Original Article

Rare Variant APOC3 R19X Is Associated With Cardio-Protective Profiles in a Diverse Population-Based Survey as Part of the Epidemiologic Architecture for Genes Linked to Environment StudyCLINICAL PERSPECTIVE

Dana C. Crawford, Logan Dumitrescu, Robert Goodloe, Kristin Brown-Gentry, Jonathan Boston, Bob McClellan, Cara Sutcliffe, Rachel Wiseman, Paxton Baker, Margaret A. Pericak-Vance, William K. Scott, Melissa Allen, Ping Mayo, Nathalie Schnetz-Boutaud, Holli H. Dilks, Jonathan L. Haines, Toni I. Pollin
https://doi.org/10.1161/CIRCGENETICS.113.000369
Circulation: Genomic and Precision Medicine. 2014;7:848-853
Originally published November 1, 2014

Jump to

Abstract

Background—A founder mutation was recently discovered and described as conferring favorable lipid profiles and reduced subclinical atherosclerotic disease in a Pennsylvania Amish population. Preliminary data have suggested that this null mutation APOC3 R19X (rs76353203) is rare in the general population.

Methods and Results—To better describe the frequency and lipid profile in the general population, we as part of the Population Architecture using Genomics and Epidemiology I Study and the Epidemiological Architecture for Genes Linked to Environment Study genotyped rs76353203 in 1113 Amish participants from Ohio and Indiana and 19 613 participants from the National Health and Nutrition Examination Surveys (NHANES III, 1999 to 2002, and 2007 to 2008). We found no carriers among the Ohio and Indiana Amish. Of the 19 613 NHANES participants, we identified 31 participants carrying the 19X allele, for an overall allele frequency of 0.08%. Among fasting adults, the 19X allele was associated with lower triglycerides (n=7603; β=−71.20; P=0.007) and higher high-density lipoprotein cholesterol (n=8891; β=15.65; P=0.0002) and, although not significant, lower low-density lipoprotein cholesterol (n=6502; β= -4.85; P=0.68) after adjustment for age, sex, and race/ethnicity. On average, 19X allele participants had approximately half the triglyceride levels (geometric means, 51.3 to 69.7 versus 134.6 to 141.3 mg/dL), >20% higher high-density lipoprotein cholesterol levels (geometric means, 56.8 to 74.4 versus 50.38 to 53.36 mg/dL), and lower low-density lipoprotein cholesterol levels (geometric means, 104.5 to 128.6 versus 116.1 to 125.7 mg/dL) compared with noncarrier participants.

Conclusions—These data demonstrate that APOC3 19X exists in the general US population in multiple racial/ethnic groups and is associated with cardio-protective lipid profiles.

Introduction

Both common and rare genetic variation is associated with lipid trait distributions. Candidate gene and genome-wide association studies in populations of mostly European descent have identified >150 common genetic variants associated with high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C), triglyceride, and total cholesterol levels.1,2 Early linkage and family-based studies have identified rare mutations linked to extreme lipid trait profiles associated with dyslipidemias.3 More recent population-based sequencing studies are bridging the gap between common genetic variation and disease-causing mutations with the discovery and catalog of additional rare and less common variation (frequency <1% in the general population) impacting lipid trait profiles in humans.4–10

Clinical Perspective on p 853

One such rare variant discovered in a Pennsylvania Old Order Amish population sample11 and recently described in the National Heart, Lung, and Blood Institute Exome Sequencing Project12,13 is APOC3 R19X (rs76353203). This null mutation was associated with cardio-protective profiles in the Amish, including significantly higher levels of HDL-C and lower levels of triglycerides and total cholesterol levels compared with noncarriers.11 Pennsylvania Amish carriers of 19X were also less likely to have detectable coronary artery calcification compared with noncarriers, which is consistent with their cardio-protective profiles.11 In contrast to the Pennsylvania Amish population, no 19X carriers were identified in a preliminary study of 214 European American adults from Baltimore, Maryland, suggesting that this variant is rare in the general population.11

To date, the rare APOC3 R19X has not yet been characterized in a large and diverse general population or other Amish populations. Therefore, to further characterize this variant in other populations, we as part of the Epidemiological Architecture for Genes Linked to Environment Study, a member of the Population Architecture using Genomics and Epidemiology (PAGE) I Study,14 genotyped APOC3 R19X in 19 613 Americans (including non-Hispanic whites, non-Hispanic blacks, and Mexican Americans) ascertained for the National Health and Nutrition Examination Surveys (NHANES). We also genotyped 1113 Old Order Amish from Ohio and Indiana ascertained for studies of aging and dementia. Overall, we found the 19X variant to be present but rare in the general American population and on the same single haplotype as in the Lancaster Amish; 19X was absent in this sample of Old Order Amish from the Midwestern United States. These data confirm the association between APOC3 R19X and cardio-protective lipid profiles and provide the first glimpse of carrier rates in a general population of Americans.

