JAX® QTL Mapping Services FAQ
What is QTL analysis?
QTL analysis uses genotype and phenotype data from the progeny of a cross to detect and localize regions in the genome that are responsible for the phenotypic variations between two parental strains. The most commonly used crosses are the backcross (N2) and intercross (F2).
How do you detect QTL?
To detect QTL, various statistical models are used to scan markers along each chromosome of the F2 or N2 mice. Each marker is evaluated for its likelihood of being associated with the phenotype of interest. The greater that likelihood, the greater that marker's LOD score (a logarithmic index of statistical significance). Only makers with LOD scores above statistically determined thresholds are considered significant. Sophisticated thresholding and modeling strategies of significant LOD score have been proposed in numerous references.
How many mice should be analyzed to indentify QTL?
The number of mice that should be analyzed depends on the variance of the phenotype(s) under study and the expected QTL effect(s). Generally, we suggest genotyping 200-300 mice. Alternatively, only mice with extreme phenotypes (about 60-70% of the total progeny) may be genotyped. To select this supset, we suggest phenotyping all the progeny.
How do I initiate a QTL analysis project?
- You contact JAX® Services using our services request form or via email at jaxservices@jax.org
- You complete a questionnaire describing your project
- To ensure that the experimental design meets your objectives, we contact you for a brief phone consultation
- We provide you a project quote for your review and acceptance
Should I send processed DNA or tail samples?
We prefer tail samples. Ship them on dry ice, individually labeled with mouse id numbers. If you send DNA, we will assess whether it is adequately purified and quantitated for mapping. If it is, we process it for SNP genotyping.
How do you conduct your analysis?
We genotype all DNA samples with a selected subset of informative SNPs from our 2,0000+ SNP marker panel. Our Computational Sciences-Statistics and Analysis group analyzes the genotype and phenotype data and generates quality control and diagnostic plots of the data. Then, you choose the depth of analysis you want performed.
How long will it take to get the genotype data and QTL report?
Typically, between six to eight weeks depending on the complexity of your project.
How do I find out about the status of my project?
You may find out about the status of your project by contacting your dedicated JAX Services Project Specialist by phone or email. You will receive project status updates at the following points:
- Upon receipt of samples to our Genetic Analysis Laboratory
- Upon completion of the genotyping
- Upon completion of the data analysis
If QC criteria are not met at any time during the study, the Project Specialist will contact you to discuss your options.
What is included in the data analysis report?
The report contents depend on whether you chose a Level 1 Analysis (sample report) or a Level 2 Analysis (sample report).
The sample reports feature a subset of data published in Peters LL, Zhang W, Lambert AJ, Brugnara C, Churchill GA, Platt OS. 2005. Quantitative trait loci for baseline white blood cell count, platelet count, and mean platelet volume. Mamm Genome 16:749-63.
Can you also perform analysis of raw genotype data I have generated?
Yes. The same analysis procedure can be applied on data you have generated.
Can you provide raw data?
Yes, raw genotyping data are included in the final report.
How and when will I be invoiced?
All QTL Service projects are priced by quotation, based upon study design. A Purchase Order is required to initiate a project. All projects are invoiced at the time of data delivery.
