DNA Copy Number Variation
The StellARray™ Technology has been designed to provide the user with multiple functions. Each primer pair has been designed to detect both RNA (as cDNA) and genomic DNA (gDNA) in separate assays. This design approach, while contrary to traditional approaches, provides the user with the direct capability to analyze both gene expression and genomic DNA copy-number variations (CNV) derived from the same primer pairs. What follows below is an experiment that demonstrates the precision and accuracy of StellARrays™ to measure genomic DNA copy-number variation as well as the power of Global Pattern Recognition™ analysis to statistically rank the variation between two groups of samples.
Experiment:
Genomic DNA Copy Number Variation - Global Pattern Recognition™ output as a demonstration of the utility of StellARays™ and GPR™ for determination of genomic DNA (gDNA) copy number variation (CNV). We analyzed individual gDNA samples (biological replicates) from five male C57BL/6J and five female C57BL/6J mice using the 384-well Lymphoma and Leukemia StellARray™ (Cat # CA0301-MM384). This StellARray™ has a total of 12 targets on the mouse X chromosome, consisting of 11 genes and our intergenic genomic control (genomic3). For these 12 targets, the expected CNV is two fold due to the females having 2 copies of the X chromosome and males having only one.
Results:
Only data for the top 32 of 384 genes are shown. This '5 vs. 5' example identified all 12 X-specific targets with statistical significance (p-value less than 0.05), ranking them as the top 12 'hitters', and providing an average Fold Change value of 2.0136 (relative to the females) with a standard deviation of 0.112.
| Rank | Gene Name | p-Value | Fold Change | Chromosome |
| 1 | Cdx4 | 1.9694 x 10-5 | 2.1984 | X |
| 2 | Rhox6 | 2.3721 x 10-5 | 2.0614 | X |
| 3 | Tro | 2.3942 x 10-5 | 2.0355 | X |
| 4 | Cd40lg | 5.5550 x 10-5 | 2.0013 | X |
| 5 | Ikbkg | 6.5947 x 10-5 | 1.7857 | X |
| 6 | Hprt1 | 8.5730 x 10-5 | 1.9999 | X |
| 7 | Btk | 1.3532 x 10-4 | 1.9606 | X |
| 8 | Gata1 | 1.6391 x 10-4 | 2.0157 | X |
| 9 | Mecp2 | 3.6731 x 10-4 | 2.0405 | X |
| 10 | Suv39h1 | 4.4394 x 10-4 | 1.9456 | X |
| 11 | Mageh1 | 6.7939 x 10-4 | 2.1936 | X |
| 12 | genomic3 | 9.9295 x 10-4 | 1.9252 | X |
| 13 | Hdac1 | 0.0027 | 1.2972 | 8 |
| 14 | Tert | 0.0398 | -1.2339 | 13 |
| 15 | Irf2 | 0.0538 | -1.1347 | 8 |
| 16 | Il6st | 0.0571 | -1.1236 | 11 |
| 17 | Hmgb2 | 0.0657 | 1.1361 | 11 |
| 18 | Tnfrsf13b | 0.0748 | -1.1386 | 5 |
| 19 | Ezh1 | 0.0802 | -1.1468 | 12 |
| 20 | Shh | 0.0871 | -1.5049 | 10 |
| 21 | Max | 0.0878 | 1.1223 | 4 |
| 22 | Cdk2 | 0.0887 | -1.1429 | 17 |
| 23 | Mib2 | 0.0908 | -1.1037 | 14 |
| 24 | Notch3 | 0.0988 | -1.1005 | 12 |
| 25 | Rb1 | 0.1045 | -1.2625 | 8 |
| 26 | Jag2 | 0.1164 | -1.4582 | 7 |
| 27 | Fanca | 0.1176 | -1.1154 | 10 |
| 28 | Mki67 | 0.1204 | 1.8320 | 3 |
| 29 | Mdm2 | 0.1295 | -1.0773 | 1 |
| 30 | Dkk2 | 0.1369 | 1.0766 | 3 |
| 31 | Psen2 | 0.1395 | -1.0853 | 10 |
| 32 | S100a9 | 0.1422 | -1.0831 | 2 |
Conclusion:
It is known that the mammalian genome is dynamic. Genomic CNVs are more frequent in humans than expected (Redon R, et al., Nature. 2006; 444; 444-454) and play a major role for disease risk, onset, and progression. This is not only true for cancer, where it is well established that changes in the DNA itself are responsible for cancer type, stage, and prognosis, but for other conditions as well, such as glomerulonephritis (Aitman TJ, et al., Nature 2006; 439; 851-855), mental retardation and dysmorphic features (Shaw-Smith C, et al., Nat Genet. 2006; 38; 1032-7). The above results illustrate the precision and accuracy of BHB's StellARray™ and GPR™ technology for measuring the small changes associated with CNVs.
Contact Information:
|
Daniel J. Shaffer |
