Genome Scans promote t he ability to multiplex by size and color in high throughput. The internal standard and PEBiosystems software promotes high accuracy. We have two marker sets available for genome scans. Contact us more more information!
Overview
- The Utah Marker Index Set. Developed here at the University of Utah, this group of 192 markers is based on tetramer repeats. It covers the somatic chromosomes at an average of 20cM with an average heterozygosity of 81%. The average multiplex is 8. Chromosome 7q is poorly covered. Because some markers have polymorphisms differing by one base, this set is most useful for projects small enough to be run on a single gel (92 samples or less).
- Applied Biosystems MD10 Linkage Mapping Set. This commercial set is a group of 400 di-nucleotide markers covering the somatic and X chromosomes at an average of 10cM. Although there is a surcharge for genotyping with this set, the average multiplex is 14. Panels are arranged by chromosome facilitating partial genome scans. There is also an HD5 Linkage Mapping Set (5cM) and an LD20 Set (20cM). The electropherogram below is a single panel of the MD10 Linkage Mapping Set composed of 17 markers.
To calculate an ESTIMATED cost for your project,
please use the table below and the highlighted cost per genotype for the service you require.
1 marker x 1 DNA = 1 genotype.
e.g. Genome scan using the UT marker set:
30 DNA samples x 192 markers = 5,760 genotypes
Using an average multiplex of 8, the cost per genotype = $1.72
Total cost = 5,760 x $1.72 = $9, 907.20
| Marker Set | Multiplex | Genome Scan | Fine Map | SNE | Allele Specific | LOH | MIN |
| 1 | 6.15 | 6.15 | 8.39 | 6.50 | 7.24 | 6.50 | |
| 2 | 3.61 | 3.61 | 5.85 | 3.96 | 4.70 | 3.96 | |
| 3 | 2.76 | 2.76 | 5.00 | 3.11 | 3.85 | 3.11 | |
| 4 | 2.34 | 2.34 | 4.57 | 2.68 | 3.43 | 2.68 | |
| Mouse or Custom Hu. | 5 | 2.08 | 2.08 | 4.32 | 2.43 | 3.17 | 2.43 |
| 6 | 1.91 | 1.91 | 4.15 | 2.26 | 3.00 | 2.26 | |
| 7 | 1.79 | 1.79 | 4.03 | 2.14 | 2.88 | 2.14 | |
| UT marker set | 8 | 1.70 | 1.70 | 3.94 | 2.05 | 2.79 | 2.05 |
| 9 | 1.63 | 1.63 | 3.87 | 1.98 | 2.72 | 1.98 | |
| 10 | 1.58 | 1.58 | 3.81 | 1.92 | 2.66 | 1.92 | |
| 11 | 1.53 | 1.53 | 3.76 | 1.88 | 2.62 | 1.88 | |
| 12 | 1.49 | 1.49 | 3.73 | 1.84 | 2.58 | 1.84 | |
| 13 | 1.46 | 1.46 | 3.69 | 1.80 | 2.55 | 1.80 | |
| ABI MD10 set | 14 | 1.43 | 1.43 | 3.66 | 1.78 | 2.52 | 1.78 |
| 15 | 1.41 | 1.41 | 3.64 | 1.75 | 2.49 | 1.75 | |
| 16 | 1.38 | 1.38 | 3.62 | 1.73 | 2.47 | 1.73 | |
| 17 | 1.37 | 1.37 | 3.60 | 1.71 | 2.45 | 1.71 | |
| 18 | 1.35 | 1.35 | 3.58 | 1.70 | 2.44 | 1.70 | |
| 19 | 1.33 | 1.33 | 3.57 | 1.68 | 2.42 | 1.68 | |
| 20 | 1.32 | 1.32 | 3.56 | 1.67 | 2.41 | 1.67 |
| Table 1 |
We will re-run missing genotypes once at no extra charge. Expect a dropout rate of 3-6%.
Estimate for Grant Proposal or Budget Please contact us and we will be glad to send you an official cost and time estimate for your project.
Custom Primers We can help you design custom primers and primer sets to achieve the most efficient multiplex. A typical pair of fluorescently tagged primers ordered from a commercial vendor costs $80-$100 for a 100nmol synthesis. We charge $10-$20 for optimizing new primers not previously used in the Core.
Off-Campus Projects will be considered if they do not interfere with University projects. Please consult with the Core Facility Manager, Michael Klein, to discuss timing. By University policy there is a 50% surcharge for off-campus NIH projects. Off-campus non-NIH projects may have additional charges.
Access to the facility is on a first-come-first-served basis for all University researchers.