Next-generation sequencing profiling of mitochondrial genomes in gout

Table 3 Positively associated alleles of MT-TA, MT-TC, MT-TH, MT-TQ, MT-TS2, MT-TT, and MT-TW identified from SKAT analysis

Gene	Position	Mutation	Location^a	Nucleotide number^b	HF (%)	Absent in control	Fre (%)^c	CI (%)	Alteration^d	Published disease association
MT-TQ ^e	4386	T➔C	D-loop	15	99.8599.61	+	1.89	64.71
MT-TW	5528	T➔C	D-loop	18	70.53	+	0.00	11.76
MT-TW	5557	T➔C	V region	48	80.18	+	0.15	47.06
MT-TW	5563	G➔A	T-loop	55	51.92	+	0.30	11.76
MT-TA	5601	C➔T	T-loop	59	77.10	+	1.37	47.06
MT-TA	5628	T➔C	AC stem	31	99.61	+	0.15	94.12	+	Hearing loss, hypertension, ophthalmoplegia and dysphagia [37,38,39]
MT-TC	5783	G➔A	T-stem	50	99.58	+	0.04	94.12	+	Encephalomyopathy, deafness, myopathy, cardiomyopathy, and renal failure [40, 41]
MT-TC	5814	T→C	D-stem	13	59.30	+	0.37	88.24	+	Encephalomyopathy [42]
MT-TH	12,172	A→G	AC loop	38	99.67	+	1.15	88.24	+
MT-TH	12,178	C→T	V region	44	71.81	+	0.00	64.71	+
MT-TS2	12,234	A→G	AC stem	42	55.90	+	0.30	58.82
MT-TS2	12,239	C→T	V region	48	66.70	+	0.96	64.71
MT-TS2	12,248	A→G	T-loop	57	99.59	+	0.11	100.00
MT-TT	15,894	G→A	ACC stem	7	99.52	+	0.04	88.24	+
MT-TT	15,940	T→C	T-loop	59	65.31	+	0.11	41.18

Abbreviations: SKAT Sequence Kernel Association Test, HF heteroplasmic fraction, CI conservation index, V variable, AC anticodon, ACC acceptor
^aThe region of transfer RNA (tRNA) (acceptor stem, D-stem, D-loop, anticodon stem, anticodon loop, variable region, T-stem, T-loop) where alleles were located (Fig. 2) ^bNucleotide numbers represent the nucleotide positions according to the conventional tRNA numbering system, as described in “Methods”
^cAllele frequency in 2704 mitochondrial genomes
^dPotential structural and functional alterations
^eTwo patients with gout had m.4386 T > C alleles

ISSN: 1478-6362