Eur J Clin Pharmacol (2008) 64:257266

DOI 10.1007/s00228-007-0409-y

PHARMACOGENETICS

Comparison of SLCO1B1 sequence variability

among German, Turkish, and African populations
Jessica Mwinyi & Karla Kpke & Melanie Schaefer &
Ivar Roots & Thomas Gerloff

Received: 5 March 2007 / Accepted: 1 November 2007 / Published online: 6 January 2008
# Springer-Verlag 2007

Abstract
Background OATP1B1 is one of the key hepatocellular
uptake transporters providing extraction of diverse compounds, including bile acids, xenobiotics, and a variety of
drugs, from portal venous blood into the liver. Polymorphisms of the SLCO1B1 gene have been demonstrated
to influence in vitro transport function and the pharmacokinetic profile of compounds.
Objective The goal of our study was the comparison of
SLCO1B1 gene sequence variability in three ethnic groups
as a basis for future genetic association studies.
Methods Eighteen exonic SLCO1B1 single nucleotide
polymorphisms (SNPs) were genotyped by PCR and RFLP
analysis in 300 German, 94 Turkish, and 115 African
subjects. Calculation of pairwise linkage disequilibrium and
estimation of population haplotype frequencies were carried
out, and haplotype block structure was determined.
Results Only eight genotyped SNPs (c.388A>G, c.411G>A,
c.463C>A, c.521T>C, c.571C>T, c.597C>T, c.1463G>>C,
c.1929A>C) were found in at least one of our German,
Turkish, or African samples. A total of 12 haplotypes with a
frequency 1% in at least one of the three populations could
be inferred. Between the Caucasian and African samples,
significant differences in sequence variability were observed
leading to a different haplotype profile in these populations.

J. Mwinyi : K. Kpke : M. Schaefer : I. Roots : T. Gerloff (*)

Institute of Clinical Pharmacology, Charit-Universittsmedizin
Berlin, Humboldt University of Berlin,
Schumannstrasse 20/21,
10098 Berlin, Germany
e-mail: thomas.gerloff@charite.de
M. Schaefer : I. Roots : T. Gerloff
Clinical Pharmacogenomics, Cenimed GmbH,
Center for Individualized Medicine,
Berlin, Germany

Conclusion Our results demonstrate a high sequence variability of OATP1B1 within different popuations. In the
future, distinct haplotypes should be taken into account
when studying the effect of OATP1B1 on drugs in different
populations.
Keywords Organic anion-transporting polypeptides .
Single neuclotide polymorphisms . Population variability .
SLCO1B1
Introduction
To provide a continuous biliary flow and hepatic clearance
of endogenous compounds and xenobiotics, hepatocytes
exhibit a variety of uptake and efflux transporter systems in
their basolateral and apical membrane domains, respectively [1]. Members of the organic anion-transporting polypeptide family (SLCO, OATP) play an important role in the
extraction of substrates from sinusoidal blood into hepatocytes [2, 14, 15]. Currently OATP1B1, OATP2B1, and
OATP1B3 are known to be expressed at the basolateral pole
of hepatocytes [1]. OATPs mediate the uptake of diverse
endogenous amphiphatic organic compounds, including
bile acids, steroid hormone conjugates, thyroid hormones,
leucotriene C4, anionic peptides, and conjugated and
unconjugated bilirubin [1]. In addition to this physiological
function, OATPs have been found to transport an increasing
number of frequently used drugs, such as different HMGCoA reductase inhibitors, fexofenadine, benzylpenicillin,
repaglinide, valsartan, and temocaprilat [312].
Recently, SLCO1B1 has become an interesting target of
pharmacogenetic research. Eighteen allelic variants were
proposed by Tirona and Nishizato [3, 13] from 14 single
neuclotide polymorphisms (SNPs) found within the 14 exons
of the gene. Most prevalent were the c.388A>G, c.463C>A,
and c.521T>C polymorphisms that resulted in the definition

