Latin American genetic studies [official archive]

[BirdMan]

NEW Brazilian study 2019 with 15,105 Sample

https://journals.plos.org/plosone/ar...0216653#sec012












Here i made some modifications so its easier to understand

Average results per region and color.




Ancestry boxplots

This study and the graphics you created are amazing. I’m actually in Rio right now for work and these results seem to correspond pretty well with the people I see on the streets.

If only they made studies segmented by self-identification and region for all of Latin America.

[Argentano]

NEW 2019 LATIN AMERICAN GENETIC STUDY INCLUDING SEVERAL COUNTRIES

https://www.ncbi.nlm.nih.gov/pubmed/31376146
https://ascpt.onlinelibrary.wiley.co....1002/cpt.1598

Genomic ancestry, CYP2D6, CYP2C9 and CYP2C19 among Latin‐Americans


Methods
Subjects, Populations and Groups
From the 6,060 individuals genotyped for CYP2D6, CYP2C9 or CYP2C19 polymorphisms13, 3,387 were analyzed for individual ancestry in the present study, with the following distribution (Table 1): (i) 1,051 Native Americans from Mexico, Costa Rica and Peru, representing North, Central and South America, respectively. They live in rural populations, are locally recognized as indigenous and are settled in regions where the population is predominantly indigenous; (ii) 38 Afro -Latin Americans, that self-reported as Afro -descendants in Costa Rica and reported to have four Black grandparents in Cuba; (iii) 163 self-reported Ashkenazi Jews from Argentina; (iv) 206 Cubans that self-reported to have four White grandparents, (v) 1,442 admixed (Mestizo) in the Hispanic America; (vi) 371 Spaniards and 116 Portuguese. For Native American populations, we followed the ethno -linguistic classification by Campbell15 (Table 1). University of Extremadura and local IRBs approved the use of studied sample for the present study.



Results

Ancestry analysis confirms that populations classified as Native American in Mexico, Costa Rica and Peru have at least 86% of Native American ancestry (Figure 1B, Table 1). The exceptions are the native Mayo population from Mexico (~40% of Old World admixture), and Bribri and Chorotega populations from Costa Rica (European ancestry 18% and 22%, respectively). We studied a broad spectrum of 31 autochthonous and admixed populations distributed across Latin America. Among urban admixed populations, Native American ancestry is predominant in admixed Peruvians (from Lima, 71%), admixed Ecuadorians (from Quito and Guayaquil, 61%) and admixed Mexicans (from Distrito Federal, 60%). Interestingly, Lima -Peru admixed have similar Old World ancestry than some populations classified as Native Americans, such as the Mayo from Mexico (61%) and the Costa Rican Chorotega (69%). European ancestry predominates in Argentinians Ashkenazi Jews (88%), Argentinians (82%), Uruguayans (78%), Brazilians (68%) and Cubans (64%), all considered admixed populations. The admixed Nicaraguans and Costa Ricans have the most balanced admixture among the studied populations (Native American, European and African ancestry, respectively: 41%, 45% and 14% for Nicaragua and 40%, 43% and 17% for Costa Rica). The populations with the highest African ancestry are the Costa Rican Blacks (86%) and Cuban Blacks (52%), where some individuals reach >90% of African ancestry.


AVERAGE RESULTS




INDIVIDUAL RESULTS BARPLOTS

Figure 1. Genomic ancestry of studied individuals and populations and African Yoruba (Nigerians) from the 1000 Genomes Project, based on the 83 ancestry informative markers (AIMs). (A) Principal Component (PC) Analysis representation. Individuals are colored according to geographic regions. (B) Vertical barplots of individual continental ancestry.