Methods

Study Population

The National Health and Nutrition Examination Surveys are conducted by the National Center for Health Statistics at the Centers for Disease Control and Prevention. The NHANES participants included in this study were ascertained as part of NHANES III phase 2 (between 1991 and 1994), NHANES 1999 to 2000, NHANES 2001 to 2002, and NHANES 2007 to 2008. NHANES is a national representative survey of noninstitutionalized Americans ascertained regardless of health status. NHANES collects data on health and lifestyle of participants via questionnaires, laboratory measures, and a physical examination administered by Centers for Disease Control (CDC) health professionals.

We accessed data for serum HDL-C, triglycerides, and total cholesterol, which were all measured using standard enzymatic methods. LDL-C was calculated using the Friedewald equation, with missing values assigned for samples with triglyceride levels >400 mg/dL. Body mass index (kg/m2) was calculated from measured height and weight as part of the physical examination in the CDC Mobile Examination Center. A total of 19 613 samples were available for study from consenting participants. All procedures were approved by the CDC Ethics Review Board and written informed consent was obtained from all participants. Because no identifying information is available to the investigators, Vanderbilt University’s Institutional Review Board determined that this study met the criteria of nonhuman subjects.

The Old Order Amish participants included in this study were originally ascertained as part of a population-based study of aging and dementia conducted between 1998 and present in the Amish communities of Adams, Elkhart, and LaGrange Counties in Indiana and Holmes County in Ohio. Study population characteristics of the Old Order Amish have been previously described.15 Briefly, the Amish immigrated to the United States from Europe in 2 waves. The first wave arrived and settled in Pennsylvania in the early 1700s and some of these families proceeded to migrate west to Ohio in the 18th and 19th centuries.16 A second wave of European Amish with distinct surnames arrived in Pennsylvania in the 1800s but continued westward to Indiana and Ohio.17,18 A third wave of immigrants from Switzerland settled in Adams County, Indiana in the mid-1800s. Written informed consent was obtained for all Old Order Amish participants or their legal guardians. A total of 1113 unique DNA samples were available for genotyping in this study, of which 143 were cases of dementia, 620 were controls, and 350 were of unknown dementia status. Biomarker data were not available on the Midwestern Amish samples.

Genotyping

Genotyping was conducted by the Vanderbilt DNA Resources Core using Applied Biosystems’ custom TaqMan assay with the following primers and probes: 5′-CCTCCTGGCGCTCCTG-3′ (forward), 5′-CCAAGTTGCCTCCACCCT-3′ (reverse), 5′-CAAGTGCTTACGGGCAGA-3′ (G allele probe), and 5′-CAAGTGCTTACAGGCAGA-3′ (A allele probe). To evaluate the assay and to assist in clustering the rare variant, 94 deidentified samples consisting of 39 Pennsylvania Amish individuals heterozygous for R19X and 55 relatives without the mutation11 were genotyped blinded by mutation status. In addition to experimental NHANES DNA, we genotyped blinded duplicates provided by CDC for concordance checks and quality control. The genotyping call rate for rs76353203 in NHANES DNA samples and the Old Order Amish samples was ≈95% and 98%, respectively.

For haplotype inference in the Pennsylvania Amish subjects, 211 individuals were genotyped for both rs7635320311 and the Illumina Omni 2.5 mol/L Beadchip. Originally 1472 individuals were genotyped for 2 443 179 single nucleotide polymorphisms (SNPs). The 6 Beadchip SNPs used in the haplotype inference (using Haploview)19 and comparison with NHANES III were among the 2 391 559 passing quality control filters, which comprised exclusion of SNPs with >2% duplicate inconsistency, >5% missing data, >5 Mendelian inconsistencies, Hardy–Weinberg Equilibrium P<10−6, mitochondrial location, minor allele frequency <0.01, as well as duplicated and nonuniquely mapped SNPs.

