The Impact of Mitochondrial and Nuclear DNA

Journal of Alzheimer’s Disease 27 (2011) 1–12 IOS Press

Supplementary Data

The Impact of Mitochondrial and Nuclear DNA Variants on Late-Onset Alzheimer’s Disease Risk Aleksandra Maruszaka,∗ , Krzysztof Safranowb , Wojciech Branickic , Katarzyna Gawe¸da-Walerycha , Ewelina Po´spiechc , Tomasz Gabryelewicza , Jeffrey A. Canterd , Maria Barcikowskaa a ˙ and Cezary Zekanowski a Department

of Neurodegenerative Disorders, Mossakowski Medical Research Centre, Polish Academy of Sciences, Warszawa, Poland b Department of Biochemistry and Medical Chemistry, Pomeranian Medical University, Szczecin, Poland c Section of Forensic Genetics, Institute of Forensic Research, Krak´ ow, Poland d Center for Human Genetic Research, Vanderbilt University Medical Center, Nashville, TN, US Handling Associate Editor: Russell Swerdlow

Accepted 6 June 2011

∗ Correspondence

to: Aleksandra Maruszak, Department of Neurodegenerative Disorders, Mossakowski Medical Research Centre, Polish Academy of Sciences, Pawinskiego 5, 02-106 Warsaw, Poland. Tel.: +4822 6086485; Fax: +4822 6685532; E-mail: [email protected].

ISSN 1387-2877/11/$27.50 © 2011 – IOS Press and the authors. All rights reserved

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A. Maruszak et al. / Mitochondrial and Nuclear DNA Variants in LOAD

Supplementary Figure 1. Summary of the main effects (A, B) and interaction model of two-factor (APOE4 status, rs1937) combinations (C) associated with high risk (dark box) or low risk (light box) for LOAD from MDR analysis (described in detail in Table 11). For each genotype combination, the number of cases (left bar in boxes) and control individuals (right bar in boxes) is displayed. APOE4+ status is indicated as 1, APOE4− as 0; TFAM rs1937 GG genotype is indicated as 2, GC as 1 and CC as 0. A) Results of MDR analysis for single locus model - APOE4 status. Testing Balanced Accuracy = 0,685, CVC 10/10, p = 0,0014; B) Results of MDR analysis for single locus model – rs1937 (Search type: forced), Testing Balanced Accuracy = 0.513, p = 0.772; D) Results of MDR analysis for two-locus model – APOE4 status × rs1937 (Search type: forced; Testing Balanced Accuracy = 0.689, p = 0.0011).

Supplementary Table 1 MtDNA polymorphisms, haplogroups and haplogroup clusters found associated with AD risk Polymorphism/Haplogroup/ haplogroup cluster m.4336T>C

m.11467A>G m.10398A>G m.12308A>G m.12372G>A, m.9698C>T m.16270C>T HV H

Effect on LOAD risk

Population

LOAD/Control group (N/N)

References

↑ ↑ ↑ ↓ ↑ ↑for males ↓for females ↑ ↑

European Caucasians (USA) German mixed (USA)* mixed (USA)* ADNI** European Caucasians (USA) European Caucasians (USA) ADNI ADNI

62/125 28/100 72/296 155/105 170/188 989/328 989/328 170/188 170/188

[27] [28] [29] [30] [25] [31] [31] [25] [25]

↑ ↑

Polish Iranian

222/252 30/100

[32] [33]

↑symbolizes an increase and↓a decrease in AD risk; * Mixed population means that it comprised Africans, Asians and Europeans; **ADNI Alzheimer’s Disease Neuroimaging Initiative.


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Supplementary Table 1 (Continued) Polymorphism/Haplogroup/ haplogroup cluster H5 J K T U

Effect on LOAD risk

Population

LOAD/Control group (N/N)

References

↑ ↑ neutralizes APOE4 effect ↓ neutralizes APOE4 effect ↑for males, ↓for females ↑ ↑

citizens of Southern and Central Italy French Canadians Italian French Canadians Italian European Caucasians(USA) Iranian ADNI

936/776 69/83 213/179 69/83 213/179 989/328 30/100 170/188

[26] [34] [35] [34] [35] [31] [33] [25]

↑symbolizes an increase and↓a decrease in AD risk; * Mixed population means that it comprised Africans, Asians and Europeans; **ADNI Alzheimer’s Disease Neuroimaging Initiative.

Supplementary Table 2 Haplogroup H subhaplogroups with defining mtDNA coding region polymorphisms. The primers used to amplify the fragment of mtDNA sequence with particular polymorphism are also presented Subhaplogroup of haplogroup H

mtDNA polymorphism

H1

3010G>A

H1-709

709G>A

H2

1438A>G

H3

6776T>C

H4a

4024T>A

H4

5004T>C

H5a

4336T>C

H7

4793A>G

H9

13020T>C

H10

14470T>A

H13

14872C>T

H14

7645T>C

H16

10394C>T

H12 H17 H23

3936C>T 3915G>A 10211C>T

H25

9620C>T

H26

11152>C

H33

11447G>C

H24 H35 H37

3333C>T 3342C>T 3531G>A

Primers (5’→3’) F R F R F R F R F R F R F R F R F R F R F R F R F R F R F R F R F R F R F R F R

F, forward, R, reverse, Tm, melting temperature.

