Table S1: Classification error rates of NAT2PRED in the 54 worldwide samples collected from the literature.
Population
(No. of individuals)
Sampling
location
No. of
screened
Reference
a
variants
Haplotyping
Classification error rate
Classification error rate
methodb
for two phenotypesc
for three phenotypesd
Sub-Saharan Africa (617)
Tswana (101)
South Africa
7
Loktionov et al. 20021
M
9,8%
16,1%
Akele Bantus (50)
Gabon
7
Patin et al. 20062
CB
14,0%
14,0%
Bakola Pygmies (40)
Cameroon
7
Patin et al. 20062
CB
2,5%
30,0%
Baka Pygmies (30)
Cameroon
7
2
CB
0%
13,3%
Patin et al. 2006
3
Yoruba (60)
Nigeria
7
HapMap data
Dendi (11)
Nigeria
7
Luca et al. 20084
Dogons (50)
Mali
7
5
Deloménie et al. 1996
6
CB
0%
11,7%
M+CB
0%
18,2%
M+CB
12,0%
22,0%
18,6%
Mandenka (97)
Senegal
7
Sabbagh et al. 2008
CB
9,3%
Somali (24)
Somalia
7
Patin et al. 20062
CB
4,2%
4,2%
Sudanese (127)
Sudan
7
Al-Yahyaee et al. 20077
CB
5,5%
6,3%
Amhara (15)
Ethiopia
7
Luca et al. 20084
M+CB
0%
0%
Oromo (12)
Ethiopia
7
Luca et al. 20084
M+CB
0%
0%
Moroccans (44)
Morocco
7
Patin et al. 20062
CB
0%
0%
Egyptians (37)
Egypt
6
Luca et al. 20084
M+CB
0%
5,4%
Spanish (1,312)
Spain
7
Agundez et al. 20088
M
0,8%
1,9%
Sardinians (49)
Sardinia
7
Patin et al. 20062
CB
0%
0%
Italians (37)
Italy
6
Luca et al. 20084
M+CB
0%
2,7%
Greeks (40)
Greece
6
Luca et al. 20084
2,5%
Europe and North Africa (4,391)
M+CB
0%
9
Turks (303)
Turkey
7
Aynacioglu et al. 1997
M+CB
0%
0%
French (60)
France
7
Deloménie et al. 19965
M+CB
0%
3,3%
UK Caucasians (112)
United Kingdom
7
Loktionov et al. 20021
M
0%
0%
10
US Caucasians (387)
United States
7
Deitz et al. 2000
CB
0,3%
0,5%
US Caucasians (60)
United States
7
HapMap data3
CB
0%
0%
Swedes (50)
Sweden
7
Patin et al. 20062
CB
0%
0%
Saami (48)
Finland
7
2
CB
0%
0%
M+CB
0,1%
0,5%
CB
0,9%
1,8%
M+CB
0%
0%
M+CB
0%
0%
Patin et al. 2006
11
Germans (844)
Germany
7
Cascorbi et al. 1995
Germans (223)
Germany
6
Schnakenberg et al. 200012
Czechs (27)
Czech Republic
6
Polish (248)
Poland
7
Luca et al. 2008
4
13
Mrozikiewicz et al. 1996
Table S1 (Continued)
Population
(No. of individuals)
Ashkenazi Jews (40)
Sampling
location
-
No. of
screened
Reference
a
variants
7
Patin et al. 20062
14
Haplotyping
Classification error rate
Classification error rate
methodb
for two phenotypesc
for three phenotypesd
CB
0%
0%
CB
0%
0%
0%
7,1%
Romanians (140)
Romania
6
Rabstein et al. 2006
Mordvins (14)
Mordovia
6
Luca et al. 20084
M+CB
Russians (290)
Russia
7
Gaikovitch et al. 2003
M+CB
0%
0%
Perm Russians (12)
Russia
6
Luca et al. 20084
M+CB
0%
8,3%
Khanty&Mansi (14)
Russia
6
Luca et al. 20084
M+CB
0%
0%
Turkmen (50)
Uzbekistan
7
Patin et al. 20062
CB
0%
0%
Kyrgyz (290)
Kyrgyzstan
6
Rabstein et al. 200614
CB
0%
0%
Central/South Asia (556)
2
Gujarati (50)
India
7
Patin et al. 2006
CB
Dravidians (166)
India
7
Anitha and Banerjee 200315
M
Han Chinese (112)
China
7
Guo et al. 200416
CB
0%
Han Chinese (45)
China
7
HapMap data3
CB
0%
0%
Chinese (44)
China
7
Patin et al. 20062
CB
0%
2,3%
Japanese (144)
Japan
7
Tanaka et al. 200217
CB
0%
0,7%
0%
0%
1,2%
10,2%
1,8%
East Asia (2,134)
18
Japanese (172)
Japan
6
Deguchi et al. 2005
CB
0%
0%
Japanese (44)
Japan
7
HapMap data3
CB
0%
0%
Koreans (288)
Korea
7
Lee et al. 200319
CB
0%
2,1%
Koreans (1,000)
Korea
6
Lee et al. 200220
0,2%
2,6%
Thai (44)
Thailand
7
M
CB
0%
0%
0%
2
Patin et al. 2006
21
Indonesians (212)
Indonesia
7
Yuliwulandari et al. 2007
CE
0%
Yakuts (16)
Siberia
6
Luca et al. 20084
M+CB
0%
0%
Chukchee (13)
Siberia
6
Luca et al. 20084
M+CB
0%
7,7%
Embera (136)
Panama
6
Jorge-Nebert et al. 200222
CC
0%
2,2%
Ngawbe (105)
Panama
6
Jorge-Nebert et al. 200222
CC
0%
2,9%
Nicaraguans (137)
Nicaragua
7
M
0%
1,5%
America (378)
23
Martinez et al. 1998
a
All population samples were genotyped for the seven common SNPs of the NAT2 gene (191G>A, 282C>T, 341T>C, 481C>T, 590G>A,
803A>G, and 857G>A), except some non-African samples where the SNP 191G>A was omitted since this is monomorphic in non-African
populations.
b
In each sample, NAT2 haplotypes were reconstructed using either molecular techniques (M), computational algorithms (C), or a combination of
both approaches (M+C; some studies indeed limited the application of molecular haplotyping to particular cases as those where an alternative
linkage pattern of mutations would have led to a change in phenotype). CB, CE and CC refer to the computational method used (when
applicable): the Bayesian algorithm implemented in PHASE24, the EM algorithm25 implemented in Haploview26, and the Clark’s method27
based on maximum parsimony, respectively.
c
Classification error rate of NAT2PRED when two phenotypic classes were considered: slow and other acetylators (intermediate and rapid
acetylators pooled together).
d
Classification error rate of NAT2PRED when three phenotypic classes were considered: slow, intermediate and rapid acetylators.
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