Comprehensive Association Testing of Common Mitochondrial DNA Variation in Metabolic Disease

Abstract

Many lines of evidence implicate mitochondria in phenotypic variation: (a) rare mutations in mitochondrial proteins cause metabolic, neurological, and muscular disorders; (b) alterations in oxidative phosphorylation are characteristic of type 2 diabetes, Parkinson disease, Huntington disease, and other diseases; and (c) common missense variants in the mitochondrial genome (mtDNA) have been implicated as having been subject to natural selection for adaptation to cold climates and contributing to “energy deficiency” diseases today. To test the hypothesis that common mtDNA variation influences human physiology and disease, we identified all 144 variants with frequency >1% in Europeans from >900 publicly available European mtDNA sequences and selected 64 tagging single-nucleotide polymorphisms that efficiently capture all common variation (except the hypervariable D-loop). Next, we evaluated the complete set of common mtDNA variants for association with type 2 diabetes in a sample of 3,304 diabetics and 3,304 matched nondiabetic individuals. Association of mtDNA variants with other metabolic traits (body mass index, measures of insulin secretion and action, blood pressure, and cholesterol) was also tested in subsets of this sample. We did not find a significant association of common mtDNA variants with these metabolic phenotypes. Moreover, we failed to identify any physiological effect of alleles that were previously proposed to have been adaptive for energy metabolism in human evolution. More generally, this comprehensive association-testing framework can readily be applied to other diseases for which mitochondrial dysfunction has been implicated.

Mitochondria play a central role in energy metabolism, are composed of >700 known proteins,¹ and are essential for generating ATP and for regulating apoptosis.² The human mitochondrial oxidative phosphorylation (OXPHOS) machinery, which synthesizes most intracellular ATP, consists of five complexes with 85 known protein subunits. Thirteen OXPHOS subunits, 2 rRNA genes, and 22 tRNA genes are encoded by the 16.6-kb mitochondrial genome (mtDNA).

Rare mutations in both nuclear-encoded OXPHOS genes and in mtDNA result in disease syndromes with neurological, muscular, or metabolic manifestations, proving that defects in mitochondrial OXPHOS can play a causal role in human disease. Mutations in nuclear-encoded components of OXPHOS complexes have been identified in many early-onset diseases, such as Leigh syndrome (MIM 256000) and cardioencephalomyopathy (MIM 604377).^2,3 Nuclear genes that encode OXPHOS assembly factors, influence mtDNA maintenance or translation, modify mitochondrial tRNA, or encode biosynthetic enzymes may be mutated in rare mitochondrial diseases.^4,5 In addition, >250 mtDNA point mutations and deletions have been linked to human disease, and several of these include glucose defects or diabetes mellitus as component phenotypes—for example, mitochondrial myopathy, encephalopathy, lactic acidosis, and stroke-like episodes (MELAS [MIM 540000]), Kearns-Sayre syndrome (KSS [MIM 530000]), and maternally inherited diabetes and deafness syndrome (MIDD [MIM 520000]).^6,7 A mutation in the mitochondrial Leu tRNA gene (A3243G) causes MIDD,⁸ and a novel substitution in a highly conserved region of the mitochondrial Ile tRNA gene (T4291C) causes hypertension, hypercholesterolemia, and hypomagnesemia (MIM 500005),⁹ suggesting that mutations in mtDNA can cause diabetes and other metabolic defects.

Alterations in the function of OXPHOS have been recognized consistently in type 2 diabetes (MIM 125853). Reduced activity of OXPHOS enzymes and fewer, smaller mitochondria are seen by transmission electron microscopy in skeletal muscle from diabetics compared with nondiabetics.^10–12 From global gene-expression–profiling studies, we and others identified a subset of OXPHOS genes that are co-coordinately downregulated in muscles from individuals with type 2 diabetes compared with healthy control individuals.^13,14 In addition, functional in vivo spectroscopy studies demonstrate that OXPHOS activity and rates of ATP synthesis are lower in the insulin-resistant offspring of diabetic individuals and in elderly insulin-resistant people.^15–17

Population genetics analysis has suggested a functional role for common variants in mtDNA. On the basis of differential conservation of missense variants in different mtDNA lineages, it was argued that positive selection influenced common mtDNA variation. Moreover, it was hypothesized that mtDNA SNPs favorable for selective adaptation to cold Northern climates during human evolution predispose to energy metabolism diseases today.^2,18,19

These many lines of evidence suggest a “mitochondrial” hypothesis of disease. Specifically, inherited defects in mitochondria may play a causal role in type 2 diabetes^20,21 and neurodegenerative diseases, such as Alzheimer (MIM 104300), Parkinson (MIM 168600), and Huntington (MIM 143100) diseases.^22,23 Population genetics analysis specifically suggests that common mtDNA variants may be functional and relevant to disease. However, no comprehensive test, even of common variation in mtDNA, has yet been performed. Several previous reports did not consistently reproduce associations of common mtDNA variants with diabetes or metabolic traits.^24–29 However, these studies tested only a subset of mtDNA variation in relatively modestly sized samples of <2,000 individuals.

The goal of the present study was to perform a comprehensive test of the hypothesis that mtDNA variants influence type 2 diabetes and metabolic traits. Specifically, we sought to (1) inventory all SNPs with frequency >1% in Europeans, (2) select tagging SNPs (tSNPs) to capture this variation efficiently, (3) test all common variants and haplogroups for association with type 2 diabetes and a range of metabolic phenotypes (although sample sizes for some traits were limited), and (4) assess studywide significance of our findings by permutation testing.

Material and Methods

Alignment of Sequences

We aligned all human mtDNA coding-region sequences from GenBank (719 sequences) and 536 sequences from Mitokor³⁰ and identified 3,240 variant sites. We excluded ∼0.8 kb of the hypervariable mtDNA D-loop promoter region from the study, since this region is best addressed by direct resequencing in case-control samples because of its high mutation rate.

Subjects and Samples

The sample consisted of 6,608 white subjects from Scandinavia (Sweden and Botnia, hereafter referred to as the “Swedish” and “Scandinavian” samples, respectively), Canada, Poland, and the United States; metabolic phenotype information was available for a subset of the subjects (table 1).^31,32 The Scandinavian and Canadian diabetic case-control samples were matched for sex, age, region, and BMI (calculated as weight in kilograms divided by the square of height in meters), whereas the Polish and U.S. case-control samples were matched for sex, age, and geographical region but not tightly for BMI. BMI, blood pressure, and cholesterol values were available for diabetic and nondiabetic subjects from all five populations, and insulinogenic index and homeostasis model assessment of insulin resistance (HOMA-IR) values were obtained for nondiabetic Scandinavian and Swedish subjects (from a 2-h oral glucose tolerance test [OGTT]). The study of human subjects was approved by the institutional review boards at parent institutions for all samples and at the Broad Institute for Harvard and MIT. Genomic DNA was extracted from blood samples and lymphoblastoid cell lines.

Table 1. .

Clinical Characteristics of the Diabetes Case-Control Study Samples and Quantitative Metabolic Traits in Subjects Used to Study Genotype-Phenotype Correlations^[Note]

Sample or Traita	n	No. of Males; Females	Age (years)	BMI	Fasting Plasma Glucose (mmol/liter)	HbA1cb (%)	Plasma Glucose by 2-h OGTT (mmol/liter)	Trait Value
Case-control sample:
Scandinavian:
DM/severe IGT	459	247; 212	60.9 ± 10.2	28.2 ± 4.6	9.8 ± 3.4	…	15.0 ± 5.3	…
NGT	459	247; 212	59.6 ± 10.4	26.3 ± 3.6	6.2 ± 1.8	…	6.8 ± 2.8	…
Swedish:
DM/severe IGT	505	264; 241	66.3 ± 11.8	27.6 ± 4.1	9.8 ± 3.4	6.5 ± 1.5	…	…
NGT	505	264; 241	66.6 ± 11.6	27.7 ± 4.1	6.2 ± 1.8	ND	ND	…
Canadian:
DM	123	67; 56	53.5 ± 7.9	29.2 ± 4.4	6.4 ± 1.8	…	12.8 ± 2.1	…
NGT	123	67; 56	52.1 ± 7.9	28.6 ± 4.1	5.1 ± 0.6	…	6.1 ± 1.1	…
U.S.c:
DM	1,214	641; 573	62.6 ± 11.0	33.0 ± 6.9	9.8 ± 3.0	8.0 ± 3.1	…	…
NGT	1,214	641; 573	60.9 ± 9.7	27.4 ± 5.2	5.1 ± 0.9	ND	ND	…
Polishc:
DM	1,003	420; 583	61.8 ± 9.6	29.6 ± 4.8	8.9 ± 4.0	7.9 ± 1.3	…	…
NGT	1,003	420; 583	58.7 ± 7.2	26.1 ± 3.6	4.8 ± 1.2	ND	ND	…
Trait:
Ins index	342	181; 161	58.5 ± 10.1	26.2 ± 3.6	…	…	…	22.6 ± 31.3
HOMA-IR	399	210; 189	59.2 ± 10.3	26.3 ± 3.7	…	…	…	2.1 ± 1.3
Cholesterol	1,274	682; 592	62.5 ± 11.1	27.4 ± 4.2	…	…	…	6.0 ± 1.2 mmol
Systolic BP	2,047	1,090; 957	62.2 ± 11.7	27.7 ± 4.2	…	…	…	144 ± 22 mm Hg
Diastolic BP	2,047	1,090; 957	62.2 ± 11.7	27.7 ± 4.2	…	…	…	83 ± 10 mm Hg

Note.— Data are means ± SD. ND = not determined.

^aBP = blood pressure; DM = diabetes mellitus, type 2; IGT = impaired glucose tolerance; Ins = insulinogenic; NGT = normal glucose tolerance.

^bHbA1c = hemoglobin A1c.

^cSample from Genomics Collaborative Inc.

Genotyping

Genotyping was performed by primer extension of multiplex products with detection by matrix-assisted laser desorption/ionization time-of-flight mass spectroscopy with use of a Sequenom platform.³³ Genotyping for the 64 tSNPs was >98%; maternal inheritance was confirmed for tSNPs by genotyping in 117 CEPH trios (not shown). Two SNPs (mt14470 and mt15884) were triallelic in this population. Duplicate genotypes were obtained for ∼20% of the sample with 22 SNPs and were highly concordant (0.1% discordant genotypes of 29,462 duplicate comparisons). For 69 samples (1.1% of samples genotyped), we observed spectral peaks for both the major and minor allele for 1–3 SNPs per sample. In total, 21 SNPs had heterozygous calls in at least one individual. These observations are consistent with either DNA contamination or heteroplasmy (more than one mtDNA haplotype arising from somatic/maternal germ line mutations or from the paternal mtDNA contribution). Signals for both alleles were seen in individuals from all populations, and no significant difference in the number of cases and controls with such genotypes was observed. For analysis, these genotypes were treated as missing data.

Results

Previous studies have tested subsets of mtDNA variants (from 10–32 sites) for association with a variety of traits,^{24–27,34–49} typically focusing on the nine canonical haplogroups.⁵⁰ We began by cataloging all common sites (frequency >1%) in 15,770 bp of mtDNA (excluding the coding region) and by evaluating how well the complete inventory is captured by these canonical haplogroups in mtDNAs of European origin. Alignment of 928 European coding-region mtDNA sequences (>15,770 bp) identified 2,349 variable sites; 144 sites had a frequency >1% in European individuals (1 site per 110 bp), including 37 nonsynonymous variants, 81 synonymous variants, 25 rRNA/tRNA variants, and 1 noncoding variant (table 2). Fifty variants with frequency >5% were identified. The common variants (frequency >1%) explained 72% of the “heterozygosity” in the European population; this is notably less than in the nuclear genome, where ∼90% of heterozygosity is due to common variants.^51–53

Table 2. .

Common European mtDNA Variants with Frequency >1%, by Gene of Origin

Genea	OXPHOS Complex	Putatively Functional	Missense Mutations	Synonymous Mutations	Total
ND1	1	…	5	5	10
ND2	1	…	6	11	17
ND3	1	…	2	1	3
ND4L	1	…	…	1	1
ND4	1	…	…	15	15
ND5	1	…	6	15	21
ND6	1	…	1	5	6
Cyt B	3	…	9	5	14
COX1	4	…	…	10	10
COXII	4	…	…	4	4
COXIII	4	…	3	4	7
ATP6	5	…	5	5	10
12SrRNA	…	6	…	…	6
16SrRNA	…	7	…	…	7
tRNA Gln	…	1	…	…	1
tRNA Ser	…	1	…	…	1
tRNA Gly	…	2	…	…	2
tRNA Arg	…	1	…	…	1
tRNA Ser2	…	1	…	…	1
tRNA Leu2	…	1	…	…	1
tRNA Glu	…	1	…	…	1
tRNA Thr	…	4	…	…	4
Noncoding	…	…	…	…	1
Total	…	25	37	81	144

^aOne ATP6 missense variant is also a synonymous ATP8 variant; no common variants in 14 tRNA genes.