ACTCAATTGATCCAATAACTTGACC GTAGATAGAAACCGACCTGGATTAC GGCTCACATCACCCCATAAA GCTTGATGCTTGTTCCTTTTG TGGCAAGAAATGGGCTACAT GTGTGTACGCGCTTCAGG GTCACCCTGAAGTTTATATTCTTATCCTAC GTGTGTCTACGTCTATTCCTACTGTAAACA CCCTTCGCCCTATTCTTCAT GGGAGGTTAGAAGTAGGGTCTTG CCATCATAGCAGGCAGTTGA AGGAATGCGGTAGTAGTTAGGA AGCATTCCCCCTCAAACCTA ATGGGCCCGATAGCTTATTT CCGGACAATGAACCATAACC TGATTGAGATGGGGGCTAGT CCCACAACAAATAGCCCTTC TGGAGTAGGGCTGAGACTGG CCCCATGCCTCAGGATACTC TGATTGTTAGCGGTGTGGTC CAACATCTCCGCATGATGAA ATTGATGAAAAGGCGGTTGA ACATGCAGCGCAAGTAGGTC GGGCATACAGGACTAGGAAGC CCCTACCATGAGCCCTACAA AATGAGGGGCATTTGGTAAA TCATGACCCTTGGCCATAAT ATTCGGCTATGAAGAATAGGG ACCACAACTCAACGGCTACA TTGTAGGGCTCATGGTAGGG GCCTTTTACCACTCCAGCCTA TGGTGAGCTCAGGTGATTGA CGCCACTTATCCAGTGAACC GGAAGTATGTGCCTGCGTTC TGACTCCCTAAAGCCCATGT TTTTGTCAGGGGGTTGAGAA CACCCAAGAACAGGGTTTGT TCGTTCGGTAAGCATTAGGA TCTTCACCAAAGAGCCCCTA GCCTAGGTTGAGGTTGACCA

Tm 60◦ C 56◦ C 60◦ C 60◦ C 59◦ C 58◦ C 56◦ C 56◦ C 56◦ C 56◦ C 54◦ C 59◦ C 56◦ C 56◦ C 56◦ C 56◦ C 56◦ C 56◦ C 56◦ C 56◦ C

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A. Maruszak et al. / Mitochondrial and Nuclear DNA Variants in LOAD Supplementary Table 3 Distribution of subhaplogroups of mtDNA haplogroups in the LOAD patients and in the control group Subhaplogroup

HV

H

H1

H2

H3 H4

H5’36

H6 H7

H8 H9 H10 H11 H13

Whole group, n (%) H1* H1a H1a1 H1a3 H1b H1c H1c1 H1f H1k H2* H2a1 H2a2b1 H2a3 H2a5 H3 H4a H4a1a1 H4a1b H5* H5a H36 H6 H7* H7a1 H7c1 H9* H10* H10a H11* H11a H13 H13a1 H13a2

H15 H16 H17 H18 H21 H24 H27 H28 H31 H34 H* HV1 HV0

V IWX

I

W

I* I1 I3 I4 W1 W3 W5 W6

HV1a1a1 HV1* HV0* HV0b’c HV6a V* V7a I1 I1a

W1b W1e W3’5 W5a

Females, n (%)

Males, n (%)

LOAD

Control group

LOAD

Control group

LOAD

Control group

29 (6.87) 2 (0.47) 3 (0.71) 0 (0.0) 18 (4.26) 24 (5.69) 2 (0.47) 1 (0.24) 1 (0.24) 4 (0.95) 7 (1.66) 1 (0.24) 2 (0.47) 1 (0.24) 11 (2.61) 0 (0.0) 1 (0.24) 1 (0.24) 3 (0.71) 20 (4.74) 1 (0.24) 9 (2.13) 3 (0.71) 1 (0.24) 1 (0.24) 2 (0.47) 1 (0.24) 3 (0.71) 0 (0.0) 3 (0.71) 7 (1.66) 1 (0.24) 2 (0.47) 1 (0.24) 1 (0.24) 6 (1.42) 1 (0.24) 2 (0.47) 1 (0.24) 2 (0.47) 1 (0.24) 1 (0.24) 1 (0.24) 0 (0.0) 25 (5.92) 0 (0.0) 2 (0.47) 2 (0.47) 3 (0.71) 1 (0.24) 9 (2.13) 4 (0.95) 2 (0.47) 1 (0.24) 3 (0.71) 1 (0.24) 1 (0.24) 2 (0.24) 2 (0.24) 6 (1.42) 0 (0.0) 3 (0.71)

17 (5.35) 2 (0.63) 3 (0.71) 3 (0.71) 7 (2.20) 14 (4.40) 1 (0.31) 0 (0.0) 0 (0.0) 3 (0.71) 5 (1.57) 1 (0.31) 1 (0.31) 1 (0.31) 11 (3.46) 1 (0.31) 1 (0.31) 0 (0.0) 4 (1.26) 8 (2.52) 0 (0.0) 8 (2.52) 3 (0.71) 2 (0.63) 1 (0.31) 0 (0.0) 1 (0.31) 2 (0.63) 2 (0.63) 1 (0.31) 5 (1.57) 0 (0.0) 2 (0.63) 0 (0.0) 0 (0.0) 0 (0.0) 0 (0.0) 3 (0.94) 0 (0.0) 1 (0.31) 0 (0.0) 1 (0.31) 1 (0.31) 1 (0.31) 15 (4.72) 1 (0.31) 1 (0.31) 1 (0.31) 1 (0.31) 0 (0.0) 4 (1.26) 4 (1.26) 2 (0.63) 2 (0.63) 2 (0.63) 0 (0.0) 0 (0.0) 0 (0.0) 0 (0.0) 2 (0.63) 1 (0.31) 1 (0.31)

