Relation of Genetic Variation in the Gene Coding for C-Reactive Protein with Its Plasma Protein...

Relation of Genetic Variation in the Gene Coding for C-ReactiveProtein with its Plasma Protein Concentrations: Findings fromthe Women’s Health Initiative Observational Cohort

Cathy C. Lee1,2, Nai-chieh Yuko You3, Yiqing Song4, Yi-Hsiang Hsu5, JoAnn Manson4,Lauren Nathan6, Lesley Tinker7, and Simin Liu1,3,81 Department of Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA 900952 VA Greater Los Angeles Healthcare System, Los Angeles, CA 900733 Department of Epidemiology, UCLA, School of Public Health, Los Angeles, CA 900954 Division of Preventive Medicine, Department of Medicine, Brigham and Women’s Hospital andHarvard Medical School, Boston, MA 022155 Molecular and Integrative Physiological Science Program, Department of Environmental Health,Harvard School of Public Health, Boston, MA 022156 Department of OB/GYN, David Geffen School of Medicine, UCLA, Los Angeles, CA 900957 Fred Hutchinson Cancer Research Center, Seattle, WA 981098 Johnson Comprehensive Cancer Center, David Geffen School of Medicine, UCLA, Los Angeles,CA 90095

AbstractBACKGROUND—Although common genetic variants of the CRP gene have been associatedwith plasma CRP concentrations (hsCRP) in several cohorts of European Americans, relativelyfew studies have comprehensively assessed this association in well-characterized multiethnicpopulations.

METHODS—In a case-control study of diabetes nested in the Women’s Health InitiativeObservational Cohort, we comprehensively evaluated the association of genetic variation in the

*To whom correspondence should be addressed at: Simin Liu, Department of Epidemiology, UCLA School of Public Health, Box951772, 650 Charles E. Young Drive South, Los Angeles, CA 90095. Tel: 310-206-5862; Fax: 310-206-6039; [email protected] and NYY contributed equally to this work.HUMAN GENES DISCUSSED IN THIS MANUSCRIPT: CRP with HUGO approved names “C-reactive protein” and “pentraxin-related” (HGNC: 2367). Alias: PTX1.CONFLICT OF INTEREST: None of the authorshad any conflicts of interest.AUTHOR CONTRIBUTIONS: Drs. You and Liu had full access to the data in the study and take responsibility for the integrity ofthe data and the accuracy of the data analysis. Dr. Lee and Dr. You contributed equally to the manuscript as joint first authors.Conception and design: Liu, YouAcquisition of data: Liu, Tinker, Nathan, MansonAnalysis and interpretation of data: You, Liu, Lee, Song, HsuDrafting of manuscript: Lee, You, LiuCritical revision for intellectual content: Lee, You, Song, Hsu, Tinker, Manson, Nathan, LiuStatistical expertise: You, Song, Hsu, LiuObtained funding: LiuAdministrative, technical, or material support: Liu, Manson, Tinker, NathanStudy supervision: Liu

NIH Public AccessAuthor ManuscriptClin Chem. Author manuscript; available in PMC 2010 April 19.

Published in final edited form as:Clin Chem. 2009 February ; 55(2): 351–360. doi:10.1373/clinchem.2008.117176.

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CRP gene with plasma hsCRP concentrations. Thirteen tagging single nucleotide polymorphisms(tSNPs) were identified and subsequently genotyped in 3,782 postmenopausal women.

RESULTS—The allele frequencies for these tSNPs and haplotype blocks defined by these tSNPsvaried significantly by ethnic group. Consistent with prior studies among Whites, rs3093068,rs1130864 and rs1417938 were significantly associated with higher hsCRP concentrations(geometric mean per minor allele change: 1.20–1.25 mg/L), while rs1205 and rs1800947 weresignificantly associated with lower hsCRP values (1.28–1.48 mg/L). The associations withrs3093068 and rs1205 appeared to be stronger in Asian/Pacific Islanders than in Whites with ageometric mean increase of 1.65 mg/L compared to 1.25 mg/L, respectively. The minor alleles,rs3093075 and rs3093059, were associated with substantially increased hsCRP concentrationswhereas rs1800947 was associated with lower hsCRP values. All haplotype-based associationresults tended to be consistent with the associations seen with single CRP SNPs.

CONCLUSION—Our large multiethnic case-control study of postmenopausal women providesevidence that common genetic variants in CRP gene are substantially associated with plasmahsCRP concentrations in this case-control subcohort. There are also suggestions of ethnicvariations in these associations.