Evaluation of previous sets of tSNPs used for disease association studies revealed that ∼30% of variants (frequency ⩾1%) are captured with r²⩾0.8 (table 3). Recently,²⁷ more-complete coverage of mtDNA variation was reported using 32 mtDNA SNPs; still, these SNPs capture less than half of the sites (42%) at r²⩾0.8. Thus, previous studies might have missed a true association simply because not all variants were captured by the tSNPs used.

Table 3. .

Estimated Fraction of mtDNA Coding-Region Variation Captured by Previous Association Studies Compared with the Present Study

			Percentage of SNPs Captured
Study	tSNPs	Testsa	r2⩾.5	r2⩾.8
Van der Walt et al.47	9b	9 HGs + 9 SNPs	35	30
Huerta et al.49	12b	9 HGs + 12 SNPs	33	26
Niemi et al.42	8	9 HGs	34	26
Mohlke et al.27	32c	9 HGs + 32 SNPs	54	42
Present study	64	All variants with frequency >1%	100	100

^aHGs = haplogroups.

^bOne D-loop–region SNP was used to specify haplogroup I; this SNP was excluded from our evaluation of the coverage of coding-region mtDNA SNPs.

^cTen SNPs chosen by Mohlke et al.²⁷ (in Finns) were observed at a frequency <1% in the 928 European sequences of the reference panel.

We selected a set of 64 SNPs that capture each of the 144 sites as well as the nine haplogroups with r²⩾0.8, using Tagger⁵⁴; tSNPs and predictive tests are listed in table 4. Details on the assay conditions are available online (Broad Institute Tagger: SNPs in human mtDNA Web site).

Table 4. .

tSNPs and Tests Used to Predict All Coding-Region Variants with Frequency >1% in European mtDNA

SNP or Haplogroup	Position (rCRSa)	Alleles (Major/Minor)	Rarer Allele Frequency (Reference Panel)	Captured by Test (tSNP or Haplotype)	Test Allele(s)	Test Allele Frequency (Reference Panel)	r2 for Test vs. Predicted Allele	SNP Type
SNP:
mt709	709	G/A	.20	mt709				tSNP
mt750	750	G/A	.01	mt750				tSNP
mt930	930	G/A	.05	mt930				tSNP
mt1189	1189	T/C	.07	mt1189				tSNP
mt1243	1243	T/C	.05	mt11674	T	.05	1
mt1438	1438	G/A	.03	mt4769	A	.02	.872
mt1719	1719	G/A	.06	mt709, mt12007, mt12705	G, G, T	.05	.836
mt1811	1811	A/G	.13	mt3348, mt9477, mt12372	A, G, A	.13	.944
mt1888	1888	G/A	.11	mt11812, mt12633	A, C	.89	.978
mt2158	2158	T/C	.01	mt11914, mt13879	G, C	.01	.838
mt2706	2706	G/A	.38	mt7028	C	.38	.982
mt3010	3010	G/A	.23	mt3010				tSNP
mt3197	3197	T/C	.06	mt9477	A	.05	.959
mt3348	3348	A/G	.02	mt3348				tSNP
mt3394	3394	T/C	.01	mt3394				tSNP
mt3480	3480	A/G	.09	mt1189, mt9716	T, T	.90	.988
mt3505	3505	A/G	.05	mt11674	T	.05	.978
mt3720	3720	A/G	.01	mt5426, mt12372	C, A	.01	1
mt3915	3915	G/A	.01	mt3915				tSNP
mt3990	3990	C/T	.01	mt10915, mt15924	C, G	.01	1
mt3992	3992	C/T	.02	mt7028, mt9123	C, A	.02	.9
mt4024	4024	A/G	.02	mt7028, mt9123	C,A	.02	1
mt4216	4216	T/C	.22	mt12705, mt9123, mt11719, mt12372	C, G, A, G	.21	.969
mt4336	4336	T/C	.02	mt4336				tSNP
mt4529	4529	A/T	.03	mt9123, mt10034	G, C	.03	1
mt4561	4561	T/C	.02	mt709, mt9716	A, C	.02	.847
mt4580	4580	G/A	.07	mt7028, mt11719, mt15218	T, G, A	.08	.844
mt4639	4639	T/C	.02	mt8869	G	.02	.88
mt4769	4769	G/A	.02	mt4769				tSNP
mt4793	4793	A/G	.01	mt4793				tSNP
mt4917	4917	A/G	.11	mt11812, mt12633	A, C	.89	.978
mt4928	4928	T/C	.02	mt4928				tSNP
mt5004	5004	T/C	.02	mt7028, mt9123	C, A	.02	.907
mt5046	5046	G/A	.05	mt709, mt12705	A, T	.05	1
mt5147	5147	G/A	.05	mt709, mt930	A, A	.05	.953
mt5263	5263	C/T	.01	mt8869	G	.02	.865
mt5390	5390	A/G	.01	mt12372, mt13020	A, C	.01	.922
mt5426	5426	T/C	.02	mt5426				tSNP
mt5460	5460	G/A	.07	mt11674, mt13879	C, T	.94	.857
mt5465	5465	T/C	.02	mt5465				tSNP
mt5495	5495	T/C	.03	mt5495				tSNP
mt5656	5656	A/G	.02	mt5656				tSNP
mt6045	6045	C/T	.01	mt5426, mt13020	C, C	.01	1
mt6152	6152	T/C	.01	mt5426, mt11812	C, A	.01	.922
mt6221	6221	T/C	.02	mt12705, mt14470, mt15884	T, C, G	.02	.898
mt6260	6260	G/A	.01	mt6260				tSNP
mt6365	6365	T/C	.02	mt6365				tSNP
mt6371	6371	C/T	.02	mt11674, mt12705, mt14470	C, T, C	.02	1
mt6719	6719	T/C	.01	mt6719				tSNP
mt6734	6734	G/A	.01	mt10034, mt10915	C, C	.01	.844
mt6776	6776	T/C	.04	mt6776				tSNP
mt7028	7028	T/C	.38	mt7028				tSNP
mt7476	7476	C/T	.01	mt13708, mt15257	A, A	.01	1
mt7768	7768	A/G	.03	mt10034, mt14182	T, C	.03	1
mt7864	7864	C/T	.04	mt709, mt12705, mt15784	A, T, T	.05	.95
mt8251	8251	G/A	.08	mt12633, mt12705, mt13020, mt13105, mt13708, mt13734, mt13879, mt13934, mt13965, mt13966, mt14182	C, T, T, A, G, T, T, C, T, A, T	.09	.959
mt8269	8269	G/A	.03	mt8269				tSNP
mt8557	8557	G/A	.01	mt8269, mt13708	A, A	.01	.916
mt8616	8616	G/T	.01	mt10915, mt12705	C, T	.01	.844
mt8697	8697	G/A	.11	mt11812, mt12633	A, C	.89	.946
mt8705	8705	T/C	.01	mt8705				tSNP
mt8869	8869	A/G	.02	mt8869				tSNP
mt8994	8994	G/A	.05	mt709, mt12705	A, T	.05	.978
mt9055	9055	G/A	.10	mt1189, mt9716	T, T	.90	.988
mt9093	9093	A/G	.01	mt11377, mt12372	A, A	.01	.922
mt9123	9123	G/A	.04	mt9123				tSNP
mt9150	9150	A/G	.01	mt9150				tSNP
mt9477	9477	G/A	.05	mt9477				tSNP
mt9612	9612	G/A	.01	mt4928, mt11719	C, A	.01	1
mt9667	9667	A/G	.01	mt9667				tSNP
mt9698	9698	T/C	.10	mt1189, mt9716	T, T	.90	.964
mt9716	9716	T/C	.02	mt9716				tSNP
mt9899	9899	T/C	.02	mt9899				tSNP
mt9947	9947	G/A	.01	mt10034, mt10915	C, C	.01	.916
mt10034	10034	T/C	.03	mt10034				tSNP
mt10044	10044	A/G	.02	mt8269, mt9123, mt15884	A, A, G	.02	.932
mt10084	10084	T/C	.01	mt10084				tSNP
mt10238	10238	T/C	.05	mt5465, mt10034	T, T	.95	.884
mt10398	10398	A/G	.20	mt1189, mt13708, mt10034	T, G, T	.78	.855
mt10463	10463	T/C	.11	mt11812, mt12633	A, C	.89	.978
mt10550	10550	A/G	.08	mt1189, mt9716	T, T	.90	.853
mt10876	10876	A/G	.01	mt12372, mt13020	A, C	.01	1
mt10915	10915	T/C	.02	mt10915				tSNP
mt11251	11251	A/G	.22	mt11812, mt12633, mt13708	A, C, G	.77	.905
mt11299	11299	T/C	.10	mt1189, mt9716	T, T	.90	1
mt11377	11377	G/A	.02	mt11377				tSNP
mt11467	11467	A/G	.20	mt12372, mt12705	A, C	.20	.993
mt11470	11470	A/G	.01	mt1189, mt15924	C, G	.01	1
mt11485	11485	T/C	.02	mt11485				tSNP
mt11674	11674	C/T	.05	mt11674				tSNP
mt11719	11719	A/G	.47	mt11719				tSNP
mt11812	11812	A/G	.08	mt11812				tSNP
mt11840	11840	C/T	.01	mt1189, mt6260	C, A	.01	1
mt11914	11914	G/A	.02	mt11914				tSNP
mt11947	11947	A/G	.05	mt709, mt12705	A, T	.05	1
mt12007	12007	G/A	.01	mt12007				tSNP
mt12239	12239	C/C	.01	mt5465, mt6719	C, C	.01	.908
mt12308	12308	A/G	.20	mt12372, mt12705	A, C	.20	1
mt12372	12372	G/A	.20	mt12372				tSNP
mt12414	12414	T/C	.02	mt12414				tSNP
mt12501	12501	G/A	.03	mt709, mt12705, mt14470	G, T, T	.03	.936
mt12612	12612	A/G	.11	mt12372, mt12705, mt11719, mt13708, mt1189	G, C, A, A, T	.11	1
mt12618	12618	G/A	.02	mt5656, mt14182, mt14470	G, C, T	.02	.943
mt12633	12633	C/A	.03	mt12633				tSNP
mt12669	12669	C/T	.02	mt5495, mt14793	C, A	.02	1
mt12705	12705	C/T	.11	mt12705				tSNP
mt13020	13020	T/C	.02	mt13020				tSNP
mt13105	13105	A/G	.01	mt13105				tSNP
mt13368	13368	G/A	.11	mt11812, mt12633	A, C	.89	.989
mt13617	13617	T/C	.05	mt9477	A	.05	1
mt13708	13708	G/A	.12	mt13708				tSNP
mt13734	13734	T/C	.02	mt13734				tSNP
mt13740	13740	T/C	.01	mt1189, mt6260	C, A	.01	1
mt13780	13780	A/G	.03	mt12705, mt15043	T, A	.03	1
mt13879	13879	T/C	.01	mt13879				tSNP
mt13934	13934	C/T	.02	mt13934				tSNP
mt13965	13965	T/C	.02	mt13965				tSNP
mt13966	13966	A/G	.02	mt13966				tSNP
mt14022	14022	A/G	.01	mt6719, mt9123	C, A	.01	1
mt14167	14167	C/T	.10	mt1189, mt9716	T, T	.90	1
mt14182	14182	T/C	.03	mt14182				tSNP
mt14233	14233	A/G	.08	mt11812	G	.08	.942
mt14365	14365	C/T	.02	mt7028, mt9123	C, A	.02	1
mt14470	14470	T/C	.03	mt14470				tSNP
mt14582	14582	A/G	.02	mt7028, mt9123	C, A	.02	1
mt14687	14687	A/G	.02	mt13965	C	.02	.932
mt14766	14766	T/C	.47	mt11719, mt11812	G, A	.47	.966
mt14793	14793	A/G	.03	mt14793				tSNP
mt14798	14798	T/C	.18	mt14798				tSNP
mt14905	14905	G/A	.11	mt11812, mt12633	A, C	.89	.989
mt15043	15043	G/A	.04	mt15043				tSNP
mt15218	15218	A/G	.02	mt15218				tSNP
mt15257	15257	G/A	.02	mt15257				tSNP
mt15452	15452	C/A	.22	mt12372, mt12705, mt11719	G, C, A	.23	.904
mt15607	15607	A/G	.11	mt11812, mt12633	A, C	.89	.989
mt15746	15746	A/A	.01	mt5465, mt6719	C, C	.01	1
mt15758	15758	A/G	.02	mt15758				tSNP
mt15784	15784	T/C	.01	mt15784				tSNP
mt15833	15833	C/C	.02	mt15833				tSNP
mt15884	15884	G/C	.06	mt15884				tSNP
mt15904	15904	C/T	.07	mt11719, mt15218, mt7028	G, A, T	.08	.844
mt15907	15907	A/G	.01	mt12372, mt13020	A, C	.01	1
mt15924	15924	A/G	.06	mt15924				tSNP
mt15928	15928	G/A	.11	mt11812, mt12633	A, C	.89	.978
Haplogroup:
mt1719, mt7028, mt10398 (X)		A,T,A	.02	mt709, mt12705, mt15043	G, T, G	.02	.868
mt1719, mt7028, mt8251, mt10398 (I)		A,T,A,G	.03	mt8269, mt10034, mt14182	G, C, T	.03	1
mt4580, mt7028, mt10398 (V)		A,T,A	.07	mt7028, mt11719, mt15218	T, G, A	.08	.844
mt7028, mt10398, mt12308 (U)		T,A,G	.13	mt1189, mt12372, mt12705	T, A, C	.13	.981
mt7028, mt10398, mt13708 (J)		T,G,A	.10	mt7028, mt12705, mt13708	T, C, A	.11	.934
mt7028, mt8251, mt10398 (W)		T,A,A	.06	mt12705, mt13966, mt15043	T, A, G	.06	.94
mt7028, mt10398, mt13368 (T)		T,A,A	.11	mt11812, mt12633	A,C	.89	.989
mt7028, mt9055, mt10398, mt12308 (K)		T,A,G,G	.07	mt1189	C	.07	.984
mt7028, mt10398 (H)		C,A	.38	mt7028	C	.38	.995

^arCRS = revised Cambridge Reference Sequence (see Human Mitochondrial DNA Revised Cambridge Reference Sequence Web site).