258

of OATP-C *1b, *4, and *5, respectively [3, 13]. There

were also considerable interethnic differences regarding
the sequence variability of SLCO1B1 among EuropeanAmericans, African-Americans, and Japanese subjects [3, 13].
Most SLCO1B1 SNPs were associated with altered in
vitro transport characteristics of the prototypic compounds
estrone sulfate and estradiol 17-D-glucuronide [13, 14].
Moreover, in vivo pharmacokinetic data demonstrated
significant effects of SLCO1B1 haplotypes on the disposition of, e.g., repaglinide and HMG-CoA reductase inhibitors such as pravastatin, pitavastatin, simvastatin,
atorvastatin, and rosuvastatin [47, 11]. Heterozygous
carriers of SLCO1B1 *15 [haplotype composed of the
variants c.388A>G (*1b) and c.521T>C (*5)] showed
significantly higher plasma levels for pravastatin and
pitavastatin compared to SLCO1B1 wild-type carriers [3,
5, 6]. Strikingly, pravastatin pharmacokinetic profiles from
subjects carrying the variant SLCO1B1 *5 revealed delayed
hepatocellular uptake, while *1b seemed to accelerate
SLCO1B1-dependent uptake of the drug [4]. The variant
SLCO1B1*5 has been associated moreover with higher
plasma levels for simvastatin and repaglinide [7, 11].
Considering that SLCO1B1 is a substantial factor in the
distribution of many drugs, interindividual and interethnic
differences in this carrier protein may explain variability in
drug response and also in its physiological function as a
transporter of endogenous compounds including bile acids.
Therefore, in the present study we investigated the allelic
frequencies of SLCO1B1 SNPs in a population of 300
German and 94 Turkish individuals in comparison to 115
African individuals and compared our genotyping results
with other studies [3, 13, 1719]. In addition, we included an
SLCO1B1 gene polymorphism found by genetic database
analysis in GenBank and three SNPs that were detected by
nucleotide sequencing of SLCO1B1 exons of some DNA
samples. A calculation of pairwise linkage disequilibrium
and an estimation of population haplotype frequencies was
carried out to allow the importance of SLCO1B1 haplotypes
in different ethnic groups to finally be evaluated.

Materials and methods

Subjects A sample of 300 healthy unrelated male subjects of
German origin from the Berlin area, a sample of 94 healthy
unrelated male and female individuals of Turkish origin living
in southeast Anatolia (kindly provided by A.S. Aynacioglu),
and 115 unrelated male and female African subjects from
Uganda (kindly provided by P.N. Mugyenyi) were investigated. All participants gave their informed consent prior to
enrollment in the study, and the protocol was approved by the
ethics committee of the Charit University Hospital, medical
school of the Humboldt University Berlin.

Eur J Clin Pharmacol (2008) 64:257266

Blood samples Whole blood (10 ml) was collected in

Vacutainer tubes containing ethylene diamine tetraacetic
acid (EDTA) as anticoagulant. DNA was either isolated
from leukocytes by a standard phenol/chloroform extraction
procedure or from native blood samples using the MagNA
Pure LC system and the MagNA Pure LC Total Nucleic
Acid Isolation kit (Roche Diagnostics) according to the
manufacturers protocols.
Genotyping Each of the 18 SNPs of the SLCO1B1 gene
(reference sequences, GenBank accession no. AJ132573)
were identified by polymerase chain reaction-restriction
fragment length polymorphism (PCR-RFLP) analysis either
by using modified procedures previously described [13] or
by newly designed assays.
Exons of interest were amplified for genotyping using
forward and reverse primer pairs (TIB Molbiol, MWG)
given in Table 1. For the polymorphisms c.455G>A (exon
4), c.521T>C (exon 4), c.2000A>G (exon 14), c.571C>T
(exon 5), and c.597C>T (exon5), mismatch primers were
used, introducing restriction cleavage sites based on the
respective SNP position. To hold the risk for artificial
enzyme errors to a minimum, PCR reactions were designed
so that a cleavage was performed in the wild-type case and
no cleavage appeared in the heterozygous (two bands) or in
the homozygous mutated case (one upper band). Homozygous mutated samples were redetermined. Genomic DNA
was added to PCR mixtures of 25 l consisting of 10 PCR
buffer [Rapidozym, 100 mM Tris-HCl (pH 8.8), 50 mM
(NH4)2SO4, 250 mM KCl, 20 mM MgSO4], 3 or 4 mM
MgCl2 (Rapidozym), 0.2 l dNTPs (Rapidozym), and 1 U
of Biotherm DNA Polymerase (Rapidozym).
PCR amplification consisted of an initial denaturation of
2 min at 94C followed by 30 cycles of denaturation at
95C for 30 s, annealing of oligonucleotides at the primer
pair-specific temperature for 30 s, and extension at 72C for
30 s. The PCR reactions were carried out in a Gene Amp
9700 PCR thermocycler (Applied Biosystems). RFLP
fragments (restriction endonucleases given in Table 2) were
separated on a 3% agarose gel (Qualex Gold Agarose) and
visualized after Sybr Green staining of the agarose gel with
the use of an ultraviolet transilluminator. Confirmation of
PCR-RFLP was done by PCR Dye-Terminator DNA
sequencing using an ABI automatic sequencing system
(ABI 310 Prism Foster, USA).
Statistical analysis Conformance with Hardy-Weinberg
equilibrium was tested with the software package Haploview, version 3.2 [20] using an exact test. Linkage
disequilibrium (LD) between pairs of variants was determined by the same software. Chi-squared tests for
significance of pairwise LD were calculated using the
program Linkdos [21]. The comparison of haplotype