18 (6.62) 2 (0.73) 2 (0.73) 0 (0.0) 9 (3.31) 14 (5.15) 2 (0.73) 1 (0.37) 1 (0.37) 2 (0.73) 6 (2.21) 1 (0.37) 1 (0.37) 1 (0.37) 8 (2.94) 0 (0.0) 1 (0.37) 1 (0.37) 2 (0.73) 13 (4.78) 0 (0.0) 8 (2.94) 2 (0.73) 0 (0.0) 0 (0.0) 1 (0.37) 1 (0.37) 3 (1.10) 0 (0.0) 2 (0.73) 4 (1.47) 0 (0.0) 1 (0.37) 1 (0.37) 1 (0.37) 3 (1.10) 0 (0.0) 1 (0.37) 1 (0.37) 2 (0.73) 1 (0.37) 1 (0.37) 1 (0.37) 0 (0.0) 17 (6.25) 0 (0.0) 1 (0.37) 2 (0.73) 1 (0.37) 1 (0.37) 5 (1.84) 2 (0.73) 0 (0.0) 1 (0.37) 1 (0.37) 1 (0.37) 1 (0.37) 2 (0.73) 0 (0.0) 5 (1.84) 0 (0.0) 2 (0.73)

14 (6.09) 0 (0.0) 3 (1.30) 2 (0.87) 4 (1.74) 9 (3.91) 0 (0.0) 0 (0.0) 0 (0.0) 1 (0.43) 4 (1.74) 1 (0.43) 1 (0.43) 1 (0.43) 9 (3.91) 1 (0.43) 0 (0.0) 0 (0.0) 1 (0.43) 8 (3.48) 0 (0.0) 5 (2.17) 2 (0.87) 2 (0.87) 1 (0.43) 0 (0.0) 1 (0.43) 2 (0.87) 1 (0.43) 1 (0.43) 5 (2.17) 0 (0.0) 0 (0.0) 0 (0.0) 0 (0.0) 0 (0.0) 0 (0.0) 2 (0.87) 0 (0.0) 1 (0.43) 0 (0.0) 0 (0.0) 1 (0.43) 1 (0.43) 10 (4.35) 1 (0.43) 0 (0.0) 1 (0.43) 1 (0.43) 0 (0.0) 2 (0.87) 4 (1.74) 2 (0.87) 2 (0.87) 2 (0.87) 0 (0.0) 0 (0.0) 0 (0.0) 0 (0.0) 1 (0.43) 1 (0.31) 1 (0.43)

11 (7.33) 0 (0.0) 1 (0.67) 0 (0.0) 9 (6.0) 10 (6.67) 0 (0.0) 0 (0.0) 0 (0.0) 2 (1.33) 1 (0.67) 0 (0.0) 1 (0.67) 0 (0.0) 3 (2.0) 0 (0.0) 0 (0.0) 0 (0.0) 1 (0.67) 7 (4.67) 1 (0.67) 1 (0.67) 1 (0.67) 1 (0.67) 1 (0.67) 1 (0.67) 0 (0.0) 0 (0.0) 0 (0.0) 1 (0.67) 3 (2.0) 0 (0.0) 0 (0.0) 0 (0.0) 0 (0.0) 3 (2.0) 1 (0.67) 1 (0.67) 0 (0.0) 0 (0.0) 0 (0.0) 0 (0.0) 0 (0.0) 0 (0.0) 8 (5.33) 0 (0.0) 1 (0.67) 0 (0.0) 2 (1.33) 0 (0.0) 4 (2.67) 2 (1.33) 2 (1.33) 0 (0.0) 2 (1.33) 0 (0.0) 0 (0.0) 0 (0.0) 2 (1.33) 1 (0.67) 0 (0.0) 1 (0.67)

3 (3.41) 2 (2.27) 0 (0.0) 1 (1.14) 3 (3.41) 5 (5.68) 1 (1.14) 0 (0.0) 0 (0.0) 2 (2.27) 1 (1.14) 0 (0.0) 0 (0.0) 0 (0.0) 2 (2.27) 0 (0.0) 1 (1.14) 0 (0.0) 3 (3.41) 0 (0.0) 0 (0.0) 3 (3.41) 1 (1.14) 0 (0.0) 0 (0.0) 0 (0.0) 0 (0.0) 0 (0.0) 1 (1.14) 0 (0.0) 0 (0.0) 0 (0.0) 2 (2.27) 0 (0.0) 0 (0.0) 0 (0.0) 0 (0.0) 1 (1.14) 0 (0.0) 0 (0.0) 0 (0.0) 1 (1.14) 0 (0.0) 0 (0.0) 5 (5.68) 0 (0.0) 1 (1.14) 0 (0.0) 0 (0.0) 0 (0.0) 2 (2.27) 0 (0.0) 0 (0.0) 0 (0.0) 0 (0.0) 0 (0.0) 0 (0.0) 0 (0.0) 0 (0.0) 1 (1.14) 0 (0.0) 0 (0.0)


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Supplementary Table 3 (Continued) Subhaplogroup