As a framework to test common mtDNA variants for association with clinical traits (fig. 1), we first enumerated all hypotheses to be tested for association. Specifically, we sought to test for association with each phenotype for each of the individual 144 variant sites with frequency >1% as well as for the nine previously codified European haplogroups. Association tests for type 2 diabetes (the dichotomous trait) were performed by 2×2 χ² comparisons, and, for quantitative phenotypes, by linear regression. Studywide significance (P_study) was empirically evaluated by permutation testing (association studies were repeated 50–1,000 times by using randomized phenotype labels within each case-control pair for diabetes and by using randomized trait values within each of five populations for quantitative traits). We also tested all pairwise combinations of single variants with a nominal P value (P_nom) <.1 (another ∼600 correlated hypotheses) for association with diabetes and BMI.⁵⁵

Figure 1. .

Procedure for identification and comprehensive disease-association testing of all common variants in the mtDNA coding region. 1 and 2, A total of 928 mtDNA sequences of European origin were aligned to identify 144 variants with frequency >1%. 3, tSNPs and multimarker haplotypes of tSNPs were selected to capture all 144 variant sites and haplogroups with r²⩾0.8 (a haplotype of tSNPs [shaded box] captures an untyped SNP [unshaded box]). 4, tSNPs were genotyped in a diabetic case-control panel with available metabolic phenotypes. 5, All hypotheses to be tested were enumerated. 6, Association tests were performed. 7, Studywide significance of results was assessed by permutation (multiple rounds of association testing with randomization of case-control labels or, for quantitative measures, shuffling within a population).

As a test of the hypothesis that common mtDNA variation plays a causal role in disease, we considered association with type 2 diabetes and metabolic traits. We genotyped each of the 64 tSNPs in a diabetes case-control sample of 6,608 subjects, with quantitative measurements available for a subset of subjects (table 1). Under the assumption of ∼100 independent tests performed in this study, this sample has >77% power to reject the null hypothesis of no association between mtDNA variants and type 2 diabetes at P<.05 for a 5% risk allele with a 1.5 genotype relative risk and has >98% power for risk alleles with frequency >10%.⁵⁶ Allele frequencies for SNPs differed across the populations tested (table 5).

Table 5. .

Allele Frequencies of SNPs and Haplogroups across Five Study Populations

		Allele Frequency in Population
SNP or Haplogroup	Allele	Scandinavia(n = 918)	Sweden(n = 1,010)	Canada(n = 246)	United States(n = 2,428)	Poland(n = 2,006)
SNP:
mt709	A	.130	.146	.199	.136	.154
mt750	A	.029	.028	.016	.026	.013
mt930	A	.026	.031	.050	.039	.058
mt1189	C	.053	.057	.073	.075	.038
mt1243	C	.029	.011	.012	.020	.019
mt1438	A	.067	.045	.017	.039	.027
mt1719	A	.031	.053	.126	.061	.049
mt1811	G	.105	.220	.140	.160	.135
mt1888	A	.074	.112	.159	.088	.123
mt2158	C	.015	.010	.033	.010	.014
mt2706	A	.460	.431	.322	.419	.404
mt3010	A	.262	.227	.149	.229	.222
mt3197	C	.161	.107	.041	.076	.113
mt3348	G	.002	.003	.000	.002	.001
mt3394	C	.018	.007	.004	.010	.005
mt3480	G	.066	.069	.094	.099	.044
mt3505	G	.029	.011	.012	.020	.019
mt3720	G	.007	.014	.000	.015	.022
mt3915	A	.012	.035	.025	.025	.020
mt3990	T	.003	.010	.004	.007	.009
mt3992	T	.010	.018	.000	.013	.013
mt4024	G	.010	.018	.000	.013	.013
mt4216	C	.149	.217	.238	.194	.221
mt4336	C	.021	.017	.025	.023	.033
mt4529	T	.011	.025	.114	.031	.018
mt4561	C	.010	.007	.017	.017	.004
mt4580	A	.061	.050	.045	.061	.056
mt4639	C	.019	.007	.004	.004	.010
mt4769	A	.067	.045	.017	.039	.027
mt4793	G	.014	.014	.008	.021	.014
mt4917	G	.074	.112	.159	.088	.123
mt4928	C	.004	.001	.000	.000	.003
mt5004	C	.010	.018	.000	.013	.013
mt5046	A	.029	.013	.017	.019	.020
mt5147	A	.025	.030	.008	.036	.054
mt5263	T	.019	.007	.004	.004	.010
mt5390	G	.007	.014	.000	.016	.023
mt5426	C	.011	.022	.000	.020	.026
mt5460	A	.044	.021	.045	.030	.033
mt5465	C	.000	.000	.000	.001	.000
mt5495	C	.020	.023	.004	.010	.015
mt5656	G	.081	.013	.012	.014	.038
mt6045	T	.007	.015	.000	.016	.022
mt6152	C	.007	.014	.000	.016	.022
mt6221	C	.001	.020	.004	.010	.006
mt6260	A	.007	.019	.020	.012	.006
mt6365	C	.003	.001	.000	.008	.006
mt6371	T	.001	.022	.004	.012	.007
mt6719	C	.000	.002	.000	.001	.004
mt6734	A	.003	.011	.008	.007	.009
mt6776	C	.043	.028	.069	.038	.016
mt7028	C	.460	.431	.322	.419	.404
mt7476	T	.010	.033	.021	.019	.008
mt7768	G	.073	.025	.020	.038	.049
mt7864	T	.026	.011	.012	.015	.015
mt8251	A	.040	.036	.149	.060	.049
mt8269	A	.023	.022	.033	.021	.026
mt8557	A	.016	.008	.033	.010	.009
mt8616	T	.003	.010	.008	.007	.009
mt8697	A	.074	.112	.159	.088	.123
mt8705	C	.027	.016	.000	.004	.003
mt8869	G	.019	.007	.004	.004	.010
mt8994	A	.029	.013	.017	.019	.020
mt9055	A	.066	.069	.094	.099	.044
mt9093	G	.013	.008	.000	.010	.012
mt9123	A	.010	.019	.000	.014	.014
mt9150	G	.000	.009	.000	.006	.002
mt9477	A	.161	.107	.041	.076	.113
mt9612	A	.004	.001	.000	.000	.001
mt9667	G	.023	.012	.000	.010	.015
mt9698	C	.066	.069	.094	.099	.044
mt9716	C	.012	.012	.021	.023	.007
mt9899	C	.016	.023	.008	.018	.030
mt9947	A	.003	.011	.008	.007	.009
mt10034	C	.011	.028	.114	.031	.018
mt10044	G	.001	.013	.000	.007	.009
mt10084	C	.001	.005	.000	.009	.005
mt10238	C	.011	.027	.114	.032	.018
mt10398	G	.146	.204	.278	.231	.168
mt10463	C	.074	.112	.159	.088	.123
mt10550	G	.066	.069	.094	.099	.044
mt10876	G	.007	.014	.000	.016	.023
mt10915	C	.006	.012	.008	.009	.010
mt11251	G	.156	.226	.250	.212	.231
mt11299	C	.066	.069	.094	.099	.044
mt11377	A	.024	.036	.004	.023	.020
mt11467	G	.267	.248	.183	.239	.254
mt11470	G	.005	.002	.000	.014	.004
mt11485	C	.009	.021	.025	.017	.012
mt11674	T	.029	.011	.012	.020	.019
mt11719	G	.477	.470	.416	.481	.457
mt11812	G	.055	.081	.114	.064	.083
mt11840	T	.007	.017	.020	.011	.004
mt11914	A	.048	.014	.004	.041	.022
mt11947	G	.029	.013	.017	.019	.020
mt12007	A	.014	.007	.049	.012	.016
mt12308	G	.267	.248	.183	.239	.254
mt12372	A	.267	.248	.183	.239	.255
mt12414	C	.034	.012	.012	.019	.019
mt12501	A	.018	.028	.135	.050	.042
mt12612	G	.073	.099	.071	.102	.067
mt12618	A	.058	.012	.012	.013	.022
mt12633	A	.018	.030	.042	.023	.038
mt12669	T	.018	.001	.004	.000	.000
mt12705	T	.059	.065	.161	.083	.070
mt13020	C	.012	.016	.004	.017	.028
mt13105	G	.012	.009	.029	.010	.008
mt13368	A	.074	.112	.159	.088	.123
mt13617	C	.161	.107	.041	.076	.113
mt13708	A	.081	.119	.087	.123	.114
mt13734	C	.007	.017	.000	.016	.023
mt13740	C	.007	.017	.020	.011	.004
mt13780	G	.010	.028	.082	.039	.019
mt13879	C	.015	.010	.033	.010	.014
mt13934	T	.004	.015	.037	.028	.031
mt13965	C	.007	.006	.000	.005	.007
mt13966	G	.015	.028	.000	.019	.014
mt14022	G	.000	.002	.000	.000	.000
mt14167	T	.066	.069	.094	.099	.044
mt14182	C	.073	.025	.029	.040	.049
mt14233	G	.055	.081	.114	.064	.083
mt14365	T	.010	.018	.000	.013	.013
mt14470	C	.001	.030	.004	.025	.019
mt14582	G	.010	.018	.000	.013	.013
mt14687	G	.007	.006	.000	.005	.007
mt14766	C	.477	.470	.416	.480	.456
mt14793	G	.067	.077	.023	.041	.072
mt14798	C	.093	.127	.100	.176	.119
mt14905	A	.074	.112	.159	.088	.123
mt15043	A	.010	.040	.082	.047	.035
mt15218	G	.033	.053	.057	.034	.049
mt15257	A	.010	.034	.021	.022	.014
mt15452	A	.149	.219	.236	.196	.222
mt15607	G	.074	.112	.159	.088	.123
mt15758	G	.012	.014	.111	.016	.005
mt15784	C	.003	.003	.008	.012	.016
mt15833	C	.004	.015	.025	.016	.024
mt15884	C	.036	.034	.012	.032	.022
mt15904	T	.061	.050	.045	.062	.056
mt15907	G	.007	.014	.000	.016	.023
mt15924	G	.017	.047	.107	.062	.036
mt15928	A	.074	.112	.159	.088	.123
Haplogroup:
X		.015	.025	.018	.024	.030
I		.011	.025	.107	.028	.018
V		.061	.050	.045	.061	.056
U		.212	.185	.106	.163	.216
J		.075	.100	.083	.106	.083
W		.031	.013	.039	.030	.037
T		.074	.112	.159	.088	.123
K		.053	.057	.073	.075	.038
H		.460	.431	.322	.419	.404

Results from association studies with type 2 diabetes and BMI are shown in tables 6, 7, and 8. For diabetes, only two hypotheses with P_nom<.05 were found, and these results were far from significant after permutation testing (50–1,000 iterations for each association test) (P_study=.55). For BMI, we found no significant association before (P_study=1.0) or after (P_study=.25) adjustment for sex and age. Tests for epistasis did not demonstrate any significant association with diabetes or BMI. Subanalysis of association with diabetes by population failed to show any strong effects in U.S., Scandinavian, and Canadian populations (tables 9 and 10). A significant association result was observed in the Polish subpopulation after permutation testing (P_Polishstudy=.02 after 1,000 permutations); however, given that mtDNA variants from five populations were tested for association with diabetes, this result is consistent with noise and thus would need to be validated by replication in other large Polish samples.

Table 6. .

Results of Association Testing of All mtDNA Variants with Type 2 Diabetes and Metabolic Traits

Phenotypea	n	Best Result	Effect Estimateb (95% CI)	Pnom	Pempiricalc
DM	6,608	mt12612 (syn ND5)	1.25 (1.05–1.49)	.011	>.55 (NS)
BMI	6,523	mt9123 (mis ND3)	−.04 (−.05 to −.03)	.0027	1.0 (NS)
Ins Index	342	mt3197 (16S rRNA); mt9477 (mis COIII); mt13617 (syn ND5)	−.14 (−.19 to −.09)	.012	>.3 (NS)
HOMA-IR	399	mt4561 (mis ND2)	.102 (.052–.152)	.042	>.26 (NS)
Cholesterol	1,274	mt15784 (syn cytB)	.10 (.07–.13)	.0003	>.08 (NS)
Systolic BP	2,047	mt4561 (mis ND2)	−.045 (−.065 to −.025)	.042	>.35 (NS)
Diastolic BP	2,047	mt3394 (tRNA S)	.022 (−.001 to .045)	.12	>.5 (NS)

^aBP = blood pressure; DM = diabetes mellitus, type 2; Ins = insulinogenic.

