in established mouse lines where a number of brother-sister matings have already been performed. If such breeding is done correctly, the genetic background variation between individuals is in the range of 2-4%.

We recommend the complete genotyping of at least three (male) animals with 250 STR markers during a targeted backcross to a defined inbred strain (recipient strain), where the offspring of a backcross generation are always mated with animals of the recipient strain. In this case, there are considerable differences between the individuals with regard to the genomic proportion of donor and recipient DNA. The complete genotyping of several individuals allows the identification of the animal with the largest amount of recipient DNA, which can then be used for the next backcrossing.

A similar situation exists after breeding failures with a foreign mouse line. Again, in this case we recommend complete genotyping of all samples.

Do you check for known phenotype-relevant mutations present in the various sub-strains of C57BL/6?

Yes, we do. Markers include genotyping of Nnt, Crb1^rd8, Dock2 and Snca.

Is the determination of the Y-chromosomal haplotype part of every test?

Yes. Genotyping of the Y chromosome is part of the small panel, mixed panel and full panel. The Y chromosomal haplotypes of the most commonly used inbred strains are already deposited with us for reference.

Technical Questions

What is the turnaround time per sample?

Turnaround time is maximum 2 weeks (10 working days). However, most of the times it is shorter.

What type of sample material can be submitted? Is it ear punches, tail tip biopsies, or finished DNA extracts?

Any tissue sample, tail biopsy, earlip or other, will be fine. Readily extracted DNA (from commercial extraction kits, no “quick-and-dirty” extractions) works equally well. In this case, please send us half of the extract and keep the other half as a retainer.

How does the sample shipment work?

Please send samples cooled, either on ice or, ideally, on dry ice, preferably at the beginning of the week to avoid samples going astray over the weekend.

What is the sample supply note?

Our Sample Supply Note can be used for identification and naming of samples.

Do you provide special packaging material?

We do not provide any packaging materials. We recommend to use simple 1.5ml Eppendorf style tubes.

Do you have a delivery address for processing samples?

Delivery to GVG can be made to the attention of Mrs. Schmidt (Tel. 0341- 392 859 21, GVG Genetic Monitoring GmbH, Deutscher Platz 5e, 04103 Leipzig). You can use our DHL account (DHL Express #144005514) for shipping. We will invoice transportation cost together with our analytical service. Simply call your local DHL Express representative to have your samples picked up.

What are the costs for genotyping, are there volume discounts?

We charge 250€ plus VAT for a full genetic analysis (Full Panel - 250 STRs plus Y chromosome and BL/6 specific mutations). We recommend to examine at least 3 male individuals per strain/line to get an overview of the genetic dispersion. In order to reduce the costs, we also offer a combination package (Mixed Panel) consisting of a full analysis (1x Full Panel) and for two samples the analysis of the Y-chromosome and genotyping BL/6-specific mutations (Small Panel - 100€), for a total price of 450€ plus VAT.

We also offer a 10% discount for orders for genotyping more than 10 samples and will be happy to discuss further discounts or a special cooperation price for larger numbers of samples/regular tests.

Do you have any further questions?

Feel free to call us at +49 (0) 341 / 39 29 86 90, send us an E-Mail or fill out the following form.

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