Testing for non‐random mating: evidence for ancestry‐related assortative mating in the Framingham heart study

Sebro, Ronnie; Hoffman, Thomas J.; Lange, Christoph; Rogus, John; Risch, Neil

doi:10.1002/gepi.20528

Cited by 51 publications

(54 citation statements)

References 14 publications

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“…Recent work from several groups suggests that genetic factors contribute to human mating preferences (5,(7)(8)(9)(10). In European populations, there is evidence that individuals tend to be attracted to people with major histocompatibility complex (MHC) regions that are distinct from their own (7,8).…”

mentioning

confidence: 99%

Genetic and socioeconomic study of mate choice in Latinos reveals novel assortment patterns

Zou

Park

Burchard

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

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Nonrandom mating in human populations has important implications for genetics and medicine as well as for economics and sociology. In this study, we performed an integrative analysis of a large cohort of Mexican and Puerto Rican couples using detailed socioeconomic attributes and genotypes. We found that in ethnically homogeneous Latino communities, partners are significantly more similar in their genomic ancestries than expected by chance. Consistent with this, we also found that partners are more closely related—equivalent to between third and fourth cousins in Mexicans and Puerto Ricans—than matched random male–female pairs. Our analysis showed that this genomic ancestry similarity cannot be explained by the standard socioeconomic measurables alone. Strikingly, the assortment of genomic ancestry in couples was consistently stronger than even the assortment of education. We found enriched correlation of partners’ genotypes at genes known to be involved in facial development. We replicated our results across multiple geographic locations. We discuss the implications of assortment and assortment-specific loci on disease dynamics and disease mapping methods in Latinos.

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mentioning

confidence: 99%

Genetic and socioeconomic study of mate choice in Latinos reveals novel assortment patterns

Zou

Park

Burchard

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

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“…Some studies have indicated that there is ancestrally related positive assortative mating in the FHS. 17 Fortunately, our method is neither influenced by assortative mating nor by non-random mating, a major advantage clearly demonstrated in our simulation. There are three groups of the FHS participants, the original cohort, the offspring cohort and the third generation cohort, which consist of 5209, 5124 and 4095 participants, respectively.…”

Section: Application To Fhs Datamentioning

confidence: 67%

Joint detection of association, imprinting and maternal effects using all children and their parents

Han

Lin

2013

Eur J Hum Genet

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Genomic imprinting and maternal effects have been increasingly explored for their contributions to complex diseases. Statistical methods have been proposed to detect both imprinting and maternal effects simultaneously based on nuclear families. However, these methods only make use of case-parents triads and possibly control-parents triads, thus wasting valuable information contained in the siblings. More seriously, most existing methods are full-likelihood based and have to make strong assumptions concerning mating-type probabilities (nuisance parameters) to avoid over-parametrization. In this paper, we develop a partial Likelihood approach for detecting Imprinting and Maternal Effects (LIME), using nuclear families with an arbitrary number of affected and unaffected children. By matching affected children with unaffected ones (within or across families) having the same triad/pair familial genotype combination, we derive a partial likelihood that is free of nuisance parameters. This alleviates the need to make strong, yet unrealistic assumptions about the population, leading to a procedure that is robust to departure from Hardy-Weinberg equilibrium. Power gain by including siblings and robustness of LIME under a variety of settings are demonstrated. Our simulation study also indicates that it is more profitable to recruit additional siblings than additional families when the total number of individuals is kept the same. We applied LIME to the Framingham Heart Study data to demonstrate its utility in analyzing real data. Many of our findings are consistent with results in the literature; potentially novel genes for hypertension have also emerged.

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“…Estimates of the number of generations since admixture in the Mexican population (Johnson et al 2011) range from 10 to 15, so it is reasonable to assume that equilibrium on the X chromosome for males and females should have been reached in the Mexican population if mating in this population is completely at random. Previous studies (Risch et al 2009;Sebro et al 2010), however, have shown evidence of nonrandom mating in Mexican populations. In the HapMap MXL, we detected significant evidence of assortative mating among mate pairs that produced an offspring, where the correlation of European and Native American ancestries on both the autosomes and the X chromosome is significantly higher for mate pairs than what would be expected under the null hypothesis of a random mating population.…”

Section: Discussionmentioning

confidence: 83%

Detecting Heterogeneity in Population Structure Across the Genome in Admixed Populations

2016

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The genetic structure of human populations is often characterized by aggregating measures of ancestry across the autosomal chromosomes. While it may be reasonable to assume that population structure patterns are similar genome-wide in relatively homogeneous populations, this assumption may not be appropriate for admixed populations, such as Hispanics and AfricanAmericans, with recent ancestry from two or more continents. Recent studies have suggested that systematic ancestry differences can arise at genomic locations in admixed populations as a result of selection and nonrandom mating. Here, we propose a method, which we refer to as the chromosomal ancestry differences (CAnD) test, for detecting heterogeneity in population structure across the genome. CAnD can incorporate either local or chromosome-wide ancestry inferred from SNP genotype data to identify chromosomes harboring genomic regions with ancestry contributions that are significantly different than expected. In simulation studies with real genotype data from phase III of the HapMap Project, we demonstrate the validity and power of CAnD. We apply CAnD to the HapMap Mexican-American (MXL) and African-American (ASW) population samples; in this analysis the software RFMix is used to infer local ancestry at genomic regions, assuming admixing from Europeans, West Africans, and Native Americans. The CAnD test provides strong evidence of heterogeneity in population structure across the genome in the MXL sample (p ¼ 1e 2 5), which is largely driven by elevated Native American ancestry and deficit of European ancestry on the X chromosomes. Among the ASW, all chromosomes are largely African derived and no heterogeneity in population structure is detected in this sample.KEYWORDS admixture; population structure; heterogeneity testing; local ancestry; assortative mating T ECHNOLOGICAL advancements in high-throughput genotyping and sequencing technologies have allowed for unprecedented insight into the genetic structure of human populations. Population structure studies have largely focused on populations of European descent, and ancestry differences among European populations have been well studied and characterized (Novembre et al. 2008;Nelis et al. 2009). Recent studies have also investigated the genetic structure of more diverse populations, including recently admixed populations, such as African-Americans (Zakharia et al. 2009;Bryc et al. 2010a) and Hispanics (Manichaikul et al. 2012;Conomos et al. 2016), who have experienced admixing within the past few hundred years from two or more ancestral populations from different continents.Both continental and fine-scale genetic structures of human populations have largely been characterized by aggregating measures of ancestry across the autosomal chromosomes. While it may be reasonable to assume that population structure patterns across the genome are similar for populations with ancestry derived from a single continent, such as populations of European descent, this may not be a reasonable assumption for admixe...

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Testing for non‐random mating: evidence for ancestry‐related assortative mating in the Framingham heart study

Cited by 51 publications

References 14 publications

Genetic and socioeconomic study of mate choice in Latinos reveals novel assortment patterns

Genetic and socioeconomic study of mate choice in Latinos reveals novel assortment patterns

Joint detection of association, imprinting and maternal effects using all children and their parents

Detecting Heterogeneity in Population Structure Across the Genome in Admixed Populations

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