Pharmacogenetics of methotrexate in patients with rheumatoid
arthritis
Wessels, J.A.M
Citation
Wessels, J. A. M. (2007, October 11). Pharmacogenetics of methotrexate in patients with
rheumatoid arthritis. Retrieved from https://hdl.handle.net/1887/12436
Version: Corrected Publisher’s Version
License: Licence agreement concerning inclusion of doctoral thesis in the
Institutional Repository of the University of Leiden
Downloaded from: https://hdl.handle.net/1887/12436
Note: To cite this publication please use the final published version (if applicable).
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Table 1. Baseline characteristics RA patients with and without hepatotoxicity.
Characteristic Baseline value
Cases (n = 6) Controls (n = 12)
Sex, female/male, % 67/33 67/33
Age ± sd, years 53.4 ± 15.1 55.7 ± 10.1
Duration of joint complaints in weeks, median (range) 22.1 (14–33) 44.9 (12–66)
DAS ± sd 4.6 ± 0.6 4.1 ± 0.8
ALAT level units/liter, median (range) 23 (9–86)† 27 (9–45)
ESR, median (range), mm/hour 38 (7–58) 45 (10–86)
RF positivety, % 67 42
CRP, median (range), mg/L 26 (3–43) 19 (6–106)
RAI, median, (range) 17 (8–25) 14 (2–21)
Number of swollen joints, median (range) 15 (8–20) 10 (6–32)
BMI, median (range), kg/m2 28 (25–34) 28 (25–36)
Alcohol consumption, % (range), units/week 67 (2–7) 67 (1–14)
ALAT = alanine aminotransferase; BMI = body mass index; CRP = C-reactive protein; DAS = disease activ- ity score in 44 joints; ESR = erythrocyte sedimentation rate; RF = rheumatoid factor; RAI = Ritchie articular index. †One case subject had initial ALAT value of 86 units/liter before methotrexate (MTX) treatment.
After starting MTX, ALAT increased to 279 units/liter. As a consequence, MTX was withdrawn and the ALAT value declined to 33 units/liter. Five cases had normal ALAT ( ≤45 units/liter) at baseline.
A
0.8 0.6 0.4 0.2
1 2
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B
0.8 0.6 0.4 0.2
1 2
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Figure 1. Simplified representation of population structure as determined with admixture correlated alle- les model in Structure®. Bars (X-axis) represent individual subjects which are grouped by population identifi- cation; cases with hepatotoxicity defined as ‘1’ (black) and controls without hepatotoxicity defined as ‘2’ (grey).
The Y-axis shows the fraction of interfering in one cluster, assuming that the number of clusters is 2 (K = 2).
A. Population structure for cases and controls based on the analysis of genotypes with >89% SNP call rate.
B. Population substructure based on the analysis of 8 most informative SNPs for clustering (Fst values range from 0.38 to 0.47). SNP Affymetrix IDs: 1512151, 1512322, 1518195, 1517662, 1510107, 1515070, 1517574, 1514120 (NCBI SNP database rs-numbers: rs 7230333, rs946816, rs725124, rs1365491, rs1321015, rs952242, rs726914, rs1517361)
Table 2. Differences between cases and controls analysed by single marker and haplotype association with Haploview®.
Chromosome No of SNPs tested * Number of haploblocks*
1 480 (9) 13 (0)
2 610 (6) 10 (0)
3 461 (9) 11 (0)
4 422 (6) 15 (0)
5 458 (7) 17 (0)
6 459 (7) 12 (0)
7 336 (2) 6 (0)
8 317 (9) 3 (0)
9 287 (0) 7 (0)
10 352 (2) 11 (0)
11 374 (3) 10 (1)
12 293 (6) 8 (0)
13 256 (4) 7 (0)
14 229 (4) 5 (0)
15 173 (4) 5 (1)
16 132 (1) 1 (0)
17 123 (2) 5 (0)
18 184 (5) 2 (1)
19 93 (1) 3 (0)
20 149 (1) 1 (0)
21 98 (1) 0 (0)
22 45 (1) 1 (0)
X males 89 (0) 0 (0)
X females 167 (0) 0 (0)
*number significant without Bonferroni correction
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FB@AM Table 3. Differences in allele distribution between cases and controls analyzed by chromosome loca- tion with the R® package Globaltest.
Chromosome No. of combined SNPs tested
(adjusted data)‡
P-value (adjusted data )‡
1 769 (355) 0.31 (0.40)
2 835 (403) 0.47 (0.55)
3 703 (347) 0.32 (0.30)
4 696 (320) 0.33 (0.28)
5 692 (315) 0.32 (0.45)
6 693 (304) 0.42 (0.42)
7 513 (246) 0.42 (0.35)
8 472 (225) 0.41 (0.38)
9 483 (235) 0.46 (0.48)
10 528 (259) 0.42 (0.50)
11 548 (229) 0.33 (0.29)
12 476 (241) 0.36 (0.48)
13 436 (204) 0.47 (0.51)
14 354 (153) 0.34 (0.38)
15 282 (120) 0.31 (0.47)
16 226 (108) 0.50 (0.59)
17 166 (86) 0.45 (0.55)
18 306 (125) 0.26 (0.48)
19 149 (70) 0.26 (0.29)
20 203 (96) 0.29 (0.25)
21 165 (90) 0.66 (0.61)
22 74 (36) 0.26 (0.19)
X males (n = 6) 263 (68) 0.20 (0.73)
X females (n = 12) 263 (155) 0.76 (0.86)
‡Genotypes were tested without any data adjustments and with data adjustments. These data adjust- ments were: removing SNPs which were missing in more than 1 case and removing SNPs which were miss- ing in more than 2 control subjects and removing SNPs with a minor allele frequency of less than 0.3.
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Case sample size required (log scale)
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Figure 2. Schematic representation of the number of cases needed to detect significant differences in a case-control (1:2) study design. Lines represent number of cases required to detect differences with sig- nificance level of 1.10–4 (10K array are lines at lower level) and 1.10–6 (Genome-wide P-value are lines in black in upper level) with 80% power depending on the minor allele frequency (MAF) in controls and hypothetical odds ratios for the occurrence of hepatotoxicity in cases relative to controls.
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