Eur J Clin Pharmacol (2008) 64:257266

259

Table 1 Nucleotide sequence of oligonucleotide primers used for amplification of SLCO1B1 exons containing distinct single nucleotide
polymorphisms (SNP)
Exon

SNP

Primer

Fragment length
(bp)

2
3
4

c.217T>C
c.245T>C
c.388A>G
c.411G>A

5-TGC CTA TTG ACA TTA TAT AGT CC-3 5-GAT AAC CAG TGG TGT AAA GCA T3
5-CTT GGA CTC TAT TTG CAT CCA TTC-3 5-CAA GGT ACT GAT AGT GGC ACAG-3
5-GCA AAT AAA GGG GAA TAT TTC TC-3 5-AGA GAT GTA ATT AAA TGT ATA C-3
Nested PCR on PCR product for A388G with mismatch primer pair:
5-TTC ATC AGA AAA TTC AAC GTC3
5GGG AGA GAT GTA ATT AAA TGT ATA C-3
Nested PCR on PCR product for A388G with mismatch primer pair:
5-TCA AAT TTT ATC ACT CAC TA-3
5-AGA GAT GTA ATT AAA TGT ATA C-3
Same as A388G
Same as A388G
5-GTT AAA TTT GTA ATA GAA ATG C-3
5-GTA GAC AAA GGG AAA GTG ATC ATA-3
and nested PCR with mismatch primer pair:
5GGT CAT ACA TGT GGA TAT ACG3
5GTA GAC AAA GGG AAA GTG ATC3
Nested PCR on first PCR product for T521C with mismatched primer pair:
5-GGA ATA GGG GAG ACT CCC ATA GTA ACA3
5-GGG GTA GAC AAA GGG AAA GTG ATC ATA3
Nested PCR on first PCR product for T521C with mismatched primer pair:
5GGG CTT TCT TAC ATT GAT GAA TT3
5-GTA GAC AAA GGG AAA GTG ATC ATA-3
Same as A720T
5-AAT CTT ACA TGA CTT ACG TTC AC-3
5-CCA CTT GGA ATA CAG TAT TTA G-3
5-CAG AAA ACT CAT ATA TGA TTA CAA C-3 5-CAT ATT ATG CAA TTG ATA TAG TG-3
5-TCT GCT TTC ACT TTA CTT CTT CC-3 5-AAA ATT GTT CAA TCT AAT CTG TGC-3
Same as A1385G
5- GTT ATT ACA CAC AAT TTA AAC TG-3
5-GTT TGG AAA CAC AGA AGC AGA AG-3
5-GTT ATT ACA CAC AAT TTA AAC TG-3
5-GTT TGG AAA CAC AGA AGC AGA AG-3
Nested PCR on PCR product for A1964G with mismatch primer pair:
5-AAA TGG AAG TGT CAT GGG TG-3
5-GTT TGG AAA CAC AGA AGC AGA AG-3

282
272
274
155

c.455G>A

c.463C>A
c.467A>G
c.521T>C

c.571C>T

c.597C>T

8
9
10
14

c.721G>A
c.1058T>C
c.1294A>G
c.1385A>G
c.1463G>C
c.1929A>C
c.1964A>G
c.2000A>G

107

274
274
260

178
137

103

303
321
276
293
293
305
305
136

frequencies between ethnic groups was done by an exact

chi-squared test using SPSS, version 12.0. Confidence
intervals were calculated according to the NewcombWilson method using binconf of the Hmisc software
package written by Frank E. Harrell Jr. (http://biostat.mc.
vanderbilt.edu/twiki/bin/view/Main/Hmisc). P<0.05 was
considered as statistically significant.

