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Thread: Latin American genetic studies [official archive]

  1. #1541
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    Quote Originally Posted by samario View Post
    I'm guessing he has higher NA than Puerto Rican average and SSA somewhere around 20%.



    Hmm. I wouldn't call him an harnizo.
    Fact. His nose seems to have SSA.
    99% Spanish_Aragon + 1% Chukchi @ 7.43

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  2. #1542
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    Colonialism and the co-evolution of ethnic and genetic structure in New Mexico

    https://www.ncbi.nlm.nih.gov/pubmed/31930496

    2.2 | Materials
    In semi-structured face-to-face interviews with 25 NMS, and in consultation with community leaders and social scientists who work in New Mexico, we identified seven ethnic terms that NMS commonly use to describe themselves: Chicanx (“x” denotes the gender forms that were used by study participants, for example, Chicano and Chicana), Hispanic, Latinx, Nuevomexicanx, Mexican American, Mexican, and Spanish (Healy et al., 2018; Hunley et al., 2018). We then conducted structured face-to-face interviews with 507 NMS. Interviews took place at the University of New Mexico in Albuquerque. Thirty-two percent of New Mexicans reside in Albuquerque, and the city is representative of the state with respect to age, education, income, English and Spanish language use, race, and ethnicity (US Census Bureau, 2016). Participants were recruited through printed mailers and advertisements on the University of New Mexico campus, public libraries, community centers, and non-profit organizations. Recruitment materials asked for volunteers who self-identified as New Mexican of Spanish-speaking descent. Though we did not exclude Native American individuals from participating, only one individual identified as “Native” in an open-ended question asked prior to showing participants the list of seven terms. We added “Other” to the list of terms and asked participants to choose the terms they used to describe themselves in order of salience in their everyday lives. Participants were permitted to choose and rank multiple terms. We also asked participants to choose the term that their mothers and fathers would use to describe themselves (“Which group do you think your mother/father belongs to?”). During the interviews, we collected mouthwash samples from which we extracted DNA and genotyped 291,917 autosomal single nucleotide polymorphisms (Illumina HumanCytoSNP-12 DNA Analysis BeadChip Kit). The SNPs were also typed in 40 Native American, 54 European, and 40 Sub-Saharan African individuals from the HGDP-CEPH (Cann et al., 2002) (Table 2). To determine whether beliefs about connections to past ancestors, as represented by ethnic terms used by NMS today, reflect the actual history of regional migrations and isolation, as ascertained from genomic data, we conducted the following analyses.


    Among groups, average European ancestry ranged from a low of 0.595 for the Mexican American group to a high of 0.744 for the Nuevomexicanx group. Average Native American ancestry ranged from 0.242 (Nuevomexicanx) to 0.368 (Mexican American), and average African ancestry ranged from 0.013 (Spanish) to 0.036 (Mexican American). The bottom row of Figure 1 shows heat maps of the pvalues for the Wilcoxon tests comparing ancestry between each pair of NMS groups, highlighting only the values that fell below 0.05. NMS who identified as Mexican American had significantly higher African and Native American ancestry and lower European ancestry than NMS who identified using all other terms except Mexican (Wilcoxon test, p < .002). The pattern of significance was similar for NMS who identified as Mexican, though only the Mexican-Nuevomexicanx and Mexican-Spanish comparisons were significant at the multiple-test adjusted threshold. Diamond-shaped points in the violin plots in Figure 1 show ancestry estimates for individuals who identified their parents as non-NMS. Eighteen NMS identified their mother as non-NMS, using terms such as Anglo, Caucasian, French, and Irish. These NMS identified themselves as Chicanx (n = 3), Hispanic (n = 4), Nuevomexicanx (n = 6), Other (n = 2), and Spanish (n = 3). The European ancestry for these NMS (mean = 0.853) was higher than it was for any of the NMS ethnic groups, and the Native American ancestry (mean = 0.142) was lower (see Table S1). Seventeen NMS identified their father as non-NMS, using terms like Anglo, Gringo, English, and Italian. These NMS identified themselves as Hispanic (n = 8), Nuevomexicanx
    (n = 5), Other (n = 2), and Spanish (n = 2). They also had relatively high European ancestry (mean = 0.838) and low Native American ancestry (mean = 0.156). These results indicate that there is ongoing gene flow into NMS from non-NMS individuals who are of European descent.


