Overview

This report compares carriers of the mitochondrial variant m.C2639T (MT-RNR2 / 16S rRNA) against non-carriers across the DOLORisk diabetic peripheral neuropathy cohort.

Carrier identification

Carriers are extracted directly from the mitochondrial VCFs at position 2639, mapped from sequencing (WTCHG) IDs to DOLORisk IDs, and matched to the cleaned phenotype table. 17 carriers are identified (euNeuP 13, eunoNeuP 4) and all match a phenotype record. Following the official QC, the 2 flagged exclude are set aside, leaving 15 in the primary comparison.

17 identified carriers → 15 analysed
Analysis status Carriers
Case — neuropathic pain 11
Control — painless 4
Excluded (DOLORisk criteria) 2
Total — 17

Haplogroup

All carrier are N1b1. The other N-clade samples are 5 divergent N1a/N9).

Phenotype differences across macro-haplogroups
Variable Type Groups (n) Statistic p
Age (years) Continuous — Kruskal-Wallis 3 / 1 / 1 / 2 / 440 / 27 / 95 / 118 / 10 / 7 / 20 / 6 / 84 / 139 / 16 / 11 / 25 / 2 12.99 0.737
BMI (kg/m²) Continuous — Kruskal-Wallis 3 / 1 / 1 / 2 / 440 / 27 / 95 / 118 / 10 / 7 / 20 / 6 / 84 / 139 / 16 / 11 / 25 / 2 10.51 0.881
HbA1c (mmol/mol) Continuous — Kruskal-Wallis 3 / 1 / 1 / 2 / 440 / 27 / 95 / 118 / 10 / 7 / 20 / 6 / 84 / 139 / 16 / 11 / 25 / 2 23.12 0.145
DN4 score Continuous — Kruskal-Wallis 3 / 1 / 1 / 2 / 440 / 27 / 95 / 118 / 10 / 7 / 20 / 6 / 84 / 139 / 16 / 11 / 25 / 2 8.69 0.949
BPI average Continuous — Kruskal-Wallis 3 / 1 / 1 / 2 / 440 / 27 / 95 / 118 / 10 / 7 / 20 / 6 / 84 / 139 / 16 / 11 / 25 / 2 19.11 0.322
TCSS (Toronto) Continuous — Kruskal-Wallis 3 / 1 / 1 / 2 / 440 / 27 / 95 / 118 / 10 / 7 / 20 / 6 / 84 / 139 / 16 / 11 / 25 / 2 19.11 0.322
MNSI score Continuous — Kruskal-Wallis 3 / 1 / 1 / 2 / 440 / 27 / 95 / 118 / 10 / 7 / 20 / 6 / 84 / 139 / 16 / 11 / 25 / 2 23.47 0.075
Pain intensity Continuous — Kruskal-Wallis 3 / 1 / 1 / 2 / 440 / 27 / 95 / 118 / 10 / 7 / 20 / 6 / 84 / 139 / 16 / 11 / 25 / 2 12.71 0.756
Sex Categorical — Fisher 3 / 1 / 1 / 2 / 440 / 27 / 95 / 118 / 10 / 7 / 20 / 6 / 84 / 139 / 16 / 11 / 25 / 2 — 0.507
Diabetes type Categorical — Fisher 3 / 1 / 1 / 2 / 440 / 27 / 95 / 118 / 10 / 7 / 20 / 6 / 84 / 139 / 16 / 11 / 25 / 2 — 0.939