JT

X

X2

J

J1

J2

T

T* T1 T2

KU

K

U

K* K1

K2 U1

U2

U3 U4

U5

Whole group, n (%) X2* X2b X2c J1* J1b1a J1c J1c1 J1c1a J1c2 J1c2c1 J1c6 J1c7 J2a J2a1 J2b J2b1a T1* T1a T2* T2b T2b4 T2c1b T2e T2f1 K1a K1a1 K1a1a K1a9 K1a11 K1b1a1 K1c U1* U1a1 U1c U2* U2e U2e1 U3* U3a U4* U4a1 U4a1c U4a2 U4a2a U4a2b U4a3 U4b1b U4c1 U5a U5a1 U5a1b1 U5a2 U5a2a U5b U5b1a U5b1b U5b1c U5b2* U5b1b1a

Females, n (%)

Males, n (%)

LOAD

Control group

LOAD

Control group

LOAD

Control group

0 (0.0) 3 (0.71) 0 (0.0) 2 (0.47) 3 (0.71) 12 (2.84) 1 (0.24) 2 (0.47) 3 (0.71) 1 (0.24) 1 (0.24) 2 (0.47) 3 (0.71) 0 (0.0) 2 (0.47) 0 (0.0) 7 (1.66) 0 (0.0) 7 (1.66) 2 (0.47) 13 (3.08) 3 (0.71) 2 (0.47) 2 (0.47) 1 (0.24) 1 (0.24) 2 (0.47) 2 (0.47) 0 (0.0) 0 (0.0) 0 (0.0) 0 (0.0) 4 (0.95) 1 (0.24) 1 (0.24) 2 (0.47) 0 (0.0) 2 (0.47) 9 (2.13) 3 (0.71) 5 (1.18) 2 (0.47) 2 (0.47) 4 (0.95) 1 (0.24) 4 (0.95) 3 (0.71) 0 (0.0) 1 (0.24) 0 (0.0) 3 (0.71) 1 (0.24) 12 (2.84) 4 (0.95) 2 (0.47) 6 (1.42) 3 (0.71) 0 (0.0) 5 (1.18) 1 (0.24) 1 (0.24) 0 (0.0)

3 (0.94) 0 (0.0) 1 (0.31) 0 (0.0) 8 (2.52) 10 (3.14) 0 (0.0) 4 (1.26) 5 (1.57) 2 (0.63) 1 (0.31) 1 (0.31) 0 (0.0) 1 (0.31) 1 (0.31) 1 (0.31) 6 (1.89) 2 (0.63) 8 (2.52) 5 (1.57) 15 (4.72) 0 (0.0) 0 (0.0) 0 (0.0) 0 (0.0) 2 (0.63) 6 (1.89) 0 (0.0) 4 (1.26) 2 (0.63) 1 (0.31) 1 (0.31) 0 (0.0) 0 (0.0) 0 (0.0) 0 (0.0) 1 (0.31) 1 (0.31) 1 (0.31) 1 (0.31) 0 (0.0) 0 (0.0) 5 (1.57) 3 (0.94) 0 (0.0) 1 (0.31) 3 (0.94) 2 (0.63) 0 (0.0) 1 (0.31) 1 (0.31) 0 (0.0) 21 (6.60) 0 (0.0) 4 (1.26) 1 (0.31) 0 (0.0) 1 (0.31) 1 (0.31) 0 (0.0) 0 (0.0) 4 (1.26)

0 (0.0) 3 (1.10) 0 (0.0) 0 (0.0) 2 (0.73) 9 (3.31) 1 (0.37) 1 (0.37) 2 (0.73) 1 (0.37) 1 (0.37) 1 (0.37) 2 (0.73) 0 (0.0) 0 (0.0) 0 (0.0) 2 (0.73) 0 (0.0) 2 (0.73) 1 (0.37) 6 (2.21) 2 (0.73) 1 (0.37) 1 (0.37) 0 (0.0) 1 (0.37) 2 (0.73) 1 (0.37) 0 (0.0) 0 (0.0) 0 (0.0) 0 (0.0) 3 (1.10) 0 (0.0) 1 (0.37) 1 (0.37) 0 (0.0) 2 (0.73) 4 (1.47) 3 (1.10) 3 (1.10) 2 (0.73) 2 (0.73) 3 (1.10) 1 (0.37) 2 (0.73) 1 (0.37) 0 (0.0) 1 (0.37) 0 (0.0) 3 (1.10) 1 (0.37) 11 (4.04) 2 (0.73) 1 (0.37) 4 (1.47) 3 (1.10) 0 (0.0) 3 (1.10) 1 (0.37) 1 (0.37) 0 (0.0)

2 (0.87) 0 (0.0) 0 (0.0) 0 (0.0) 4 (1.74) 6 (2.61) 0 (0.0) 2 (0.87) 2 (0.87) 2 (0.87) 1 (0.43) 0 (0.0) 0 (0.0) 1 (0.43) 1 (0.43) 1 (0.43) 5 (2.17) 1 (0.43) 7 (3.04) 4 (1.74) 12 (5.22) 0 (0.0) 0 (0.0) 0 (0.0) 0 (0.0) 2 (0.87) 3 (1.30) 0 (0.0) 2 (0.87) 2 (0.87) 1 (0.43) 1 (0.43) 0 (0.0) 0 (0.0) 0 (0.0) 0 (0.0) 1 (0.43) 0 (0.0) 1 (0.43) 1 (0.43) 0 (0.0) 0 (0.0) 4 (1.74) 1 (0.43) 0 (0.0) 0 (0.0) 3 (1.30) 2 (0.87) 0 (0.0) 0 (0.0) 1 (0.43) 0 (0.0) 16 (6.96) 0 (0.0) 3 (1.30) 0 (0.0) 0 (0.0) 0 (0.0) 1 (0.43) 0 (0.0) 0 (0.0) 4 (1.74)