With respect to genotypes, 1 codes for homozygous status

(according to reference sequence), 2 for heterozygous
status, and 3 for homozygous mutated status. With respect
to the haplotypes, 1 denotes the reference sequence at this
position, and 2 denotes the variant.

Haplotype analysis The software package PHASE (version

2.0) [22, 23] was used to infer haplotype pairs from
genotype data and to estimate the population haplotype
frequencies. Haplotypes were analyzed as combinations of
the eight detected variants in the order c.388A>G,
c.411G>A, c.463C>A, c.521T>C, c.571C>T, c.597C>T,
c.1463G>C, and c.1929A>C. Genotypes and haplotypes
are given as a sequence of these eight variants as follows:

Results
Allelic frequencies of SLCO1B1 SNPs
A total of 18 genetic SLCO1B1 variants (Table 3) were
genotyped in a sample of 300 German subjects, in 94
individuals of Turkish origin and in 115 African subjects.
Interestingly, the majority of the tested polymorphisms

260

Eur J Clin Pharmacol (2008) 64:257266

Table 2 Restriction endonucleases and RFLP fragment sizes resolved based on the reference sequence or polymorphisms
Exon

SNP

Amino acid
exchange

Fragment length
of PCR product
(bp)

Enzyme

Cleavage pattern: wt
mut

c.217T>C

F73L

282

HindIII

c.245T>C

V82A

272

CviRI

c.388A>G

N130D

274

ClaI

c.411G>A

S137S

155

SalI

c.455G>A

R152K

107

BfaI

c.463C>A

P155T

274

HphI

c.467A>G

E156G

274

BstNI

c.521T>C

V174A

178

FnuDII

c.571C>T

L191L

137

BseNI

c.597C>T

F199F

103

EcoRI

c.721G>A

D241N

303

MboI + BglII

c.1058T>C

I353T

321

BseNI

c.1294A>G

N432D

276

BbsI

10

c.1385A>G

D462G

293

Fnu4HI

c.1463G>C

G488A

293

Fnu4HI

c.1929A>C

Leu643Phe

305

VspI

c.1964A>G

D655G

305

EcoRV

c.2000A>G

E667G

136

HphI

194/88
282
15/257
15/94/163
274
119/155
19/136
155
18/89
107
185/89
274
274
197/77
178
20/158
137
32/105
20/83
103
209/94
303
102/219
102/80/139
276
68/208
293
148/145
293
222/71
116/189
305
155/150
305
28/108
136

14

wt Wild type, mut mutation

could not be detected in our samples. Only eight of the

investigated SNPs were found in at least one of the three
populations analyzed in this study. In our African sample,
the genotyping resulted in only six detectable polymorphisms. SNP frequencies of our Caucasian and Turkish
samples were similar except for c.388A>G (Table 3), which
was more prevalent in Turks (46.3%, 95% CI: 3953.7%)
than in Caucasians (36.5%, 95% CI: 32.640.5%). Interestingly, c.388A>>G was most prevalent in our African
individuals (77.8%, 95% CI: 71.983%). The SNPs
c.571C>T and c.597C>T were frequent in Germans and
Turks, but were rare (c.571C>T) or not observed
(c.597C>T) in Africans. For the variants c.411G>A,
c.463C>A, and c.521T>C, we found frequencies between

12.2 and 16.0% in Germans and Turks, while in Africans

these SNPs were less frequent or did not occur at all
(c.411G>A). In contrast c.1463G>C was not detected in
German and Turkish individuals of this study, but was
found in our African sample with a frequency of 1.7%. The
variant c.1929A>C was rare in all of our three ethnic
samples with frequencies between 3.1 and 7.3%. None of
the genetic variants showed any significant deviation from
Hardy-Weinberg equilibrium.
Because of missing genotypes, the pairwise LD and the
estimated haplotypes for the variant c.1929A>C were
calculated for a reduced number of individuals (German
subjects: n=276; Turkish subjects: n=78; African subjects:
n=109). Figure 1 shows a graphical representation of the