KeywordsC-Reactive Protein; CRP; Women’s Health Initiative; WHI

INTRODUCTIONC-Reactive Protein (CRP) is an acute phase reactant secreted by the liver that has long beenused to characterize systemic inflammation. Increased circulating concentrations of high-sensitivity CRP (hsCRP) have been associated with obesity, type 2 diabetes (T2DM)(1–4),and atherosclerotic cardiovascular disease(5–11). In a prospective case-control study of3,782 postmenopausal women nested in the Women’s Health Initiative observational study(WHI-OS), increased circulating concentrations of hsCRP were significantly associated withan increased risk of clinical diabetes(3). Further, racial and ethnic differences in plasmahsCRP values have also been noted in these populations(12–14). More recently, commongenetic variants in the CRP gene were found to be associated with plasma hsCRPconcentrations in several cohorts of European Americans(15–20). To date, however,relatively few studies have examined the associations of common variants in the genecoding for CRP with its plasma hsCRP concentrations in a multiethnic-population.Therefore, we conducted a comprehensive assessment of the association of genetic variationin the CRP gene with plasma hsCRP values in a large case-control study nested in the WHI-OS, an ethnically diverse cohort of postmenopausal women aged over 50 years includingWhite/Caucasian, Black/African, Hispanic and Asian/Pacific Islander participants. Inparticular, we examined whether any genetic effect on plasma hsCRP concentrations differby ethnicity.

MATERIALS AND METHODSStudy Participants

Details regarding our case-control study design have been described elsewhere(3;21).Briefly, of the 93,676 postmenopausal women enrolled in the WHI-OS(21), approximately82,069 had no prior history of cardiovascular disease and/or diabetes at baseline. Followingthe principle of risk-set sampling, 1,584 diabetes cases were individually matched with2,198 controls on age (±2.5 years), ethnicity, clinical center, time of blood draw (±0.10hours), and length of follow-up. The ethnic groups represented in this study include Whites

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(n=1,936), Blacks (n=1,098), Hispanics (n=455), and Asian/Pacific Islanders (n=293).Further details about the ethnic distribution and demographics have already been describedpreviously(3). The Institutional Review Board (IRB) at UCLA has previously approved theoriginal study, and all study subjects have signed informed consent forms prior to studyenrollment in the WHI.

Tagging SNP SelectionAs described previously(22), we implemented a two-stage approach in choosing haplotypetagging Single Nucleotide Polymorphisms (tSNPs). First, we surveyed common geneticvariation using the National Center for Biotechnology Information database SNP (NCBIdbSNP) supplemented by HapMap database(23). Our goal was to capture the commonhaplotype patterns in the genetic region covering the 30 kb 5′ upstream and 30 kb 3′downstream of the CRP gene (3.1kb). The initial set of SNPs were selected based on thefollowing criteria: 1) Functionality priority: nonsynonymous coding SNPs (cSNPs) andsplicing-site SNPs (ssSNPs) must be kept; the priority order of picking SNPs based on theirpotential functions is: nonsynonymous SNPs > ssSNPs > synonymous SNPs > 5′ UTR SNPs> 3′ UTR SNPs > intronic SNPs; 2) minor allele frequency (MAF) ≥ 5% in at least oneethnic group; and 3) SNP density: SNPs should be relatively evenly spaced across the generegion(24).

In the second stage, we identified tSNPs based on the Linkage Disequilibrium (LD) patternsof those selected SNPs among 61 individuals from each ethnic population. Pair-wise LDbetween SNPs was assessed using the squared correlation statistic r2. The Haploviewprogram was used to calculate the LD coefficient and define haplotype blocks(25;26). Fromthe initial set of SNPs, a total of 13 tSNPs that account for most of the genetic variationwithin the CRP locus across all four ethnic groups were selected and genotyped in all thecase-control samples.

SNP Genotyping MethodFor these 13 tSNPs, large-scale genotyping was performed using the TaqMan allelicdiscrimination method. Specific primers and probes were custom-designed by AppliedBiosystems (Applied Biosystems, ABI). Following polymerase chain reaction (PCR)amplification, end-point fluorescence was read using the ABI Primer 7900HT instrumentand genotypes were scored using SDS2.2.2 Allelic Discrimination Software (AppliedBiosystems). To evaluate reproducibility we performed blind duplicate genotyping in arandomly-selected subset of 5% of samples. Concordance rate was >99%.

Measurement of hsCRP concentrationsSince all incident cases and controls were free of clinical diabetes at baseline, baselinehsCRP concentrations were not influenced by clinical diabetes status. According to astandardized protocol, fasting blood specimens were collected from each participant atbaseline and processed locally into separate aliquots containing serum, plasma, and buffycoat. Detailed sample preparation and handling procedures are described elsewhere(3).hsCRP was measured on the Hitachi 911 analyzer (Roche Diagnostics) using animmunoturbidimetric assay with reagents and calibrators from Denka Seiken Co Ltd. Thecoefficient of variation was 1.61% for hsCRP(3).

