Estimates of European American Ancestry in African Americans Using HFE p.C282Y

Abstract

Background:

HFE p.C282Y (chromosome 6p22.2; exon 4, c.845G>A; rs1800562), a hemochromatosis-associated polymorphism in European Americans, is absent in sub-Saharan West African blacks.

Methods:

We estimated European American ancestry in African Americans (M) using published p.C282Y allele frequencies of sub-Saharan West African blacks; and ≥50 unselected African Americans and ≥50 unselected European Americans in the same city/region.

Results:

p.C282Y allele frequency in 870 West African blacks (The Gambia, Ghana, Nigeria, Senegal, Sierra Leone) was 0.0000 (confidence interval [95% CI 0.0000-0.0027]). p.C282Y allele frequencies in European Americans were 0.0600 (12,592 participants; five single-site studies) and 0.0673 (54,882 participants; two multisite studies). p.C282Y allele frequencies in African Americans were 0.0102 (3084 participants; five single-site studies) and 0.0122 (30,762 participants; two multisite studies). M for all data was 0.1803 (standard error 0.0049; [95% CI 0.1706-0.1900]). City/region estimates of M differed 1.8-fold: 0.1321, Rochester, NY; 0.1456, Birmingham, AL; 0.1569, Upper Savannah Region, SC; 0.1612, Portland, OR; 0.1746, San Diego, CA; 0.1780, Hartford, CT; 0.1957, District of Columbia; 0.2377, Oakland, CA; and 0.2429, Irvine, CA.

Conclusions:

Estimates of M using p.C282Y are consistent with those using other autosomal markers, differ across nine cities/regions, and reflect paternal and maternal contributions of European American ancestry in African Americans.

Introduction

The p.C282Y mutation of the high-iron gene (HFE, chromosome 6p22.2; exon 4, c.845G>A; rs1800562) is a hemochromatosis-associated polymorphism in western European whites and derivative populations (Merryweather-Clarke et al., 2000; Barton et al., 2015). Among whites of western European descent who have hemochromatosis phenotypes, ∼90% are p.C282Y homozygotes (Feder et al., 1996; Barton et al., 2015; Edwards and Barton, 2019). Hemochromatosis phenotypes in typical referred patients before treatment include the following: elevated serum iron, transferrin saturation, and serum ferritin levels; low hepcidin expression; increased iron absorption; and increased hepatic iron deposition (Edwards and Barton, 2019). Some p.C282Y homozygotes, especially men, develop severe iron overload and consequent cirrhosis, primary liver cancer, arthropathy, diabetes, other endocrinopathies, cardiomyopathy, and cutaneous hyperpigmentation (Edwards and Barton, 2019).

In European American participants in two large U.S. multisite screening studies, the prevalence of HFE p.C282Y homozygosity was 0.0042 and 0.0064, respectively, and the p.C282Y allele frequency was 0.0683 and 0.0633, respectively (Barton et al., 2005; Pankow et al., 2008). In African American participants in the same studies, the prevalence of p.C282Y homozygosity was 0.0001 and 0.0003, respectively, and the p.C282Y allele frequency was 0.0119 and 0.0143, respectively (Barton et al., 2005; Pankow et al., 2008).

African Americans are descendants of enslaved black Africans, most of whom were taken from contiguous areas of sub-Saharan West Africa (Law, 1989; Sluiter, 1997; Beckles, 2002; Salas et al., 2005; Hall, 2007; Lovejoy, 2012). In four reports of sub-Saharan West African blacks who resided in areas from which enslaved black Africans were previously taken for transport to the region of the present United States, HFE p.C282Y was not detected (Merryweather-Clarke et al., 1997; Roth et al., 1997; Jeffery et al., 1999; IGSR, 2020). Thus, European American ancestry would explain the occurrence of p.C282Y in African Americans.

European American ancestry in African Americans can be estimated using phenotypes or alleles restricted to European or European American whites and others restricted to sub-Saharan West African blacks (Reed, 1969a; Reitnauer et al., 1982; Chakraborty et al., 1992; Parra et al., 1998; Destro-Bisol et al., 1999). p.C282Y is a suitable autosomal allele for such estimates.

Using published HFE p.C282Y allele frequencies, we estimated the proportion of European American ancestry in African Americans (M) (Bernstein, 1931; Reed, 1969a) and postulated that M varies significantly across cities/regions of the United States. We used p.C282Y allele frequencies in sub-Saharan West African blacks; and cohorts of ≥50 unselected African Americans and ≥50 unselected European Americans who resided in the same city/region. We compare our results with those of ancestry studies of African Americans that used other autosomal phenotype or allele markers, explore the significance of our results in understanding the epidemiology of iron overload in African Americans, and discuss strengths, limitations, and uncertainties of this study.