  3. #1543
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    Quote Originally Posted by Duffmannn View Post
    En España los ecuatorianos se ven muy indígenas, al nivel de peruanos o bolivianos, hay incluso algún negroide.

    Sacar un 75% euro en un test genético como el chaval del otro día debe ser una proeza en Ecuador.
    Aquí en Nueva York varían bastante. Los hay mestizos, los hay indígenas, los hay harnizos e incluso castizos. Muchos son de la costa ecuatoriana y otros de la sierra. Ellos son el 5to. grupo latino más común acá después de los dominicanos, los boricuas, los mexicanos y los colombianos.

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    Verdad yo iba a la escuela con un ecuatoriano que se veía blanco aquí en Nueva York quando estaba en middle school ni me di cuenta que era latino hasta que dijo que era ecuatoriano, pero si tenía nariz e ojos como de alguien de la zona andina. Entonces tampoco me sorprendió mucho. Creo que en Nueva York hay más variedad que en otros lugares del mundo para ser te honesto, e eso que no fue en ningún escuela de ricos si no una escuela da área clase media baja

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    Yo conozco un montón e incluso anduve con una de Portoviejo. Me recordaba a Laura Pausini pero más atractiva (tenía buen cuerpo ella por cierto). Para mí en aquel entonces se veía criolla pero realmente no tenía ojos antropológicos. La última vez que supe andaba con otro dominicano pero más mulato. Nosotros fuimos a la universidad juntos en mis primeros 2 años e hicimos el CLIP también en BCC.

  6. #1546
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    2020 brazilian genetic study (Sao Paulo)

    https://journals.plos.org/plosone/ar...l.pone.0227260

    The Brazilian TP53 mutation (R337H) and sarcomas


    Materials and methods
    Study subjects
    A total of 701 patients treated at the Barretos Cancer Hospital between 2008 and 2016 were included in the study. Because a large proportion of the cases did not have blood samples available, frozen tumor tissue was analyzed for the purposes of this study. Samples were selected from the Institutional Biobank, macrodissected and revised by a board of pathologists who decided the best area to be analyzed (areas with tumor content higher than 60% and necrosis lower than 20%). A total of 199 cases were excluded due to different issues, mainly because of insufficient material, leading to a total of 502 sarcomas analyzed. In cases where the R337H mutation could be identified in the tumor, DNA from blood or normal tissue was analyzed when available.

    Clinical and histopathological data as well as information regarding the family history of cancer were collected from the patient’s clinical chart. This study was approved by the local institutional ethical committee (approval number 866/2014). All patients provided written informed consent.

    Genotyping
    Genomic DNA was extracted from peripheral blood leukocytes or tumor tissue using a DNA Blood and Tissue kit (Qiagen), following the manufacturer’s instructions. For the detection of TP53 p.Arg337His, samples were PCR-amplified and analyzed by RFLP using the HhaI enzyme as described elsewhere [15]. Samples with a PCR-RFLP profile suggestive of positivity were confirmed by bidirectional Sanger sequencing. Moreover, in cases where the mutation was identified in tumor DNA, available blood or normal tissue samples were used to confirm the mutation by bidirectional Sanger sequencing.

    Ancestry analysis
    A panel of 46 AIM-INDELs was performed to evaluate the population admixture proportions considering four continental origins (Africa, Europe, East Asia and Native South America) [16,17,18]. Primer sequences and PCR conditions were obtained according to Pereira et al [16]. For that purpose, a 46-multiplex PCR followed by capillary electrophoresis was performed on an ABI 3500 xL Genetic Analyzer (Applied Biosystems) according to the manufacturer’s instructions. The electropherograms were evaluated, and genotypes were automatically assigned with GeneMapper v4.1 (Applied Biosystems).