Statistical AnalysisWe assessed each SNP for allele frequency and Hardy-Weinberg Equilibrium (HWE) testusing the Proc Allele procedure in SAS (v9.1.3, SAS Institute, Cary, NC). We also tested forheterogeneity of genotype distributions across ethnic groups using the Chi-square test. For

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hsCRP concentrations with markedly skewed distributions, we made logarithmictransformations to enhance compliance with normality assumption then calculated geometricmean differences. To determine the effect of genetic variants on plasma hsCRPconcentrations, we calculated the geometric mean differences in plasma hsCRP according toeach tSNP genotyped by fitting general linear models (GLM) treating plasma hsCRPconcentration as a dependent variable and tSNPs as independent variables. An additiveinheritance model was used in single gene analysis, and the results of this analysis wereexpressed as the geometric mean increase in hsCRP per each additional copy of the minorallele. All the linear models included matching factors and potential confounders (case/control status, alcohol consumption, cigarette smoking, body mass index (BMI), hormonereplacement therapy (HRT) used, and physical activity) as covariates in each of the fourethnic groups. Likelihood ratio tests were used to test the interaction effects between thegenotypes and ethnicity on diabetes risk.

The Haploview program was used to characterize the LD patterns between tSNPs(25;26). Inhaplotype-based analysis, we estimated haplotype frequency using an “expectation-substitution” algorithm(27), which treated expected haplotype scores (calculated under auser-specified inheritance model) as observed covariates in analysis, and stored theseexpected scores in an auxiliary data set for customized analyses. Only haplotypes withestimated frequencies ≥ 1% in the combined controls were included for further analyses. Toexamine the association between the resulting haplotype/haplotype combinations and hsCRPconcentrations, the estimate of haplotype dosage was treated as a surrogate variable for thetrue haplotype.

Further, to account for potential false positives due to multiple comparisons, we calculatedthe false discovery rate (FDR) by incorporating all p-values from multiple tests performedfor SNPs and haplotypes in the GLM analysis(28). Proc Multtest procedure in SAS 9.1.3was used to obtain the adjusted p-values.

RESULTSLD Patterns in the CRP gene defined by tagging SNPs

Table 1 summarizes the genetic variation within the CRP locus defined by the 13 tSNPs ineach of the four ethnic groups. The allele frequencies for all tSNPs varied significantly byethnicity (all P < 0.0001). The specific locations of these thirteen tSNPs are schematicallypresented in Figure 1, based on NCBI Entrez gene for the CRP gene structure(NT_004487.18), and contig position for each SNP based on NCBI build 36 and dbSNPb129. None of the SNPs, except for rs3093068 in Whites, showed statistically significantdeviation from HWE among controls in each ethnic group (data not shown).

Single-marker association analysisOf the 13 tSNPs genotyped, eleven tSNPs were significantly associated with plasma hsCRPconcentrations after adjustment for matching factors and other potential confounders (seeSupplemental Data Table 1 available at www.clinchem.org with the online version of thispaper). Supplemental Data Figure 1 shows the different pattern in the mean differences(without logarithmic transformations) and 95% confidence intervals (CIs) of hsCRPconcentrations for each SNP, as estimated by an additive genetic model. In an additivemodel, geometric mean differences in plasma hsCRP concentrations were associated with anincreasing number of minor alleles as compared to those homozygous major alleles (i.e. thegenotypes were coded as 0=homozygous major alleles, 1=heterozygotes, and2=homozygous minor alleles). For six tSNPs, carriers of each additional copy of the minorallele were associated with decreased hsCRP concentrations: the geometric mean per-allele

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decrease ranging from 1.07 to 1.46 mg/L(all P < 0.05). In contrast, the minor alleles of fivetSNPs (rs3093059, rs1417938, rs1130864, rs3093075, and rs3093068) were associated withincreased hsCRP concentrations with the geometric mean per-allele increase ranging from1.17 to 1.27mg/L (all P < 0.05). The tSNPs that were associated with plasma hsCRPconcentrations also varied by ethnicity (Supplemental Data Table 2). Figure 2 shows thedifferent pattern in the mean differences (without logarithmic transformations) and 95% CIsof hsCRP values for each SNP by ethnicity, as estimated by an additive genetic model. Nineout of 13 tSNPs were significantly associated with plasma hsCRP concentrations in Whitesand Asian/Pacific Islanders, and eight of these nine tSNPs were common to both ethnicgroups. The one significantly different tSNP, rs1417938 in Whites, rs4275453 in Asian/Pacific Islanders, was associated with increased hsCRP concentrations. The association ofthese tSNPs with higher hsCRP concentrations in Whites and Asian/Pacific Islanders wassignificantly different from that in Blacks and Hispanics where no association with hsCRPconcentrations was observed. In contrast, only four of the 13 tSNPs among Blacks andHispanics were significantly associated with plasma hsCRP concentrations. There was nooverlap in the four significant tSNPs between Blacks and Hispanics.