Methods

Ethics statement

Western Institutional Review Board granted an exemption determination for performance of this study under 45 CFR 46.101(b)(4) (submission no. 2539985-44189619) (JCB). Obtaining informed consent was not required because this study was based entirely on compilation and analyses of previously published data. There was no direct involvement of human subjects.

Terminology

African Americans were defined as self-identified non-Hispanic blacks or blacks (Barton et al., 2005). We interpreted “Negro” in some publications as a synonym. European Americans were defined as self-identified non-Hispanic whites, whites, or Caucasians (Barton et al., 2005).

Data sources

We identified studies with HFE p.C282Y allele frequencies using computerized and manual literature searches. We tabulated data from studies of West African blacks who resided in areas of sub-Saharan West Africa from which slaves were taken for transport to the areas in the United States (Law, 1989; Sluiter, 1997; Beckles, 2002; Salas et al., 2005; Hall, 2007; Lovejoy, 2012). We stipulated that each U.S. study has interpretable p.C282Y allele frequencies on ≥50 African American and ≥50 European American participants who resided in the same city/region and that participants were unselected for specific diagnoses or conditions.

We excluded data for “Africans” from the Genome Aggregation Database (Broad Institute, 2019) because the database specifies no geographic region within Africa and the “Africans” data may include observations in African Americans (Karczewski et al., 2020). We excluded HFE p.C282Y data from 286 residents of Angola, São Tomé and Principe, and Cape Verde (Martins et al., 2005). Although some African Americans have Angolan ancestry (Sluiter, 1997), Angolan data were not tabulated separately (Martins et al., 2005). The Portuguese enslaved black natives from São Tomé and Principe and Cape Verde and transported them to the Caribbean and Brazil (Beckles, 2002).

Statistics

We calculated M as an estimate of HFE p.C282Y ancestry in African Americans as previously described (Bernstein, 1931; Reed, 1969a). We defined qA, the allele frequency of p.C282Y in presumed African ancestors of African Americans, as 0.0000, because p.C282Y was not detected in 870 sub-Saharan West African blacks (The Gambia, Ghana, Nigeria, Senegal, Sierra Leone) (Table 1). We defined qW as the allele frequency of p.C282Y in European Americans; and qB as the allele frequency of p.C282Y in African Americans. We calculated M = (qB − qA)/(qW − qA) (Reed, 1969a). Because qA is defined as zero, M can be expressed simply as the proportion of qB by qW. The standard error (SE) of M was calculated as previously described (Reed, 1969a). The 95% confidence interval (CI) of M was computed as M ± (1.96 × SE).

Table 1.

Eight Hundred Seventy Subjects from West Africa^a Tested for HFE p.C282Y^b

West Africans	Subjects (n)	Alleles (n)	References
Esan in Nigeria	99	198	IGSR (2020)
Gambians	39	78	Merryweather-Clarke et al. (1997)
Gambians in Western Division, The Gambia	138	276	IGSR (2020)
Ghanians	97	194	Jeffery et al. (1999)
Mandeka in Senegal	94	188	Roth et al. (1997)
Mende in Sierra Leone	85	170	IGSR (2020)
Nigerians	80	160	Merryweather-Clarke et al. (1997)
Senegalese	130	260	Merryweather-Clarke et al. (1997)
Yoruba in Ibadan, Nigeria	108	216	IGSR (2020)
Total	870	1740

The “Slave Coast” of West Africa from the early 16th Century to the late 19th Century was that part of coastal West Africa along the Bight of Benin located between the Volta River and the Lagos Lagoon (Law, 1989). Some enslaved black Africans transported to the region of the present United States were probably taken from other areas in sub-Saharan West Africa (Law, 1989; Sluiter, 1997; Beckles, 2002; Salas et al., 2005; Hall, 2007; Lovejoy, 2012).

None of these 870 subjects had p.C282Y.

HFE, high-iron gene.

Descriptive data are displayed as enumerations and proportions. Proportions were compared using Fisher's exact test (two-tailed). Values of p < 0.05 were defined as significant. Analyses were performed with Excel 2000^® (Microsoft Corp., Redmond, WA) and GraphPad Prism8^® (2018; GraphPad Software, San Diego, CA).

