Sanger-based Gene Resequencing
Gene Mutation Detection
Resequencing provides a fast, simple method of detecting variants in cancer related genes. It allows an entire gene to be evaluated in a single experiment. The SMF performs this assay using custom designed primers. The table below lists the genes available for this service.
The SMF provides custom design and optimization services. Cost depends on gene sequence complexity and the number of amplicons/sequences necessary to cover the regions of interest.
New gene assay design and optimization are provided at no charge with a minimum of five samples submitted for each amplicon.
Resequencing Service Includes
- Quantification and normalization of samples
- PCR Amplification and purification
- Sanger Sequencing (AB3730XL)-both directions (where possible)
- Comparative alignment to reference sequence (SeqScape Software – Applied Biosystems)
- Reanalysis (if needed)
- Report of all mutations found and all sequences generated
Assay Development Form
Resequencing Submission Form
General Pricing
| Service | MD Anderson Investigators | Non-MD Anderson Investigators |
|---|---|---|
| Assay Design | No Cost-5+ samples required | Not available |
| Mutation Detection | $20/amplicon (2 sequences) | $41/amplicon (2 sequences) |
Resequencing Gene List
| Gene Symbol | Exons | Coverage | Cost/Sample | Amplicons |
|---|---|---|---|---|
| ALK | Exon 25 (R1275Q) | selected SNPs | 20 | 1 |
| AKT1 | Exon 4 (E17K) | selected SNPs | 20 | 1 |
| AURKA | 1, 3-11, UTR (3') | selected exons | 280 | 14 |
| BRAF | Exon 15 (V600E) | selected SNPs | 20 | 1 |
| BRCA1 | 1-24, a*, UTR (5') | all transcripts | 882 | 42 |
| BRCA2 | 1-28 | all transcripts | 1134 | 54 |
| CDK4 | Exon 2 (R24C) | selected SNPs | 20 | 1 |
| CHEK2 | 1-18 | full coding - select transcript | 0 | |
| Dip2C | 2-37 | selected exons | 700 | 35 |
| EGFR | 18-21 | selected exons | 80 | 4 |
| FBXW7 (a.k.a. CDC4) | Exons 8 (R465C), 10 (R505C) and 11 (S582L) | selected SNPs | 60 | 3 |
| FGFR3 | Exon 8 (G370C and S371C) | selected SNPs | 40 | 2 |
| FLT1 | 17-26 | selected exons | 200 | 10 |
| FLT4 | 17-26 | selected exons | 200 | 10 |
| GAL3 | 1, 4** | selected exons | 40 | 2 |
| HRAS+ | 1-4, 4a | selected exons | 100 | 5 |
| ID1 | 1 | all transcripts | 80 | 4 |
| KIT (a.k.a. c-KIT) | Exon 13 (K642E) | selected SNPs | 20 | 1 |
| KRAS | 2-6 | all transcripts | 100 | 5 |
| LKB11/STK11a | 1, 4-8 | select transcript | 100 | 5 |
| MDM2 | 1-4, 4a, 5-11 | all transcripts | 240 | 12 |
| mP53 (mouse) | 1-11 | all transcripts | 140 | 7 |
| mPTEN (mouse) | 1-9, UTR (5' and 3') | all transcripts | 460 | 23 |
| NHERF-2 | Exon 3 (R171W) | selected SNPs | 20 | 1 |
| P53 | 1-11, a, b, UTR (5')* 1-11 | all transcripts exons only | 450 364 | 21 17 |
| PHLLPP2 | Exon 18 (L1016S) | selected SNPs | 20 | 1 |
| PIK3CA | 2, 8 | selected exons | 60 | 3 |
| PIK3R1 | 1-15 | full coding - select transcript | 280 | 14 |
| PIK3R2 | 1-15, 5' regulatory | full coding | 340 | 17 |
| PRKAG2 | Exon 15 (R531Q) | selected SNPs | 20 | 1 |
| PTCH1 | 1-23, UTR (3') | full coding - select transcript | 640 | 32 |
| PTEN | 1-9 | all transcripts | 190 | 9 |
| SART1 | 1-22 | all transcripts | 220 | 11 |
| SNON (SK1L) | 1, 4 | selected exons | 80 | 4 |
| SRC | 1-12 | all transcripts | 195 | 9 |
| TRK2 | 4-21 | full coding - select transcript | 340 | 17 |
| UBCH10 | 1-5 | all transcripts | 100 | 5 |
| VEGFA (a.k.a. VPF) | Promoter (partial) | selected exons | 60 | 3 |
| VBP1 | 1-6 | all transcripts | 160 | 8 |
| VHL | 1-3, UTR | full coding - select transcript | 120 | 6 |