Haplotype association analysisThe lengths and locations of specific haplotype blocks by ethnicity are presented in Figure 3.Haplotype frequencies and the specific haplotype blocks varied with ethnicity (Figure 3 andTable 2). In Whites, there were three haplotypes in block 1 and five haplotypes in block 2.The 0-0 carriers in block 1 and carriers of 0-1-1-0-0-0-0-0-1-0 in block 2 (where 0 coded formajor allele and 1 coded for minor allele) exhibited the highest hsCRP values withgeometric mean difference in hsCRP concentrations of 1.27 mg/L and 1.21 mg/L comparedwith non-carriers, respectively. We only identified 3 haplotypic blocks of this CRP gene inother ethnicities, each containing two to five haplotypes within each block. Blacks andHispanics had haplotype blocks with similar boundaries whereas block 2 in Asian/PacificIslanders was significantly different from the other ethnic groups. In block 2 for Blacks andHispanics, haplotype 0-0-0-0-0-0-0 carriers had increased hsCRP concentrations (1.23 and1.58 mg/L, respectively) compared with non-carriers.

In addition to examining the haplotype block identified in our study population, we alsoreplicated the haplotypes found in other studies (i.e., rs1130864-rs1205-rs3093068 byDehghan et al(16), and rs1180947-rs1130864-rs1205 by Timpson et al(17) (Table 3 andSupplemental Data Table 3). Among the rs1130864-rs1205-rs3093068 haplotypes, 0-0-1carriers appeared to have increased plasma hsCRP compared with non-carriers, and thisrelationship was consistently observed in all four ethnicities (geometric mean difference =1.24, 1.36, 1.31, and 1.60 mg/L, respectively).

DISCUSSIONIn this large multiethnic cohort of postmenopausal women, common genetic variants in theCRP gene were highly associated with plasma hsCRP concentrations. In particular, thesegenotype-phenotype relationships appeared to vary significantly across ethnic groups.

Several tSNPs (rs1130864, rs1205, rs3093068, rs1800947, rs2794521) identified in ourstudy have been reported previously in both White and African American men and women(15–20). Although the specific effects of these variants on plasma hsCRP concentrationsremain to be determined, it has been estimated in a previous family study that 30–40% of thevariation in plasma hsCRP concentrations may be due to genes(29). In our multi-ethniccohort, common genetic variants in the CRP gene accounted for 4% of the total variation ofplasma hsCRP in Whites, 5% of the variation in Blacks, and 10% of the variation inHispanics and Asian/Pacific Islanders.

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Consistent with prior studies among Whites (19), carriers of minor alleles of rs3093068,rs1130864 and rs1417938 were found to have significantly higher hsCRP concentrations,whereas rs1205 and rs1800947 were associated with lower plasma hsCRP concentrationscompared to non-carriers. The tSNPs rs1130864 and rs1205 appeared to have even greatereffects on plasma hsCRP concentrations in Asian/Pacific Islanders (hsCRP concentrationsincrease by 1.62 mg/L with rs1130864 and decrease by 1.57 mg/L with rs1205). Similarethnic differences were also found for rs3093075 and rs3093059 where greater magnitude ofassociations appeared more evident in Asians and Hispanics than that in Whites (i.e.geometric mean hsCRP values increase by 1.5 to 1.7 mg/L vs. 1.2 mg/L). In contrast,rs1800947 was significantly associated with lower hsCRP concentrations in Whites but notin Hispanics, a finding that has been reported previously(20). The tSNP rs2794521 has notbeen found to be associated with plasma hsCRP concentrations in other studies but has beenreported to be associated with T2DM in Pima Indians(30) and coronary disease in ethnicHan Chinese(31). In the current study, both rs2794521 and rs2808634 were significantlyassociated with lower hsCRP concentrations in Hispanics but not in Whites. The directionand magnitude of associations for rs1205, rs3093075, rs2808629 and rs1470515 weresimilar in Blacks compared to Whites.

Several reasons for the ethnic differences of the gene-phenotype relationships have beennoted previously. The apparently distinct LD patterns of this CRP gene by ethnicity were anovel observation and a unique strength of our multiethnic study, as previous studies havemainly examined tSNPs or haplotypes in European Americans. In prior reports(15;32),rs3091244 was found to be a functional triallelic SNP in the CRP promoter region with highLD to other SNPs (i.e., rs113084, rs1417938 and rs2795421), possibly explaining thesignificant associations found in those studies. There may be further population stratification(33–35) within each ethnic subgroup.I If such stratification is present, the significant ethnicdifferences we found in our study would only be biased toward the null.