Statistical Analysis

Allele frequencies were calculated for 19X. Tests of association were limited to fasting (≥8 hours since last meal) adults (≥18 years of age), and study population characteristics are given in Table 1. We performed an SNP test of association assuming a dominant genetic model using linear regression. HDL-C, LDL-C, triglycerides each were the dependent variables as continuous traits. Models were adjusted for age, sex, and self-reported race/ethnicity. Logistic regressions were performed for each NHANES (III, 1999 to 2002, and 2007 to 2008) with SAS v9.2 (SAS Institute, Cary, NC) using the Analytic Data Research by E-mail portal of the CDC Research Data Center in Hyattsville, MD. Meta-analyses were conducted using a fixed-effects inverse-variance weighted approach using METAL.20 METAL also implements Cochran Q-test for heterogeneity. To facilitate comparisons of the genetic effect of 19X across lipid traits across studies, we also calculated the geometric means by carrier status. Haplotypes were inferred using PHASE v2.1.121,22 for 35 genetic variants in the APOA5/A4C3/A1 gene cluster on chromosome 11. The 35 genetic variants included APOC3 R19X and genetic variants selected as tagSNPs (based on data from Fullerton et al)23 and genotyped in NHANES III for previous lipid trait genetic association studies24,25 (Table I in the Data Supplement). These Genetic NHANES data are available for secondary analysis via the CDC.

View this table:
Table 1.

NHANES Study Population Characteristics for Fasting Adults by Survey

Results

General Population

To estimate the prevalence of the APOC3 19X allele in a general population from the United States, we genotyped rs76353203 in a total of 19 613 DNA samples from participants ascertained as part of NHANES III, NHANES 1999 to 2002, and NHANES 2007 to 2008. We identified a total of 31 carriers of the 19X allele among all participants genotyped. The overall frequency of the 19X allele was 0.08% in this US population. Among the 3 major NHANES racial/ethnic groups, the 19X allele was observed at a higher frequency among Mexican Americans (0.23% allele frequency) and non-Hispanic whites (0.20% allele frequency) compared with non-Hispanic blacks (0.0124% allele frequency).

We next characterized the haplotype background containing APOC3 19X in the 10 carriers identified in NHANES III to establish the number of haplotype backgrounds associated with the mutation event. A total of 35 genetic variants spanning the APOA5/A4/C3/A1 gene cluster on chromosome 11 were available for haplotype inference in NHANES III only (Table I in the Data Supplement). All 10 19X alleles in NHANES III were inferred on a single haplotype background, suggesting that this mutation occurred once (Table II in the Data Supplement). This haplotype background was identical to the second most common haplotype in the population at all loci except R19X. Using data from 211 individuals in the Pennsylvania Amish genotyped for both APOC3 R19X and the Illumina Omni 2.5 mol/L Beadchip, we identified 6 polymorphic markers genotyped in both the Amish and NHANES samples. These 6 markers along with APOC3 R19X uniquely tagged 8 of the 10 common haplotypes and collapsed 2 pairs of haplotypes. The Amish haplotype containing the APOC3 R19X variant was identical to the NHANES III R19X haplotype, but found at a frequency of 0.028 versus 0.0007 in NHANES III consistent with a founder effect and genetic drift (Table III in the Data Supplement; also shows frequency of haplotypes in the 1000 Genomes Project).

To assess the relationship between APOC3 R19X and lipid profiles in the general population, we performed a test of association between the rare variant and HDL-C, LDL-C, and triglycerides among fasting adults (Table 1). Overall, the 19X allele was associated with lower triglycerides (β=−71.20±26.45 [SEM] ln mg/dL; P=0.007) and higher HDL-C (β=+15.65±4.23 mg/dL; P=2.1×10−4) after adjustment for age, sex, and race/ethnicity (Table 2). The 19X allele was not significantly associated with LDL-C in adjusted analyses (β=−4.85±11.65 mg/dL; P=0.68). There was no evidence for heterogeneity for any of the 3 meta-analyzed lipids traits (pheterogeneity=0.226, 0.794, and 0.997 for HDL-C, LDL-C, and triglycerides, respectively). On average, participants with the 19X allele had approximately half the triglyceride levels, >20% higher HDL-C levels, and, although not statistically significant, had lower LDL-C levels compared with RR homozygotes (Table 3). In contrast, there was no association between the 19X allele and body mass index (β=2.16±1.82; P=0.234), as was the case in the Pennsylvania Amish.11

View this table:
Table 2.

Meta-Analysis Results for APOC3 R19X and Lipid Traits in NHANES

View this table:
Table 3.