0 (0.0) 0 (0.0) 0 (0.0) 2 (1.33) 1 (0.67) 3 (2.0) 0 (0.0) 1 (0.67) 1 (0.67) 0 (0.0) 0 (0.0) 1 (0.67) 1 (0.67) 0 (0.0) 2 (1.33) 0 (0.0) 5 (3.33) 0 (0.0) 5 (3.33) 1 (0.67) 7 (4.67) 1 (0.67) 1 (0.67) 1 (0.67) 1 (0.67) 0 (0.0) 0 (0.0) 1 (0.67) 0 (0.0) 0 (0.0) 0 (0.0) 0 (0.0) 1 (0.67) 1 (0.67) 0 (0.0) 1 (0.67) 0 (0.0) 0 (0.0) 5 (3.33) 1 (0.67) 2 (1.33) 0 (0.0) 0 (0.0) 1 (0.67) 0 (0.0) 2 (1.33) 2 (1.33) 0 (0.0) 0 (0.0) 0 (0.0) 0 (0.0) 0 (0.0) 1 (0.67) 2 (1.33) 1 (0.67) 2 (1.33) 0 (0.0) 0 (0.0) 2 (1.33) 0 (0.0) 0 (0.0) 0 (0.0)

1 (1.14) 0 (0.0) 1 (1.14) 0 (0.0) 4 (4.54) 4 (4.54) 0 (0.0) 2 (2.27) 3 (3.41) 0 (0.0) 0 (0.0) 1 (1.14) 0 (0.0) 0 (0.0) 0 (0.0) 0 (0.0) 1 (1.14) 1 (1.14) 1 (1.14) 1 (1.14) 3 (3.41) 0 (0.0) 0 (0.0) 0 (0.0) 0 (0.0) 0 (0.0) 3 (3.41) 0 (0.0) 2 (2.27) 0 (0.0) 0 (0.0) 0 (0.0) 0 (0.0) 0 (0.0) 0 (0.0) 0 (0.0) 0 (0.0) 1 (1.14) 0 (0.0) 0 (0.0) 0 (0.0) 0 (0.0) 1 (1.14) 2 (2.27) 0 (0.0) 1 (1.14) 0 (0.0) 0 (0.0) 0 (0.0) 1 (1.14) 0 (0.0) 0 (0.0) 5 (5.68) 0 (0.0) 1 (1.14) 1 (1.14) 0 (0.0) 1 (1.14) 0 (0.0) 0 (0.0) 0 (0.0) 0 (0.0)

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A. Maruszak et al. / Mitochondrial and Nuclear DNA Variants in LOAD Supplementary Table 3 (Continued) Subhaplogroup

Whole group, n (%)

N

R* M

N1

Y A R2 R0 C D M37

Males, n (%)

Control group

LOAD

Control group

LOAD

Control group

0 (0.0) 0 (0.0) 0 (0.0) 0 (0.0) 2 (0.47) 0 (0.0) 1 (0.24) 1 (0.24) 4 (0.95) 1 (0.24) 1 (0.24) 0 (0.0) 0 (0.0) 1 (0.24) 1 (0.24) 1 (0.24) 1 (0.24) 0 (0.0)

4 (0.94) 1 (0.31) 1 (0.31) 1 (0.31) 2 (0.63) 2 (0.63) 0 (0.0) 0 (0.0) 3 (0.94) 0 (0.0) 0 (0.0) 1 (0.31) 1 (0.31) 0 (0.0) 1 (0.31) 1 (0.31) 1 (0.31) 4 (1.26)

0 (0.0) 0 (0.0) 0 (0.0) 0 (0.0) 1 (0.37) 0 (0.0) 0 (0.0) 1 (0.37) 3 (1.10) 1 (0.37) 1 (0.37) 0 (0.0) 0 (0.0) 1 (0.37) 1 (0.37) 1 (0.37) 0 (0.0) 0 (0.0)

2 (0.87) 1 (0.43) 1 (0.43) 1 (0.43) 1 (0.43) 2 (0.87) 0 (0.0) 0 (0.0) 2 (0.87) 0 (0.0) 0 (0.0) 1 (0.43) 1 (0.43) 0 (0.0) 1 (0.43) 1 (0.43) 0 (0.0) 3 (1.30)

0 (0.0) 0 (0.0) 0 (0.0) 0 (0.0) 1 (0.67) 0 (0.0) 1 (0.67) 0 (0.0) 1 (0.67) 0 (0.0) 0 (0.0) 0 (0.0) 0 (0.0) 0 (0.0) 0 (0.0) 0 (0.0) 1 (0.67) 0 (0.0)

2 (2.27) 0 (0.0) 0 (0.0) 0 (0.0) 1 (1.14) 0 (0.0) 0 (0.0) 0 (0.0) 1 (1.14) 0 (0.0) 0 (0.0) 0 (0.0) 0 (0.0) 0 (0.0) 0 (0.0) 0 (0.0) 0 (0.0) 0 (0.0)

U5b2a1 U5b2a2 U5b2c U7 U8

Females, n (%)

