SNP mapping by TAMS assays
We have developed a novel rapid method for mapping gene mutations ("positional cloning") based on SNPs as markers, and on tag-array mini-sequencing (TAMS) as genotyping assay.
For a detailed description please see Chen, D.*, Ahlford, A.*, Schnorrer, F.*, Kalchhauser, I., Fellner, M., Viragh, E., Kiss, I., Syvänen, A.C., and Dickson, B.J.D. High-resolution, high-throughput SNP mapping in Drosophila melanogaster. Nat Methods 5(4), 323-329 (2008).
In total, 293 TAMS assays for all major chromosome arms (56 - 60 assays each) were experimentally verified. TAMS primers were designed to detect equidistant SNPs at an average resolution of 391.3kb.
They were designed to distinguish between selected stocks (see table below), but should also cover polymorphisms of other stock pairs.
A detailed list of TAMS assay PCR primers, mini-sequencing primers (including tags) and anti-tag sequences is provided as comma-separated text or as Excel file (one sheet per chromosome arm).
| Chrom. arm | Verified TAMS assays | Resolution (kb) | Stock pair (used for assay design) |
|---|---|---|---|
| X | 58 | 386.5 | CS[X] - Rec. mar.[X] |
| 2L | 59 | 366.7 | CS[2] - OR[2] |
| 2R | 60 | 336.0 | CS[2] - OR[2] |
| 3L | 56 | 412.1 | CS[3] - Rec. mar.[3L] |
| 3R | 60 | 455.0 | CS[3] - Rec. mar.[3R] |
To facilitate usage of the TAMS method for fine mapping, we have additionally designed in total 1417 TAMS assays. These pre-computed primer sets cover the regions between the two EP insertions of each 2EP stock.
A detailed list of TAMS assay PCR primers, mini-sequencing primers (including tags) and anti-tag sequences is provided as Excel file (one sheet per chromosome arm).
| Chrom. arm | Pre-computed TAMS assays |
|---|---|
| X | 373 |
| 2L | 360 |
| 2R | 322 |
| 3L | 313 |
| 3R | 49 |