Using Population Descriptors in Genetics and Genomics Research A New Framework for an Evolving Field (2023) / Chapter Skim
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2 A Multiplicity of Descriptors in Genetics and Genomics Research
2 A Multiplicity of Descriptors in Genetics and Genomics Research
Pages 57-90
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From page 57... ...
. As a result, genetics researchers who deem it necessary to incorporate some kind of population descriptor in their work face a choice about which descriptor(s)
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From page 58... ...
Hence it is important to think clearly about the myriad possibilities for population descriptors and make a reasoned, deliberate choice when conducting genomics research. In addition, this chapter considers the conceptualization and inclusion of environmental variables in human genetics and genomics research.
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From page 59... ...
Not all of an individual's genealogical ancestors are their genetic ancestors, that is, have contributed DNA to that focus individual; in fact, most did not. Genetic ancestry: the paths through an individual's family tree by which they have inherited DNA from specific ancestors.
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From page 60... ...
The final section of this chapter explores the inclusion of environmental variables in genetics research, which could be used independently or along with other descriptors. A RANGE OF DESCENT-ASSOCIATED POPULATION DESCRIPTORS Ancestry Each person has a family tree, a set of biological ancestors consisting of their parents, grandparents, great-grandparents, and so forth.
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From page 61... ...
, individuals living in close proximity in Europe today, who might be characterized as of some particular regional ancestry or of "European ancestry," trace much of their genetic ancestry also to both central Asia and the Middle East only 8,000 years ago (Haak et al., 2015) , and farther back in the past their genetic ancestors lived in Africa (Wohns et al., 2022)
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From page 62... ...
As indicated, the overlap between family trees that indicate genealogical ancestors happens much more recently than the common ancestor events in the "gene trees" that describe the relationship of genetic ancestors. Who is most closely related genetically to whom varies along a genome, as shown in the inset panel.
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From page 63... ...
: the models are approximately correct for gene mapping despite the assumptions being precisely wrong. While genetic ancestry is often the descriptive framing used by researchers to describe individuals or groups in their samples, "most statements about ancestry are really statements about genetic similarity" (Coop, 2022; Mathieson and Scally, 2020)
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From page 64... ...
Alternatively, and especially in genetics, the interest may be in the descent-associated notion of geographical ancestry, that is, where an individual's genealogical ancestors lived at some time point in the past. Geographical ancestry, like genetic ancestry, thus requires having to specify a timescale.
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From page 65... ...
Continental-scale population descriptors are problematic for two main reasons: the heterogeneity that exists within continents along nearly any dimension of interest, and the important fact that continent boundaries have no relevance for genetics studies. As examples, neither the classical divide of Asia and Europe in the Bosporus Strait nor separating Asia and Africa at the Suez Canal are meaningful indicators of genetic ancestry.
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As with the use of genetic ancestry as a population descriptor, careful consideration of the intended uses of a geographic descriptor is essential in every genomics study. Ethnicity Ethnicity is often mentioned alongside race without clarifying the relationship between the two.
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It is useful, then, to draw a distinction between the separate logics at their core in order to clarify the concepts of difference that are in play when researchers design and assess genomics research. The type of group that is recognized as an ethnicity varies widely.
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From page 68... ...
Linguistic patterns are also likely to deviate from other descent-associated population descriptors. But to the extent that a researcher may wish to capture an ethnic sense of belonging; gauge familiarity with the worldviews, norms, and values expressed through a particular language; or link exposure to particular ethnic practices or institutions, language may be of real use as a descent-associated population descriptor.
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. However, the concept of indigeneity is distinguished from these other population descriptors by its emphasis on the continuity of geographic location over time as well as shared culture, traditions, and other connections (Bello-Bravo, 2019)
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From page 70... ...