Geometric Means and SD of HDL-C, LDL-C, and TG Levels Among Fasting Adults by APOC3 19X Carrier Status and NHANES

Midwestern US Amish Population

The original discovery of APOC3 R19X involved Amish participants from Pennsylvania.11 Given the migration patterns and history of the Amish in the Americans, we sought to estimate the prevalence of 19X in a non-Pennsylvania Amish population to determine if the cardio-protective variant is common in the Amish that settled in Ohio and Indiana. Among the 1113 Amish participants from Indiana and Ohio genotyped for APOC3 R19X, no carriers were detected. Detailed examination of the pedigree connections between the sampled Ohio/Indiana Amish and the Pennsylvania Amish indicate that only 2 founders of the sampled Ohio/Indiana Amish were directly descended from the most recent common ancestor of all Pennsylvania Amish individuals possessing the R19X variant.11 This suggests that the 19X allele was either lost in this sample because of chance nontransmission, the variant is much less frequent compared with the Pennsylvania Amish, or the variant was not detected because of genotyping error.

Discussion

We estimated the prevalence of the APOC3 19X allele to be 0.08% in a general population from the United States ascertained regardless of health status, with allele frequencies highest among Mexican Americans (0.23%) and non-Hispanic whites (0.20%) and lowest among non-Hispanic blacks (0.0124%). We also replicated the association between APOC3 rs76353203 and cardio-protective lipid profiles first described in a Pennsylvania Amish population. APOC3 19X carriers in NHANES on average had significantly higher HDL-C (geometric means, 64 versus 52 mg/dL) and lower triglycerides (geometric means, 62 versus 137 mg/dL) compared with noncarriers, similar to the effects reported in the Pennsylvania Amish carriers of 19X (median HDL-C, 67 versus 55 mg/dL; median triglycerides, 31 versus 57 mg/dL).11 We also observed a trend for lower LDL-C levels among APOC3 19X carriers versus noncarriers (117 versus 122 mg/dL), which, although not statistically significant, was in the same direction as was seen in the Pennsylvania Amish (116 versus 140 mg/dL).11

We did not identify any APOC3 19X carriers among 1113 Amish from Ohio and Indiana. These data coupled with NHANES data of an overall frequency of 0.08% suggest that APOC3 19X is a rare variant in most populations. Interestingly, among the 31 carriers identified in NHANES, the overwhelming majority were either self-identified non-Hispanic white or Mexican American. Indeed, frequency of 19X in non-Hispanic blacks is >15 times less than that for the other 2 groups. Furthermore, the mutation was observed on a single haplotype background in all NHANES III participants and the Amish subjects. In the National Heart, Lung, and Blood Institute Exome Sequencing Project, the 19X allele was less common in European Americans than in NHANES (allele frequency 0.03% [3/8588 alleles] in 4294 individuals) but nonexistent (0/4402 alleles) in blacks.12,13 Collectively, these data suggest that the founding mutation event occurred once.

Since the writing of this article, Tachmazidou and colleagues26 published frequency estimates of APOC3 R19X in a Greek population isolate. Among 1267 individuals, 3.8% were identified as carriers of the 19X allele, with an overall allele frequency of 1.9% in this isolated population.26 In contrast, the 19X allele was found only among 4 of the 3621 participants whole genome sequenced from the UK10K project,27 for an overall allele frequency of 0.05%. The allele frequency estimated by the UK10K project (0.05%) is similar to the overall frequency estimated in NHANES (0.08%), reflecting the fact that both surveys ascertained participants without regard to disease unlike the Exome Sequencing Project, which ascertained cases and controls of various diseases and extremes of quantitative trait distributions for ≥7 studies. In the case of the UK10K project, the whole genome sequence data were generated on well-phenotyped controls from the TwinsUK and Avon Longitudinal Study of Parents and Children Study.27 Also like NHANES, Tachmazidou et al26 found the 19X allele on a single haplotype background in both the Greek population isolate and the UK10K data sets, suggesting a single origin of the mutation. And, Tachmazidou et al26 replicated the association between 19X and lower triglyceride levels and higher HDL-C levels compared with noncarriers. Together, these data establish the association between 19X and cardioprotective lipid profiles in both isolate and outbred populations.