Since comprehensive screening of SNPs was conducted in the current study, we were able todefine haplotype structures for each ethnic group beyond those reported in previousstudies(16;17). The haplotype frequencies for Whites were similar to those reported forEuropean Americans(16;17). For example, Timpson et al(17) showed that carriers of C-A-Cin rs1800947, rs1130864, and rs1205 (i.e. 0-1-0 in Table 3 and Supplemental Data Table 3)have the highest plasma hsCRP values whereas GGT carriers have the lowest hsCRPconcentrations. In our study, plasma hsCRP concentrations were 1.21 mg/L (Standard error(SE)=1.04) higher in haplotype 0-1-0 carriers, and 1.49 mg/L (SE=1.07) lower in 1-0-1carriers compared with that of non-carriers. Similar trends were also found in Black andAsian carriers (i.e., carriers of haplotype 0-1-0 carriers had higher hsCRP values comparedto non-carriers). In contrast, carriers of the same haplotypes had lower hsCRPconcentrations than did non-carriers among Hispanics (p>0.05). In the report by Dehghan etal(16), the highest contrast of plasma hsCRP values was found in comparing carriers of theCCG haplotype (defined by three SNPs, rs1130754, rs1205, and rs3093068, same as 0-0-1in Table 3 and Supplemental Data Table 3) with carriers of the most common haplotypeCTC (i.e., 0-1-0 in Supplemental Data Table 3).

More importantly, minor allele frequencies, haplotype structure, and LD patterns varied byethnic group. For example, we observed similar haplotype frequencies in Whites as well assimilar magnitudes of effects on plasma hsCRP concentrations associated with thehaplotypes to those seen in the Dehghan et al study(16) (i.e., increased hsCRPconcentrations by 1.24 mg/L in carriers of 0-0-1 and decreased hsCRP concentrations by1.29 mg/L in carriers of 0-1-0 haplotype). However, no significant associations were foundbetween hsCRP and these haplotypes in the other ethnic groups. In general, our haplotype-based analysis was consistent with the single SNP- plasma hsCRP associations in terms of

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direction and magnitude. We also observed that the direction of the effect remained the samebut the magnitude of the effect varied with ethnicity.

In conclusion, we found that common genetic variants in the CRP gene were substantiallyand independently associated with plasma hsCRP concentrations in this large multiethniccase–control study of postmenopausal women. These associations may differ by ethnicity.Further studies will be warranted to confirm the ethnic differences of CRP gene varianceand the potential direct role of these genetic variants on T2DM risk.

Supplementary MaterialRefer to Web version on PubMed Central for supplementary material.

AcknowledgmentsWe would like to acknowledge all WHI centers, principal investigators and committed participants in this research.The WHI is funded by the National Heart, Lung, and Blood Institute, and U.S. Department of Health and HumanServices. This study was supported by the National Institute of Diabetes and Digestive and Kidney Diseases R01DK062290 from the National Institutes of Health.

ABBREVIATIONS

CRP C-Reactive Protein

tSNPs haplotype tagging SNPs

hsCRP high-sensitivity C-Reactive Protein

T2DM type 2 diabetes mellitus

IRB Institutional Review Board

UCLA University of California, Los Angeles,

WHI-OS Women’s Health Initiative Observational Study

SNP single nucleotide polymorphism

NCBI dbSNP National Center for Biotechnology Information database SNP

ssSNPs splicing-site SNPs

cSNPs nonsynonymous coding SNPs

UTR Untranslated Region

PCR polymerase chain reaction

ABI Applied Biosystems

MAF minor allele frequency

LD linkage disequilibrium

HWE Hardy-Weinberg Equilibrium

GLM general linear models

BMI body mass index

HRT hormone replacement therapy

FDR false discovery rate

SE standard error

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Figure 1.Human C-Reactive Protein (CRP) gene (Chromosome 1q21-q23)

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Figure 2.The adjusted mean difference of plasma hsCRP concentrations (95% confidence intervals)according to CRP gene variation based on an additive genetic model, by ethnicity

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Figure 3.Haploview plot defining ethnic-specific LD structures between the 13 tSNPs within or nearCRP gene among control participants. Each diamond for each SNP combination indicatesthe pairwise LD between all tSNPs. LD strength between the chosen SNPs is determined bythe 90% confidence limits of D′ statistic.

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Tabl

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8)B

lack

s (n=

732)

His

pani

cs (n

=303

)A

sian

/Pac

ific

Isla

nder

s (n=

195)

Pool

ed (n

=2,1

98)