^bOR for DM and standardized regression coefficient (β) for all other phenotypes (the quantitative traits).

^cNS = not significant.

Table 7. .

Association Testing with Type 2 Diabetes, BMI, and Metabolic Traits^[Note]

Variable	Type 2 Diabetes	BMI	Insulinogenic Index	HOMA-IR	Cholesterol	Systolic BP	Diastolic BP
n	6,608	6,523	342	399	1,274	2,047	2,047
Populations	All	All	Scandinavian/Swedish	Scandinavian/Swedish	All	All	All
Diabetics and controls	Yes	Yes	Controls only	Controls only	Yes	Yes	Yes
Log taken	…	Yes	Yes	Yes	No	No	No
Best result	mt12612	mt9123	mt3197, mt9477, mt13617	mt4561	mt15784	mt4561	mt3394
Minimum P	.0106	.0027	.0439	.0415	.0003	.04	.1197
Maximum test statistic (OR or β)	1.25	−.0250	−.10	.21	2.15	−10.24	−3.550
No. of SNPs with Pnom < .05	3	26	3	2	13	1.00	0
No. of SNPs with Pnom < .01	3	26	3	2	13	1.00	0
Pstudy	>.55	1.00	>.45	>.26	>.08	>.35	>.5
Adjusted Pstudy	NA	>.25	>.5	>.42	>.08	>.1	>.6
Adjusted for	NA	Age, sex	Age, sex, BMI	Age, sex, BMI	Age, sex, BMI	Age, sex, BMI	Age, sex, BMI

Note.— BP = blood pressure; NA = not applicable.

Table 8. .

Results of Association Testing of Each SNP and Haplogroup with Type 2 Diabetes, BMI, and Metabolic Traits^[Note]