This study has many strengths, including sample size (≈20 000 total DNA samples) and diversity (3 racial/ethnic groups). Despite these strengths, this study also has several weaknesses. First, given that the allele frequency in African-descent populations is low, the sample size for non-Hispanic blacks in NHANES is not sufficient for accurate estimates especially given the error rate of the assay is nearly equal to the frequency estimate of the overall population. Second, the Ohio and Indiana Amish population genotyped here was ascertained for studies related to aging and dementia, and it is possible that ascertainment bias may be an explanation for the lack of 19X carriers in the non-Pennsylvania Amish. However, given that most of the genotyped Amish were free of dementia and were older than a general population, the sample was likely biased toward more 19X carriers. These data coupled with examination of the pedigrees suggest that the founder mutation described in the Pennsylvania Amish was lost by chance nontransmission in the Ohio and Indiana Amish (although differences in frequency of the mutation between Amish samples or genotyping error cannot yet be ruled out). Third, while we replicated the genetic association between APOC3 19X and cardio-protective profiles in NHANES, we were limited to HDL-C, LDL-C, and triglyceride levels. NHANES does not regularly measure other lipid traits such as non-HDL or very low-density lipoprotein. NHANES also does not determine coronary artery calcification in participants. Finally, given the wide age range of NHANES (children to older adults), NHANES has few cases of myocardial infarction or other clinical outcomes. Therefore, this study was limited in exploring the extent of cardio-protection afforded by APOC3 19X in NHANES.

There are other limitations worth noting that may have affected the allele frequency estimations presented here. The frequencies presented here were not weighted to account for the complex survey design used to ascertain participants for NHANES. The sample design differs by survey, and NHANES provides sampling weights by survey (and by variable, if applicable). NHANES does not yet provide sampling weights for analyses combining all Genetic NHANES (NHANES III, 1999 to 2002, and 2007 to 2008). It is, in fact, unclear if sampling weights can be calculated for the Genetic NHANES data set given the original surveys were conducted during different census years. Given the lack of sampling weights, we have analyzed the data unweighted, and this may have slightly overestimated the point estimate of the allele frequencies for all racial/ethnic groups presented here. It is difficult, however, to assess the extent of overestimation given that the genotyping performed here may have also introduced both false positives and false negatives. TaqMan genotyping assays are generally associated with low error rates of 0.1%,28 with published error rates as low as <1 in 2000 genotypes or 0.05%.29 On the basis of these error rates, we would expect 10 to 20 genotyping errors among 19 613 NHANES participants genotyped for rs76353203 using this assay. Given the PAGE I Study only supported genotyping, we were unable to verify the 31 identified carriers of the 19X via resequencing. Comparisons of the frequencies estimated here to the UK10K Project described above and replication of the associations between 19X and HDL-C and triglycerides as reported in several populations, however, suggest that the effect of the absence of sample weights or genotyping error is minimal.

Despite these limitations, these data establish APOC3 R19X as a variant present in the general outbred population at an appreciable, albeit low, frequency with favorable effects on lipid profiles similar to that observed in the Pennsylvania Amish. Recent Phase I clinical trials have shown that inhibition of apoC-III leads to reductions in plasma apoC-III and triglycerides in humans,30 both of which are associated with risk of cardiovascular disease. Further studies are needed to establish the relevance of APOC3 in cardiovascular disease prediction, drug therapy, and other possible clinical applications.

Acknowledgments

We at Epidemiological Architecture for Genes Linked to Environment would like to thank Dr Geraldine McQuillan and Jody McLean for their help in accessing the Genetic NHANES data and Keith Tanner for technical assistance in assembling the Pennsylvania Amish positive control samples. The Vanderbilt University Center for Human Genetics Research, Computational Genomics Core provided computational or analytic support for this work. The findings and conclusions in this report are those of the authors and do not necessarily represent the views of the National Institutes for Health or the Centers for Disease Control and Prevention.

Sources of Funding

Genotyping in National Health and Nutrition Examination Surveys (NHANES) was supported in part by the Epidemiological Architecture for Genes Linked to Environment Study (U01HG004798 and its ARRA supplements) as part of the Population Architecture using Genomics and Epidemiology Study established by the National Human Genome Research Institute. Select NHANES III data presented here were genotyped under funding provided by the University of Washington’s Center for Ecogenetics and Environmental Health supported by the National Institute of Environmental Sciences (5 P30 ES007033-12). Also, genotyping services for select NHANES III single nucleotide polymorphism (SNPs) presented here were provided by the Johns Hopkins University under federal contract number (N01-HV-48195) from National Heart, Lung, and Blood Institute. Genotyping and analysis in Pennsylvania Amish samples supported by National Institutes of Health (NIH) R01 HL088119, R01 AR046838, U01 HL72515, R01 AG18728, U01 HL084756, R01 HL104193, and R01 CA122844; General Clinical Research Centers Program, National Center for Research Resources, NIH; the University of Maryland General Clinical Research Center, grant M01 RR 16500; University of Maryland Nutrition and Obesity Research Center grant P30 DK072488. The collection and genotyping of the Indiana/Ohio Amish samples was supported by the NIH grants AG019085 (to Dr Haines and Dr Pericak-Vance) and AG019726 (to Dr Scott). We thank Dr Julie Douglas for kindly sharing the Illumina Omni 2.5 mol/L Beadchip SNP genotypes obtained in the Old Order Amish as part of R01 CA122844.