0.0
0.0
36.5

16.0

0.0
16.0

0.0
15.0

34.5

37.5

0.0
0.0
0.0
0.0
0.0
3.1
0.0
0.0

c.217T>C
c.245T>C
c.388A>G

c.411G>A

c.455G>A
c.463C>A

c.467A>G
c.521T>C

c.571C>T

c.597C>T

c.721G>A
c.1058T>C
c.1294A>G
c.1385A>G
c.1463G>C
c.1929A>Cb
c.1964A>G
c.2000A>G

0.00.5
0.00.5
32.6
40.5
13.2
19.2
0.00.5
13.2
19.2
0.00.5
12.2
18.1
30.7
38.5
33.6
41.5
0.00.5
0.00.5
0.00.5
0.00.5
0.00.5
1.84.9
0.00.5
0.00.5

95% CIa

0.0
0.0
0.0
0.0
0.0
5.1
0.0
0.0

36.2

38.3

0.0
12.2

0.0
13.8

13.8

0.0
0.0
46.3

Turkish
subjects
this
study
(n=94)

31.3
45.7
29.3
43.5
0.01.6
0.01.6
0.01.6
0.01.6
0.01.6
2.29.9
0.01.6
0.01.6

0.01.6
7.917.8

0.01.6
9.219.6

0.01.6
0.01.6
39.0
53.7
9.219.6

95% CIa

0.0
0.0
0.0
0.0
1.7
7.3
0.0
0.0

0.0

6.1

0.0
3.9

0.0
2.2

0.0

0.0
0.0
77.8

African
subjects
this study
(n=115)

0.01.3
0.01.3
0.01.3
0.01.3
0.54.4
4.311.7
0.01.3
0.01.3

0.01.3

3.410.0

0.01.3
1.87.3

0.01.3
0. 15.0

0.01.3
0.01.3
71.9
83.0
0.01.3

95% CIa

nd
2.0
1.0
1.0
0.0
nd
2.0
2.0

nd

nd

2.0
14.3

nd
16.3

nd

2.0
2.0
30.6

European
Americans
[13] (n=49)

nd
0.0
0.0
0.0
9.1
nd
0.0
34.1

nd

nd

0.0
2.3

nd
2.3

nd

0.0
0.0
75.0

African
Americans
[13]
(n=22)

0.0
nd
nd
nd
nd
nd
nd
nd

nd

nd

nd
11.1

0.0
nd

nd

nd
nd
64.0

Japanese
[17]
(n=267)

nd
nd
nd
nd
nd
nd
nd
nd

42.9

64.2

nd
15.8

nd
nd

nd

nd
0.0
62.9

Japanese
[3]
(n=120)

nd Not determined
a
If the number of variants equals zero, the confidence intervals become one-sided, and the entire 0.05 tail area goes into one tail
b
Frequencies calculated for a reduced number of individuals. German subjects: n=276, Turkish subjects: n=78, African subjects: n=109

German
subjects
this study
(n=300)

SNP

Table 3 SLCO1B1 allelic frequencies (%) in subjects of different ethnic origins

nd
nd
nd
nd
nd
4.0
nd
nd

46.4

46.8

nd
20.2

nd
13.1

13.1

nd
nd
46.2

Finnish
[18]
(n=468)

nd
nd
nd
nd
nd
nd
0.0
0.0

50.0

26.0

nd
13.0

nd
0.0

100

nd
nd
79.5

Chinese
[19]
(n=100)

nd
nd
nd
nd
nd
nd
nd
nd

50.0

23.5

nd
11.0

nd
2.5

97.5

nd
nd
87.0

Malay
[19]
(n=100)

nd
nd
nd
nd
nd
nd
nd
nd

21.5

43.5

nd
6.5

nd
1.5

98.5

nd
nd
57.0

Indian
[19]
(n=100)

Eur J Clin Pharmacol (2008) 64:257266

261

262

c.411G>A

c.463C>A

c.521T>C

c.571C>T

c.597C>T

c.1463G>C

c.1929A>C

c.411G>A

c.463C>A

c.521T>C

c.571C>T

c.597C>T

c.1463G>C

c.1929A>C

TURKS

c.463C>A

c.521T>C

c.571C>T

c.597C>T

c.1463G>C

c.1929A>C

AFRICANS

c.411G>A

c.388A>G

GERMANS

c.388A>G

c.388A>G

Fig. 1 Pairwise linkage

disequilibrium plot (r2 color
scheme) of SLCO1B1 in
Germans (a), Turks (b), and
Africans (c). Plots were
generated in Haploview v3.2.
Gray-shading of the boxes indicates the r2 value expressed as
the correlation coefficient
between two loci