Pd

rs42

7545

35′

flan

king

T/C

37.1

55.7

30.8

26.9

42.0

<0.0

001

rs28

0863

45′

flan

king

C/T

29.7

17.9

21.3

14.0

23.3

<0.0

001

rs30

9305

95′

flan

king

T/C

7.0

23.7

9.1

12.8

13.6

<0.0

001

rs27

9452

15′

flan

king

T/C

30.1

17.6

20.9

12.9

23.2

<0.0

001

rs14

1793

8In

tron1

T/A

29.9

11.7

30.5

7.8

21.9

<0.0

001

rs18

0094

7Ex

on2

G/C

6.0

1.8

3.3

8.3

4.3

<0.0

001

rs11

3086

4Ex

on2

C/T

29.3

16.6

31.9

8.2

23.5

<0.0

001

rs12

05Ex

on2

C/T

32.5

22.0

35.4

64.4

31.7

<0.0

001

rs30

9307

53′

flan

king

C/A

6.8

24.3

9.6

11.8

13.7

<0.0

001

rs30

9306

83′

flan

king

C/G

8.4

24.1

9.0

12.5

14.3

<0.0

001

rs28

0862

93′

flan

king

G/A

32.5

22.9

36.1

64.9

32.1

<0.0

001

rs23

6914

63′

flan

king

G/A

25.0

37.3

20.9

14.9

28.0

<0.0

001

rs14

7051

53′

flan

king

G/A

37.5

28.8

40.8

62.6

36.8

<0.0

001

a From

the

Nat

iona

l Cen

ter f

or B

iote

chno

logy

Info

rmat

ion

(NC

BI)

dbS

NP

data

base

.

b SNP

loca

tion

is b

ased

on

NC

BI E

ntre

z ge

ne fo

r the

CR

P ge

ne st

ruct

ure

(NT_

0044

87.1

8), a

nd c

ontig

pos

ition

for e

ach

SNPs

bas

ed o

n N

CB

I bui

ld 3

6 an

d db

SNP

b129

.

c Maj

or/M

inor

Alle

le b

ased

on

the

NC

BI d

bSN

P.

d P-va

lues

wer

e es

timat

ed b

y a

chi-s

quar

e te

st (d

f=3)

for g

enot

ype

dist

ribut

ion

acro

ss th

e fo

ur e

thni

c gr

oups

.


NIH


NIH


NIH


Lee et al.

Tabl

e 2

Ass

ocia

tions

bet

wee

n et

hnic

-spe

cific

hap

loty

pes o

f CR

P ge

ne a

nd p

lasm

a hs

CR

P co

ncen

tratio

ns

Hap

loty

pe F

requ

ency

Hap

loty

pea

Cas

esC

ontr

ols

Geo

met

ric

Mea

n D

iffer

ence

±(SE

)bP

(FD

R)c

Whi

tes

(n=9

68)

(n=9

68)

Blo

ck 1

rs14

7051

5-rs

2369

146

0-0

40.9

33.2

1.27

± 1

.04

<0.0

01(<

0.00

1)

1-0

35.4

41.8

−1.

20 ±

1.0

3<0

.001

(<0.

001)

0-1

23.4

24.9

−1.

05 ±

1.0

40.

20

Blo

ck 2

rs28

0862

9-rs

3093

068-

rs30

9307

5-rs

1205

-rs1

1308

64-r

s180

0947

-rs1

4179

38-r

s279

4521

-rs3

0930

59-r

s280

8634

0-0-

0-0-

1-0-

1-0-

0-0

32.2

25.7

1.19

± 1

.04

<0.0

01(<

0.00

1)

0-0-

0-0-

0-0-

0-1-

0-1

28.0

27.9

−1.

02 ±

1.0

40.

64

1-0-

0-1-

0-0-

0-0-

0-0

23.4

29.0

−1.

18 ±

1.0

4<0

.001

(<0.

001)

1-0-

0-1-

0-1-

0-0-

0-0

5.0

7.8

−1.

48 ±

1.0

7<0

.001

(<0.

001)

0-1-

1-0-

0-0-

0-0-

1-0

6.9

6.1

1.21

± 1

.07

0.00

4(0.

005)

Bla

cks

(n=3

66)

(n=7

32)

Blo

ck1

rs14

7051

5-rs

2369

146-

rs28

0862

9

0-0-

039

.530

.81.

38 ±

1.0

6<0

.001

(<0.

001)

0-1-

05.

636

.8−1.

06 ±

1.0

60.

31

1-0-

118

.024

.9−1.

29 ±

1.0

7<0

.001

(0.0

02)

1-0-

06.

66.

6−1.

22 ±

1.1

10.

07

Blo

ck2

rs30

9307

5-rs

1205

-rs1

1308

64-r

s180

0947

-rs1

4179

38-r

s279

4521

-rs3

0930

59

1-0-

0-0-

0-0-

124

.123

.21.

07 ±

1.0

60.

27

0-0-

0-0-

0-0-

023

.119

.31.

23 ±

1.0

70.

001(

0.00

5)

0-1-

0-0-

0-0-

016

.323

.2−1.

33 ±

1.0

7<0

.001

(<0.

001)

0-0-

0-0-

0-1-

015

.417

.5−1.

14 ±

1.0

70.

06

0-0-

1-0-

1-0-

012

.610

.51.

08 ±

1.0

90.

35

0-0-

1-0-

0-0-

05.

83.

721.

22 ±

1.1

30.