Results

General data

Aggregate HFE p.C282Y allele frequencies in European Americans were 0.0600 (12,592 participants in five single-site studies) and 0.0673 (54,882 participants in two multisite studies). Aggregate p.C282Y allele frequencies in African Americans were 0.0102 (3084 participants in five single-site studies) and 0.0122 (30,762 participants in two multisite studies) (Table 2). These data represent five states and nine cities/regions in the United States, including the District of Columbia (Table 2). p.C282Y allele frequencies were significantly greater for European Americans than African Americans in each city/region (p ≤ 0.0004) except Hartford, Connecticut (0.0500 vs. 0.0089, respectively; p = 0.0985) (Table 2).

Table 2.

HFE p.C282Y Allele Frequencies in European and African Americans

City/region of United States (study population)	European Americans, allele frequency (n subjects)	African Americans, allele frequency (n subjects)	References
Rochester, New York (primary care screening)	0.0507 (3227)	0.0067 (1123)	Phatak et al. (2002)
Birmingham, Alabama (HEIRS Study)	0.0742 (9316)	0.0108 (9670)	Acton et al. (2006)
Upper Savannah Region, South Carolina (cord blood screening)	0.0771 (765)	0.0121 (536)	MacClenahan et al. (2000)
Portland, Oregon^a (HEIRS Study)	0.0670 (12,217)	0.0108 (279)	Acton et al. (2006)
HEIRS Study (primary care screening) (aggregate)^b	0.0683 (44,082)	0.0119 (27,077)	Acton et al. (2006)
San Diego, California (health appraisal clinic screening)	0.0630 (7864)	0.0110 (371)	Beutler et al. (2000)
Hartford, Connecticut (multiethnic controls testing)	0.0500 (100)	0.0089 (56)	Marshall et al. (1999)
District of Columbia (HEIRS Study)	0.0649 (855)	0.0127 (16,589)	Acton et al. (2006)
Irvine, California (HEIRS Study)	0.0597 (4428)	0.0145 (345)	Acton et al. (2006)
ARIC Study^c (community-based epidemiologic study)	0.0633 (10,800)	0.0143 (3685)	Pankow et al. (2008)
Oakland, California (cord blood screening)	0.0547 (996)	0.0130 (998)	Hoppe et al. (2006)

Participants were recruited from northwest Oregon/southwest Washington.

Includes participants in London, Ontario, Canada (Adams et al., 2005).

The ARIC Study enrolled subjects ages 45-64 years in: Forsyth County, North Carolina; Jackson, Mississippi; seven northwestern suburbs of Minneapolis, Minnesota; and Washington County, Maryland. Black residents were oversampled in Forsyth County, North Carolina. Enrollment at the Jackson, Mississippi site was restricted to black residents (The ARIC Investigators, 1989).

ARIC Study, Atherosclerosis Risk in Communities Study; HEIRS Study, Hemochromatosis and Iron Overload Screening Study.

Estimates of M using HFE p.C282Y allele frequencies

Aggregate M for all data was 0.1803 (SE 0.0049; 95% CI [0.1706-0.1900]). There was a 1.8-fold difference in M across nine cities/regions (0.1321-0.2429) (Table 3). There was a 1.3-fold difference of M between the two multisite studies (0.1742-0.2259) (Table 3). There was 1.7-fold difference across the four different sites of participant recruitment in the United States for the Hemochromatosis and Iron Overload Screening (HEIRS) Study (0.1456-0.2429) (Table 3).

Table 3.

Estimates of M Using HFE p.C282Y Allele Frequencies

City/region of United States (study population)	M	SE	95% CI	References
Rochester, New York (primary care screening)	0.1321	0.0347	0.0642-0.2001	Phatak et al. (2002)
Birmingham, Alabama (HEIRS Study)	0.1456	0.0107	0.1246-0.1666	Acton et al. (2006)
Upper Savannah Region, South Carolina (cord blood screening)	0.1569	0.0455	0.0678-0.2461	MacClenahan et al. (2000)
Portland, Oregon^a (HEIRS Study)	0.1612	0.0654	0.0330-0.2894	Acton et al. (2006)
HEIRS Study^b (primary care screening) (aggregate)	0.1742	0.0072	0.1602-0.1883	Acton et al. (2006)
San Diego, California (health appraisal clinic screening)	0.1746	0.0610	0.0550-0.2942	Beutler et al. (2000)
Hartford, Connecticut (multiethnic controls testing)	0.1780^c	0.1858^c	0-0.5421	Marshall et al. (1999)
District of Columbia (HEIRS Study)	0.1957	0.0203	0.1559-0.2355	Acton et al. (2006)
ARIC Study^d (community-based epidemiologic study)	0.2259	0.0769	0.1815-0.2702	Pankow et al. (2008)
Oakland, California (cord blood screening)	0.2377	0.0514	0.1370-0.3383	Hoppe et al. (2006)
Irvine, California (HEIRS Study)	0.2429	0.0770	0.0921-0.3936	Acton et al. (2006)

Participants were recruited from northwest Oregon/southwest Washington.

