Development of a small panel of SNPs to infer ancestry in Chileans that distinguishes Aymara and Mapuche components

BACKGROUND: Current South American populations trace their origins mainly to three continental ancestries, i.e. European, Amerindian and African. Individual variation in relative proportions of each of these ancestries may be confounded with socio-economic factors due to population stratification. Therefore, ancestry is a potential confounder variable that should be considered in epidemiologic studies and in public health plans. However, there are few studies that have assessed the ancestry of the current admixed Chilean population. This is partly due to the high cost of genome-scale technologies commonly used to estimate ancestry. In this study we have designed a small panel of SNPs to accurately assess ancestry in the largest sampling to date of the Chilean mestizo population (n = 3349) from eight cities. Our panel is also able to distinguish between the two main Amerindian components of Chileans: Aymara from the north and Mapuche from the south. RESULTS: A panel of 150 ancestry-informative markers (AIMs) of SNP type was selected to maximize ancestry informativeness and genome coverage. Of these, 147 were successfully genotyped by KASPar assays in 2843 samples, with an average missing rate of 0.012, and a 0.95 concordance with microarray data. The ancestries estimated with the panel of AIMs had relative high correlations (0.88 for European, 0.91 for Amerindian, 0.70 for Aymara, and 0.68 for Mapuche components) with those obtained with AXIOM LAT1 array. The country's average ancestry was 0.53 ± 0.14 European, 0.04 ± 0.04 African, and 0.42 ± 0.14 Amerindian, disaggregated into 0.18 ± 0.15 Aymara and 0.25 ± 0.13 Mapuche. However, Mapuche ancestry was highest in the south (40.03%) and Aymara in the north (35.61%) as expected from the historical location of these ethnic groups. We make our results available through an online app and demonstrate how it can be used to adjust for ancestry when testing association between incidence of a disease and nongenetic risk factors. CONCLUSIONS: We have conducted the most extensive sampling, across many different cities, of current Chilean population. Ancestry varied significantly by latitude and human development. The panel of AIMs is available to the community for estimating ancestry at low cost in Chileans and other populations with similar ancestry.

Prevalencia del virus de la inmunodeficiencia humana, virus de la hepatitis B y Treponema pallidum en reclusos del Centro de Detención Preventiva de Arica, Chile / Prevalence of HIV, hepatitis B virus and Treponema pallidum in inmates in the Preventive Detention Center of Arica, Chile

Resumen Introducción: Los grupos de riesgo para las infecciones de transmisión sexual (ITS) son trabajadores sexuales, drogadictos, la población joven de inicio sexual precoz, así como la población penal. Objetivo: Determinar la prevalencia de infección por virus de inmunodeficiencia humana (VIH), Treponema pallidum y virus de hepatitis B (VHB) en reclusos (hombres) del Centro de Detención Preventiva (CDP) de Arica. Material y Métodos: El estudio se efectuó en 140 reclusos, con consentimiento informado. Se realizó encuesta epidemiológica y toma de muestra sanguínea. Los exámenes positivos se enviaron al Hospital Regional de Arica para confirmación y posteriormente al Instituto de Salud Pública. Resultados: La prevalencia de ITS fue de 13,6%. La mayor frecuencia se observó en VDRL positivos (7,1%), seguido por infección por VIH (5,7%) y VHB (2,9%). Por edad, la mayor frecuencia (57,9%) se presentó en individuos bajo 31 años. El 63,2% se encontraban en situación de hacinamiento, en 42,1% la edad de inicio de la actividad sexual fue antes de los 15 años y 94,7% declaró ser consumidor de drogas. Conclusiones: El estudio reafirma los factores predisponentes a la transmisión de las ITS, como edad, inicio sexual precoz, consumo de drogas y hacinamiento, destacando que las prisiones son ambientes altamente vulnerables, donde la sobrepoblación, condición sexual, inicio sexual precoz, alto consumo de drogas y la carente visita conyugal proporcionan un contexto epidemiológico favorable para el incremento de ITS.

Background: The risk groups for sexual transmitted diseases (STDs) are sex workers, drug addicts, young people in early sexual initiation, and population in prison. Aim: To determine the prevalence of HIV, Treponema pallidum and hepatitis B Virus (HBV) in male inmates at the Preventive Detention Center (CDP) of Arica. Methods: The study was conducted in 140 inmates, with informed consent. Epidemiological survey and blood sampling was conducted. The positive tests were sent to the Hospital Regional of Arica for confirmation and the National Reference Laboratory for confirmation. Results: STD prevalence was 13.6%. The most prevalent was VDRL positive (7.1%) followed by HIV infection (5.7%) and HBV (2.9%). The highest rate (57.9%) occurred in individuals under 31 years old. 63.2% were in an overcrowded situation, 42.1% of cases corresponded to those whose age of sexual activity onset of was before age 15 and 94.7% used drugs. Conclusions: The study reasserts the predisposing factors for the transmission of STDs as age, early sexual debut, drug abuse and overcrowding, noting that prisons are highly vulnerable environments where overcrowding, sexual condition, early sexual initiation, high drug abuse and the lacking spouses visits provide an epidemiological context favorable for increased STD.