10

0-1-

0-1-

0-0-

01.

21.

75−1.

29 ±

1.2

50.

25

Blo

ck3

rs28

0863

4-rs

4275

453

0-0

42.5

45.2

−1.

06 ±

1.0

50.

28


NIH


NIH


NIH


Lee et al.

Hap

loty

pe F

requ

ency

Hap

loty

pea

Cas

esC

ontr

ols

Geo

met

ric

Mea

n D

iffer

ence

±(SE

)bP

(FD

R)c

0-1

41.9

37.3

1.14

± 1

.05

0.01

(0.0

4)

1-1

15.6

17.5

−1.

14 ±

1.0

70.

06

His

pani

cs(n

=152

)(n

=303

)

Blo

ck1

rs14

7051

5-rs

2369

146-

rs28

0862

9

0-0-

041

.032

.61.

24 ±

1.0

80.

007(

0.03

)

1-0-

134

.237

.7−1.

07 ±

1.0

80.

41

0-1-

019

.623

.1−1.

08 ±

1.0

90.

39

1-0-

04.

55.

6−1.

42 ±

1.1

80.

03(0

.07)

Blo

ck2

rs30

9307

5-rs

1205

-rs1

1308

64-r

s180

0947

-rs1

4179

38-r

s279

4521

-rs3

0930

59

0-1-

0-0-

0-0-

030

.933

.7−1.

04 ±

1.0

80.

59

0-0-

1-0-

1-0-

031

.129

.21.

04 ±

1.0

90.

67

0-0-

0-0-

0-1-

017

.724

.1−1.

34 ±

1.1

00.

002(

0.00

6)

1-0-

0-0-

0-0-

19.

46.

31.

57 ±

1.1

4<0

.001

(0.0

05)

0-0-

0-0-

0-0-

06.

21.

01.

58 ±

1.1

90.

01(0

.02)

0-1-

0-1-

0-0-

03.

23.

1−1.

02 ±

1.2

50.

93

Blo

ck3

rs28

0863

4-rs

4275

453

0-0

69.9

67.0

1.13

± 1

.08

0.10

1-1

18.2

24.7

−1.

36 ±

1.1

00.

001(

0.00

3)

0-1

11.7

8.4

1.20

± 1.

120.

12

Asi

ans/

Paci

fic Is

land

ers

(n=9

8)(n

=195

)

Blo

ck1

rs14

7051

5-rs

2369

146

1-0

47.1

68.2

−1.

45 ±

1.1

20.

001(

0.00

2)

0-0

37.8

18.4

1.61

± 1

.14

<0.0

01(<

0.00

1)

0-1

15.0

13.2

−1.

00 ±

1.1

80.

98

Blo

ck2

rs28

0862

9-rs

3093

068-

rs30

9307

5-rs

1205

-rs1

1308

64

1-0-

0-1-

049

.671

.7−1.

57 ±

1.1

2<0

.001

(<0.

001)

0-0-

0-0-

016

.213

.01.

08 ±

1.1

90.

66

0-1-

1-0-

014

.79.

71.

48 ±

1.1

90.

02(0

.003

)

0-0-

0-0-

116

.64.

81.

69 ±

1.2

10.

007(

0.01

)

Blo

ck3

rs28

0863

4-rs

4275

453


NIH


NIH


NIH


Lee et al.

Hap

loty

pe F

requ

ency

Hap

loty

pea

Cas

esC

ontr

ols

Geo

met

ric

Mea

n D

iffer

ence

±(SE

)bP

(FD

R)c

0-0

68.5

77.7

−1.

40 ±

1.1

40.

008(

0.01

)

0-1

17.4

9.9

1.89

± 1

.19

<0.0

01(<

0.00

1)

1-1

13.1

12.2

−1.

01 ±

1.1

90.

96

a Hap

loty

pes o

bser

ved

with

≥0.

01 fr

eque

ncy

in a

t lea

st o

ne e

thni

c gr

oup

in th

e m

ultie

thni

c pa

nel (

1=m

ajor

alle

le, 2

=min

or a

llele

).

b Geo

met

ric m

ean

diff

eren

ce a

nd st

anda

rd e

rror

for e

ach

geno

type

was

cal

cula

ted

usin

g ge

nera

l lin

ear r

egre

ssio

n m

odel

s with

adj

ustm

ent f

or m

atch

ing

fact

ors (

age,

eth

nici

ty, c

linic

al c

ente

r, an

d tim

e of

bloo

d dr

aw),

T2D

M, a

nd o

ther

con

foun

ders

incl

udin

g B

MI,

horm

one

repl

acem

ent t

hera

py, a

lcoh

ol c

onsu

mpt

ion,

cig

aret

te sm

okin

g, a

nd p

hysi

cal a

ctiv

ity.

c Adj

uste

d p-

valu

e fo

r p<0

.05

afte

r FD

R


NIH


NIH


NIH


Lee et al.