Pain status Categorical — Fisher 3 / 1 / 1 / 2 / 440 / 27 / 95 / 118 / 10 / 7 / 20 / 6 / 84 / 139 / 16 / 11 / 25 / 2 — 0.982
NPalgo grade Categorical — Fisher 3 / 1 / 1 / 2 / 440 / 27 / 95 / 118 / 10 / 7 / 20 / 6 / 84 / 139 / 16 / 11 / 25 / 2 — 0.921
N1b1 (carrier lineage) vs all other haplogroups
Variable Contrast Type N1b1 Other Effect (95% CI) p
Age (years) N1b1 vs Other Wilcoxon n=15 · 66.0 (58.0–69.5) n=992 · 68.0 (60.0–73.0) Δ -3.0 (-8.0, 2.0) 0.254
BMI (kg/m²) N1b1 vs Other Wilcoxon n=15 · 29.4 (26.5–33.1) n=970 · 29.4 (26.4–33.6) Δ -0.2 (-2.8, 2.5) 0.861
HbA1c (mmol/mol) N1b1 vs Other Wilcoxon n=11 · 54.0 (48.0–66.5) n=853 · 56.0 (48.0–67.0) Δ -0.0 (-8.0, 7.0) 0.913
DN4 score N1b1 vs Other Wilcoxon n=14 · 4.0 (3.0–5.8) n=893 · 4.0 (2.0–6.0) Δ -0.0 (-1.0, 1.0) 0.825
BPI average N1b1 vs Other Wilcoxon n=14 · 3.0 (1.0–4.5) n=550 · 4.0 (2.0–6.0) Δ -1.0 (-3.0, 0.0) 0.083
TCSS (Toronto) N1b1 vs Other Wilcoxon n=14 · 8.5 (7.2–12.0) n=967 · 11.0 (8.0–14.0) Δ -1.0 (-3.0, 1.0) 0.287
MNSI score N1b1 vs Other Wilcoxon n=11 · 5.0 (4.0–7.0) n=473 · 5.0 (3.0–7.0) Δ 0.0 (-1.0, 2.0) 0.886
Pain intensity N1b1 vs Other Wilcoxon n=15 · 2.0 (0.0–4.0) n=977 · 2.0 (0.0–5.0) Δ -0.0 (-2.0, 1.0) 0.791
Sex N1b1 vs Other Fisher n=15 n=992 OR 0.54 (0.10, 2.00) 0.412
Diabetes type N1b1 vs Other Fisher n=14 n=881 OR 0.00 (0.00, 3.82) 0.616
Pain status N1b1 vs Other Fisher n=15 n=992 OR 1.41 (0.42, 6.14) 0.784
NPalgo grade N1b1 vs Other Fisher n=15 n=992 — 0.708
Within macro-haplogroup N: N1b1 vs sister clades1
Variable Contrast Type N1b1 (n) Other N (n) Effect (95% CI) p
Age (years) Within N Wilcoxon 15 5 Δ -5.0 (-14.0, 7.0) 0.457
BMI (kg/m²) Within N Wilcoxon 15 4 Δ -0.3 (-9.7, 5.8) 0.961
HbA1c (mmol/mol) Within N Wilcoxon 11 4 Δ 2.0 (-35.0, 22.0) 0.844
DN4 score Within N Wilcoxon 14 5 Δ 1.0 (-2.0, 3.0) 0.639
BPI average Within N Wilcoxon 14 2 Δ 1.0 (-2.0, 7.0) 0.294
TCSS (Toronto) Within N Wilcoxon 14 5 Δ -3.0 (-8.0, 3.0) 0.264
MNSI score Within N Wilcoxon 11 2 Δ -0.0 (-6.0, 4.0) 0.919
Pain intensity Within N Wilcoxon 15 5 Δ 1.0 (-0.0, 5.0) 0.074
Sex Within N Fisher 15 5 OR 1.00 (0.06, 65.43) 1.000
Diabetes type Within N Fisher 14 5 — NA
Pain status Within N Fisher 15 5 OR 3.81 (0.31, 62.48) 0.290
NPalgo grade Within N Fisher 15 5 — 0.477
1 Other N = N1a, N9, etc. Very small sample; interpret as directional only.