Disclosures

None.

  • Received October 1, 2013.
  • Accepted September 16, 2014.

References

  1. 1.↵
    Global Lipids Genetics Consortium. Discovery and refinement of loci associated with lipid levels. Nat Genet. 2013;45:1274–1283.
    OpenUrlCrossRefPubMed
  2. 2.↵
    1. Teslovich TM,
    2. Musunuru K,
    3. Smith AV,
    4. Edmondson AC,
    5. Stylianou IM,
    6. Koseki M,
    7. et al
    . Biological, clinical and population relevance of 95 loci for blood lipids. Nature. 2010;466:707–713.
    OpenUrlCrossRefPubMed
  3. 3.↵
    1. Hegele RA
    . Plasma lipoproteins: genetic influences and clinical implications. Nat Rev Genet. 2009;10:109–121.
    OpenUrlCrossRefPubMed
  4. 4.↵
    1. Cohen JC,
    2. Kiss RS,
    3. Pertsemlidis A,
    4. Marcel YL,
    5. McPherson R,
    6. Hobbs HH
    . Multiple rare alleles contribute to low plasma levels of HDL cholesterol. Science. 2004;305:869–872.
    OpenUrlAbstract/FREE Full Text
  5. 5.↵
    1. Cohen J,
    2. Pertsemlidis A,
    3. Kotowski IK,
    4. Graham R,
    5. Garcia CK,
    6. Hobbs HH
    . Low LDL cholesterol in individuals of African descent resulting from frequent nonsense mutations in PCSK9. Nat Genet. 2005;37:161–165.
    OpenUrlCrossRefPubMed
  6. 6.↵
    1. Kotowski IK,
    2. Pertsemlidis A,
    3. Luke A,
    4. Cooper RS,
    5. Vega GL,
    6. Cohen JC,
    7. et al
    . A spectrum of PCSK9 alleles contributes to plasma levels of low-density lipoprotein cholesterol. Am J Hum Genet. 2006;78:410–422.
    OpenUrlCrossRefPubMed
  7. 7.↵
    1. Musunuru K,
    2. Pirruccello JP,
    3. Do R,
    4. Peloso GM,
    5. Guiducci C,
    6. Sougnez C,
    7. et al
    . Exome sequencing, ANGPTL3 mutations, and familial combined hypolipidemia. N Engl J Med. 2010;363:2220–2227.
    OpenUrlCrossRefPubMed
  8. 8.↵
    1. Rios J,
    2. Stein E,
    3. Shendure J,
    4. Hobbs HH,
    5. Cohen JC
    . Identification by whole-genome resequencing of gene defect responsible for severe hypercholesterolemia. Hum Mol Genet. 2010;19:4313–4318.
    OpenUrlAbstract/FREE Full Text
  9. 9.↵
    1. Romeo S,
    2. Pennacchio LA,
    3. Fu Y,
    4. Boerwinkle E,
    5. Tybjaerg-Hansen A,
    6. Hobbs HH,
    7. et al
    . Population-based resequencing of ANGPTL4 uncovers variations that reduce triglycerides and increase HDL. Nat Genet. 2007;39:513–516.
    OpenUrlCrossRefPubMed
  10. 10.↵
    1. Lange L,
    2. Hu Y,
    3. Zhang H,
    4. Xue C,
    5. Schmidt E,
    6. Tang ZZ,
    7. et al
    . Whole-exome sequencing identifies rare and low-frequency coding variants associated with LDL cholesterol. Am J Hum Genet. 2014;94:233–245.
    OpenUrlCrossRefPubMed
  11. 11.↵
    1. Pollin TI,
    2. Damcott CM,
    3. Shen H,
    4. Ott SH,
    5. Shelton J,
    6. Horenstein RB,
    7. et al
    . A null mutation in human APOC3 confers a favorable plasma lipid profile and apparent cardioprotection. Science. 2008;322:1702–1705.
    OpenUrlAbstract/FREE Full Text
  12. 12.↵
    1. Tennessen JA,
    2. Bigham AW,
    3. O’Connor TD,
    4. Fu W,
    5. Kenny EE,
    6. Gravel S,
    7. et al
    . Evolution and functional impact of rare coding variation from deep sequencing of human exomes. Science. 2012;337:64–69.
    OpenUrlAbstract/FREE Full Text
  13. 13.↵
    1. Fu W,
    2. ‘Connor TD,
    3. Jun G,
    4. Kang HM,
    5. Abecasis G,
    6. Leal SM,
    7. et al
    . Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants. Nature. 2013;493:216–220.
    OpenUrlCrossRefPubMed
  14. 14.↵
    1. Matise TC,
    2. Ambite JL,
    3. Buyske S,
    4. Carlson CS,
    5. Cole SA,
    6. Crawford DC,
    7. et al
    ; PAGE Study. The next PAGE in understanding complex traits: design for the analysis of Population Architecture Using Genetics and Epidemiology (PAGE) Study. Am J Epidemiol. 2011;174:849–859.
    OpenUrlAbstract/FREE Full Text
  15. 15.↵
    1. Edwards DR,
    2. Gilbert JR,
    3. Jiang L,
    4. Gallins PJ,
