. Author manuscript; available in PMC: 2021 Mar 10.

Published in final edited form as: Eur J Immunol. 2020 Jun 17;50(9):1307–1320. doi: 10.1002/eji.201948495

Table 1.

Target nucleotide mutation frequency in DGYW/WRCH mutation hotspots within framework regions (FR) and complementarity-determining regions (CDR) of T cell receptor (TCR) variable region (V) segments

V segment	Hotspot motif	Region	# G/C Bases	% G/C	S/N	Observed G/C mutations	Expected G/C mutations	MI^a)	χ² p^b)
TCRαδV-TCRαC	DGYW/WRCH	FR	11008	1.9	1.27	140	5.9	23.62	0.0000
		CDR	2997	0.5	1.94	58	2.6	22.73
		All	14005	2.4	1.41	198	8.3	23.96	0.0000
	Outside motif		568931		0.03	146	335.7	0.43
TCRαδV-TCRδC	DGYW/WRCH	FR	4012	4.2	0.65	26	2.3	11.15	0.0000
		CDR	714	0.7	0.84	6	0.5	11.15
		All	4726	4.9	0.68	32	2.9	11.15	0.0000
	Outside motif		90762		0.03	26	55.1	0.47
TCRβV	DGYW/WRCH	FR	5476	9.8	0.29	16	5.5	2.92	0.0000
		CDR	925	1.7	0.32	3	0.7	4.28
		All	6401	11.5	0.30	19	6.2	3.07	0.0000
	Outside motif		49435		0.07	35	47.8	0.73
TCRγV	DGYW/WRCH	FR	3099	5.6	0.42	13	3.4	3.78	0.0000
		CDR	581	1.0	0.69	4	0.4	11.27
		All	3680	6.6	0.46	17	3.7	4.58	0.0000
	Outside motif		51898		0.08	39	52.3	0.75
IgHV-TCRδC	DGYW/WRCH	FR	4604	6.2	0.56	26	6.0	4.37	0.0000
		CDR	1995	2.7	1.10	22	3.5	6.33
		All	6599	8.9	0.73	48	9.4	5.12	0.0000
	Outside motif		67254		0.08	57	95.6	0.60
NTCRV	DGYW/WRCH	FR	644	14.6	0.47	3	1.7	1.80	0.2240
		CDR	102	2.3	2.94	3	2.1	1.44
		All	746	16.9	0.80	6	3.6	1.69	0.1542
	Outside motif		3664		0.41	15	17.4	0.86
STCRδV	DGYW/WRCH	FR	1019	11.3	0.20	2	1.4	1.40	0.5413
		CDR	279	3.1	0.00	0	0.1	0.00
		All	1298	14.3	0.15	2	1.6	1.27	0.7161
	Outside motif		7754		0.12	9	9.4	0.96

DGYW/WRCH (G/C is the mutable position; D = A/G/T, Y = C/T, W = A/T, R = A/G, and H = T/C/A); “ALL” refers to G and C nucleotides found within hotspot motifs along the entire V segment (FR and CDR); “Outside motif” refers to G and C nucleotides outside a hotspot motif; S/N = substitutions per nucleotide; MI = mutability index^a); %G/C = proportion of all nucleotides in that category that are G or C. TCRαδV-TCRαC, alpha; TCRαδV-TCRδC, delta; TCRβV, beta; TCRγV, gamma; IgHV-TCRδC, trans-rearrangements between immunoglobulin heavy chain (IgH) and delta TCR constant regions; NTCRV and STCRδV, components of NARTCR.

^a)

Mutability index is the observed number of mutations of a specific nucleotide divided by the expected number of mutations of that nucleotide, with a value of 1.00 indicating random mutation.

^b)

χ² analysis was used to compare observed and expected numbers of mutations between (a) FR and CDR regions and (b) all mutations inside and outside hotspot motifs for each V segment type.