LOAD

U8a1 U8b N1a N1a1 N1b Y1b A8 R2* R0a

C* D4/G M37a

L2 Unclassified

Supplementary Table 4 Odds ratios of LOAD, when the individuals that do not carry H5 subhaplogroup or APOE4 are the reference group (OR = 1) H5 subhaplogroup

APOE4 status

Control group, n

LOAD patients, n

OR

+ +

243 11 63 1

179 2 220 21

1 0.25 4.74 28.51

+ +

Supplementary Table 5 Odds ratios for LOAD with aggregated mitochondrial haplogroups and subhaplogroups harboring variants in CYTB and/or ATP6. Statistical analysis was performed using χ2 test or Fisher’s exact test Aggregated mtDNA haplogroups

Whole group

Females

Males

and subhaplogroups

OR

95% CI

p

OR

95% CI

p

OR

95% CI

p

U4 + U5a1 + K U4 + U5a1 + K + J U4 + U5a1 + K + J1c U4 + U5a1 + K + J1c + J2 U4 + U5a1 + K+J1c+J2 + T U4 + U5a1 + K + J + T UKJT

0.58 0.58 0.59 0.61 0.62 0.58 0.69

0.38–0.89 0.41–0.83 0.41–0.85 0.43–0.88 0.45–0.84 0.42–0.79 0.51–0.92

0.013 0.002 0.005 0.008 0.003 0.0006 0.012

0.70 0.72 0.77 0.75 0.58 0.56 0.68

0.42–1.15 0.47–1.09 0.50–1.20 0.49–1.16 0.39–0.85 0.38–0.82 0.48–0.97

0.161 0.124 0.246 0.195 0.005 0.003 0.035

0.38 0.34 0.32 0.39 0.68 0.62 0.68

0.17–0.88 0.20–0.69 0.16–0.64 0.20–0.75 0.39–1.19 0.36–1.07 0.40–1.15

0.024 0.002 0.001 0.005 0.179 0.087 0.152

Supplementary Table 6 Nucleotide substitutions in the mtDNA control region of LOAD patients and the control group as compared with revised Cambridge Reference Sequence Nucleotide position in mtDNA 3 55 57 60 64 72 73 89 93 95

Nucleotide change T>C T>C T>C T>C C>T T>C A>G T>C A>G A>C

Locus

LOAD patients, n

Control individuals, n

7S DNA 7S DNA 7S DNA, HVSII 7S DNA, HVSII 7S DNA, HVSII 7S DNA, HVSII 7S DNA, HVSII 7S DNA, HVSII 7S DNA, HVSII 7S DNA, HVSII

0 1 1 0 3 16 199 0 14 1

1 0 0 1 2 9 119 3 7 0


7

Supplementary Table 6 (Continued) Nucleotide position in mtDNA 114 119 143 146 150 151 152 153 185 186 188 189 193 194 195 196 198 199 200 203 204 207 210 211 214 215 217 222 225 226 227 228 235 236 239 240 242 247 248 249 250 252 257 259 262 263 279 282 285 288 292 293 295 296 297 310 316 319 326

Nucleotide change C>T T>C G>A T>C C>T C>T T>C A>G G>A C>A A>G A>G A>G C>T T>C T>C C>T T>C A>G G>A T>C G>A A>G A>G A>G A>G T>C C>T G>A T>C A>G G>A A>G T>C T>C A>G C>T G>A A>G A>G T>C T>C A>G A>G C>T A>G T>C T>C C>T A>G T>C T>C C>T C>A A>G T>C G>A T>C A>G

Locus

LOAD patients, n


7S DNA, OH, HVSII 7S DNA, OH, HVSII 7S DNA, OH, HVSII 7S DNA, OH, HVSII 7S DNA, OH, HVSII 7S DNA, OH, HVSII 7S DNA, OH, HVSII 7S DNA, OH, HVSII 7S DNA, OH, HVSII 7S DNA, OH, HVSII 7S DNA, OH, HVSII 7S DNA, OH, HVSII 7S DNA, OH, HVSII 7S DNA, OH, HVSII 7S DNA, OH, HVSII 7S DNA, OH, HVSII 7S DNA, OH, HVSII 7S DNA, OH, HVSII 7S DNA, OH, HVSII 7S DNA, OH, HVSII 7S DNA, OH, HVSII OH, HVSII OH, HVSII OH, HVSII OH, CSB1, HVSII OH, CSB1, HVSII OH, CSB1, HVSII OH, CSB1, HVSII OH, CSB1, HVSII OH, CSB1, HVSII OH, CSB1, HVSII OH, CSB1, HVSII OH, CSB1, HVSII OH, HVSII OH, TFX, HVSII OH, TFX, HVSII OH, TFX, HVSII OH, TFX, HVSII OH, TFX, HVSII OH, TFX, HVSII OH, TFX, HVSII OH, TFX, HVSII OH, TFX, HVSII OH, TFX, HVSII OH, TFX, HVSII OH, TFX, HVSII OH, TFY, HVSII OH, TFY, HVSII OH, TFY, HVSII OH, TFY, HVSII OH, TFY, HVSII OH, TFY, HVSII OH, TFY, HVSII OH, TFY, HVSII OH, TFY, HVSII OH, TFY, HVSII OH, TFY, HVSII OH, TFY, HVSII OH, TFY, HVSII

5 1 2 29 33 6 96 3 22 1 7 13 1 10 74 1 1 14 2 1 25 17 1 1 2 3 13 1 3 3 1 18 1 0 13 1 6 1 0 1 8 1 6 1 1 421 2 2 3 1 1 1 33 0 1 10 0 3 0

