Type 1 diabetes loci display a variety of native American and African ancestries in diseased individuals from Northwest Colombia

Table 1 Genetic ancestry of type 1 diabetes patients compared to Colombians living in Medellin control population

Chromosomal region	Ancestry	T1D, median (IQR)	CLM, median (IQR)	P value1
Overall AIMs	EUR	61.58 (52.84-69.85)	62.06 (49.67-73.74)	0.675
	NAT	27.34 (21.36-34.05)	25.46 (16.12- 32.90)	0.106
	AFR	10.28 (4.0-16.83)	10.65 (6.05-16.75)	0.575
Chr2_EFR3B	EUR	60.27 (34.05-80.79)	47.88 (34.04-76.43)	0.189
	NAT	24.30 (0.01-51.24)	37.10 (1.61-62.49)	0.02
	AFR	7.17 (0.01-25.05)	0.01 (0.01-15.67)	0.06
Chr2_CTLA4	EUR	46.24 (16.82-69.52)	58.26 (30.82-82.79)	0.167
	NAT	27.96 (0.04-41.31)	25.01 (0.01-45.16)	0.829
	AFR	20.54 (0.01-41.72)	11.78 (0.01-36.59)	0.183
Chr2_RNASEH1	EUR	56.91 (31.33-73.91)	58.80 (32.75-78.43)	0.482
	NAT	27.41 (11.69-46.36)	24.81 (0.01-48.84)	0.241
	AFR	8.37 (0.01-28.24)	13.04 (0.01-23.87)	0.430
Chr2_IFIH1	EUR	42.42 (0.01-77.63)	52.01 (16.33-82.16)	0.05
	NAT	32.07 (0.01-56.74)	14.99 (0.01-41.35)	0.246
	AFR	14.99 (0.01-32.31)	17.83 (0.01-42.31)	0.181
Chr5_IL7R	EUR	11.56 (1.04-41.14)	24.75 (7.20-46.98)	7.0 × 10-3
	NAT	52.18 (3.74-98.06)	39.18 (0.04-52.80)	1.0 × 10-4
	AFR	15.21 (3.0-35.75)	33.89 (11.23-59.94)	1.56 × 10-5
Chr6_MHC	EUR	51.35 (32.92-70.32)	55.86 (32.61-71.21)	0.76
	NAT	23.28 (8.92-40.0)	21.61 (5.83-43.13)	0.835
	AFR	18.87 (1.63-36.08)	19.53 (0.3-34.11)	0.660
Chr10_NRP1	EUR	63.32 (23.70-63.32)	0.03 (0.001-20.34)	2.2 × 10-16
	NAT	36.67 (7.93-36.67)	0.003 (0.001-7.93)	2.2 × 10-16
	AFR	0.03 (0.001-30.91)	94.23 (53.94-99.99)	2.2 × 10-16

¹Data from Mann-Whitney U test. AIMs: Ancestry informative markers; IQR: Interquartile range; CLM: Colombians living in Medellin from 1,000 genomes database; Chr: Chromosome; EUR: European; NAT: Native American; AFR: African; T1D: Type 1 diabetes.

Table 2 Significant findings in an exploratory association analysis

CHR	SNP	A1	MAF		ORa	95%CI	P value1	EMP1
			T1D	CLM
2	rs798364	A	0.18	0.27	0.62	0.40-0.96	0.034	0.035
2	rs1606237	T	0.33	0.26	1.55	1.04-2.30	0.031	0.031
5	rs700164	T	0.56	0.35	2.38	1.62-3.48	5.56 × 10-6	3.0 × 10-6
6	rs9378428	C	0.38	0.48	0.61	0.42-0.89	0.010	0.018
6	rs2523747	G	0.42	0.30	1.68	1.13-2.51	0.010	0.012
6	rs2395656	G	0.23	0.28	0.63	0.41-0.98	0.040	0.041
10	rs3123687	G	0.15	0.86	0.04	0.02-0.08	8.70 × 10-19	1.0 × 10-6

¹Odds ratio and P value adjusted for genetic admixture. This table extracts the significant findings shown in Supplementary Table S2. CHR: Chromosome; A1: Minor allele; MAF: Minor allele frequency; CI: Confidence interval; EMP1: Empirical P value obtained by permutation tests; OR: Odds ratio; SNP: Single nucleotide polymorphism; T1D: Type 1 diabetes; CLM: Colombians living in Medellin.