    5. Caywood L,
    6. Creason M,
    7. et al
    . Successful aging shows linkage to chromosomes 6, 7, and 14 in the Amish. Ann Hum Genet. 2011;75:516–528.
    OpenUrlCrossRefPubMed
  16. 16.↵
    1. Walt J,
    2. Scott W,
    3. Slifer S,
    4. Gaskell PC,
    5. Martin E,
    6. Welsh-Bohmer K,
    7. et al
    . Maternal lineages and Alzheimer disease risk in the Old Order Amish. Hum Genet. 2005;118:115–122.
    OpenUrlCrossRefPubMed
  17. 17.↵
    1. Hostetler JA
    Amish Society. Baltimore, MD: Johns Hopkins University Press; 1993.
  18. 18.↵
    1. Hostetler JA
    Hutterite Society. Baltimore, MD: Johns Hopkins University Press; 1997.
  19. 19.↵
    1. Barrett JC,
    2. Fry B,
    3. Maller J,
    4. Daly MJ
    . Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics. 2005;21:263–265.
    OpenUrlAbstract/FREE Full Text
  20. 20.↵
    1. Willer CJ,
    2. Li Y,
    3. Abecasis GR
    . METAL: fast and efficient meta-analysis of genomewide association scans. Bioinformatics. 2010;26:2190–2191.
    OpenUrlAbstract/FREE Full Text
  21. 21.↵
    1. Stephens M,
    2. Smith NJ,
    3. Donnelly P
    . A new statistical method for haplotype reconstruction from population data. Am J Hum Genet. 2001;68:978–989.
    OpenUrlCrossRefPubMed
  22. 22.↵
    1. Stephens M,
    2. Scheet P
    . Accounting for decay of linkage disequilibrium in haplotype inference and missing-data imputation. Am J Hum Genet. 2005;76:449–462.
    OpenUrlCrossRefPubMed
  23. 23.↵
    1. Fullerton SM,
    2. Buchanan AV,
    3. Sonpar VA,
    4. Taylor SL,
    5. Smith JD,
    6. Carlson CS,
    7. et al
    . The effects of scale: variation in the APOA1/C3/A4/A5 gene cluster. Hum Genet. 2004;115:36–56.
    OpenUrlCrossRefPubMed
  24. 24.↵
    1. Dumitrescu L,
    2. Carty CL,
    3. Taylor K,
    4. Schumacher FR,
    5. Hindorff LA,
    6. Ambite JL,
    7. et al
    . Genetic determinants of lipid traits in diverse populations from the population architecture using genomics and epidemiology (PAGE) study. PLoS Genet. 2011;7:e1002138.
    OpenUrlCrossRefPubMed
  25. 25.↵
    1. Keebler ME,
    2. Sanders CL,
    3. Surti A,
    4. Guiducci C,
    5. Burtt NP,
    6. Kathiresan S
    . Association of blood lipids with common DNA sequence variants at 19 genetic loci in the multiethnic United States National Health and Nutrition Examination Survey III/CLINICAL PERSPECTIVE. Circ Cardiovasc Genet. 2009;2:238–243.
    OpenUrlAbstract/FREE Full Text
  26. 26.↵
    1. Tachmazidou I,
    2. Dedoussis G,
    3. Southam L,
    4. Farmaki AE,
    5. Ritchie GRS,
    6. Xifara DK,
    7. et al
    . A rare functional cardioprotective APOC3 variant has risen in frequency in distinct population isolates. Nat Commun. 2013;4:2872.
    OpenUrlPubMed
  27. 27.↵
    1. Muddyman D,
    2. Smee C,
    3. Griffin H,
    4. Kaye J
    . Implementing a successful data-management framework: the UK10K managed access model. Genome Med. 2013;5:100.
    OpenUrlCrossRefPubMed
  28. 28.↵
    1. De La Vega FM,
    2. Isaac H,
    3. Collins A,
    4. Scafe CR,
    5. Halldorsson BV,
    6. Su X,
    7. et al
    . The linkage disequilibrium maps of three human chromosomes across four populations reflect their demographic history and a common underlying recombination pattern. Genome Res. 2005;15:454–462.
    OpenUrlAbstract/FREE Full Text
  29. 29.↵
    1. Ranade K,
    2. Chang MS,
    3. Ting CT,
    4. Pei D,
    5. Hsiao CF,
    6. Olivier M,
    7. et al
    . High-throughput genotyping with single nucleotide polymorphisms. Genome Res. 2001;11:1262–1268.
    OpenUrlAbstract/FREE Full Text
  30. 30.↵
    1. Graham MJ,
    2. Lee RG,
    3. Bell TA III.,
    4. Fu W,
    5. Mullick AE,
    6. Alexander VJ,
    7. et al
    . Antisense oligonucleotide inhibition of apolipoprotein C-III reduces plasma triglycerides in rodents, nonhuman primates, and humans. Circ Res. 2013;112:1479–1490.
    OpenUrlAbstract/FREE Full Text