			Type 2 Diabetes		BMI		InsulinogenicIndex		HOMA-IR		Cholesterol		Systolic BP		Diastolic BP
SNP or Haplogroup	Allele	Allele Name	OR (95% CI)	Pnom	β	Pnom	β	Pnom	β	Pnom	β	Pnom	β	Pnom	β	Pnom	Percentage of Data
SNP:
mt709	A	12SrRNA	.92 (.80–1.05)	.212	−.001	.621	.02	.688	.01	.824	.09	.3860	−.91	.509	−.32	.626	99.3
mt750	A	12SrRNA	1.08 (.78–1.50)	.627	.000	.997	.01	.924	.07	.407	.15	.4683	.41	.891	−1.76	.217	99.4
mt930	A	12SrRNA	.88 (.69–1.12)	.288	−.002	.744	−.06	.754	.04	.689	.01	.9745	.41	.884	.08	.951	99.1
mt1189	C	12SrRNA	.84 (.68–1.03)	.100	−.002	.561	.07	.412	.02	.734	.09	.4912	.09	.965	.08	.933	99.7
mt1243	C	12SrRNA	1.16 (.81–1.65)	.424	.003	.700	.01	.953	−.05	.481	.12	.6131	.95	.793	1.27	.462	99.5
mt1438	A	12SrRNA	1.05 (.82–1.35)	.678	−.003	.619	.09	.293	.08	.120	.20	.1577	−2.80	.206	−1.38	.191	98.7
mt1719	A	16SrRNA	1.04 (.84–1.28)	.744	−.001	.752	.01	.918	.02	.790	−.08	.6530	1.00	.648	−.82	.429	98.5
mt1811	G	16SrRNA	.89 (.77–1.02)	.082	.000	.989	.02	.722	.00	.903	−.09	.3176	−.57	.673	−.62	.337	97.8
mt1888	A	16SrRNA	.89 (.76–1.05)	.160	−.002	.560	.04	.639	−.03	.585	.13	.2933	−.49	.761	−.07	.923	97.5
mt2158	C	16SrRNA	1.25 (.81–1.92)	.322	−.004	.633	.23	.093	.06	.506	.26	.4245	−.22	.956	.52	.782	98.7
mt2706	A	16SrRNA	.99 (.90–1.09)	.884	.002	.446	.06	.135	.01	.572	.10	.1296	−.26	.789	−.17	.717	99.7
mt3010	A	16SrRNA	.99 (.88–1.11)	.854	−.004	.089	.04	.354	.01	.829	.02	.8391	−.54	.639	−.19	.725	99.0
mt3197	C	16SrRNA	1.10 (.93–1.29)	.264	−.004	.252	−.10	.044	−.03	.314	−.06	.5465	−.75	.620	−1.12	.120	98.5
mt3348	G	synND1	.37 (.10–1.34)	.131	.039	.097	.04	.915	.16	.522	.05	.9285	6.53	.505	−1.38	.767	99.4
mt3394	C	misND1	1.29 (.77–2.18)	.336	−.006	.571	.02	.817	.05	.473	−.74	.0141	−7.96	.097	−3.55	.120	98.5
mt3480	G	synND1	.84 (.69–1.01)	.059	−.004	.298	.06	.436	.04	.395	.10	.4205	−.77	.683	−.17	.845	98.7
mt3505	G	misND1	1.16 (.81–1.65)	.424	.003	.700	.01	.953	−.05	.481	.12	.6131	.95	.793	1.27	.462	99.5
mt3720	G	synND1	1.22 (.82–1.80)	.327	.016	.041	−.31	.380	−.20	.422	.09	.8383	−2.87	.613	−1.43	.596	99.7
mt3915	A	synND1	1.05 (.76–1.45)	.763	.016	.013	−.01	.959	.07	.488	.14	.5599	−3.00	.333	.58	.694	98.2
mt3990	T	synND1	1.10 (.62–1.93)	.753	−.001	.941	−.35	.156	−.06	.742	.47	.3338	5.27	.387	−.89	.758	99.1
mt3992	T	misND1	.68 (.44–1.05)	.081	−.025	.004	−.02	.920	−.16	.141	.16	.5830	5.72	.176	1.25	.535	99.4
mt4024	G	misND1	.68 (.44–1.05)	.081	−.025	.004	−.02	.920	−.16	.141	.16	.5830	5.72	.176	1.25	.535	99.4
mt4216	C	misND1	.97 (.86–1.10)	.642	.001	.566	−.07	.188	−.02	.635	.06	.5276	−.60	.629	.02	.968	98.4
mt4336	C	tRNA Q	.87 (.64–1.19)	.384	.001	.873	.02	.847	−.05	.511	−.17	.4813	−3.62	.293	−.80	.625	99.5
mt4529	T	synND2	1.09 (.81–1.48)	.568	.013	.034	−.35	.157	−.06	.736	.34	.2124	.35	.902	1.37	.310	98.7
mt4561	C	misND2	.86 (.54–1.38)	.536	−.007	.484	.03	.837	.21	.042	−.44	.2737	−10.24	.042	−2.89	.230	99.1
mt4580	A	synND2	1.18 (.96–1.46)	.114	.003	.512	.09	.294	−.04	.474	.40	.0046	−3.00	.158	−.37	.715	99.5
mt4639	C	misND2	1.51 (.88–2.58)	.135	−.010	.344	−.01	.978	.23	.189	−.70	.0086	.31	.946	.35	.873	99.3
mt4769	A	synND2	1.05 (.82–1.35)	.678	−.003	.619	.09	.293	.08	.120	.20	.1577	−2.80	.206	−1.38	.191	98.7
mt4793	G	synND2	.96 (.65–1.41)	.831	.009	.257	.10	.522	−.13	.207	−.60	.0326	.87	.833	.63	.752	99.2
mt4917	G	misND2	.89 (.76–1.05)	.160	−.002	.560	.04	.639	−.03	.585	.13	.2933	−.49	.761	−.07	.923	97.5
mt4928	C	synND2	1.51 (.43–5.30)	.522	−.002	.938	−.34	.341	−.27	.263	−.59	.3957	2.00	.874	3.68	.540	99.2
mt5004	C	synND2	.68 (.44–1.05)	.081	−.025	.004	−.02	.920	−.16	.141	.16	.5830	5.72	.176	1.25	.535	99.4
mt5046	A	misND2	1.10 (.77–1.55)	.608	.001	.841	.02	.832	−.08	.245	.18	.4425	−2.74	.445	.10	.954	99.3
mt5147	A	synND2	.88 (.68–1.13)	.314	−.001	.879	−.06	.763	.04	.684	−.05	.8222	1.76	.568	−.33	.821	98.7
mt5263	T	misND2	1.51 (.88–2.58)	.135	−.010	.344	−.01	.978	.23	.189	−.70	.0086	.31	.946	.35	.873	99.3
mt5390	G	synND2	1.29 (.87–1.90)	.201	.016	.042	−.31	.379	−.20	.420	.09	.8404	−2.86	.613	−1.41	.601	99.4
mt5426	C	synND2	1.08 (.76–1.52)	.673	.012	.087	−.15	.453	−.06	.617	.05	.8639	−4.80	.257	−1.34	.508	99.7
mt5460	A	misND2	1.20 (.91–1.59)	.187	.001	.917	.09	.277	−.01	.842	.17	.3751	.43	.873	.95	.461	99.0
mt5465	C	synND2	1.01 (.06–16.09)	.997	.111	.045											99.3
mt5495	C	synND2	1.09 (.72–1.64)	.683	−.009	.274	.05	.736	−.07	.425	−.24	.3009	1.61	.652	.92	.590	98.8
mt5656	G	ncnc	.89 (.67–1.18)	.426	−.003	.561	−.13	.062	−.06	.177	−.09	.5272	.85	.732	.53	.654	99.4
mt6045	T	synCO1	1.17 (.79–1.72)	.437	.017	.033	−.31	.380	−.20	.422	.09	.8383	−2.04	.710	−.36	.889	99.7
mt6152	C	synCO1	1.19 (.81–1.76)	.380	.017	.030	−.31	.380	−.20	.422	.09	.8383	−2.87	.613	−1.43	.596	99.7
mt6221	C	synCO1	1.22 (.74–2.04)	.437	.003	.740	.39	.260	−.01	.973	−.05	.9119	−2.97	.526	1.16	.603	99.3
mt6260	A	synCO1	.80 (.50–1.27)	.341	−.001	.908	.11	.542	.04	.758	.00	.9962	3.23	.422	−.02	.991	98.7
mt6365	C	synCO1	.94 (.49–1.83)	.863	−.005	.708	.09	.712	−.09	.589	−.62	.2985	−14.10	.196	−2.14	.681	99.3
mt6371	T	synCO1	1.16 (.72–1.88)	.547	.002	.832	.39	.263	−.01	.972	−.05	.9128	−1.92	.668	1.91	.372	98.9
mt6719	C	synCO1	1.60 (.53–4.84)	.407	−.025	.251					.76	.5213	−11.58	.452	−4.65	.527	99.3
mt6734	A	synCO1	1.17 (.67–2.05)	.575	−.003	.806	−.35	.155	−.06	.736	.11	.8173	2.63	.643	−1.13	.676	99.7
mt6776	C	synCO1	1.09 (.82–1.43)	.557	.004	.438	−.04	.598	.03	.583	.20	.2676	1.76	.487	−1.25	.302	99.5
mt7028	C	synCO1	.99 (.90–1.09)	.884	.002	.446	.06	.135	.01	.572	.10	.1296	−.26	.789	−.17	.717	99.7
mt7476	T	tRNA S	.98 (.67–1.44)	.915	.007	.393	.31	.126	.08	.555	−.39	.0993	.86	.793	−1.90	.222	98.9
mt7768	G	synCOII	.87 (.69–1.11)	.267	.007	.141	−.14	.054	−.02	.691	.25	.0985	2.15	.372	−.93	.418	98.0
mt7864	T	synCOII	1.14 (.78–1.69)	.497	−.003	.663	.02	.832	−.10	.153	.06	.8159	−3.99	.299	−1.18	.517	99.3
mt8251	A	synCOII	1.18 (.95–1.47)	.134	−.003	.437	−.07	.531	.01	.857	−.29	.1104	2.21	.332	−.51	.641	96.6
mt8269	A	nc	1.02 (.74–1.40)	.911	−.016	.012	.04	.716	−.07	.332	.23	.3098	1.69	.589	.49	.745	99.2
mt8557	A	synATP8; misATP6	1.29 (.81–2.05)	.281	−.016	.094	.22	.095	.06	.518	.23	.4652	−1.87	.646	−.80	.680	99.1
mt8616	T	misATP6	1.28 (.73–2.25)	.381	.003	.797	−.35	.156	−.06	.742	.47	.3338	3.89	.507	−1.42	.610	99.2
mt8697	A	synATP6	.89 (.76–1.05)	.160	−.002	.560	.04	.639	−.03	.585	.13	.2933	−.49	.761	−.07	.923	97.5
mt8705	C	misATP6	1.04 (.61–1.76)	.896	−.016	.122	.01	.896	−.06	.396	−.18	.4415	3.75	.277	−.65	.694	99.5
mt8869	G	misATP6	1.51 (.88–2.58)	.135	−.010	.344	−.01	.978	.23	.189	−.70	.0086	.31	.946	.35	.873	99.3
mt8994	A	synATP6	1.10 (.77–1.55)	.608	.001	.841	.02	.832	−.08	.245	.18	.4425	−2.74	.445	.10	.954	99.3
mt9055	A	misATP6	.84 (.69–1.01)	.059	−.004	.298	.06	.436	.04	.395	.10	.4205	−.77	.683	−.17	.845	98.7
mt9093	G	synATP6	1.52 (.93–2.47)	.091	.001	.892	−.01	.955	−.01	.933	−.27	.3518	1.86	.706	2.51	.285	99.3
mt9123	A	synATP6	.76 (.50–1.15)	.194	−.025	.003	−.02	.928	−.16	.146	.16	.5823	5.72	.178	1.25	.537	99.0
mt9150	G	synATP6	2.38 (1.07–5.32)	.034	.030	.048					.53	.3708	.15	.985	1.49	.687	99.5
mt9477	A	misCOIII	1.10 (.93–1.29)	.264	−.004	.252	−.10	.044	−.03	.314	−.06	.5465	−.75	.620	−1.12	.120	98.5
mt9612	A	misCOIII	2.51 (.52–12.26)	.254	−.041	.246	−.34	.341	−.27	.263	−.59	.3957	2.00	.874	3.68	.540	99.2
mt9667	G	misCOIII	1.27 (.83–1.94)	.280	−.001	.929	−.09	.474	−.04	.687	.55	.0268	−1.50	.709	1.29	.500	99.6
mt9698	C	synCOIII	.84 (.69–1.01)	.059	−.004	.298	.06	.436	.04	.395	.10	.4205	−.77	.683	−.17	.845	98.7
mt9716	C	synCOIII	.80 (.54–1.20)	.290	−.008	.320	.01	.936	.09	.284	.12	.7185	−4.65	.290	−1.34	.524	98.8
mt9899	C	synCOIII	1.04 (.74–1.45)	.826	−.002	.765	.17	.214	.02	.798	.26	.3337	1.25	.726	−.53	.755	98.7
mt9947	A	misCOIII	1.17 (.67–2.05)	.575	−.003	.806	−.35	.155	−.06	.736	.11	.8173	2.63	.643	−1.13	.676	99.7
mt10034	C	tRNA G	1.08 (.80–1.46)	.602	.015	.013	−.35	.155	−.06	.736	.36	.1523	.30	.915	1.15	.389	99.7
mt10044	G	tRNA G	.75 (.43–1.32)	.322	−.025	.030	.00				.16	.6998	9.15	.118	2.10	.453	99.0
mt10084	C	misND3	.61 (.31–1.17)	.138	−.005	.705	.15	.669	.02	.938	−.41	.5478	7.00	.433	3.62	.396	99.5
mt10238	C	synND3	1.10 (.82–1.49)	.523	.017	.005	−.35	.156	−.06	.739	.36	.1620	.35	.901	1.18	.375	99.0
mt10398	G	misND3	1.04 (.92–1.18)	.501	.002	.464	.05	.321	.02	.588	−.05	.5965	.80	.519	.30	.617	98.6
mt10463	C	tRNA R	.89 (.76–1.05)	.160	−.002	.560	.04	.639	−.03	.585	.13	.2933	−.49	.761	−.07	.923	97.5
mt10550	G	synND4L	.84 (.69–1.01)	.059	−.004	.298	.06	.436	.04	.395	.10	.4205	−.77	.683	−.17	.845	98.7
mt10876	G	synND4	1.29 (.87–1.90)	.201	.016	.042	−.31	.379	−.20	.420	.09	.8404	−2.86	.613	−1.41	.601	99.4
mt10915	C	synND4	1.15 (.69–1.92)	.586	−.004	.708	−.29	.151	.00	.975	.57	.1545	6.83	.187	−1.02	.679	99.2
mt11251	G	synND4	1.02 (.91–1.15)	.740	−.001	.668	.05	.308	.00	.928	−.05	.5786	.13	.915	−.01	.988	96.7
mt11299	C	synND4	.84 (.69–1.01)	.059	−.004	.298	.06	.436	.04	.395	.10	.4205	−.77	.683	−.17	.845	98.7
mt11377	A	synND4	1.09 (.79–1.50)	.589	−.003	.660	.13	.272	.04	.638	−.44	.0188	1.52	.603	.04	.978	99.3
mt11467	G	synND4	.94 (.84–1.06)	.314	.001	.773	.08	.050	.02	.516	.00	.9659	.50	.659	.18	.739	99.6
mt11470	G	synND4	.75 (.42–1.32)	.314	.012	.277	−.07	.785	−.13	.354	.09	.8644	2.33	.779	−.54	.891	99.7
mt11485	C	synND4	1.03 (.69–1.53)	.893	−.005	.505	.11	.539	.04	.760	−.07	.7835	1.58	.679	−1.05	.564	99.2
mt11674	T	synND4	1.16 (.81–1.65)	.424	.003	.700	.01	.953	−.05	.481	.12	.6131	.95	.793	1.27	.462	99.5
mt11719	G	synND4	1.04 (.95–1.15)	.399	.001	.592	.03	.463	.02	.485	.02	.7837	.55	.574	.00	.996	99.6
mt11812	G	synND4	.87 (.73–1.05)	.158	−.003	.417	−.03	.760	−.04	.497	.09	.4970	−1.49	.416	−.53	.541	99.5
mt11840	T	synND4	.88 (.53–1.45)	.606	.002	.830	.11	.543	.04	.764	−.20	.4944	2.51	.547	−.70	.725	99.7
mt11914	A	synND4	.91 (.69–1.21)	.511	.000	.999	−.03	.737	.03	.603	−.06	.7572	−.76	.803	1.42	.328	99.2
mt11947	G	synND4	1.10 (.77–1.55)	.608	.001	.841	.02	.832	−.08	.245	.18	.4425	−2.74	.445	.10	.954	99.3
mt12007	A	synND4	1.43 (.94–2.16)	.095	−.005	.522	.21	.152	.04	.678	.35	.2934	−2.22	.576	−.12	.947	99.2
mt12308	G	tRNA L2	.94 (.84–1.06)	.314	.001	.773	.08	.050	.02	.516	.00	.9659	.50	.659	.18	.739	99.6
mt12372	A	synND5	.94 (.84–1.05)	.300	−.001	.759	−.08	.050	−.02	.516	.00	.9659	−.50	.659	−.18	.739	99.6
mt12414	C	synND5	1.15 (.81–1.62)	.435	.005	.461	−.04	.696	−.09	.149	.04	.8653	−.68	.843	1.23	.454	99.4
mt12501	A	synND5	1.01 (.80–1.28)	.928	.004	.408	−.32	.110	−.03	.854	.37	.1120	−1.50	.564	.37	.764	98.8
mt12612	G	synND5	1.25 (1.05–1.49)	.011	−.003	.441	−.08	.229	−.04	.337	.21	.0900	−2.51	.149	−.19	.819	98.9
mt12618	A	synND5	.97 (.70–1.35)	.862	.005	.443	−.13	.122	−.03	.547	−.06	.7141	2.21	.440	.20	.886	99.1
mt12633	A	synND5	.94 (.71–1.27)	.703	.001	.815	.16	.228	.02	.846	.24	.3547	2.52	.409	1.18	.415	97.9
mt12669	T	synND5	1.57 (.61–4.02)	.347	−.013	.510	.00	.996	−.02	.847	−.04	.9000	1.62	.767	2.51	.337	98.8
mt12705	T	synND5	1.08 (.9–1.30)	.384	.002	.513	.01	.949	−.06	.272	.11	.4386	−1.69	.361	.61	.492	99.7
mt13020	C	synND5	1.18 (.83–1.67)	.369	.009	.224	−.20	.325	−.13	.276	−.26	.4577	−1.10	.811	.23	.916	99.5
mt13105	G	misND5	1.06 (.65–1.72)	.812	−.005	.610	.04	.841	.29	.042	−.26	.3799	1.36	.748	.96	.636	98.8
mt13368	A	synND5	.89 (.76–1.05)	.160	−.002	.560	.04	.639	−.03	.585	.13	.2933	−.49	.761	−.07	.923	97.5
mt13617	C	synND5	1.10 (.93–1.29)	.264	−.004	.252	−.10	.044	−.03	.314	−.06	.5465	−.75	.620	−1.12	.120	98.5
mt13708	A	misND5	1.15 (.98–1.34)	.079	.001	.859	.06	.340	.02	.609	−.21	.0768	1.54	.342	.27	.727	99.0
mt13734	C	synND5	1.18 (.80–1.73)	.399	.016	.047	−.31	.375	−.20	.418	.08	.8423	−1.24	.816	−1.49	.559	98.4
mt13740	C	synND5	.88 (.53–1.45)	.606	.002	.830	.11	.543	.04	.764	−.20	.4944	2.51	.547	−.70	.725	99.7
mt13780	G	misND5	1.22 (.91–1.62)	.187	.013	.025	−.35	.155	−.06	.736	.36	.1937	.13	.966	1.29	.376	99.4
mt13879	C	misND5	1.27 (.83–1.96)	.272	−.003	.768	.22	.095	.06	.518	.25	.4270	−.26	.947	.51	.788	99.5
mt13934	T	misND5	1.00 (.73–1.37)	.988	.010	.132	−.08	.815	.11	.521	.33	.4052	−1.80	.670	1.92	.341	99.0
mt13965	C	synND5	.73 (.38–1.38)	.333	−.006	.659	−.13	.457	−.11	.323	1.21	.0076	−2.09	.741	−.60	.843	97.3
mt13966	G	misND5	.90 (.63–1.3)	.574	−.007	.365	.17	.283	−.08	.405	−.24	.3534	.32	.926	1.40	.395	99.5
mt14022	G	synND5															99.3
mt14167	T	synND6	.84 (.69–1.01)	.059	−.004	.298	.06	.436	.04	.395	.10	.4205	−.77	.683	−.17	.845	98.7
mt14182	C	synND6	.88 (.69–1.11)	.279	.007	.144	−.14	.054	−.02	.691	−.25	.0985	1.77	.456	−1.05	.354	98.2
mt14233	G	synND6	.87 (.73–1.05)	.158	−.003	.417	−.03	.760	−.04	.497	.09	.4970	−1.49	.416	−.53	.541	99.5
mt14365	T	synND6	.68 (.44–1.05)	.081	−.025	.004	−.02	.920	−.16	.141	.16	.5830	5.72	.176	1.25	.535	99.4
mt14470	C	synND6	1.28 (.90–1.81)	.170	.005	.488	.40	.252	−.01	.984	−.33	.3817	2.31	.558	1.83	.327	98.2
mt14582	G	misND6	.68 (.44–1.05)	.081	−.025	.004	−.02	.920	−.16	.141	.16	.5830	5.72	.176	1.25	.535	99.4
mt14687	G	tRNA E	.73 (.38–1.38)	.333	−.006	.659	−.13	.457	−.11	.323	1.21	.0076	−2.09	.741	−.60	.843	97.3
mt14766	C	misCyt B	1.04 (.95–1.15)	.405	−.001	.624	−.03	.463	−.02	.485	−.02	.7837	−.55	.574	.00	.996	99.4
mt14793	G	misCyt B	1.16 (.94–1.42)	.174	−.003	.489	−.11	.211	.06	.260	−.06	.6519	1.38	.498	.58	.544	96.8
mt14798	C	misCyt B	.93 (.81–1.07)	.296	−.002	.591	.05	.371	.04	.274	.03	.8101	1.13	.473	.59	.427	99.2
mt14905	A	synCyt B	.89 (.76–1.05)	.160	−.002	.560	.04	.639	−.03	.585	.13	.2933	−.49	.761	−.07	.923	97.5
mt15043	A	synCyt B	1.03 (.80–1.32)	.846	.013	.012	−.35	.155	−.06	.749	.28	.2715	−1.49	.591	.67	.613	98.5
mt15218	G	misCyt B	1.16 (.91–1.48)	.232	−.007	.133	−.15	.137	−.09	.223	.11	.5128	2.70	.251	.99	.380	98.8
mt15257	A	misCyt B	.87 (.61–1.23)	.428	.006	.393	.31	.126	.09	.549	−.45	.0515	.39	.903	−1.94	.207	99.5
mt15452	A	misCyt B	.96 (.85–1.09)	.538	.002	.497	−.07	.156	−.02	.569	.06	.4695	−.60	.625	.00	.995	99.2
mt15607	G	synCyt B	.89 (.76–1.05)	.160	−.002	.560	.04	.639	−.03	.585	.13	.2933	−.49	.761	−.07	.923	97.5
mt15758	G	misCyt B	.90 (.61–1.34)	.603	.017	.030	−.13	.608	.13	.450	−.02	.9565	−2.87	.359	2.26	.130	98.9
mt15784	C	synCyt B	.94 (.58–1.51)	.795	−.001	.937			.18	.459	2.15	.0003	10.48	.176	1.97	.594	99.6
mt15833	C	synCyt B	1.14 (.78–1.65)	.508	.003	.696	.20	.430	−.30	.086	.23	.5210	.58	.898	1.76	.411	99.5
mt15884	C	misCyt B	1.00 (.74–1.34)	.987	.002	.748	−.01	.902	−.08	.174	.04	.8212	1.96	.473	.88	.498	94.3
mt15904	T	tRNA T	1.18 (.96–1.45)	.122	.003	.513	.09	.295	−.04	.481	.40	.0047	−3.02	.155	−.38	.707	99.0
mt15907	G	tRNA T	1.29 (.87–1.90)	.201	.016	.042	−.31	.379	−.20	.420	.09	.8404	−2.86	.613	−1.41	.601	99.4
mt15924	G	tRNA T	1.00 (.79–1.26)	.989	.011	.017	−.11	.470	−.09	.351	−.08	.6910	.88	.717	.77	.507	98.6
mt15928	A	tRNA T	.89 (.76–1.05)	.160	−.002	.560	.04	.639	−.03	.585	.13	.2933	−.49	.761	−.07	.923	97.5
Haplogroup:
X			.88 (.64–1.20)	.410	−.010	.098	.10	.480	−.01	.921	−.20	.4564	−1.14	.736	1.43	.373	98.8
I			1.07 (.78–1.46)	.677	.015	.016	−.35	.156	−.06	.736	.34	.2121	.63	.828	1.75	.208	98.8
V			1.18 (.96–1.46)	.114	.003	.512	.09	.294	−.04	.474	.40	.0046	−3.00	.158	−.37	.715	99.5
U			.99 (.87–1.12)	.857	.000	.989	.12	.010	.03	.369	.05	.5499	.74	.558	.24	.694	99.3
J			1.23 (1.04–1.45)	.017	−.003	.452	−.06	.379	−.03	.500	.21	.0822	−2.02	.241	−.25	.763	98.9
W			.98 (.74–1.30)	.882	−.003	.589	.00	.973	−.07	.274	.25	.2813	−3.03	.353	.06	.969	99.4
T			.89 (.76–1.05)	.160	−.002	.560	.04	.639	−.03	.585	.13	.2933	−.49	.761	−.07	.923	97.5
K			.84 (.68–1.03)	.100	−.002	.564	.07	.412	.02	.734	.09	.4912	.09	.965	.08	.933	99.7
H			.99 (.90–1`.09)	.884	.002	.446	.06	.135	.01	.572	.10	.1296	−.26	.789	−.17	.717	99.7