Tabl

e 3

Geo

met

ric m

ean

diff

eren

ces i

n pl

asm

a hs

CR

P co

ncen

tratio

ns a

ccor

ding

to sp

ecifi

c C

RP

hapl

otyp

e an

d et

hnic

ity e

stim

ated

by

an a

dditi

ve g

enet

ic e

ffec

tm

odel

Hap

loty

pe sp

ecifi

c G

eom

etri

c M

ean

Diff

eren

ce±

(SE

)b

Hap

loty

pea

Whi

teB

lack

His

pani

csA

sian

/Pac

ific

Isla

nder

sA

llc

rs11

3086

4– rs

120

5 –

rs30

9306

8d

0-0-

01.

02 ±

1.0

4−1.

09 ±

1.0

6−1.

10 ±

1.0

91.

10 ±

1.1

9−1.

02 ±

1.0

3

0-1-

0−1.

29 ±

1.0

4***

−1.

34 ±

1.0

7***

−1.

03 ±

1.0

9−1.

56 ±

1.1

2***

−1.

30 ±

1.0

3***

1-0-

01.

20 ±

1.0

4***

1.06

± 1

.09

1.02

± 1

.09

1.70

± 1

.21*

1.17

± 1

.03*

**

0-0-

11.

24 ±

1.0

7***

1.36

± 1

.07*

**1.

31 ±

1.1

41.

60 ±

1.1

9*1.

29 ±

1.0

4***

1-0-

12.

18 ±

1.4

91.

37 ±

1.1

6−1.

20 ±

1.4

5-

1.40

± 1

.12*

*

rs 1

8009

47 -

rs11

3086

4 –

rs 1

205e

0-0-

01.

09 ±

1.0

4*1.

13 ±

1.0

61.

01 ±

1.0

81.

38 ±

1.1

4*1.

10 ±

1.0

3***

0-0-

1−1.

19 ±

1.0

4***

−1.

31 ±

1.0

7***

−1.

01 ±

1.0

9−1.

34 ±

1.1

1*−1.

23 ±

1.0

3***

0-1-

01.

21 ±

1.0

4***

1.13

± 1

.08

1.01

± 1

.09

1.70

± 1

.21*

1.20

± 1

.03*

**

1-0-

1−1.

49 ±

1.0

7***

−1.

40 ±

1.3

0−1.

03 ±

1.2

4−1.

51 ±

1.2

4−1.

47 ±

1.0

6***

a Hap

loty

pes o

bser

ved

with

≥0.

01 fr

eque

ncy

in a

t lea

st o

ne e

thni

c gr

oup

in th

e m

ultie

thni

c pa

nel (

0=m

ajor

alle

le, 1

=min

or a

llele

).

b Geo

met

ric m

ean

diff

eren

ce a

nd st

anda

rd e

rror

for e

ach

geno

type

was

cal

cula

ted

usin

g ge

nera

l lin

ear r

egre

ssio

n m

odel

s with

adj

ustm

ent f

or m

atch

ing

fact

ors (

age,

clin

ical

cen

ter,

and

time

of b

lood

dra

w),

T2D

M, a

nd o

ther

con

foun

ders

incl

udin

g B

MI,

horm

one

repl

acem

ent t

hera

py, a

lcoh

ol c

onsu

mpt

ion,

cig

aret

te sm

okin

g, a

nd p

hysi

cal a

ctiv

ity.

c Geo

met

ric m

ean

diff

eren

ce a

nd st

anda

rd e

rror

for e

ach

geno

type

was

cal

cula

ted

usin

g ge

nera

l lin

ear r

egre

ssio

n m

odel

s with

adj

ustm

ent f

or m

atch

ing

fact

ors (

age,

eth

nici

ty, c

linic

al c

ente

r, an

d tim

e of

blo

oddr

aw),

T2D

M, a

nd o

ther

con

foun

ders

incl

udin

g B

MI,

horm

one

repl

acem

ent t

hera

py, a

lcoh

ol c

onsu

mpt

ion,

cig

aret

te sm

okin

g, a

nd p

hysi

cal a

ctiv

ity.

d Hap

loty

pe st

ruct

ure

from

the

Deh

ghan

et a

l.(20

07)(

16)

e Hap

loty

pe st

ruct

ure

from

Tim

pson

et a

l (20

05)(

17)

* Adj

uste

d p-

valu

e<0.

05 a

fter F

DR

**A

djus

ted

p-va

lue<

0.01

afte

r FD

R

*** A

djus

ted

p-va

lue<

0.00

1 af

ter F

DR


Relation of Genetic Variation in the Gene Coding for C-Reactive Protein with Its Plasma Protein...

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Transcript of Relation of Genetic Variation in the Gene Coding for C-Reactive Protein with Its Plasma Protein...