Includes participants in London, Ontario, Canada (Adams et al., 2005).

SE for Hartford was greater than the estimate of M.

CI, confidence interval; M, estimate of European American (self-identified non-Hispanic white, white, or Caucasian) ancestry in African Americans (self-identified non-Hispanic blacks or blacks); SE, standard error of M.

The lowest estimate of M was computed using data from Rochester, New York (0.1321) (Table 3). Estimates of M computed using data from Alabama and South Carolina were 0.1456 and 0.1569, respectively. Estimates of M in three study sites in California were higher (0.1746, 0.2377, and 0.2429) (Table 3).

SEs and 95% CIs of M are displayed in Table 3. The smallest SE was that of the aggregate estimate M for the HEIRS Study (Table 3). The city/region with the smallest cohort was Hartford, Connecticut. The SE of M for this region was greater than the estimate of M (Table 3). Inspection of the 95% CIs revealed that the estimate of M for Birmingham, Alabama, is significantly lower than that of the Atherosclerosis Risk in Communities (ARIC) Study (Table 3). No other significant differences in estimates of M were observed.

Discussion

This study reports using HFE p.C282Y as a novel means of estimating the proportion of European American ancestry in African Americans (M). Using the aggregate p.C282Y allele frequency in 870 sub-Saharan West African blacks who reside in The Gambia, Ghana, Nigeria, Senegal, and Sierra Leone (Merryweather-Clarke et al., 1997; Roth et al., 1997; Jeffery et al., 1999; IGSR, 2020) and p.C282Y allele frequencies in 67,834 European Americans and 33,846 African Americans who participated in five single-site (Marshall et al., 1999; Beutler et al., 2000; MacClenahan et al., 2000; Phatak et al., 2002; Hoppe et al., 2006) and two multisite (Barton et al., 2005; Pankow et al., 2008) studies, we observed an aggregate estimate of M of 0.1803 for all data and a 1.8-fold difference in estimates of M across nine cities/regions in the United States.

Other alleles with “zero” frequency in sub-Saharan West African blacks used to estimate M include Duffy allele Fy^a and Gm allotype Gm¹^,5 (Steinberg, 1967; Reed, 1969a, 1969c). In the present study, the estimate of M for Oakland, California, was 0.238. In previous studies, an estimate of M for Oakland that used Fy^a was 0.220 (Reed, 1968; Reed, 1969b) and another estimate for Oakland that used Gm allotypes was 0.273 (Reed, 1969c). The estimate of M for Birmingham, Alabama, in the present study was 0.146. In another report, the European American ancestry in African Americans in Birmingham estimated using nine erythrocyte antigen markers was 0.179 (Reitnauer et al., 1982).

Estimates of M for the District of Columbia in this study were 0.196. In a report from Baltimore that used Rh (R⁰), M was 0.216 (Glass, 1955). In the present study, the estimate of M for the Upper Savannah Region of South Carolina in this study was 0.157. In a study that used 10 “population-specific” autosomal alleles that occur only in persons of African ancestry or for which the allele frequencies between Africans and Europeans differ by >48%, estimates of M for Charleston, South Carolina, were 0.116 and 0.122, depending on the method of calculation (Parra et al., 1998). Aggregate estimates of M from two multisite studies (Barton et al., 2005; Pankow et al., 2008) in the present report were 0.174 and 0.226, respectively. Taken together, these observations indicate that the present estimates of M for these respective cities/regions are consistent with those of previous reports that used different single alleles.

Average European ancestry in African Americans was 13% in a study that used 1327 nuclear microsatellite and insertion/deletion markers, although admixture proportions varied across individuals (Tishkoff et al., 2009). In a genome-wide ancestry study of self-identified African Americans based on data from 23andMe customers, the average proportion of European ancestry was 24%, although proportions varied significantly by region (Bryc et al., 2015). In the same study, by-state differences in levels of European ancestry of African Americans were similar to those of the present study (Bryc et al., 2015). Average European ancestry in African Americans was 14% in a study that used autosomal short tandem repeat markers (Tang et al., 2006). In a study based on ancestry informative markers, European ancestry in African Americans was 18% (Fernandez et al., 2003).