1: African Yoruba from Nigeria, 1000 Genomes Project;
2: Spaniards from Extremadura,
3: Portuguese;
4: Ashkenazi from Argentina;
5: Ashaninka from Peru;
6: Shimaa from Peru;
7: Aymara from Peru;
8: Mexicaneros from Mexico;
9: Seris from Mexico,
10: Tepehuanos from Mexico;
11: Tarahumaras from Mexico;
12: Guarijios from Mexico;
13: Huicholes from Mexico;
14: Coras from Mexico;
15: Lacandones from Mexico;
16: E. Lacandones from Mexico;
17: Tzeltales from Mexico;
18: Mayos from Mexico;
19: Costa Rica populations: 1st: Bribri, 2nd: Chorotega, 3rd: Guaymí, 4th: Admixed population, 5th AfroCaribbeans;
20: Admixed from Mexico (DF);
21: Admixed from Chiapas, Mexico
22: Admixed from Peru;
23: Admixed from Nicaragua;
24: Admixed from Brazil;
25: Cuban,
26: Afro-Caribbeans from Cuba,
27: Admixed from Cuba;
28: Admixed from Ecuador;
29: Admixed from Argentina;
30: Admixed from Uruguay.






SAMPLES/RESULTS

[Argentano]

CHILE ATACAMA

https://www.ncbi.nlm.nih.gov/pubmed/31384924
https://academic.oup.com/gbe/advance...evz172/5544110
https://oup.silverchair-cdn.com/oup/...5G5CRDK6RD3PGA

Adaptation to extreme environments in an admixed human population from the Atacama Desert.


Materials and Methods
Study subjects
Subjects were invited to participate after signing an informed consent. Cases were recruited among patients treated for primary BC between 2013 and 2015 at the state-owned Hospital Regional de Antofagasta, which is the regional referral center for all major health problems occurring in northern Chile. The study was approved by the Ethics Committee of the Faculty of Medicine from Clínica Alemana/ Universidad del Desarrollo in Santiago. Based on this approval, it was subsequently authorized for execution by local authorities of the Hospital Regional de Antofagasta. Control subjects were individuals with no prior history of genitourinary malignancies. They were enrolled at the outpatient center of the same hospital and matched to the case patients by age (~5 years) and sex. Epidemiologic and clinical data (demographics, smoking history, medical history and ORFs) were collected during an in-person interview by trained nurses using a validated questionnaire. A blood sample was obtained at the same time. Smoking status was assigned according to current WHO-classification, with never smokers defined as individuals who had smoked none or <100 cigarettes during lifetime, and ever smokers as individuals who had smoked ≥100 cigarettes during lifetime.

[Erronkari]

CHILE ATACAMA

https://www.ncbi.nlm.nih.gov/pubmed/31384924
https://academic.oup.com/gbe/advance...evz172/5544110
https://oup.silverchair-cdn.com/oup/...5G5CRDK6RD3PGA

Adaptation to extreme environments in an admixed human population from the Atacama Desert.


Materials and Methods
Study subjects
Subjects were invited to participate after signing an informed consent. Cases were recruited among patients treated for primary BC between 2013 and 2015 at the state-owned Hospital Regional de Antofagasta, which is the regional referral center for all major health problems occurring in northern Chile. The study was approved by the Ethics Committee of the Faculty of Medicine from Clínica Alemana/ Universidad del Desarrollo in Santiago. Based on this approval, it was subsequently authorized for execution by local authorities of the Hospital Regional de Antofagasta. Control subjects were individuals with no prior history of genitourinary malignancies. They were enrolled at the outpatient center of the same hospital and matched to the case patients by age (~5 years) and sex. Epidemiologic and clinical data (demographics, smoking history, medical history and ORFs) were collected during an in-person interview by trained nurses using a validated questionnaire. A blood sample was obtained at the same time. Smoking status was assigned according to current WHO-classification, with never smokers defined as individuals who had smoked none or <100 cigarettes during lifetime, and ever smokers as individuals who had smoked ≥100 cigarettes during lifetime.

Interesting!
Looks quite more Euro than Salta or Jujuy.
It seems that Chile is more homogeneous...

[Argentano]

Rotator cuff tear susceptibility is associated with variants in genes involved in tendon extracellular matrix homeostasis

https://www.ncbi.nlm.nih.gov/pubmed/31444797

Between 2012 and 2016, 778 individuals were recruited at the Hospital São Paulo/ UNIFESP, Brazil.


