This review explores the limitations of self-reported race, ethnicity, and genetic ancestry in biomedical research. Various terminologies are used to classify human differences in genomic research including race, ethnicity, and ancestry. Although race and ethnicity are related, race refers to a person’s physical appearance, such as skin color and eye color. Ethnicity, on the other hand, refers to communality in cultural heritage, language, social practice, traditions, and geopolitical factors. Genetic ancestry inferred using ancestry informative markers (AIMs) is based on genetic/genomic data. Phenotype-based race/ethnicity information and data computed using AIMs often disagree. For example, self-reporting African Americans can have drastically different levels of African or European ancestry. Genetic analysis of individual ancestry shows that some self-identified African Americans have up to 99% of European ancestry, whereas some self-identified European Americans have substantial admixture from African ancestry. Similarly, African ancestry in the Latino population varies between 3% in Mexican Americans to 16% in Puerto Ricans. The implication of this is that, in African American or Latino populations, self-reported ancestry may not be as accurate as direct assessment of individual genomic information in predicting treatment outcomes. To better understand human genetic variation in the context of health disparities, we suggest using “ancestry” (or biogeographical ancestry) to describe actual genetic variation, “race” to describe health disparity in societies characterized by racial categories, and “ethnicity” to describe traditions, lifestyle, diet, and values. We also suggest using ancestry informative markers for precise characterization of individuals’ biological ancestry. Understanding the sources of human genetic variation and the causes of health disparities could lead to interventions that would improve the health of all individuals.

/pdf/self-reported-race-ethnicity-in-the-age-of-genomic-research-5c52di3tf2.pdf

Self-reported race/ethnicity in the age of genomic research: its potential impact on understanding health disparities

Polynesia consists of several islands that are scattered across a vast triangle in the Pacific, and include New Zealand, Hawaii, and the Pacific islands. There are reported differences in the types of cancer and epidemiologies seen among communities in these islands, the reasons for which are diverse and complex. In this Review, we describe patterns of cancer incidence, mortality, and survival in indigenous populations compared with populations of European origin in Polynesia, and highlight the limited available data for Pacific populations. Additionally, we document the current knowledge of the underlying biology of cancers in these populations, and report risk factors that differ between ethnicities, including smoking, viral infections, and obesity. Disparities in measures of health are highlighted, as are evident differences in knowledge of tumour biology and cancer management between majority and minority populations.

https://www.thelancet.com/pdfs/journals/lanonc/PIIS1470-2045(08)70127-X.pdf

Cancer disparities in indigenous Polynesian populations: Māori, Native Hawaiians, and Pacific people

Publisher Summary
This chapter gives an account of Nutrigenomics, which plays an important role in integrating genomic approaches into nutrition research. Nutrigenomics (sometimes called nutritional genomics) considers the interactions between foods or dietary supplements and an individual's genome and the consequent downstream effects on their phenotype. It offers a multi-level systems biology model that is both flexible and rigorous. Some newer tools provide a sensitivity that has been previously lacking. The Nutrigenomics New Zealand model provides an approach towards personalized, genotype-based nutrition that has the potential to provide food products and personalized advice to benefit health at the individual or population level. There is convincing evidence that single nucleotide polymorphisms (SNPs) in certain genes may profoundly influence the biological response to nutrients. However, effects of single-gene variants on risk or risk factor levels of a complex disease tend to be small and inconsistent. Increased sensitivity of current biological measurements and methods of integrating information on combinations of relevant SNPs or copy-number variants in different genes have become necessary to move the field to a higher dimension. There are only sporadic examples of clinical trials utilizing these technologies and many of the challenges are in bioinformatics, especially in relation to reducing the complexity of multidimensional data sets.

Chapter 23 – Nutrigenomics: Integrating Genomic Approaches into Nutrition Research