Note.— Some SNPs were monomorphic for subsets of individuals used for analysis; hence, values for those SNPs are missing. Standardized regression coefficients (β) for best results are listed in table 6. BP = blood pressure.

Table 9. .

Results of Association Testing of All mtDNA Variants with Type 2 Diabetes, by Population

Sample	n	Best Result	OR (95% CI)	Pnom	Pempiricala
Scandinavian	918	mt8869 (misATP6); mt5263 (misND2); mt4639 (misND2)	7.67 (2.18–27.04)	.0015	>.5 (NS)
Swedish	1,010	mt8251 (synCOII)	2.56 (1.25–5.26)	.0105	>.5 (NS)
Canadian	246	mt15218 (misCytB)	3.93 (1.16–13.28)	.0277	1 (NS)
U.S.b	2,428	mt5495 (synND2)	3.60 (1.42–9.12)	.0070	>.3 (NS)
Polandb	2,006	mt12612 (synND5)	2.07 (1.44–2.98)	.000085	.02

^aNS = not significant.

^bSample from Genomics Collaborative Inc.

Table 10. .

Results of Association Testing of Each SNP and Haplogroup with Type 2 Diabetes, by Population^[Note]

		Scandinavia		Sweden		Canada		United States		Poland
SNP or Haplogroup	Allele	OR (95% CI)	Pnom	OR (95% CI)	Pnom	OR (95% CI)	Pnom	OR (95% CI)	Pnom	OR (95% CI)	Pnom
SNP:
mt709	A	.95 (.64–1.39)	.77788	1.04 (.73–1.48)	.8202	.71 (.38–1.34)	.2872	.92 (.73–1.17)	.5037	.87 (.69–1.11)	.27722
mt750	A	1.73 (.79–3.79)	.16969	1.00 (2.12–0.47)	.9957	1.02 (.14–7.34)	.9868	.93 (.57–1.54)	.7896	1.08 (.49–2.38)	.85038
mt930	A	1.69 (.74–3.87)	.21450	.41 (.89–0.19)	.0242	.70 (.22–2.24)	.5437	1.17 (.77–1.76)	.4637	.74 (.51–1.09)	.12453
mt1189	C	.96 (.54–1.71)	.88946	.76 (1.31–0.45)	.3280	.61 (.23–1.61)	.3185	.87 (.64–1.17)	.3550	.83 (.52–1.30)	.41337
mt1243	C	1.00 (.46–2.19)	.99543	4.53 (1.11–18.42)	.0349	2.00 (.19–21.34)	.5661	.84 (.48–1.50)	.5617	1.31 (.68–2.53)	.41544
mt1438	A	1.07 (.64–1.81)	.78927	.96 (1.74–0.53)	.8896	1.01 (.14–7.28)	.9933	1.12 (.74–1.69)	.5998	1.01 (.59–1.74)	.96710
mt1719	A	2.56 (1.15–5.72)	.02158	1.35 (.77–2.38)	.2903	1.59 (.73–3.45)	.2413	.80 (.57–1.11)	.1845	.92 (.61–1.38)	.68233
mt1811	G	.74 (.48–1.13)	.16548	.76 (1.04–0.56)	.0864	.69 (.33–1.43)	.3144	.96 (.77–1.19)	.7146	.97 (.75–1.25)	.80347
mt1888	A	.88 (.53–1.46)	.62894	.86 (1.27–0.58)	.4465	.61 (.30–1.23)	.1654	1.11 (.84–1.47)	.4713	.79 (.60–1.03)	.08576
mt2158	C	.39 (.13–1.20)	.10167	.67 (2.36–0.19)	.5313	1.72 (.41–7.26)	.4577	1.30 (.57–2.97)	.5349	2.53 (1.14–5.62)	.02222
mt2706	A	1.00 (.77–1.30)	.97143	1.00 (.78–1.29)	.9710	.78 (.46–1.33)	.3614	.97 (.82–1.13)	.6678	1.04 (.87–1.25)	.64907
mt3010	A	.76 (.57–1.02)	.06835	1.33 (.99–1.80)	.0584	.68 (.33–1.39)	.2904	1.03 (.85–1.24)	.7900	.96 (.78–1.19)	.71873
mt3197	C	.94 (.66–1.33)	.70875	1.25 (.83–1.89)	.2942	1.55 (.43–5.59)	.5014	1.35 (1.00–1.83)	.0494	.94 (.71–1.24)	.66619
mt3348	G	1.00 (.06–16.11)	.99752	.50 (5.28–0.05)	.5643			.25 (.03–1.88)	.1775
mt3394	C	.46 (.16–1.30)	.14431	6.01 (.93–38.79)	.0593			1.31 (.57–2.98)	.5257	2.38 (.64–8.85)	.19679
mt3480	G	.70 (.41–1.19)	.18747	.85 (1.39–0.52)	.5269	.61 (.26–1.47)	.2733	.85 (.65–1.11)	.2230	.95 (.62–1.45)	.80851
mt3505	G	1.00 (.46–2.19)	.99543	4.53 (1.11–18.42)	.0349	2.00 (.19–21.34)	.5661	.84 (.48–1.50)	.5617	1.31 (.68–2.53)	.41544
mt3720	G	.99 (.20–4.95)	.99357	2.50 (.81–7.72)	.1113			1.47 (.76–2.84)	.2472	.87 (.48–1.58)	.64860
mt3915	A	.57 (.17–1.92)	.36280	1.13 (.57–2.24)	.7270	.50 (.09–2.70)	.4200	1.40 (.83–2.34)	.2072	.85 (.45–1.61)	.62083
mt3990	T	.51 (.05–5.43)	.57874	1.51 (.43–5.32)	.5250			1.13 (.43–2.92)	.8090	.90 (.34–2.33)	.82373
mt3992	T	.80 (.21–2.98)	.73763	1.00 (2.53–0.39)	.9932			.68 (.34–1.38)	.2824	.49 (.22–1.09)	.08073
mt4024	G	.80 (.21–2.98)	.73763	1.00 (2.53–0.39)	.9932			.68 (.34–1.38)	.2824	.49 (.22–1.09)	.08073
mt4216	C	.74 (.51–1.07)	.11273	.99 (1.33–0.73)	.9280	.63 (.34–1.14)	.1273	1.14 (.93–1.40)	.1960	.93 (.76–1.15)	.52925
mt4336	C	.58 (.23–1.46)	.24638	1.45 (.55–3.81)	.4554	2.03 (.38–10.95)	.4084	.64 (.37–1.09)	.1008	1.03 (.63–1.68)	.89781
mt4529	T	4.04 (.96–17.01)	.05732	1.07 (.49–2.38)	.8594	1.63 (.74–3.63)	.2284	.76 (.48–1.21)	.2515	1.26 (.65–2.45)	.49148
mt4561	C	.12 (.02–0.71)	.01937	2.46 (.50–12.1)	.2664	.98 (.14–7.10)	.9866	.82 (.45–1.51)	.5282	2.51 (.51–12.27)	.25489
mt4580	A	2.20 (1.25–3.87)	.00611	1.52 (.86–2.71)	.1529	.84 (.25–2.83)	.7790	1.05 (.75–1.46)	.7945	.96 (.66–1.41)	.83729
mt4639	C	7.67 (2.18–27.04)	.00153	.40 (1.96–0.08)	.2597			.66 (.19–2.34)	.5228	1.23 (.51–2.98)	.64660
mt4769	A	1.07 (.64–1.81)	.78927	.96 (1.74–0.53)	.8896	1.01 (.14–7.28)	.9933	1.12 (.74–1.69)	.5998	1.01 (.59–1.74)	.96710
mt4793	G	1.18 (.39–3.53)	.76772	.55 (1.63–0.19)	.2800	1.03 (.06–16.58)	.9860	.99 (.56–1.73)	.9596	1.08 (.50–2.30)	.84636
mt4917	G	.88 (.53–1.46)	.62894	.86 (1.27–0.58)	.4465	.61 (.30–1.23)	.1654	1.11 (.84–1.47)	.4713	.79 (.60–1.03)	.08576
mt4928	C	3.10 (.36–26.62)	.30349							.67 (.11–3.97)	.65919
mt5004	C	.80 (.21–2.98)	.73763	1.00 (2.53–0.39)	.9932			.68 (.34–1.38)	.2824	.49 (.22–1.09)	.08073
mt5046	A	1.00 (.46–2.19)	.99095	3.31 (.97–11.25)	.0556	2.97 (.34–26.13)	.3254	.67 (.37–1.21)	.1830	1.37 (.73–2.57)	.33308
mt5147	A	1.57 (.68–3.65)	.29093	.36 (.80–0.16)	.0116			1.24 (.81–1.90)	.3296	.76 (.52–1.12)	.16931
mt5263	T	7.67 (2.18–27.04)	.00153	.40 (1.96–0.08)	.2597			.66 (.19–2.34)	.5228	1.23 (.51–2.98)	.64660
mt5390	G	1.00 (.20–5.00)	.99571	2.53 (.82–7.79)	.1072			1.61 (.84–3.06)	.1492	.92 (.51–1.65)	.77333
mt5426	C	.66 (.19–2.33)	.51804	1.75 (.74–4.17)	.2041			1.34 (.76–2.37)	.3124	.79 (.45–1.37)	.39715
mt5460	A	.73 (.38–1.38)	.33182	1.64 (.68–3.95)	.2742	1.80 (.52–6.20)	.3546	1.00 (.63–1.60)	.9943	1.73 (1.04–2.86)	.03442
mt5465	C							1.00 (.06–15.98)	.9991
mt5495	C	1.26 (.49–3.21)	.63062	.78 (1.78–0.34)	.5495			3.60 (1.42–9.12)	.0070	.52 (.24–1.12)	.09332
mt5656	G	.89 (.55–1.43)	.62761	.44 (1.40–0.14)	.1650	2.02 (.19–21.5)	.5613	.94 (.47–1.86)	.8515	.95 (.60–1.50)	.81851
mt6045	T	.99 (.20–4.95)	.99357	2.00 (.69–5.77)	.2001			1.38 (.72–2.64)	.3266	.87 (.48–1.58)	.64860
mt6152	C	.99 (.20–4.95)	.99357	2.50 (.81–7.72)	.1113			1.38 (.72–2.64)	.3266	.87 (.48–1.58)	.64860
mt6221	C			1.51 (.61–3.69)	.3711			.92 (.42–2.02)	.8309	1.60 (.53–4.86)	.40589
mt6260	A	.50 (.09–2.64)	.41267	.89 (2.20–0.36)	.7960	.66 (.11–3.98)	.6514	.87 (.42–1.79)	.7082	.72 (.23–2.26)	.56962
mt6365	C	.50 (.05–5.27)	.56306					1.22 (.50–2.94)	.6641	.84 (.25–2.75)	.76877
mt6371	T			1.19 (.51–2.78)	.6872			1.00 (.48–2.05)	.9909	1.60 (.53–4.84)	.40999
mt6719	C							2.00 (.19–21.04)	.5649
mt6734	A	.50 (.05–5.27)	.56306	1.20 (.36–3.95)	.7643			1.28 (.47–3.43)	.6288	1.01 (.40–2.55)	.98979
mt6776	C	.61 (.32–1.17)	.13893	.86 (1.82–0.40)	.6896	1.48 (.55–4.00)	.4403	1.21 (.80–1.85)	.3696	1.68 (.82–3.42)	.15645
mt7028	C	1.00 (.77–1.30)	.97143	1.00 (.78–1.29)	.9710	.78 (.46–1.33)	.3614	.97 (.82–1.13)	.6678	1.04 (.87–1.25)	.64907
mt7476	T	1.26 (.34–4.69)	.73514	.94 (1.89–0.47)	.8687	.24 (.03–1.84)	.1693	.95 (.52–1.71)	.8560	1.51 (.54–4.23)	.43224
mt7768	G	.94 (.56–1.56)	.80245	.46 (1.05–0.20)	.0638	.67 (.11–4.01)	.6580	1.12 (.74–1.71)	.5869	.79 (.52–1.19)	.25418
mt7864	T	1.01 (.45–2.27)	.98696	4.46 (1.09–18.21)	.0370			.63 (.32–1.23)	.1775	1.43 (.68–2.99)	.34545
mt8251	A	1.99 (.99–4.00)	.05416	2.56 (1.25–5.26)	.0105	1.91 (.92–3.97)	.0834	.82 (.58–1.15)	.2553	1.11 (.74–1.68)	.61329
mt8269	A	.50 (.20–1.24)	.13380	1.00 (.43–2.33)	.9962	1.70 (.40–7.15)	.4721	1.08 (.62–1.90)	.7795	1.18 (.68–2.05)	.55420
mt8557	A	.40 (.13–1.24)	.11350	1.68 (.4–6.95)	.4760	1.70 (.40–7.15)	.4721	1.50 (.68–3.34)	.3168	2.03 (.77–5.32)	.15049
mt8616	T	.51 (.05–5.43)	.57874	1.51 (.43–5.32)	.5250			1.43 (.55–3.75)	.4663	1.01 (.40–2.55)	.98461
mt8697	A	.88 (.53–1.46)	.62894	.86 (1.27–0.58)	.4465	.61 (.30–1.23)	.1654	1.11 (.84–1.47)	.4713	.79 (.60–1.03)	.08576
mt8705	C	1.28 (.58–2.84)	.54662	1.29 (.48–3.48)	.6142			.50 (.13–1.95)	.3164	.66 (.11–3.93)	.65108
mt8869	G	7.67 (2.18–27.04)	.00153	.40 (1.96–0.08)	.2597			.66 (.19–2.34)	.5228	1.23 (.51–2.98)	.64660
mt8994	A	1.00 (.46–2.19)	.99095	3.31 (.97–11.25)	.0556	2.97 (.34–26.13)	.3254	.67 (.37–1.21)	.1830	1.37 (.73–2.57)	.33308
mt9055	A	.70 (.41–1.19)	.18747	.85 (1.39–0.52)	.5269	.61 (.26–1.47)	.2733	.85 (.65–1.11)	.2230	.95 (.62–1.45)	.80851
mt9093	G	1.42 (.45–4.48)	.55082	.59 (2.46–0.14)	.4725			1.77 (.79–3.97)	.1688	1.88 (.80–4.40)	.14472
mt9123	A	.79 (.21–2.97)	.73265	1.10 (.44–2.73)	.8340			.78 (.40–1.54)	.4743	.55 (.26–1.19)	.12787
mt9150	G			2.02 (.52–7.89)	.3137			1.82 (.62–5.35)	.2795
mt9477	A	.94 (.66–1.33)	.70875	1.25 (.83–1.89)	.2942	1.55 (.43–5.59)	.5014	1.35 (1.00–1.83)	.0494	.94 (.71–1.24)	.66619
mt9612	A	3.10 (.36–26.62)	.30349							1.01 (.06–16.11)	.99660
mt9667	G	.91 (.38–2.17)	.83321	.71 (2.24–0.23)	.5590			2.45 (1.04–5.77)	.0398	1.23 (.59–2.56)	.58585
mt9698	C	.70 (.41–1.19)	.18747	.85 (1.39–0.52)	.5269	.61 (.26–1.47)	.2733	.85 (.65–1.11)	.2230	.95 (.62–1.45)	.80851
mt9716	C	.10 (.02–0.52)	.00640	1.41 (.45–4.44)	.5613	.66 (.11–3.94)	.6447	.85 (.49–1.45)	.5463	1.33 (.46–3.84)	.59560