Eur J Clin Pharmacol (2008) 64:257266

pairwise LD measure r2 for the eight detected SNPs in three

different populations. For Germans and Turks, the variants
c.411G>A and c.463C>A were in a perfect LD, but this was
not true for Africans. In this population, the c.411G>A
variant was not detected and the c.463C>A variant was rare.
In summary, in Germans and Turks a significant pairwise
LD was found between most of the eight genetic SLCO1B1
variants, but in contrast, no significant pairwise LD was
observed in Africans.
SLCO1B1 haplotypes
The eight SNPs found in our samples constituted a total of
49 genotypes. For these genotypes, 35 haplotypes were
predicted by PHASE: 13 haplotypes for Germans, 16 for
Turks, and 22 for Africans. These resulted in 12 haplotypes

no comparison possible

0.00>= r2 <0.10

II

0.10>= r2 <0.20

III

0.20>= r2 <0.30

IV

0.30>= r2 <0.40

0.40>= r2 <0.80

VI

0.80>= r2 <=1.00

with frequencies of more than 1% in at least one population

(Table 4). The frequencies of these 12 haplotypes sums to
99.4% for the German, 99.2% for the Turkish, and 97.1%
for the African population.
Several haplotypes calculated from our data, including
combinations with the SNPs c.411G>A, c.571C>T, and
c.597C>T were not mentioned in the reference publication
of Tirona et al. [13]. Therefore, the schematic of SLCO1B1
allelic variants by Tirona et al. [13] was extended by
additional variants that were included in our analysis
(Table 3). Based on this revised scheme, the haplotype
analysis was performed. Haplotype analysis revealed that
the alleles formerly designated as *1a and *1b can now be
separated into two and five different haplotypes, respectively, including SNPs that were not considered by Tirona
et al. [13] (Table 4). However, as we expect additional

1
1
1
2
2
2
2
2
2
2
2
2

SLCO1B1_1b
SLCO1B1_4b
SLCO1B1_6
SLCO1B1_9b
SLCO1B1_10b
SLCO1B1_12
SLCO1B1_8b
SLCO1B1_11
SLCO1B1_5b
SLCO1B1_7b
SLCO1B1_3
SLCO1B1_2

1
1
1
1
1
1
1
1
1
1
1
2

c.411G>Aa

1
1
1
1
1
1
1
1
1
1
1
2

c.463C>A

1
1
2
1
1
1
1
2
1
1
2
1

c.521T>C

1
2
2
1
1
1
2
1
2
2
2
1

c.571C>Ta

1
1
2
1
1
1
1
1
2
2
2
2

c.597C>Ta

1
1
1
1
1
2
1
1
1
1
1
1

c.1463G>C

n.p. Not predicted

1 denotes the reference sequence at the respective sequence position, and 2 denotes the variant
Haplotype order chosen according to the rank order in Germans, followed by the rank order in Turks and Africans
a
SNPs originally not considered by [8] and [17]
b
Originally assigned as *1a and *1b, respectively

c.388A>G

Haplotype

SLCO1B1 SNPs

Table 4 Distribution of major SLCO1B1 haplotypes among different ethnic groups

1
1
1
1
2
1
1
1
1
2
1
1

c.1929A>Ca

49.1
11.3
3.0
0.000
n.p.
n.p.
2.2
n.p.
4.0
2.5
11.9
15.4

Germans
(n=276)
45.9
6.4
1.4
2.1
n.p.
n.p.
10.3
n.p.
5.1
4.3
9.4
14.1

Turks
(n=78)
19.0
2.8
n.p.
62.9
5.9
1.8
1.4
3.2
n.p.
n.p.
n.p.
n.p.

