Mapping the landscape of tandem repeat variability by targeted long read single molecule sequencing in familial X-linked intellectual disability

Table 1 Initial selection of possible targets for subsequent probe design, and final selection of tandem repeats for capture and sequencing

#	Selection groups	Predicted variability	Total repeat length	Unit length	Copy number	N	Results of modified probe design (final selection)
#	Selection groups	Predicted variability	Total repeat length	Unit length	Copy number	N	1 probes	2 probes	3 probes	4 probes	All targeted		Not included
1	Coding repeats	Any SERV	Any total length	Any unit	Any copy num.	368					305	82,88%	63	17,12%
	Coding repeats	Any SERV	Repeat length ≤ 500 bp	Any unit	Any copy num.	353	36	37	74	158
2	Regulatory repeats (top variability)	SERV ≥1	Any total length	Any unit	Any copy num.	181					149	82,32%	32	17,68%
	Regulatory repeats (top variability)	SERV ≥1	Repeat length ≤ 500 bp	Any unit	Any copy num.	174	23	36	78	12
3	Regulatory repeats (lower variability)	0,4 < SERV < 1	Repeat length ≤ 520 bp (all)	Any unit	Any copy num.	390	62	55	100	101	318	81,54%	72	18,46%
4	Additional regulatory repeats within 1 kb from the genes involved in XLID (not yet included in groups 2–3)	Any SERV (−0,92 ̶ 0,37)	Any total length (< 250 bp)	Any unit	Any copy num.	68	2	5	19	39	65	95,59%	3	4,41%
	Total (‘functional’)					1007	123	133	271	310	837	83,12%	170	>16,88%
5	Intronic repeats only	SERV > 0,8	Repeat length ≤ 500 bp	Unit ≥2 bp	≥ 15 copies	3431	filtered out	filtered out	516	24	540	15,74%	2891	84,26%
6	Intergenic repeats only	SERV > 1	Repeat length ≤ 500 bp	Unit ≥2 bp	≥ 15 copies	4126	filtered out	filtered out	440	20	460	11,15%	3666	88,85%
	Total (‘unknown significance’)					7557			956	44	1000	>13,23%	6557	86,77%
	Total (all)					8564>	123	133	1227	354	1837	21,45	6727	78,55%

ISSN: 1755-8794