In addition to its association with geographical rootedness over time, indigeneity often carries a connotation of "purity" or absence of admixture with non-Indigenous peoples. In such interpretations, indigeneity functions as a racial category, complete with the kind of references to blood quantum (as in half-blood or full-blood)
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and Indigenous genetic ancestry, distinguishing them from First Nations and Inuit Indigenous peoples (Bartlett et al., 2007)
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. Across these varied settings, race is fundamentally a sociopolitically constructed system for classifying and ranking human beings according to subjective beliefs about shared ancestry and innate biological similarities.
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. The history of race, science, and society is important for contemporary genetics and genomics researchers to understand, because it illustrates that race emerged as a political project well before the development of population genetics or the evolutionary theory that sustains it.
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census-taker instructions.census-taker instructions. Octoroon: Someone with Octoroon: "one-eighthSomeone with "one-eighth or any trace of black blood." or any trace of black blood." Multiracial: Two or more racesTwo or more races Multiracial: Indian Indian Although American Although American Indians living in Indians living in white society were white society were included in the included in the What Census What Census census before 1890, the 1890 census was the first to census before 1890, the 1890 census was the first to Other Calls UsCalls Us include a complete count of American Indians on tribal include a complete count of American Indians on tribal In 1910, the vast A HistoricalA Timeline Historical Timeline land as well.
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Eskimo Eskimo Eskimo or Alaska Native or Alaska Native Indian American Indian IndianIndian American (American) Indian (American)
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, race makes for a poor proxy of human biological variation. However, it may be a useful population descriptor for researchers who wish to measure a consequential form of social status and affiliation, in the absence of other data (notably, the case where race may be a proxy for the experience of racism in health disparities studies, see Chapter 5)
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From page 77... ...
Hence, it will be increasingly valuable to incorporate epigenetic measurements into studies of human genetic variation. Genes, Environments, and their Interactions It has long been recognized that phenotypes are the result of interplay between an individual's genome and their environment (Li et al., 2018; Seabrook and Avison, 2010; Strickberger, 1985)
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198-199) For any given study, a researcher has to identify which environmental factors to examine and how to measure them accurately, as with any descent-associated population descriptors.
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Some genetics studies can correct this effect in part using genetic markers, but the etiologic factor is lead. Yet in both examples, recognition of the environmental agent is central to understanding the outcomes and phenotypes that result from both genetic and environmental effects.
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In addition, most environmental factors are correlated with each other as they may be determined by the same upstream cause, e.g., structural racism. These limitations represent key challenges for the interpretation of genetics and genomics studies but compel us to begin to make meaningful strides toward defining the roles of selected and plausible common and unique environments in the traits studied, though admittedly, this is a much harder task for some phenotypes than for others. Consequently, there may be merit to studies of the epigenome that can capture some of the cellular consequences of environmental effects even when the specific environment is unknown.
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From page 81... ...
phenotype similarity between two individuals can arise from genes only, environments only, genes in one and the environment in the other, or from the interactions between genes and the environment in the same individual, and (2) despite the different proximal causes, the distal molecular causes of the effects of environmental perturbations and those of genetic variants can converge on the same molecular process and the same molecules, at some rate-limiting step (Chakravarti and Turner, 2016)
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From page 82... ...
. Whenever feasible, these should be measured at the individual research participant level similar to how genotypes are measured.
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2015. The genetic ancestry of African Americans, Latinos, and European Americans across the United States.
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2023. Genetic similarity versus genetic ancestry groups as sample descriptors in hu man genetics.
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2011. Different differences: The use of ‘genetic ancestry' versus race in biomedical human genetic research.
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2017. Al mena: A comprehensive resource of human genetic variants integrating genomes and exomes from Arab, Middle Eastern and north African populations.
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2021. Dissect ing the role of Amerindian genetic ancestry and the ApoE ε4 allele on Alzheimer disease in an admixed Peruvian population.
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2011. Still invisible: Enumeration of indigenous peoples in census questionnaires internationally.
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2018. Europe's only recognized indigenous peoples live in Sweden.
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2022. The representation of indigenous peoples in chronic disease clinical trials in Australia, Canada, New Zealand, and the United States.
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