Africans
(n=109)

Haplotype frequencies in different

ethnic groups

*1b
*15
*1b
*1b
*15
*14

*1a
*1a
*5
*1b
*1b

Tirona et al. [13],

Nozawa [17]

Former defined
haplotypes

Eur J Clin Pharmacol (2008) 64:257266

263

264

SNPs to be identified in SLCO1B1 in different ethnic

populations, we would suggest the use of a nomenclature
scheme derived from determined haplotype frequencies in
different populations. As shown in Table 4, 12 haplotypes,
occurring at frequencies above 0.01 in at least one of our
ethnic samples, are referred to as SLCO1B1_1 through
SLCO1B1_12 according to their rank order in Germans,
followed by the rank order in Turks and Ugandese.
The SLCO1B1 haplotype distributions were significantly
different for all three ethnic populations (P<0.001) (Fig. 1).
The most common haplotype in the German (49.5%) and in
the Turkish population (46.3%) was SLCO1B1_1, which
was identical to the reference sequence, formerly designated as allele *1a. This haplotype was less common in
Africans, with a frequency of 18.6%. In contrast, the most
common haplotype in the African population with a
frequency of 62.9% was not detectable in Caucasians.
Frequencies higher than 5% were estimated for four
haplotypes in Germans, for six haplotypes in Turks, and
only for two haplotypes in Africans. All other haplotypes
appeared at lower frequencies.

Discussion
Genetic variants of SLCO1B1 are of interest, as it has
become evident that OATP1B1 is involved in the transport
of numerous important endogenous and exogenous compounds from portal venous blood into the liver cells. For
example, pravastatin, an effective drug for the treatment of
hypercholesterolemia [24], and rifampicin were demonstrated to be substrate drugs of OATP1B1 [25, 26]. To
increase knowledge about drug safety and efficacy, it is
important to determine SNP and haplotype frequencies in
genes coding for transport proteins in different ethnic
groups to be able to effectively investigate their influence
on drug transport. An investigation of SNP frequencies in
different populations helps to evaluate the probability of
changed drug pharmacokinetics and possible adverse
effects.
We analyzed SLCO1B1 SNP frequencies in a large
sample of German and Turkish subjects as well as in
individuals from Uganda. Our data revealed that only
8 SNPs (c.388A>G, c.463C>A, c.521T>C, c.411G>A,
c.571C>T, c.597C>T, c.1463G>C, and c.1929A>C) of the
18 known polymorphisms and the haplotypes arising from
them seem to be relevant for further functional investigations in Caucasians, Turks, and Africans, as only these
8 polymorphisms could be detected in the three populations. Several of the analyzed polymorphisms (c.411G>A,
c.571C>T and c.597C>T) are silent (synonymous), leading
to no amino acid exchanges in the protein. Interestingly, the
SNPs c.217T>C, c.245T>C, c.467A>G, c.1058T>C,

Eur J Clin Pharmacol (2008) 64:257266

c.1294A>G, c.1385A>G, and c.2000A>G, originally

detected by cloning methods and sequencing based on
cDNA derived from reverse transcribed human liver sample
mRNA [13], could not be found in our populations. A
possible explanation could be that these rarely detected
genetic variants could be somatic mutations that cannot be
found in gametic cells. We conclude without much doubt
that these described SNPs are not germline variants.
When comparing our data with published studies, the
most often occurring SNP in our German population,
c.388A>G, (36.5%, 95% CI: 32.640.5%) had a similar
frequency in European Americans (30.0% [13]). Noticeably, the c.388A>G SNP frequency among Japanese
individuals (62.9%, 95% CI: 56.569.0% [3] and 64.0%,
95% CI: 59.868.1% [17]) was about twice the frequency
observed in Caucasians and even higher in Africans
(77.8%, 95% CI 71.983.0%). A very recently published
study found a slightly higher frequency for c.388A>G [18]
in a Finnish population (46.2%) compared to our German
group. Jada et al. [19] determined the c.388A>G frequencies in a Chinese and Malay population to be 79.5 and
87%, respectively. These frequencies were higher than the
frequencies found for Japanese samples (64% [3], 62.9%
[17]). The high frequency variability of the SNP c.388A>G
in different populations is in particular responsible for the
different haplotype frequencies found in Germans, Turks
and Africans (see Table 4).
The c.571C>T variant occurred considerably more often
in a Japanese group (64.2%, 95% CI: 57.870.2%) [3] and
in a Chinese group [18] (74.0%, 95% CI: 67.980.1%) as
compared to the frequency found here in the German
(34.5%, 95% CI: 30.738.5%) and Turkish populations
(38.3%, 95% CI: 31.345.7%). The frequency of c.571C>T
determined for the German sample was however a bit lower
compared to the frequency found in a Finnish population
(46.8%) [18]. In contrast, this SNP appeared less often in
our sample of African individuals (6.1%, 95% CI 3.4
10%). The variant c.463C>A occurred seldom in Africans
(2.2%) but was common in Caucasians (16%, 95% CI:
13.219.2%) and Turks (13.8%, 95%: 9.219.6%) and
comparable to the frequency found by Parsanen et al.
(13.1%) [18].
The SNP SLCO1B1*5 (c.521T>C), which has been
mainly associated with alterations in OATP-C-dependent
drug transport, was earlier found to be common in Japanese
and Chinese groups [3, 17, 19] with frequencies of about
1116%. The variant c.521T>C occurred comparably often
in our German sample (15%). Similar frequencies of
c.521T>C were found for a Finnish population (20.2%
[18]) and for European Americans (14% [13]). The SNP
c.521T>C seems, however, to occur relatively seldom in
Africans (3.9%, 95% CI: 1.87.3%, our study) and African
Americans (2% [13]). Interestingly, the SNP c.2000A>G,

