Genome-wide detection of short tandem repeat expansions by long-read sequencing

BMC Bioinformatics

Table 3 The estimation of the normal/abnormal repeat status of CAG repeats in ATXN3 according to RepeatHMM-DB compared with the determination by prior literature knowledge of normal repeat range

Subject	True counts	Prior knowledge		RepeatHMM-DB
Subject	True counts	Allele	Subject	Score	Allele	Subject
SRR5363334	14, 77	N, P	P	− 2.2, 8.4	N, P	P
SRR5363452	30, 66	N, P	P	0.5, 6.6	N, P	P
SRR5363453	14, 69	N, P	P	− 2.2, 7.1	N, P	P
SRR5363454	14, 71	N, P	P	− 2.2, 7.4	N, P	P
SRR5363455	21, 72	N, P	P	− 1.0, 7.6	N, P	P
SRR5363456	14, 77	N, P	P	− 2.2, 8.4	N, P	P
SRR5363457	26, 71	N, P	P	− 0.2, 7.4	N, P	P
SRR5363458	14, 63	N, P	P	− 2.2, 6.1	N, P	P
SRR5363459	29, 70	N, P	P	0.3, 7.2	N, P	P
SRR5363460	27, 71	N, P	P	0.0, 7.4	N, P	P
SRR5363461	34, 75	N, P	P	1.2, 8.1	N, P	P
SRR5363462	28, 89	N, P	P	0.2, 10.4	N, P	P
SRR5363463	61, 61	P, P	P	5.7, 5.7	P, P	P
SRR5363464	26, 65	N, P	P	− 0.2, 6.4	N, P	P
SRR5363465	14, 89	N, P	P	− 2.2, 10.4	N, P	P
SRR5363466	40, 67	P, P	P	2.2, 6.7	P, P	P
SRR5363467	37, 68	N, P	P	1.7, 6.9	N, P	P
SRR5363468	28, 40	N, P	P	0.2, 2.2	N, P	P
SRR5363469	14, 82	N, P	P	− 2.2, 9.2	N, P	P
SRR5363470	14, 68	N, P	P	− 2.2, 6.9	N, P	P
SRR5363471	14, 14	N, N	N	− 2.2, − 2.2	N, N	N
SRR5363472	27, 35	N, N	N	0.0, 1.3	N, N	N
SRR5363473	28, 28	N, N	N	0.2, 0.2	N, N	N
SRR5363480	14, 14	N, N	N	− 2.2, − 2.2	N, N	N
SRR5363632	14, 19	N, N	N	− 2.2, − 1.3	N, N	N

The true repeat counts for 20 patients with SCA3 and 5 control subjects were determined by capillary electrophoresis or Sanger sequencing. The estimated normal repeat range of CAG repeat is 11–28. The ‘Allele’ column shows the pathogenic inference for each allele, while the ‘Subject” column shows the disease status prediction for each subject. ‘N’: normal, ‘P’: pathogenic/patient

ISSN: 1471-2105