1 0 1 17 29 4 56 3 23 2 7 6 0 5 66 0 2 8 4 1 12 8 0 1 0 3 2 2 2 1 1 21 0 1 8 0 9 1 1 0 6 0 1 0 1 315 0 2 1 1 0 0 34 1 0 7 0 1 1

8

A. Maruszak et al. / Mitochondrial and Nuclear DNA Variants in LOAD Supplementary Table 6 (Continued) Nucleotide position in mtDNA 338 340 373 385 430 456 461 462 477 482 489 497 499 507 508 513 515 516 533 538 560 16051 16066 16067 16069 16070 16071 16075 16080 16086 16092 16093 16104 16108 16111 16111 16113 16114 16114 16124 16126 16129 16129 16134 16136 16140 16144 16145 16146 16147 16147 16148 16153 16157 16160 16162 16163 16167 16168 16169

Nucleotide change C>T C>T A>G A>G T>C C>T C>T C>T T>C T>C T>C C>T G>A T>C A>G G>A A>G C>T A>G A>G C>T A>G A>G C>T C>T A>G C>T T>C A>G T>C T>A T>C C>T C>T C>G C>T A>C C>A C>G T>C T>C G>A G>C C>T T>C T>C T>C G>A A>G C>A C>T C>T G>A T>C A>G A>G A>G C>T C>T C>T

Locus

LOAD patients, n


OH, TFY, HVSII OH, TFY, HVSII OH, mt4H, HVSII OH, mt3H, HVSII OH, PL, HVSII, mtTF1 binding site HVSIII HVSIII HVSIII HVSIII HVSIII HVSIII HVSIII HVSIII HVSIII HVSIII HVSIII HVSIII HVSIII HVSIII, mtTF1 binding site HVSIII, mtTF1 binding site HVSIII, PH1 HVSI HVSI HVSI HVSI HVSI HVSI HVSI HVSI HVSI HVSI HVSI HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, TAS, HVSI 7S DNA, TAS, HVSI 7S DNA, TAS, HVSI 7S DNA, TAS, HVSI 7S DNA, TAS, HVSI 7S DNA, TAS, HVSI 7S DNA, TAS, HVSI

1 8 1 2 2 24 1 26 27 3 35 4 18 1 13 6 0 1 1 1 2 17 0 1 33 1 0 3 5 2 10 22 1 1 1 3 1 1 4 0 71 16 14 4 0 2 0 13 3 2 1 2 10 2 1 2 7 1 0 0

0 3 0 0 0 13 0 31 15 4 35 14 15 0 3 2 1 1 0 1 0 7 2 2 34 0 1 1 0 1 4 17 0 1 0 1 0 0 3 1 72 13 3 3 1 2 4 14 2 0 1 2 7 0 0 6 10 1 1 1


9

Supplementary Table 6 (Continued) Nucleotide position in mtDNA 16172 16174 16176 16179 16181 16182 16183 16184 16185 16186 16188 16188 16189 16189 16192 16193 16195 16209 16212 16214 16216 16218 16221 16222 16223 16224 16227 16230 16231 16234 16235 16239 16240 16241 16245 16247 16248 16249 16255 16256 16257 16258 16260 16261 16263 16264 16265 16266 16266 16270 16271 16272 16274 16278 16284 16286 16287 16288 16289 16290

Nucleotide change T>C C>T C>A C>T A>G A>C A>C C>T C>T C>T C>G C>T T>A T>C C>T C>T T>C T>C A>G C>T A>G C>T C>T C>T C>T T>C A>G A>G T>C C>T A>G C>T A>G A>T C>T A>G C>T T>C G>A C>T C>T A>G C>T C>T T>C C>T A>G C>A C>T C>T T>C A>G G>A C>T A>G C>T C>A T>C A>G C>T

Locus

LOAD patients, n


7S DNA, TAS, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, mt5, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI

13 2 4 4 1 3 24 1 0 7 1 2 0 67 31 4 1 8 1 1 2 0 2 5 35 11 1 1 4 5 1 2 0 0 0 1 3 3 0 31 1 1 0 12 2 1 4 1 5 34 0 2 3 14 0 1 1 2 0 1

14 0 3 2 0 2 14 0 2 10 1 0 1 55 29 3 0 5 0 1 2 2 0 5 22 19 0 0 1 5 1 1 1 1 1 0 1 4 2 28 1 0 3 14 1 1 3 0 1 35 1 2 4 11 1 0 0 0 1 1

10

A. Maruszak et al. / Mitochondrial and Nuclear DNA Variants in LOAD Supplementary Table 6 (Continued) Nucleotide position in mtDNA 16291 16292 16293 16294 16295 16296 16297 16298 16299 16300 16302 16304 16309 16310 16311 16316 16318 16319 16320 16324 16325 16327 16335 16342 16343 16344 16354 16355 16356 16357 16360 16362 16366 16368 16380 16390 16391 16398 16399 16400 16456 16465 16482 16483 16497 16519 16526 16527

Nucleotide change C>T C>T A>G C>T C>A C>T T>C T>C A>G A>G A>G T>C A>G G>A T>C A>G A>T G>A C>T T>C T>C C>T A>G T>C A>G C>T C>T C>T T>C T>C C>T T>C C>T T>C C>T G>A G>A G>A A>G C>T G>A C>T A>G G>A A>G T>C G>A C>T