CLINICAL PERSPECTIVE

Decades of genetic studies spanning linkage studies, candidate gene and genome-wide association studies, and contemporary sequencing studies have identified hundreds of rare and common genetic variants associated with lipid profiles within the normal range as well as extreme lipid profiles associated with dyslipidemia. One recently identified variant in a Pennsylvania Old Order Amish population is rs76353203 (R19X), a rare null variant in apolipoprotein C III (APOC3) that was associated with cardio-protective profiles including significantly higher levels of high density lipoprotein (HDL) cholesterol and lower levels of triglycerides and total cholesterol levels compared with noncarriers of the mutation. Preliminary data in European-descent outbred populations suggested that APOC3 19X is rare in the general population. In this study, we sought to further characterize the frequency of APOC3 rs76353203 and replicate the reported associations in 19 613 participants from 3 National Health and Nutrition Examination Surveys (NHANES III, NHANES 1999 to 2002, and NHANES 2007 to 2008). We estimated the prevalence of the APOC3 19X allele to be 0.08% in a general population from the United States ascertained regardless of health status, with allele frequencies highest among Mexican Americans (0.23%) and non-Hispanic whites (0.20%) and lowest among non-Hispanic blacks (0.0124%). We also replicated the association between APOC3 rs76353203 and cardio-protective lipid profiles. These data establish APOC3 19X is present in the general outbred population at an appreciable, albeit low, frequency with favorable effects on lipid profiles. Further studies are needed to establish the relevance of APOC3 in cardiovascular disease prediction, drug therapy, and other possible clinical applications.

View Abstract

This Issue

Jump to

Article Tools

  • Print
  • Citation Tools
  • Article Alerts
  • Save to my folders

Share this Article

  • Email
  • Rare Variant APOC3 R19X Is Associated With Cardio-Protective Profiles in a Diverse Population-Based Survey as Part of the Epidemiologic Architecture for Genes Linked to Environment StudyCLINICAL PERSPECTIVE
    Dana C. Crawford, Logan Dumitrescu, Robert Goodloe, Kristin Brown-Gentry, Jonathan Boston, Bob McClellan, Cara Sutcliffe, Rachel Wiseman, Paxton Baker, Margaret A. Pericak-Vance, William K. Scott, Melissa Allen, Ping Mayo, Nathalie Schnetz-Boutaud, Holli H. Dilks, Jonathan L. Haines and Toni I. Pollin
    Circulation: Genomic and Precision Medicine. 2014;7:848-853, originally published November 1, 2014
    https://doi.org/10.1161/CIRCGENETICS.113.000369
    del.icio.us logo Digg logo Reddit logo Twitter logo CiteULike logo Facebook logo Google logo Mendeley logo

Related Articles

Cited By...

Subjects