The smallest SE we observed for a single study was that of the aggregate estimate of M for the HEIRS Study, the largest cohort. The smallest cohort represented the Hartford, Connecticut city/region. The SE of M for Hartford was greater than the corresponding estimate of M. SEs of M were larger than M itself for other small cohorts studied using different markers (Reed, 1969a). The estimate of M for Birmingham, Alabama, is significantly lower than that of the ARIC Study.

HFE p.C282Y has health-related consequences in African Americans, although the prevalence of p.C282Y homozygosity in African Americans is 13-64-fold lower than that of European Americans (Barton et al., 2005; Pankow et al., 2008). In a genome-wide admixture and association study of African Americans unselected for hemochromatosis, p.C282Y was linked to levels of serum iron, transferrin saturation, total serum iron-binding capacity, and serum ferritin (Li et al., 2015). In 2001, it was reported that an African American man from Alabama referred for evaluation of hypogonadism had p.C282Y homozygosity and a hemochromatosis phenotype (Barton and Acton, 2001), consistent with an earlier prediction (Barton and Acton, 2000). Five African American participants in three screening programs were discovered to have p.C282Y homozygosity (MacClenahan et al., 2000; Barton et al., 2005; Pankow et al., 2008). Iron overload unexplained by erythrocyte transfusion or dietary or parenteral iron excess that is not associated with p.C282Y homozygosity also occurs in African Americans (Monaghan et al., 1998; Barton et al., 2003; Gordeuk et al., 2003).

The present results suggest that the proportion of European white ancestry that would account for p.C282Y heterozygosity and homozygosity in African Americans is lower in Rochester, New York, Upper Savannah Region of South Carolina, and Birmingham, Alabama, and higher in Washington, D.C., Portland, Oregon, and three cities/regions in California. Nonetheless, we did not observe significant differences in estimates of M across these cities/regions using a 95% CI criterion. The proportional geographic distribution of African Americans in the United States is greatest in coastal states from Maryland to Texas (Gibson and Jung, 2002; U.S. Census Bureau, 2006). The absolute majority of African Americans have always lived in the American South (U.S. Census Bureau, 2015). Other factors that could influence diagnosis of p.C282Y homozygosity and hemochromatosis in African Americans include subpopulation differences in proportions of European Americans and African Americans, physician referral patterns, and differences in health care availability and utilization.

Strengths of the present study include the following: the numbers of participants in most of the studies from which we tabulated data are great and permit estimates of M with low SEs; the present subjects were unselected for specific diagnoses or conditions; European American and African American participants in respective studies resided in the same city/region; and HFE p.C282Y is an autosomal marker that reflects both paternal and maternal contributions of European American ancestry in African Americans. Race/ethnicity of the subjects in this study was classified according to self-reports. Some subjects may have reported their race/ethnicity according to social identity or preference, not genetic history or attributes. Differences in city/region estimates of M that we observed may have been influenced by biased selection of study sites or populations. A limitation of this study is that estimates of M are available for only nine cities/regions. Another limitation is that each of the previously published reports of HFE p.C282Y allele frequency data that we used was based on cross-sectional data. Thus, we could not evaluate changes in estimates of M in the same cities/regions over time. Studies of African American ancestry using X- and Y-chromosome and mtDNA markers reveal substantial European male and African female contributions (Parra et al., 1998; Lind et al., 2007; Bryc et al., 2015). Differential parental contributions to ancestry cannot be inferred from the present estimates of M.

We conclude that estimates of M using p.C282Y are consistent with those using other autosomal markers, differ across nine cities/regions, and reflect paternal and maternal contributions of European American ancestry in African Americans. p.C282Y may be useful for estimating European American or western European white ancestry in other race/ethnicity groups.

Footnotes

Authors' Contributions

R.T.A. conceived this project. R.T.A., H.W.W., and J.C.B. compiled and analyzed data. J.C.B. drafted the article. R.T.A., H.W.W., and J.C.B. approved the final form of the article.

Author Disclosure Statement

No competing financial interests exist.

Funding Information

This work was funded, in part, by the Southern Iron Disorders Center, Birmingham, Alabama. The funding source had no input into the interpretation of data, the writing of the report, or the decision to submit the article for publication.

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