    Structure v2.3.3 software [19] was used to estimate the ancestry proportions of each patient. Considering the historical formation of Brazil’s population, we assumed the four major population groups (Native Americans, Europeans, Africans and East Asians, K = 4) applied to the genetic makeup of the Brazilian population. The structure consisted of 100,000 burn-in steps followed by 100,000 Markov Chain Monte Carlo (MCMC) iterations. The option ‘Use population Information to test for migrants’ was used with the Admixture model, taking into account the allele frequencies that were correlated, and allele frequencies were updated using only individuals with POPFLAG = 1. (HGDP-CEPH samples were used as references).



    Considering the declared ethnicity, 60% of the patients from our cohort were white. Ancestry analysis was performed for 411 patients, and the results are compatible with the declared data, reporting that the median value for European ancestry was 67.1%, followed by African (15.9%), East Asian (7.2%) and Native American (9.8%) (Fig 4). Among the mutated cases, a total of 39 patients with the Brazilian founder pathogenic variant in TP53 (c.1010G>A; p.Arg337His) were analyzed (Fig 4). For these 39 individuals, the average ancestry proportions were 66.3% for European, followed by African (15.6%), East Asian (10.7%) and Native American (7.4%). Using the Mann-Whitney test, we did not find any correlation between the ancestral profile and the presence/absence of the pathogenic variant in TP53 (p.Arg337His).


  7. #1547
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    BRAZIL 2020

    https://www.nature.com/articles/s41598-020-58540-3#Sec7


    Material and Methods
    Study population
    The patients come from a prospective randomized clinical trial (Resistant Hypertension Optimal Treatment - ReHOT) that was conducted between 2012 and 2014. It included hypertensive patients from 26 sites located in different states in Brazil20. The Ethics Committee for Human Medical Research of the Clinical Hospital of the School of Medicine, University of São Paulo approved the study protocol (protocol number 0758/09) and all individuals signed an informed consent form in accordance with the Declaration of Helsinki and good clinical practice guidelines. This study was registered at clinicaltrials.gov under the number NTC1643434.

    Genotyping data
    Individuals from the ReHOT project were genotyped using genomic DNA in the Open Array platform with QuantStudioTM 12 K FlexTM. A commercial genotyping custom chip from Applied BiosystemsTM, containing 192 single nucleotide polymorphisms (SNPs which can be seen in Supplementary Table 1), was used to perform genotyping through real-time PCR. In this method, each chip had enough arrays to obtain the 192 genotypes of 15 individuals at the same time and a further negative control reaction to evaluate the quality of genotyping. Estimates of individual admixture using this 192 AIM panels were highly correlated with estimates using ~370 000 genome-wide SNPs: 91%, 92%, and 74% of, respectively, African, European, and Native American ancestry components21.


    Results
    Samples from 1,358 patients were analyzed for the proportions of EUR, AFR and AMR ancestry. From these, 165 were resistant hypertensive patients. Table 1 shows general and clinical characteristics of patients according to self-declared race/color groups. The average age was 54.7 years for whites and 52.9 years for non-whites. The mean blood pressure was 172.5/102.6 mmHg and 42% of the patients were males and 58% females. As expected there was a highly significant association between genetic ancestry (GA) and self-declared race/color (Supplementary Table 2). Table 2 shows that the proportion of ancestry was not associated with resistant or nonresistant hypertensive patients. The GA proportions were similar in both groups with 52.0% European, 36.7% African and 11.3% Amerindian for resistant and 54.0% European, 34.4% African and 11.6% Amerindian (p > 0.05) for nonresistant patients.

  8. #1548
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    Quote Originally Posted by Argentano View Post
    BRAZIL 2020

    https://www.nature.com/articles/s41598-020-58540-3#Sec7

    The mean blood pressure was 172.5/102.6 mmHg and 42% of the patients were males and 58% females. As expected there was a highly significant association between genetic ancestry (GA) and self-declared race/color (Supplementary Table 2). Table 2 shows that the proportion of ancestry was not associated with resistant or nonresistant hypertensive patients. The GA proportions were similar in both groups with 52.0% European, 36.7% African and 11.3% Amerindian for resistant and 54.0% European, 34.4% African and 11.6% Amerindian (p > 0.05) for nonresistant patients.
    hypertensive patients is a disease that mainly attacks black Africans.

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