Table 3 Genetic ancestry for type 1 diabetes patients stratified according to autoimmunity

Chromosomal region	Ancestry	T1AD, median (IQR)	T1BD, median (IQR)	P value1
Overall AIMs	EUR	61.92 (53.57-70.89)	59.79 (49.70-68.03)	0.333
	NAT	27.07 (20.82-33.48)	29.16 (21.57-37.06)	0.312
	AFR	10.19 (2.88-16.01)	11.54 (5.55-17.80)	0.344
Chr2_EFR3B	EUR	60.28 (36.24-83.66)	59.79 (32.34-80.01)	0.551
	NAT	25.16 (0.01-51.24)	21.92 (0.01-45.95)	0.979
	AFR	4.53 (0.01-23.32	14.41 (0.01-27.36)	0.119
Chr2_CTLA4	EUR	53.34 (16.82-70.53)	41.16 (16.62-60.86)	0.231
	NAT	26.28 (4.55-41.31)	32.69 (9.35-50.25)	0.343
	AFR	20.54 (0.01-41.73)	19.47 (0.01-42.52)	0.764
Chr2_RNASEH1	EUR	58.96 (37.72-73.87)	47.50 (26.38-78.10)	0.506
	NAT	26.92 (14.19-45.66)	31.59 (0.01-51.98)	0.885
	AFR	6.85 (0.01-28.24)	11.71 (0.01-27.86)	0.657
Chr2_IFIH1	EUR	41.90 (0.01-76.72)	42.42 (0.01-67.93)	0.708
	NAT	32.56 (0.01-55.56)	27.39 (2.01-56.89)	0.985
	AFR	14.99 (0.01-42.31)	0.01 (0.01-36.48)	0.654
Chr5_IL7R	EUR	13.27 (1.02-43.73)	9.19 (1.77-33.67)	0.555
	NAT	50.94 (38.08-98.60)	53.12 (31.82-95.13)	0.984
	AFR	14.68 (3.17-33.94)	17.98 (2.75-41.01)	0.634
Chr6_MHC	EUR	52.31 (37.26-72.43)	45.73 (19.25-67.03)	0.087
	NAT	20.32 (7.12-37.06)	31.88 (17.65-44.62)	0.019
	AFR	18.50 (3.21-36.04)	21.13 (0.53-36.56)	0.905
Chr10_NRP1	EUR	63.32 (28.61-69.09)	63.31 (6.89-63.32)	0.092
	NAT	36.67 (7.93-36.67)	36.67 (7.93-59.79)	0.282
	AFR	0.25 (1e-05-26.0)	0.52 (1e-05-37.80)	0.848

¹Mann-Whitney U test. AIMs: Ancestry informative markers; IQR: Interquartile range; Chr: Chromosome; EUR: European; NAT: Native American; AFR: African; T1AD: Autoimmune type 1 diabetes; T1BD: Idiopathic type 1 diabetes.

Table 4 Genetic ancestry for type 1 diabetes patients stratified according to age at onset

Chromosomal region	Ancestry	Early age at onset, ≤ 5 yr	Late age at onset, > 5 yr	P value1
Overall AIMs	EUR	62.06 (54.50-71.38)	61.12 (51.66-68.68)	0.420
	NAT	25.40 (18.14-33.55)	27.75 (21.86-34.35)	0.345
	AFR	11.09 (3.90-17.25)	10.19 (3.88-16.91)	0.927
Chr2_EFR3B	EUR	57.65 (34.05-82.17)	62.45 (42.04-80.67)	0.419
	NAT	25.16 (1.27-52.11)	24.30 (0.01-51.73)	0.607
	AFR	5.02 (0.01-27.29)	7.37 (0.01 23.32)	0.941
Chr2_CTLA4	EUR	58.49 (24.63-78.80)	46.09 (12.90-66.30)	0.180
	NAT	26.28 (3.98-39.82)	30.19 (4.55-42.10)	0.362
	AFR	18.05 (0.01-37.80)	20.68 (0.01-41.72)	0.701
Chr2_RNASEH1	EUR	56.84 (44.50-72.18)	56.91 (28.02-74.15)	0.672
	NAT	27.22 (0.01-31.22)	28.03 (8.15-48.58)	0.472
	AFR	3.38 (0.01-31.22)	8.62 (0.01-27.20)	0.917
Chr2_IFIH1	EUR	41.35 (0.01-66.94)	42.42 (4.44-76.73)	0.126
	NAT	33.05 (0.67-57.49)	29.05 (0.01-53.09)	0.339
	AFR	14.57 (0.01-42.31)	1.01 (0.01-42.31)	0.796
Chr5_IL7R	EUR	9.38 (0.33-41.70)	12.86 (1.73-43.11)	0.338
	NAT	53.83 (39.76-99.60)	50.94 (30.21-88.75)	0.197
	AFR	6.17 (1.01-29.03)	19.96 (9.6-37.36)	0.023
Chr6_MHC	EUR	51.67 (32.23-63.29)	52.07 (34.26-71.84)	0.596
	NAT	30.57 (13.47-43.21)	26.71 (7.69-37.39)	0.480
	AFR	15.03 (4.46-36.05)	20.52 (1.08-36.73)	0.118
Chr10_NRP1	EUR	63.32 (23.70-63)	63.32(43.07-69.08)	0.357
	NAT	36.68 (7.93-36.67)	36.67 (7.93-36.68)	0.797
	AFR	0.16 (0.001-39-1)	0.38 (0.001-63.3)	0.498

¹Mann-Whitney U test. AIMs: Ancestry informative markers; IQR: Interquartile Range; Chr2: Chromosome 2; Chr6: Chromosome 6; EUR: European; NAT: Native American; AFR: African.