Locus

LOAD patients, n


7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA, HVSI 7S DNA 7S DNA 7S DNA 7S DNA 7S DNA 7S DNA 7S DNA 7S DNA 7S DNA 7S DNA 7S DNA 7S DNA 7S DNA

9 20 9 48 3 21 0 21 2 0 0 42 1 0 52 1 0 4 5 3 3 2 2 2 9 1 7 4 32 2 3 36 1 2 0 10 8 1 17 1 1 1 8 1 1 263 11 1

10 8 9 40 0 21 1 11 0 2 1 30 2 2 47 0 1 1 3 2 3 1 0 2 0 0 5 1 23 0 0 24 0 1 1 5 6 1 21 1 2 2 8 0 0 206 9 2

HVSI-III- hypervariable segment I-III; TFX, TFY - mtTF1 binding sites; mtTF1 - mitochondrial transcription factor; OH - H-strand origin; CSB1–3 - Conserved sequence block 1–3; mt3H, mt4H, mt5H – regulatory elements on H-strand; PL – L-strand promoter; TAS – termination associated sequence; PH1 – Major H-strand promoter.


11

Supplementary Table 7 Distribution of deletions and insertions detected in mtDNA control region of LOAD patients and the control group LOAD patients, n

Control group, n

2 0 5 43 1

1 1 0 28 0

0 231 58 0 2 413 3 37 18

1 173 35 1 1 308 3 33 9

Deletions 249D 307–309D 498D 523–524D 16257D Insertions 42.1G 309.1C 309.2C 309.3C 310.1T 315.1C 455.1T 523.1C 523.2A 573nC

Supplementary Table 8 Single nucleotide heteroplasmic substitutions detected in the mitochondrial control region of LOAD patients and in the control group Heteroplasmic substitution

LOAD patients, n

Control group, n

m.152T/C m.195T/C m.204T/C m.310C/T m.497C/T m.499G/A m.16093C/T m.16129G/A m.16183C/A m.16189C/T m.16192C/T m.16193C/T m.16291C/T m.16294C/T m.16301C/T m.16519T/C

3 0 2 1 0 0 1 0 1 2 1 0 1 0 0 0

0 0 1 1 0 1 0 0 0 0 1 1 0 1 1 0

Supplementary Table 9 Variants in the mitochondrial control region not described in MITOMAP and Human Mitochondrial Genome database Variant Variant m.203G>C m.273C>T m.299D m.16474G>T m.16290C>G m.16213G>C m.16078A>C m.490.1C m.42.1G m.16179C>G

LOAD patients, n

Control group, n

Haplogroup, subhaplogroup

Locus

APOE

1 1 1 1 1 1 1 0 0 0

0 0 0 0 0 0 0 1 1 1

H2 H6 H6 K1c A8 H1c U3 J1c H11 J1c

HVSII, OH OH, TFY, HVSII CSB2, TFY, HVSII – HVSI, 7S DNA HVSI, 7S DNA HVSI HVSIII 7S DNA 7S DNA, HVSI

33 34 34 33 33 44 44 33 33 24

D- deletion; F- female, M- male; HVSI-III- hypervariable segment I-III; TFY - mtTF1 binding site, OH - H-strand origin; CSB2 - Conserved sequence block 2.

12

A. Maruszak et al. / Mitochondrial and Nuclear DNA Variants in LOAD Supplementary Table 10 Odds ratios for LOAD risk associated with the variants m.217T>C, m.242C>T, m.497C>T, m.16126T>C, m.16343A>G, m.16129G>C and m.16224T>C. Statistical analysis was performed using Fisher’s exact test and multivariate logistic regression controlling for APOE4 status, AAO/age and gender Control region polymorphism m.217T>C m.242C>T m.497C>T m.16126T>C m.16343A>G m.16129G>C m.16224T>C

Univariate analysis

Multivariate logistic regression

p

OR

95% CI

p

OR

95% CI

0.019 0.036 0.003 0.049 0.012 0.012 0.024

5.02 0.25 0.21 0.69 ∞ 4.77 0.42

1.26– 20.03 0.07–0.92 0.07–0.61 0.48–0.996 1.80–∞ 1.45–15.64 0.20–0.88

0.079 0.039 0.002 0.052 n.a. 0.129 0.028

4.42 0.20 0.15 0.66 n.a. 2.94 0.38

0.84–23.19 0.04–0.92 0.05–0.50 0.43–1.00 n.a. 0.73–11.82 0.16–0.90

Supplementary Table 11 Testing balanced accuracy and cross validation consistency for the best MDR models for the prediction of LOAD risk with one to four loci # of loci

Model

1 2 3 4

APOE4 status APOE4 status × rs1937 APOE4 status × rs1937 × rs8192678 APOE4 status × rs1937 × rs8192678 × U5b

Testing Balanced Accuracy

Cross Validation Consistency (CVC)

p

0.6849 0.6857 0.6692 0.6771

10/10 10/10 7/10 10/10

0.0014 0.0013 0.0036 0.0025

Supplementary Table 12 Multivariate logistic regression for LOAD including APOE4 status, rs1937, subhaplogroup H5, gender, AAO/age and interactions H5 × APOE4 status, rs1937 × APOE4 status and rs1937 × haplogroup H5 Covariates APOE4 status H5 subhaplogroup rs1937 genotype APOE4 status × H5 rs1937 × APOE4 status rs1937 × H5 AAO/age gender

p

OR

95% CI

0.020 0.027 0.133 0.021 0.017 0.152