Table 1 Summary of the ten individuals with known STR alleles
From: STRetch: detecting and discovering pathogenic short tandem repeat expansions
Sample | Disease | Gene | Repeat unit | Type | Position | Allele ref | Pathogenic range | Allele PCR | Allele STRetch | Rank (internal control) | p value (internal control) | Rank (reference control) | p value (reference control) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | SCA1 | ATXN1 | CAG | Coding | chr6:16327865-16327955 | 30.3 | 39–70 | 51 | 50.5 | 1 | 4.71E-25 | 1 | 2.46E-14 |
2 | Unaffected relative of Sample 1 | ATXN1 | CAG | Coding | chr6:16327865-16327955 | 30.3 | 39–70 | 29/32 | 32.2 | – | – | – | – |
3 | SCA3 | ATXN3 | CAG | Coding | chr14:92537355-92537396 | 14 | 60–87 (≥52) | 73 | 65.4 | 793 | 0.22 | 3 | 4.15E-09 |
4 | SCA6 | CACNA1A | CAG | Coding | chr19:13318673-13318712 | 13.3 | 20–33 (≥19) | 22 | No call- 0 STR reads in all samples | – | – | – | – |
5 | SBMA | AR | CAG | Coding | chrX:66765159-66765261 | 33.3 | ≥38 (≥36) | 41 | 43.3 | 9 | 6.90E-09 | 11 | 5.19E-05 |
6 | SBMA | AR | CAG | Coding | chrX:66765159-66765261 | 33.3 | ≥38 (≥36) | 47 | 35.1 (0 STR reads) | – | – | – | – |
7 | FTDALS1 | C9orf72 | GGGGCC | Intronic | chr9:27573482-27573544 | 10.8 | >60 (>30) | >50 | 41.5 | 959 | 0.6 | 5 | 1.20E-06 |
8 | DM2 | ZNF9 | CCTG | Intronic | chr3:128891419-128891502 | 20.8 | 75–11,000 | >75 | 38.4a | 1 | 3.84E-23 | 1 | 4.05E-16 |
9 | DM1 | DMPK | CAG | Non-coding | chr19:46273462-46273524 | 20.7 | >50 | >150 | 79.3 | 1 | 3.24E-48 | 1 | 1.13E-32 |
10 | FRDA | FXN | GAA | Intronic | chr9:71652203-71652205 | 6 | 66–1300 (≥44) | ~ 850 | 17.7b | 2b | 1.83e-08b | NA | NA |