Eur J Clin Pharmacol (2008) 64:257266

which was detected in African Americans at a relatively

high frequency by Tirona et al. [8], could not be found in
any of our populations.
Computer-based haplotype analysis of our data revealed
12 haplotypes that occur at a frequency of more than 1% in
at least one of the studied populations. These determined
haplotypes should be included in the nomenclature scheme
set up by Tirona et al. [13].
Highly significant differences in haplotype frequencies
were found between Caucasians and Africans. Moreover, we
combined both the Japanese samples of Nozawa et al. [17]
and Nishizato et al. [3] and compared them to our German
and Turkish samples in terms of the allele definition given
by Tirona et al. [13]. Since the SNP c.463C>A was not
studied in the Japanese population, subjects from our
samples carrying the *14 allele were included in the group
of allele *1b. Comparison of the haplotype distribution
between Japanese and either Germans or Turks revealed
highly significant differences (P<0.001). Notably, the former
allele *1a was common in Caucasians and more rarely found
in Asians. The opposite was the case with allele *1b.
Different haplotypes rather than single variants should be of
major interest for functional investigations. In vivo studies
revealed a significant influence of SLCO1B1 alleles on
pravastatin kinetics [35]. Nishizato et al. [3] showed that
the AUC of pravastatin is increased in homozygous *15
carriers, while homozygous carriers of *1b alone show a
significantly lower AUC. We could demonstrate that haplotypes containing either the polymorphism c.388A>G or
c.521T>C have complementary effects on pravastatin kinetics [4]. The c.521T>C variant can be found in three different
haplotypes: SLCO1B1_3, SLCO1B1_6, and SLCO1B1_11
(see Table 4), i.e. in combination with both c.388A and
c.388G allelic forms as well as in combination with further
allelelic variants. Thus, haplotype analysis rather than SNP
analysis can lead to more meaningful results in clinical
studies.
Based on our results in this study, we would suggest that
different haplotypes of SLCO1B1 have to be taken into
consideration in future genotype-phenotype correlation
studies on SLCO1B1, based on the population to be
investigated. It is therefore important to study the variants
c.388A>G, c.411G>A, c.463C>A, c.521T>C, c.571C>T,
c.597C>T, and c.1929A>C, which are part of the haplotypes SLCO1B1_1, _4, _6, _8, _5, _7, _3, and _2, in
Caucasian samples. For African samples we would suggest
determining the variants c.388A>G, c.463C>A, c.521T>C,
c.571C>T, c.1463G>C, and c.1929A>C (thereby studying
the haplotypes SCLO1B1_1, _4, _9, _10, _12, _8, _11) in
clinical studies investigating OATP-C substrate drugs.
In conclusion, our data suggest genetic similarities of
SLCO1B1 between Turkish and German populations, but
major differences in SNP and haplotype frequencies among

265

Caucasians, Africans, and Asians. Our results demonstrate

that analysis of sequence variability and comprehensive
haplotype analysis of ethnically different populations are
essential prerequisites for adequate results in genotypephenotype correlation studies.
Acknowledgements We thank Mrs. Ulrike Ehlert and Mrs. Kristin
Krostitz for skillful technical assistance. Supported by the German
Federal Ministry of Education and Research (BMBF), grant no. 03/
4507 (InnoRegio Health Region Berlin-Buch - Pharmacogenomic
optimization of drug therapy and drug development) given to Cenimed
GmbH, Center for Individualized Medicine, Berlin, and by grant no.
031U209B (Berlin Centre for Genome Based Bioinformatics) given to
Charit - Universittsmedizin Berlin.

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