Ancestry comparison between Non hispanic whites, African Americans and Hispanics 2020

[Argentano]

Ancestry comparison between Non hispanic whites, African Americans and Hispanics 2020

https://www.biorxiv.org/content/10.1...755v1.full.pdf

Population structure and pharmacogenomic risk stratification in the United States


Materials and Methods
Study Cohort
Self-identified race and ethnicity (SIRE) information and whole genome genotypes for Americans over the age of 50 and their spouses were collected as part of a nationally-representative longitudinal panel study called the Health and Retirement Study (HRS)33 . For the current study, only HRS participants with both SIRE and genotype information were considered (8,912 participants). The 284 participants who did not identify with one of the three largest racial/ethnic categories in the HRS data – non-Hispanic White (5,927), nonHispanic Black (1,527), and Hispanic/Latino of any race (1,174) – were excluded from this analysis. This yielded a total of 8,628 individuals in our final analysis cohort.

Results
Self-identified race/ethnicity (SIRE) and Genetic
Ancestry (GA) in the US
We compared SIRE to GA for a cohort of 8,628 individuals characterized as part of the Health and Retirement Study (HRS), for whom both SIRE information and whole genome genotypes were available (Table 1). HRS participants self-identified according to racial and ethnic labels defined by the US Government Office of Management and Budget (OMB). OMB defines five racial groups and two ethnic groups to assess disparities in health and environmental risks45 . HRS participants were asked to select one or more race category and a single ethnic designation as Hispanic/Latino or not. We considered the race and ethnicity selections together and focused on the three largest categories in the HRS cohort: non-Hispanic White (5,927; 68.7%), non-Hispanic Black (1,527; 17.7%), and Hispanic/Latino of any race (1,174; 13.6%). We refer to these three groups here as White, Black, and Hispanic. The percentages of each SIRE group in the HRS cohort resemble the demographics of the US: White=72.4%, Black=12.6%, and Hispanic=16.3%45 .

Continental ancestry profiles were inferred for members of the HRS cohort by comparing their whole genome genotypes to whole genome sequence and genotype data for reference populations from Europe, Africa, and the Americas as described in the Materials and Methods. Each HRS participant was assigned European, African, and Native American ancestry proportions, and the resulting ancestry profiles were then clustered into three distinct (non-overlapping) GA groups using kmeans clustering. GA groups were defined without reference to SIRE group labels, using unsupervised clustering on continental ancestry fractions alone, and
the choice to cluster ancestry profiles into three groups was made to allow for direct comparison with the three SIRE groups and in light of known patterns of continental ancestry in the US46 . Permutation analysis was used to confirm the stability of the resulting GA groups and their robustness to changes in sample size (Supplementary Figure 1). The distributions of continental ancestry fractions were compared for the three SIRE groups – White, Black, and Hispanic – and the three GA groups (Figure 1).

The three objectively defined GA groups appear to correspond well to the SIRE groups, with respect to the distributions of individuals’ continental ancestry fractions (Figure 1 – top row). GA groups 1, 2, and 3
correspond to the White, Black, and Hispanic SIRE groups, respectively. The distributions of continental ancestry fractions for the SIRE and their corresponding GA groups are compared in Supplementary Figure 2.
Despite the apparent similarity between SIRE and GA, ternary plots underscore the broader distribution of ancestry fractions within SIRE groups compared to the non-overlapping GA groups delineated by k-means
clustering (Figure 1 – middle row). This is especially true for the Hispanic group, consistent with the fact that it may include individuals who identify as any race. Overall, SIRE and the GA groups show similar average
continental ancestry percentages: White/Group 1 show ~99% European ancestry, Black/Group2 have ~82% African ancestry, and Hispanic/Group 3 show predominantly European ancestry (~60%) with the
highest levels of Native American ancestry (~37%) and the greatest variance in continental ancestry for any of the three groups. The correspondence between the SIRE and GA groups was quantified by haracterizing the overlap of membership assignments across the two groupings (Supplementary Figure 3). Overall, individuals’ membership in the three SIRE and corresponding GA groups show 96.2% concordance. The highest concordance is seen for the White/Group 1 pair, followed by Black/Group 2, with Hispanic/Group 3 showing the lowest concordance. The levels of concordance vary according to which grouping system is
taken as the reference for comparison. This distinction is most obvious for the Hispanic/Group 3 pairing: 96.6% of Group 3 members self-identify as Hispanic, while only 77.1% of self-identified Hispanics fall into Group 3.

[Argentano]

The one called SIRE Group is the real sample.

The Genetic Ancestry groups are groups they created eliminating the white latinos and black latinos from the hispanic group and adding them to the other 2 categories (non hispanic white and african american). That is not representative of the latino sample


So the hispanic sample is 60% european 37% native american 9% SSA

[gixajo]

The one called SIRE Group is the real sample.