mt9899	C	.66 (.23–1.85)	.42724	1.57 (.68–3.64)	.2914			1.09 (.59–2.00)	.7912	1.04 (.62–1.74)	.89486
mt9947	A	.50 (.05–5.27)	.56306	1.20 (.36–3.95)	.7643			1.28 (.47–3.43)	.6288	1.01 (.40–2.55)	.98979
mt10034	C	4.05 (.96–17.07)	.05642	.86 (1.83–0.41)	.7015	1.63 (.74–3.63)	.2284	.82 (.51–1.29)	.3891	1.26 (.65–2.45)	.49152
mt10044	G			.86 (2.57–0.29)	.7829			.63 (.25–1.63)	.3422	.70 (.27–1.84)	.47261
mt10084	C			1.51 (.25–8.96)	.6507			.61 (.26–1.47)	.2748	.42 (.11–1.58)	.20139
mt10238	C	4.17 (1.00–17.5)	.05071	.93 (1.99–0.43)	.8453	1.65 (.74–3.66)	.2195	.84 (.53–1.33)	.4550	1.21 (.62–2.36)	.58387
mt10398	G	.89 (.61–1.28)	.52021	1.10 (.81–1.50)	.5386	1.01 (.57–1.77)	.9810	.93 (.77–1.13)	.4784	1.28 (1.01–1.62)	.04098
mt10463	C	.88 (.53–1.46)	.62894	.86 (1.27–0.58)	.4465	.61 (.30–1.23)	.1654	1.11 (.84–1.47)	.4713	.79 (.60–1.03)	.08576
mt10550	G	.70 (.41–1.19)	.18747	.85 (1.39–0.52)	.5269	.61 (.26–1.47)	.2733	.85 (.65–1.11)	.2230	.95 (.62–1.45)	.80851
mt10876	G	1.00 (.20–5.00)	.99571	2.53 (.82–7.79)	.1072			1.61 (.84–3.06)	.1492	.92 (.51–1.65)	.77333
mt10915	C	.68 (.11–4.07)	.67551	1.41 (.45–4.44)	.5613			1.10 (.47–2.60)	.8280	1.01 (.42–2.44)	.98377
mt11251	G	.76 (.53–1.10)	.14209	1.06 (.79–1.43)	.6847	.66 (.37–1.20)	.1761	1.09 (.90–1.33)	.3731	1.08 (.87–1.33)	.49302
mt11299	C	.70 (.41–1.19)	.18747	.85 (1.39–0.52)	.5269	.61 (.26–1.47)	.2733	.85 (.65–1.11)	.2230	.95 (.62–1.45)	.80851
mt11377	A	1.22 (.52–2.84)	.65089	.99 (1.93–0.51)	.9854			.99 (.58–1.68)	.9624	1.36 (.72–2.55)	.34438
mt11467	G	.82 (.61–1.10)	.19156	.76 (1.01–0.57)	.0625	.85 (.44–1.62)	.6208	1.06 (.88–1.28)	.5415	.99 (.81–1.21)	.91817
mt11470	G	.67 (.11–3.97)	.65737	.99 (15.94–0.06)	.9966			.89 (.45–1.75)	.7298	.33 (.07–1.52)	.15606
mt11485	C	1.03 (.26–4.13)	.96985	1.10 (.46–2.61)	.8291	.50 (.09–2.72)	.4259	1.16 (.63–2.16)	.6346	.92 (.41–2.10)	.84714
mt11674	T	1.00 (.46–2.19)	.99543	4.53 (1.11–18.42)	.0349	2.00 (.19–21.34)	.5661	.84 (.48–1.50)	.5617	1.31 (.68–2.53)	.41544
mt11719	G	.84 (.65–1.09)	.19783	1.12 (.88–1.44)	.3564	.98 (.59–1.63)	.9394	.98 (.83–1.15)	.7929	1.02 (.86–1.22)	.81946
mt11812	G	1.00 (.56–1.76)	.99367	.66 (1.04–0.42)	.0742	.73 (.33–1.61)	.4352	1.10 (.79–1.52)	.5829	.80 (.58–1.10)	.16912
mt11840	T	.50 (.09–2.65)	.41575	1.12 (.43–2.93)	.8164	.66 (.11–3.94)	.6447	.86 (.39–1.85)	.6918	1.00 (.25–4.01)	.99887
mt11914	A	.99 (.54–1.82)	.97616	.75 (2.16–0.26)	.5877			.88 (.58–1.31)	.5197	.91 (.50–1.66)	.76814
mt11947	G	1.00 (.46–2.19)	.99095	3.31 (.97–11.25)	.0556	2.97 (.34–26.13)	.3254	.67 (.37–1.21)	.1830	1.37 (.73–2.57)	.33308
mt12007	A	.44 (.14–1.39)	.16011	1.34 (.30–5.98)	.7025	3.21 (.90–11.42)	.0710	.93 (.45–1.93)	.8377	2.92 (1.35–6.33)	.00662
mt12308	G	.82 (.61–1.10)	.19156	.76 (1.01–0.57)	.0625	.85 (.44–1.62)	.6208	1.06 (.88–1.28)	.5415	.99 (.81–1.21)	.91817
mt12372	A	.82 (.61–1.10)	.19156	.76 (1.01–0.57)	.0625	.85 (.44–1.62)	.6208	1.06 (.88–1.28)	.5415	.98 (.80–1.20)	.87760
mt12414	C	.93 (.45–1.90)	.84046	3.03 (.87–10.57)	.0820	2.03 (.19–21.66)	.5564	.87 (.49–1.56)	.6462	1.38 (.72–2.65)	.32421
mt12501	A	4.47 (1.41–14.21)	.01107	1.31 (.62–2.80)	.4793	1.82 (.85–3.89)	.1220	.78 (.54–1.12)	.1775	.86 (.56–1.34)	.50957
mt12612	G	.68 (.41–1.13)	.13447	1.44 (.95–2.19)	.0861	.90 (.33–2.41)	.8290	1.10 (.84–1.43)	.5011	2.07 (1.44–2.98)	.00009
mt12618	A	.92 (.52–1.61)	.76225	.33 (1.15–0.09)	.0826	2.02 (.19–21.5)	.5613	1.06 (.52–2.16)	.8657	1.21 (.66–2.20)	.53536
mt12633	A	.60 (.22–1.65)	.32172	1.75 (.83–3.69)	.1396	.42 (.11–1.59)	.2010	1.11 (.65–1.90)	.6962	.80 (.50–1.27)	.33851
mt12669	T	1.68 (.61–4.62)	.31301
mt12705	T	1.62 (.93–2.83)	.09073	1.64 (.98–2.73)	.0587	2.07 (1.03–4.17)	.0417	.77 (.57–1.02)	.0725	1.08 (.77–1.52)	.66678
mt13020	C	.83 (.25–2.73)	.75609	2.23 (.79–6.29)	.1305			1.48 (.80–2.75)	.2130	.93 (.55–1.58)	.78339
mt13105	G	2.70 (.75–9.72)	.12933	1.26 (.34–4.70)	.7332	.38 (.08–1.90)	.2410	.71 (.32–1.6)	.4119	1.49 (.53–4.18)	.44614
mt13368	A	.88 (.53–1.46)	.62894	.86 (1.27–0.58)	.4465	.61 (.30–1.23)	.1654	1.11 (.84–1.47)	.4713	.79 (.60–1.03)	.08576
mt13617	C	.94 (.66–1.33)	.70875	1.25 (.83–1.89)	.2942	1.55 (.43–5.59)	.5014	1.35 (1.00–1.83)	.0494	.94 (.71–1.24)	.66619
mt13708	A	.70 (.43–1.13)	.14564	1.37 (.93–2.01)	.1113	.88 (.36–2.17)	.7887	1.06 (.83–1.35)	.6467	1.41 (1.07–1.87)	.01525
mt13734	C	1.00 (.20–4.96)	.99566	2.21 (.78–6.25)	.1336			1.28 (.68–2.42)	.4442	.91 (.51–1.64)	.76543
mt13740	C	.50 (.09–2.65)	.41575	1.12 (.43–2.93)	.8164	.66 (.11–3.94)	.6447	.86 (.39–1.85)	.6918	1.00 (.25–4.01)	.99887
mt13780	G	3.59 (.82–15.71)	.09011	1.55 (.72–3.33)	.2590	2.38 (.89–6.34)	.0826	.78 (.52–1.18)	.2396	1.80 (.94–3.46)	.07579
mt13879	C	.39 (.13–1.22)	.10522	.67 (2.36–0.19)	.5292	1.71 (.41–7.20)	.4650	1.41 (.62–3.17)	.4107	2.53 (1.14–5.60)	.02270
mt13934	T	.98 (.14–7.02)	.98766	1.14 (.41–3.16)	.8039	.50 (.12–1.98)	.3202	1.32 (.81–2.15)	.2663	.79 (.47–1.32)	.36476
mt13965	C	.20 (.03–1.43)	.10900	.50 (2.67–0.09)	.4201			1.16 (.39–3.46)	.7903	.85 (.29–2.55)	.77797
mt13966	G	1.34 (.46–3.88)	.59012	1.56 (.73–3.35)	.2523			.67 (.38–1.21)	.1840	.70 (.33–1.47)	.34686
mt14022	G
mt14167	T	.70 (.41–1.19)	.18747	.85 (1.39–0.52)	.5269	.61 (.26–1.47)	.2733	.85 (.65–1.11)	.2230	.95 (.62–1.45)	.80851
mt14182	C	.94 (.56–1.56)	.80245	.46 (1.05–0.20)	.0646	1.36 (.30–6.16)	.6933	1.08 (.72–1.62)	.7233	.78 (.52–1.18)	.24376
mt14233	G	1.00 (.56–1.76)	.99367	.66 (1.04–0.42)	.0742	.73 (.33–1.61)	.4352	1.10 (.79–1.52)	.5829	.80 (.58–1.10)	.16912
mt14365	T	.80 (.21–2.98)	.73763	1.00 (2.53–0.39)	.9932			.68 (.34–1.38)	.2824	.49 (.22–1.09)	.08073
mt14470	C			1.30 (.62–2.69)	.4861			1.06 (.63–1.77)	.8292	1.72 (.89–3.32)	.10541
mt14582	G	.80 (.21–2.98)	.73763	1.00 (2.53–0.39)	.9932			.68 (.34–1.38)	.2824	.49 (.22–1.09)	.08073
mt14687	G	.20 (.03–1.43)	.10900	.50 (2.67–0.09)	.4201			1.16 (.39–3.46)	.7903	.85 (.29–2.55)	.77797
mt14766	C	.84 (.65–1.09)	.19783	1.12 (.88–1.44)	.3564	.98 (.59–1.63)	.9394	.98 (.84–1.15)	.8257	1.01 (.85–1.21)	.87667
mt14793	G	.96 (.55–1.66)	.87265	1.02 (.64–1.62)	.9347	3.93 (.50–30.57)	.1916	1.56 (1.03–2.35)	.0356	1.05 (.75–1.48)	.78017
mt14798	C	.64 (.40–1.01)	.05530	1.09 (.75–1.59)	.6345	.67 (.29–1.57)	.3546	.94 (.77–1.16)	.5936	.97 (.74–1.27)	.82976
mt14905	A	.88 (.53–1.46)	.62894	.86 (1.27–0.58)	.4465	.61 (.30–1.23)	.1654	1.11 (.84–1.47)	.4713	.79 (.60–1.03)	.08576
mt15043	A	3.52 (.80–15.47)	.09524	1.10 (.58–2.07)	.7716	2.31 (.87–6.17)	.0937	.82 (.56–1.20)	.2983	1.00 (.62–1.61)	.98972
mt15218	G	.87 (.42–1.80)	.70133	.89 (1.55–0.51)	.6774	3.93 (1.16–13.28)	.0277	1.63 (1.04–2.55)	.0349	.96 (.64–1.43)	.82791
mt15257	A	1.26 (.34–4.71)	.73015	.88 (1.75–0.44)	.7182	.25 (.03–1.90)	.1782	.96 (.56–1.66)	.8895	.75 (.35–1.59)	.44968
mt15452	A	.74 (.51–1.06)	.09985	.97 (1.31–0.72)	.8596	.63 (.34–1.14)	.1275	1.11 (.90–1.35)	.3229	.95 (.77–1.17)	.61947
mt15607	G	.88 (.53–1.46)	.62894	.86 (1.27–0.58)	.4465	.61 (.30–1.23)	.1654	1.11 (.84–1.47)	.4713	.79 (.60–1.03)	.08576
mt15758	G	4.55 (1.12–18.51)	.03434	.55 (1.64–0.19)	.2850	1.31 (.59–2.92)	.5109	.49 (.25–0.94)	.0325	1.50 (.43–5.30)	.52502
mt15784	C	1.96 (.19–20.80)	.57476	2.00 (.19–21.07)	.5654			.75 (.35–1.58)	.4457	1.13 (.56–2.28)	.72367
mt15833	C	.33 (.04–2.86)	.31519	1.13 (.41–3.15)	.8099	2.09 (.39–11.20)	.3912	1.00 (.53–1.89)	.9939	1.29 (.73–2.30)	.37879
mt15884	C	.83 (.41–1.66)	.59473	1.13 (.57–2.24)	.7271	2.03 (.19–21.66)	.5564	.99 (.61–1.59)	.9631	1.00 (.54–1.84)	.99182
mt15904	T	2.21 (1.26–3.88)	.00595	1.53 (.86–2.71)	.1509	.83 (.25–2.80)	.7683	1.04 (.74–1.45)	.8268	.96 (.65–1.40)	.82022
mt15907	G	1.00 (.20–5.00)	.99571	2.53 (.82–7.79)	.1072			1.61 (.84–3.06)	.1492	.92 (.51–1.65)	.77333
mt15924	G	1.51 (.54–4.26)	.43223	.96 (1.73–0.53)	.8923	1.45 (.64–3.30)	.3698	1.04 (.74–1.44)	.8366	.77 (.48–1.24)	.28244
mt15928	A	.88 (.53–1.46)	.62894	.86 (1.27–0.58)	.4465	.61 (.30–1.23)	.1654	1.11 (.84–1.47)	.4713	.79 (.60–1.03)	.08576
Haplogroup:
X		1.36 (.47–3.93)	.57301	1.25 (.56–2.77)	.5881			.83 (.49–1.41)	.4886	.61 (.36–1.04)	.06825
I		4.14 (.99–17.37)	.05238	.92 (2.05–0.42)	.8474	1.41 (.62–3.21)	.4066	.80 (.49–1.30)	.3599	1.21 (.62–2.36)	.58179
V		2.20 (1.25–3.87)	.00611	1.52 (.86–2.71)	.1529	.84 (.25–2.83)	.7790	1.05 (.75–1.46)	.7945	.96 (.66–1.41)	.83729
U		.80 (.58–1.09)	.16011	.80 (1.10–0.58)	.1671	1.18 (.52–2.66)	.6944	1.16 (.93–1.44)	.1824	1.02 (.82–1.26)	.87963
J		.68 (.41–1.12)	.13275	1.46 (.96–2.21)	.0787	1.02 (.41–2.54)	.9689	1.07 (.83–1.39)	.6023	1.79 (1.29–2.47)	.00047
W		1.01 (.48–2.15)	.97179	2.25 (.71–7.14)	.1672	3.76 (.85–16.73)	.0819	.73 (.45–1.16)	.1839	.97 (.61–1.54)	.90282
T		.88 (.53–1.46)	.62894	.86 (1.27–0.58)	.4465	.61 (.30–1.23)	.1654	1.11 (.84–1.47)	.4713	.79 (.60–1.03)	.08576
K		.96 (.54–1.71)	.88946	.76 (1.31–0.45)	.3280	.61 (.23–1.61)	.3185	.87 (.64–1.17)	.3550	.83 (.52–1.30)	.41337
H		1.00 (.77–1.30)	.97143	1.00 (.78–1.29)	.9710	.78 (.46–1.33)	.3614	.97 (.82–1.13)	.6678	1.04 (.87–1.25)	.64907