Cases 209 samples 70.8% european 10.2% Amerindian 16.3% African
Controls 449 samples 63.2% european 11% amerindian 23.5% African

[Argentano]

https://www.dovepress.com/influence-...t-article-DMSO

Influence of genomic ancestry and self-reported color-race in CKD in a nationwide admixed sample of Brazilian patients with type 1 diabetes

Methods: This is a multicenter, observational, cross-sectional study with 1564 patients, conducted between August 2011 and August 2014 in 14 public clinics from 10 Brazilian cities. The ethnic aspects of the patients were evaluated using self-reported color-race and genomic ancestry (divided in European, African, and Amerindian). We divided the patients into groups: normal renal function and CKD.

DNA extraction and AIM-Indel genotyping
We used the commercial kit SP QIA symphony by automation with QIA symphony equipment, following manufacturer’s instructions (Qiagen, USA) to extract Genomic DNA from peripheral blood. The global and individual GA were inferred using a panel of 46 AIM-INDEL, with a protocol described by Pereira et al.

The median EUR ancestry in our sample was 68.0 AFR was 16.3 and NAM was 10.2

[Argentano]

2019 SAO PAULO RIBEIRAO PRETO

https://www.ncbi.nlm.nih.gov/pubmed/31505868

HLA-G Polymorphisms Are Associated with Non-Segmental Vitiligo among Brazilians

Population Sample

We studied 50 non-segmental vitiligo patients from the Ribeirão Preto region, located in the northern region of the State of São Paulo, southeastern Brazil, and followed up at the Dermatology Outpatient Clinic of the University Hospital of the Ribeirão Preto Medical School, University of Sao Paulo. These individuals, 33 women and 17 men, with ages ranging from 18 to 75 years, filled out a questionnaire, signed an informed consent form and donated a 10-mL blood sample, which was stored in a Vacutainer
® EDTA-containing tube. A total of 393 healthy individuals, 186 women and 207 men, with ages ranging from 18 to 80 years, were selected within the Ribeirão region for the control group and were submitted to the same procedures.

Results

The ancestry background of the vitiligo group was 58.5% European, 29.7% African, and 11.7% Asian/Amerindian (Figure 1). In contrast, the control group’s ancestry background was 72.3% European, 19.9% African, and 7.8% Asian/Amerindian (Figure 1). This indicates a higher African and lower European ancestry among Brazilian vitiligo patients when compared to controls.

[Argentano]

https://www.nature.com/articles/s41598-019-49611-1

[Argentano]

https://onlinelibrary.wiley.com/doi/...1002/cam4.2434

Self‐Identified African Americans and prostate cancer risk: West African genetic ancestry is associated with prostate cancer diagnosis and with higher Gleason sum on biopsy


AIMs estimates of individual WA, EU, and NA ancestry for 96 self‐identified African American and 59 self‐identified European American patients undergoing standard‐of‐care systematic prostate biopsy. The mean percentage of WA genetic ancestry for the AA men was 80% (SD 12%) and for the EA men was 7% (SD 12%), and the means were significantly different P < .0001. The mean percentage of EA ancestry was 89% (SD 14%) for the EA men and 17% (SD 12%) for the AA men, and the means were significantly different P < .0001. The mean percentage of NA ancestry was 3% (SD 4%) for AA men and 4% (SD 4%) for EA men (no significant difference). NA ancestry was not included in the analyses

[Tenma de Pegasus]

https://www.dovepress.com/influence-...t-article-DMSO

Influence of genomic ancestry and self-reported color-race in CKD in a nationwide admixed sample of Brazilian patients with type 1 diabetes

Methods: This is a multicenter, observational, cross-sectional study with 1564 patients, conducted between August 2011 and August 2014 in 14 public clinics from 10 Brazilian cities. The ethnic aspects of the patients were evaluated using self-reported color-race and genomic ancestry (divided in European, African, and Amerindian). We divided the patients into groups: normal renal function and CKD.

DNA extraction and AIM-Indel genotyping
We used the commercial kit SP QIA symphony by automation with QIA symphony equipment, following manufacturer’s instructions (Qiagen, USA) to extract Genomic DNA from peripheral blood. The global and individual GA were inferred using a panel of 46 AIM-INDEL, with a protocol described by Pereira et al.

The median EUR ancestry in our sample was 68.0 AFR was 16.3 and NAM was 10.2

Diabetes type 1! Its a very good way to measure a country genetic because diabetes type 1 affects all races and social classes equally!

Type 2 is not good because it has behavior influences/habits and those things like food quality change according to social class.