The Genetic Ancestry groups are groups they created eliminating the white latinos and black latinos from the hispanic group and adding them to the other 2 categories (non hispanic white and african american). That is not representative of the latino sample


So the hispanic sample is 60% european 37% native american 9% SSA

59.8+36.8+9.4=106%

In the other 5 total percentages are ok(aprox), but not in this case.

[Argentano]

59.8+36.8+9.4=106%

In the other 5 total percentages are ok(aprox), but not in this case.

lol yes you are right

if you look at the boxplot it looks more like 53-54% euro that would make more sense still very similar result doesent change anything

[Thetruth]

Not surprised, Hispanic/Latino Americans come from very mixed places already with the bulk of us being Mexican, Puerto Rican, Dominican, Central American(Salvi, Guatemalan, Honduran), Cuban, Colombian and Ecuadorian. Based on this White non-Hispanic Americans solely European, African Americans are mixed to a small degree and Latinos are mainly Euro-leaning mestizos with a decent amount of African ancestry but also generally encompassing various degrees of admixture from all three groups(Euro, Native and African)

[Thetruth]

Ancestry comparison between Non hispanic whites, African Americans and Hispanics 2020

https://www.biorxiv.org/content/10.1...755v1.full.pdf

Population structure and pharmacogenomic risk stratification in the United States


Materials and Methods
Study Cohort
Self-identified race and ethnicity (SIRE) information and whole genome genotypes for Americans over the age of 50 and their spouses were collected as part of a nationally-representative longitudinal panel study called the Health and Retirement Study (HRS)33 . For the current study, only HRS participants with both SIRE and genotype information were considered (8,912 participants). The 284 participants who did not identify with one of the three largest racial/ethnic categories in the HRS data – non-Hispanic White (5,927), nonHispanic Black (1,527), and Hispanic/Latino of any race (1,174) – were excluded from this analysis. This yielded a total of 8,628 individuals in our final analysis cohort.

Results
Self-identified race/ethnicity (SIRE) and Genetic
Ancestry (GA) in the US
We compared SIRE to GA for a cohort of 8,628 individuals characterized as part of the Health and Retirement Study (HRS), for whom both SIRE information and whole genome genotypes were available (Table 1). HRS participants self-identified according to racial and ethnic labels defined by the US Government Office of Management and Budget (OMB). OMB defines five racial groups and two ethnic groups to assess disparities in health and environmental risks45 . HRS participants were asked to select one or more race category and a single ethnic designation as Hispanic/Latino or not. We considered the race and ethnicity selections together and focused on the three largest categories in the HRS cohort: non-Hispanic White (5,927; 68.7%), non-Hispanic Black (1,527; 17.7%), and Hispanic/Latino of any race (1,174; 13.6%). We refer to these three groups here as White, Black, and Hispanic. The percentages of each SIRE group in the HRS cohort resemble the demographics of the US: White=72.4%, Black=12.6%, and Hispanic=16.3%45 .

Continental ancestry profiles were inferred for members of the HRS cohort by comparing their whole genome genotypes to whole genome sequence and genotype data for reference populations from Europe, Africa, and the Americas as described in the Materials and Methods. Each HRS participant was assigned European, African, and Native American ancestry proportions, and the resulting ancestry profiles were then clustered into three distinct (non-overlapping) GA groups using kmeans clustering. GA groups were defined without reference to SIRE group labels, using unsupervised clustering on continental ancestry fractions alone, and
the choice to cluster ancestry profiles into three groups was made to allow for direct comparison with the three SIRE groups and in light of known patterns of continental ancestry in the US46 . Permutation analysis was used to confirm the stability of the resulting GA groups and their robustness to changes in sample size (Supplementary Figure 1). The distributions of continental ancestry fractions were compared for the three SIRE groups – White, Black, and Hispanic – and the three GA groups (Figure 1).

The three objectively defined GA groups appear to correspond well to the SIRE groups, with respect to the distributions of individuals’ continental ancestry fractions (Figure 1 – top row). GA groups 1, 2, and 3
correspond to the White, Black, and Hispanic SIRE groups, respectively. The distributions of continental ancestry fractions for the SIRE and their corresponding GA groups are compared in Supplementary Figure 2.
Despite the apparent similarity between SIRE and GA, ternary plots underscore the broader distribution of ancestry fractions within SIRE groups compared to the non-overlapping GA groups delineated by k-means
clustering (Figure 1 – middle row). This is especially true for the Hispanic group, consistent with the fact that it may include individuals who identify as any race. Overall, SIRE and the GA groups show similar average
continental ancestry percentages: White/Group 1 show ~99% European ancestry, Black/Group2 have ~82% African ancestry, and Hispanic/Group 3 show predominantly European ancestry (~60%) with the
highest levels of Native American ancestry (~37%) and the greatest variance in continental ancestry for any of the three groups. The correspondence between the SIRE and GA groups was quantified by haracterizing the overlap of membership assignments across the two groupings (Supplementary Figure 3). Overall, individuals’ membership in the three SIRE and corresponding GA groups show 96.2% concordance. The highest concordance is seen for the White/Group 1 pair, followed by Black/Group 2, with Hispanic/Group 3 showing the lowest concordance. The levels of concordance vary according to which grouping system is
taken as the reference for comparison. This distinction is most obvious for the Hispanic/Group 3 pairing: 96.6% of Group 3 members self-identify as Hispanic, while only 77.1% of self-identified Hispanics fall into Group 3.