Note.— The best results are shaded. An absence of values indicates a monomorphic SNP.

The remaining quantitative metabolic traits were studied only in nondiabetic controls, and sample sizes for these additional studies were significantly smaller than for diabetes or BMI (tables 6, 7, and 8). No significant associations were identified using unadjusted models for insulin resistance (HOMA-IR), insulin secretion (insulinogenic index), cholesterol levels, and systolic and diastolic blood pressure (table 6) or after adjustment for sex, age, and BMI (tables 7 and 8).

We specifically examined the results for the three missense variants that were hypothesized to have been adaptive in cold climates and to be related to “energy deficiency” diseases today.^18,19 No association with increased risk of diabetes, obesity, or other metabolic traits was observed (table 11). The putative association of mt16189C with type 2 diabetes reported elsewhere^24–26 was not replicated here (n=6,608; odds ratio [OR] 1.03; 95% CI 0.88–1.21; P_nom=.36), which is consistent with other recent reports that did not support this hypothesis.^27,28 With this sample size (under the assumption of an OR of 1.5 and an mt16189C allele frequency of 14%, consistent with previous reports), we have >99% power to reject the null hypothesis (of no association) at the P<.01 level.⁵⁶

Table 11. .

Results of Association Testing of Three European mtDNA Variants Predicted to Be Selected for Adaptation to Cold Climates

		mt4917G(ND2 N150D)		mt14798C(cytB F18L)		mt15257A(cytB D171N)
Phenotypea	n	Effect Estimateb	Pnom	Effect Estimateb	Pnom	Effect Estimateb	Pnom
DM	6,608	.89 (.76–1.05)	.16	.93 (.81–1.07)	.30	.87 (.61–1.23)	.47
BMI	6,523	−.002	.56	−.002	.59	.006	.39
Ins index	342	.04	.29	.05	.37	.31	.13
HOMA-IR	399	−.03	.59	.04	.27	.09	.55
Cholesterol	1,274	.13	.29	.03	.81	−.45	.05
Systolic BP	2,047	−.49	.76	1.13	.47	.39	.90
Diastolic BP	2,047	−.07	.92	.59	.43	−1.94	.21

^aBP = blood pressure; DM = diabetes mellitus, type 2; Ins = insulinogenic.

^bOR (95% CI) for DM and β for all other phenotypes.

Discussion

We set out to develop a comprehensive approach to mtDNA association testing that (a) captures all common coding-region mtDNA variants and haplogroups efficiently by use of linkage disequilibrium, (b) tests all common variants for association, and (c) accounts for the multiple comparisons implicit in testing the many variants in mtDNA. Compared with the methods in the literature, this approach provides a more complete and statistically conservative assessment of the role of common mtDNA variants in disease; the current application to diabetes and BMI provides a sample size threefold larger than any previous study.

Despite this well-powered evaluation, our analyses do not support the hypothesis that common mtDNA variants play a role in type 2 diabetes and BMI, at least in the European samples studied. The results from our association tests of all common mtDNA variants and the risk of type 2 diabetes show that there is no single common coding-region mtDNA variant in European populations that strongly influences risk of type 2 diabetes or BMI, which is consistent with recent results obtained by Mohlke et al.²⁷ Haplogroup association results for type 2 diabetes were also consistent with noise. There may be population-specific variants that confer altered risk of diabetes (as in the Polish sample tested here), and further studies, including replication and complete resequencing,⁵⁷ will be needed to explore that hypothesis. Our results showed no significant association of mtDNA variants with other metabolic traits (blood pressure, cholesterol, insulin secretion, and insulin resistance traits); however, this study was not as well powered for these traits.

It is interesting and perhaps surprising that we could not detect any phenotypic consequence of missense variants that were predicted to have been selected for in colder climates.^2,19,58 Although our study does not directly address the hypothesis that climatic influences have led to selective adaptation of mtDNA variants, if common mtDNA variation does influence such traits, it is not reflected in glucose-stimulated insulin secretion, insulin resistance, body weight, blood pressure, cholesterol level, or type 2 diabetes.

This study does not address the role of mtDNA heteroplasmy in diabetes. Acquired somatic mtDNA mutations in tissues of relevance to type 2 diabetes are undetected in the blood samples used here. Typically, blood DNA exhibits much less heteroplasmy than nondividing tissues.⁵⁹ In the 6,608 DNA samples tested, a very small amount of heteroplasmy was observed (1.1% of samples had one or more “heterozygous” calls), although the mass spectroscopy–based genotyping platform is sensitive to low-frequency spectral peaks corresponding to the alternate allele. Rare mitochondrial diseases exhibit more pronounced heteroplasmy, perhaps because cells with mutant alleles are inviable without wild-type mtDNA molecules. Thus, we think it is unlikely that mtDNA heteroplasmy for inherited variants significantly influenced our results.

These results should not be taken as addressing the broader hypothesis that mitochondrial OXPHOS plays a causal role in type 2 diabetes; there are >70 nuclear-encoded OXPHOS subunits and an estimated 1,500 mitochondrial proteins that are as yet untested. Moreover, although the mtDNA variants tested here do not appear to influence metabolic disease, inherited variation in mtDNA may influence risk of other diseases, such as Alzheimer disease, Parkinson disease, cardiovascular disease, cardiomyopathy, HIV lipodystrophy, and prostate cancer. A systematic evaluation of mtDNA and nuclear mitochondrial genes for a causal role in these diseases and an investigation of epistatic interactions between the two genomes will reveal the extent to which mitochondrial defects play a causal role in human disease.