Table 3 Performance of LUSTR and ExpansionHunter in identifying STR variants reported in the GIAB database (Chinese Trio)
Loci | Father | Mother | Child | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
Call by GIAB | Call by LUSTR (merged) | Call by EH (merged) | Call by GIAB | Call by LUSTR (merged) | Call by EH (merged) | Call by GIAB | Call by LUSTR (merged) | Call by EH (merged) | Call by LUSTR (MGI merged) | Call by EH (MGI merged) | |
ATN1 (CAG) 12:7045880–938 | -5/ + 4 | -5 (31 ± 23%)  + 4 (69 ± 23%) | -5/ + 4 | NA | 0 (50 ± 12%)  + 2 (50 ± 12%) | 0/ + 2 | NA | 0 (26 ± 19%)  + 4 (74 ± 19%) | 0/ + 4 | 0 (44 ± 16%)  + 4 (56 ± 16%) | 0/ + 4 |
ATXN1 (TGC) 6:16327865–955 | NA | -3 (40 ± 60%) -1 (60 ± 60%) | -3/-1 | NA | -1 (16 ± 16%) [+ 4.2, + 13.7] (76 ± 25%) | -1/ + 3 | NA | -1 (100 ± 0%) | -1/-1 | -1 (100 ± 0%) | -1/-1 |
ATXN2 (GCT) 12:112036754–823 | NA | -4 (8 ± 26%) -1 (92 ± 26%) | -1/-1 | NA | -1 (100 ± 0%) | -1/-1 | NA | -1 (100 ± 0%) | -1/-1 | -1 (70 ± 41%) | -1/-1 |
ATXN3 (CTG) 14:92537355–96 | NA | 0 (100 ± 0%) | 0/0 | 0/ + 6 | 0 (59 ± 7%)  + 6 (41 ± 7%) | 0/ + 6 | NA | 0 (100 ± 0%) | 0/0 | 0 (100 ± 0%) | 0/0 |
ATXN7 (GCA) 3:63898361–423 | NA | 0 (100 ± 0%) | 0/ + 2 | NA | 0 (51 ± 36%)  + 2 (49 ± 36%) | 0/ + 2 | 0/ + 2 | 0 (81 ± 51%)  + 2 (19 ± 51%) | 0/ + 2 | 0 (84 ± 84%) |  + 2/ + 9 |
ATXN10 (ATTCT) 22:46191235–304 |  + 3/ + 7 |  + 2.8 (23 ± 37%)  + 3 (37 ± 37%) [+ 7.9, + 9.7] (40 ± 25%) |  + 3/ + 6 | NA | -0.2 (34 ± 15%) 0 (66 ± 15%) | 0/0 | NA | 0 (53 ± 24%)  + 4.2 (47 ± 24%) | 0/ + 6 | 0 (33 ± 23%)  + 7 (67 ± 23%) | 0/ + 7 |
C9ORF72 (GCCCCG) 9:27573483–544 | NA | -1 (100 ± 0%) | -1/-1 | -1/ + 3 | -1 (45 ± 27%)  + 3 (54 ± 27%)  + 40 (1 ± 5%) | -1/ + 3 | -1/-1 | -1 (100 ± 0%) | -1/-1 | -1 (100 ± 0%) | -1/-1 |
CACNA1A (CTG) 19:13318673–712 | NA | 0 (49 ± 19%)  + 1 (51 ± 19%) | 0/ + 1 | NA | 0 (100 ± 0%) | 0/0 | NA | 0 (100 ± 0%) | 0/0 | 0 (36 ± 36%) | 0/0 |
CBL (CGG) 11:119077000–33 | 0/ + 1 | 0 (67 ± 17%)  + 1 (33 ± 17%) | 0/ + 1 | NA | 0 (100 ± 0%) | 0/0 | NA | 0 (100 ± 0%) | 0/0 | 0 (100 ± 0%) | 0/ + 1 |
DMPK (CAG) 19:46273463–524 | -5/-4 | -5 (56 ± 15%) -4 (44 ± 15%) | -5/-4 | NA | -7 (100 ± 0%) | -7/-7 | -7/-4 | -7 (43 ± 9%) -4 (57 ± 9%) | -7/-4 | -7 (53 ± 8%) -4 (47 ± 8%) | -7/-4 |
HTT (CAG) 4:3076604–67 | -2/-1 | -2 (17 ± 27%) -1 (83 ± 27%) | -2/-1 | -2/-1 | -2 (29 ± 23%) -1 (71 ± 23%) | -2/-1 | -1/-1 | -1 (96 ± 14%) 0 (4 ± 14%) | -1/-1 | -1 (100 ± 0%) | -1/-1 |
JPH3 (GCT) 16:87637889–935 | -1/ + 2 | -1 (42 ± 12%)  + 2 (58 ± 12%) | -1/ + 2 | NA | 0 (100 ± 0%) | 0/0 | 0/ + 2 | 0 (29 ± 9%)  + 2 (71 ± 9%) | 0/ + 2 | 0 (37 ± 5%)  + 2 (63 ± 5%) | 0/ + 2 |
PPP2R2B (GCT) 5:146258291–322 | NA |  + 6 (55 ± 13%)  + 8 (45 ± 13%) |  + 6/ + 8 | NA |  + 3 (46 ± 14%)  + 6 (54 ± 14%) |  + 3/ + 6 |  + 3/ + 6 |  + 3 (62 ± 11%)  + 6 (38 ± 11%) |  + 3/ + 6 |  + 3 (44 ± 7%)  + 6 (56 ± 7%) |  + 3/ + 6 |