Primary comparison: carrier vs non-carrier

Continuous phenotypes are compared with the Wilcoxon rank-sum test, categorical phenotypes with Fisher’s exact test.

Missing values are preserved, not imputed. Each test uses pairwise deletion, for a given phenotype, records missing that value are dropped for that test only , so the effective sample size varies by phenotype (the n= in each row of the table). No imputation is applied in this primary comparison; imputation is reserved for a separate sensitivity analysis.

The phenotypes tested carry very different amounts of missingness, which sets which are imputation candidates:

Missingness of tested phenotypes (analysis set)
Phenotype Missing % Carrier n Tier
MNSI score 69.2 11 High (≥40%) — describe only
HbA1c (mmol/mol) 53.2 11 High (≥40%) — describe only
BPI average 52.2 14 High (≥40%) — describe only
Diabetes type 41.5 14 High (≥40%) — describe only
TCSS (Toronto) 38.9 14 Impute candidate (5–40%)
DN4 score 35.0 14 Impute candidate (5–40%)
BMI (kg/m²) 21.0 15 Impute candidate (5–40%)
Pain intensity 9.9 15 Impute candidate (5–40%)
Age (years) 0.2 15 Near-complete (<5%)
Sex 0.2 15 Near-complete (<5%)
NPalgo grade 0.2 15 Near-complete (<5%)
Pain status 0.0 15 Near-complete (<5%)
m.C2639T carrier vs non-carrier — all phenotypes
Variable Type Carrier Non-carrier Effect (95% CI)1 p
Age (years) Continuous — median (IQR) n=15 · 66.0 (58.0–69.5) n=2407 · 64.0 (54.0–72.0) Δ 0.0 (-5.0, 6.0) 0.880
BMI (kg/m²) Continuous — median (IQR) n=15 · 29.4 (26.5–33.1) n=1902 · 27.8 (24.5–31.8) Δ 1.6 (-1.1, 4.4) 0.237
HbA1c (mmol/mol) Continuous — median (IQR) n=11 · 54.0 (48.0–66.5) n=1126 · 56.0 (48.0–68.0) Δ -1.0 (-9.0, 7.0) 0.859
DN4 score Continuous — median (IQR) n=14 · 4.0 (3.0–5.8) n=1564 · 5.0 (3.0–6.0) Δ -1.0 (-2.0, 1.0) 0.330
BPI average Continuous — median (IQR) n=14 · 3.0 (1.0–4.5) n=1147 · 4.0 (2.0–6.0) Δ -1.0 (-3.0, 0.0) 0.066
TCSS (Toronto) Continuous — median (IQR) n=14 · 8.5 (7.2–12.0) n=1469 · 10.0 (7.0–13.0) Δ -1.0 (-3.0, 2.0) 0.540
MNSI score Continuous — median (IQR) n=11 · 5.0 (4.0–7.0) n=738 · 5.0 (3.0–7.0) Δ 0.0 (-1.0, 2.0) 0.839
Pain intensity Continuous — median (IQR) n=15 · 2.0 (0.0–4.0) n=2172 · 3.0 (0.0–5.0) Δ -0.0 (-2.0, 1.0) 0.637
Sex Categorical — Fisher n=15 n=2408 OR 0.42 (0.08, 1.57) 0.192
Diabetes type Categorical — Fisher n=14 n=1406 OR 0.00 (0.00, 2.74) 0.385
Pain status Categorical — Fisher n=15 n=2413 OR 1.16 (0.34, 5.03) 1.000
NPalgo grade Categorical — Fisher n=15 n=2408 — 0.181
1 Δ = Hodges–Lehmann median difference (carrier − non-carrier); OR from 2×2 Fisher. '—' where no single effect size is defined (multi-level).

Forest plot with CI also include here as the small sample size we have.

Marginal differences: binned age & sex

First the demographic marginals, whether carrier status itself associates with age band or sex (potential confounders). Then the marginal phenotype differences (carrier vs non-carrier) within each stratum.

Sex-stratified tests

Each phenotype is re-tested within males and within females separately. Note the female carrier stratum has only ~3 individuals, so those p-values are shown for completeness.

Carrier vs non-carrier, stratified by sex
Variable Male n Male p Female n Female p
Age (years) 12 0.643 3 0.487
BMI (kg/m²) 12 0.284 3 0.738
HbA1c (mmol/mol) 8 0.699 3 0.372
DN4 score 11 0.582 3 0.363
BPI average 11 0.503 3 0.023
TCSS (Toronto) 11 0.294 3 0.734
MNSI score 9 0.744 2 0.856
Pain intensity 12 0.825 3 0.222
Diabetes_type 11 0.612 3 1.000
Pain_status 12 0.761 3 1.000
N_palgo 12 0.394 3 0.501

NPalgo extremes: grade 0 vs grade 4

Restricting the neuropathic-pain axis to : grade 0 (no neuropathic pain) vs grade 4 (definite neuropathic pain) .

Nociceptor phenotype (QST)

The QST-based irritable (IN) vs non-irritable (NIN) nociceptor classification 15 of 17 carriers carry a nociceptor phenotype.

Carriers are only marginally more often irritable (≈20% vs 16%), with no significant difference

Pain by nociceptor phenotype, within carriers

Among carriers the nociceptor groups are 3 IN vs 12 NIN (and only 2 IN carriers have a BPI score), so small for test, I only present this as a indicated future direction

Carrier pain by nociceptor phenotype (descriptive)
Nociceptor phenotype Carriers BPI (median) Pain intensity (median) DN4 (median)
IN (irritable) 3 1.5 0.0 1
NIN (non-irritable) 12 3.0 2.5 4

Direction: the 3 irritable-nociceptor carriers report lower pain than the 12 non-irritable ones

Robustness: exact tests & FDR correction

I also quick check with the 20,000 permutation and across the 12 primary tests we control the false discovery rate (Benjamini–Hochberg q-value).

Exact tests and FDR-adjusted significance
Phenotype Method p (primary) p (exact/perm) q (BH-FDR)
BPI average Permutation (Wilcoxon) 0.066 0.065 0.711
NPalgo grade Fisher (exact) 0.181 0.181 0.711
Sex Fisher (exact) 0.192 0.192 0.711
BMI (kg/m²) Permutation (Wilcoxon) 0.237 0.237 0.711
DN4 score Permutation (Wilcoxon) 0.330 0.330 0.769
Diabetes type Fisher (exact) 0.385 0.385 0.769
TCSS (Toronto) Permutation (Wilcoxon) 0.540 0.544 0.933
Pain intensity Permutation (Wilcoxon) 0.637 0.645 0.966
MNSI score Permutation (Wilcoxon) 0.839 0.842 0.966
HbA1c (mmol/mol) Permutation (Wilcoxon) 0.859 0.861 0.966
Age (years) Permutation (Wilcoxon) 0.880 0.885 0.966
Pain status Fisher (exact) 1.000 1.000 1.000