Do you think that result for the Latin group would change if it included even more Latinos from other regions besides those from what I’m assuming is Mexicans, Caribbean and Central American Latinos living in the USA ? Do you think it would stay the same if it included South Americans more ?

[Argentano]

Do you think that result for the Latin group would change if it included even more Latinos from other regions besides those from what I’m assuming is Mexicans, Caribbean and Central American Latinos living in the USA ? Do you think it would stay the same if it included South Americans more ?

well its hard to answer because "south america" is a very heterogeneous group. Uruguay vs Bollivia or Peru vs Brazil is completely different.

[Thetruth]

well its hard to answer because "south america" is a very heterogeneous group. Uruguay vs Bollivia or Peru vs Brazil is completely different.

Bolivia and Peru don’t have half the population of Brazil and Argentina combined Not even with Ecuador included, Brazil, the Southern Cone, Colombia and Venezuela all outnumber Peruvians and Bolivians, not to mention you’re average Peruvian, Ecuadorian and Bolivian already has a decent amount of euro ancestry even if it is low on average.

1). Brazil has a population of 210,147,125 making it the most most populated country in South America and on average is overwhelmingly European. On average Brazil is 62% European, 21% African and 17% Native American


2). Colombia and Venezuela have a population of 79,259,542 combined, making it the second region in South America to be most populated. On Average Colombia is 62% European, 27% Amerindian and 9% African while Venezuela is 56% European, 25% Amerindian and 19% African.

3). The Southern Cone(Argentina, Chile, Uruguay and Paraguay) have a population of 74,692,339 combined, this region is also overwhelmingly European.
Argentina is 79% European, 18% Amerindian and 3% African. Chile is 51.8% European, 44.3% Amerindian and 3.8% African. Paraguay is 59.9% European, 30.9% Amerindian and 9.2% African. Uruguay is 77.1% European, 13.2% Amerindian and 9.8% African.

4). The Andean region(Ecuador, Peru and Bolivia) have a population of 61,336,961 combined, making it the smallest of the bunch and this region is overwhelmingly Amerindian. Ecuador is 56% Amerindian, 39.5% European and 4.5% African. Peru is 64% Amerindian, 29% European and 7% African. Bolivia is 78% Amerindian, 21% European and 1% African.

5). The Guianas(Guyana, Suriname and French Guiana) have a population of 1,653,072 combined, this region isn’t part of the Latin South American group and identifies more with the Caribbean. It is overwhelmingly Black and Indian. Couldn’t find any data on they’re genetic compositions

Taken this all into account I would say South America is predominantly European with the rest being mostly Amerindian and some African

[Argentano]

Bolivia and Peru don’t have half the population of Brazil and Argentina combined Not even with Ecuador included, Brazil, the Southern Cone, Colombia and Venezuela all outnumber Peruvians and Bolivians, not to mention you’re average Peruvian, Ecuadorian and Bolivian already has a decent amount of euro ancestry even if it is low on average.

1). Brazil has a population of 210,147,125 making it the most most populated country in South America and on average is overwhelmingly European. On average Brazil is 62% European, 21% African and 17% Native American


2). Colombia and Venezuela have a population of 79,259,542 combined, making it the second region in South America to be most populated. On Average Colombia is 62% European, 27% Amerindian and 9% African while Venezuela is 56% European, 25% Amerindian and 19% African.

3). The Southern Cone(Argentina, Chile, Uruguay and Paraguay) have a population of 74,692,339 combined, this region is also overwhelmingly European.
Argentina is 79% European, 18% Amerindian and 3% African. Chile is 51.8% European, 44.3% Amerindian and 3.8% African. Paraguay is 59.9% European, 30.9% Amerindian and 9.2% African. Uruguay is 77.1% European, 13.2% Amerindian and 9.8% African.

4). The Andean region(Ecuador, Peru and Bolivia) have a population of 61,336,961 combined, making it the smallest of the bunch and this region is overwhelmingly Amerindian. Ecuador is 56% Amerindian, 39.5% European and 4.5% African. Peru is 64% Amerindian, 29% European and 7% African. Bolivia is 78% Amerindian, 21% European and 1% African.

5). The Guianas(Guyana, Suriname and French Guiana) have a population of 1,653,072 combined, this region isn’t part of the Latin South American group and identifies more with the Caribbean. It is overwhelmingly Black and Indian. Couldn’t find any data on they’re genetic compositions

Taken this all into account I would say South America is predominantly European with the rest being mostly Amerindian and some African

Yes i agree with mostof the things you are saying