Adult cigarette smokers usually become dependent on cigarettes during adolescence. Despite recent advances in addiction genetics, little data delineates the genetic factors that account for the vulnerability of humans to smoke tobacco. We studied the operant nicotine self-administration (SA) behavior of six inbred strains of adolescent male rats (Fisher 344, Brown Norway, Dark Agouti, Spontaneous Hypertensive Rat, Wistar Kyoto and Lewis) and six selected F1 hybrids. All rats were trained to press a lever to obtain food starting on postnatal day (PN) 32, and then nicotine (0.03 mg/kg/infusion, i.v.) reinforcement was made available on PN41-42 (10 consecutive daily 2 h sessions). Of the 12 isogenic strains, Fisher rats self-administered the fewest nicotine infusions (1.45±0.36/d) during the last 3 d, while Lewis rats took the most nicotine (13.0±1.4/d). These strains sorted into high, intermediate and low self-administration groups in 2, 2, and 8 strains, respectively. The influence of heredity on nicotine SA (0.64) is similar to that reported for humans. Therefore, this panel of isogenic rat strains effectively models the overall impact of genetics on the vulnerability to acquire nicotine-reinforced behavior during adolescence. Separate groups of rats responded for food starting on PN41. The correlation between nicotine and food reward was not significant. Hence, the genetic control of the motivation to obtain nicotine is distinctly different from food reward, indicating the specificity of the underlying genetic mechanisms. Lastly, the behavior of F1 hybrids was not predicted from the additive behavior of the parental strains, indicating the impact of significant gene-gene interactions on the susceptibility to nicotine reward. Taken together, the behavioral characteristics of this model indicate its strong potential to identify specific genes mediating the human vulnerability to smoke cigarettes.

/pdf/genetic-factors-control-nicotine-self-administration-in-y4mu3fyvqc.pdf

Genetic Factors Control Nicotine Self-Administration in Isogenic Adolescent Rat Strains

Aims To determine the prevalence of functional alleles for drug metabolising genes in a sample of Maori and compare allele frequencies with Caucasians estimates. Procedures DNA from 60 Maori volunteers was genotyped for cytochrome P450 polymorphisms-CYP2A6, CYP2C9, CYP2C19, and CYP2D6-and allele frequencies calculated and compared with Caucasian estimates. Results Absolute allele frequency differences between Maori and Caucasian groups ranged from 1% to 16% for the polymorphisms tested. Conclusions Functional allele frequencies of drug metabolising genes differed between Maori and European groups warranting larger general population surveys. These findings may also bear thinking about when conducting pharmacogenetic studies or clinical trials in New Zealand cohorts because patients with Maori ancestry may respond differently to certain medicines based on genotype.

Allele frequency differences of cytochrome P450 polymorphisms in a sample of New Zealand Māori.

Aims To estimate (a) the prevalence of gene variants associated with slow nicotine metabolism in the general Maori population and (b) nicotine intake and metabolic rate in Maori and European smokers. Methods The procedure involved (a) genotyping 85 Maori participants for cytochrome P-450 2A6 (CYP2A6) gene variants, which are associated with reduced nicotine metabolic rate (ie CYP2A6*9 and *4); and (b) measuring salivary cotinine (COT) and trans-3'-hydroxycotinine (3-HC) as biomarkers of nicotine intake and metabolic rate in 12 female smokers from the Hawke's Bay Region (6 Maori and 6 European). Results (a) The frequencies of the slow nicotine metabolising variants, CYP2A6*9 and *4, were significantly higher in Maori compared to European (p<0.01). Indeed, the prevalence of the CYP2A6*9 variant in these Maori was among the highest in the world (~20%). (b) In smokers, the Maori group had ~35% lower 3-HC:COT ratios indicating a reduced metabolic rate, as well as 2-fold lower cotinine levels per cigarette smoked, indicating reduced nicotine intake (p<0.05). The CYP2A6*9 allele was significantly more frequent in Maori smokers (70%) compared to Europeans (30%), p=0.03. Conclusions The findings of this study provide evidence that Maori are genetically slower nicotine metabolisers compared to Europeans. Although more research is required, this study may help explain ethnic differences in smoking initiation and may also have important implications for smoking cessation programs—since metabolic differences between groups with varying ancestry implies that different optimal dosages of nicotine replacement therapy may be required for successful quitting. In New Zealand (NZ), the prevalence of cigarette smoking is around 22% for the general population. However the smoking rates are markedly higher for Maori (~46%) compared to Europeans (20%) and, for reasons that are unclear, the rates for female Maori are among the highest in the world—52% nationally and up to 60% in some regions. 1 Extensive targeted campaigns for smoking cessation in the 1990s has led to a reduction in tobacco consumption in NZ, yet the high prevalence of smoking for Maori has not decreased. 1 High rates of smoking are associated with elevated rates of smoking-related diseases, and it has been estimated that smoking is responsible for around 30% of Maori deaths compared to about 17% nationally. 2 As these statistics emphasise, identifying the determinants of the high smoking prevalence in Maori and using this information to develop new targeted cessation strategies is of major public health importance in NZ.

Ethnic differences in nicotine metabolic rate among New Zealanders

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Ethnic differences in nicotine metabolic rate among New Zealanders