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Long read sequencing data, particularly those derived from the Oxford Nanopore (ONT) sequencing platform, tend to exhibit a high error rate. Here, we present NextDenovo, a highly efficient error correction and assembly tool for noisy long reads, which achieves a high level of accuracy in genome assembly. NextDenovo can rapidly correct reads; these corrected reads contain fewer errors than other comparable tools and are characterized by fewer chimeric alignments. We applied NextDenovo to the assembly of high quality reference genomes of 35 diverse humans from across the world using ONT Nanopore long read sequencing data. Based on thesede novogenome assemblies, we were able to identify the landscape of segmental duplications and gene copy number variation in the modern human population. The use of the NextDenovo program should pave the way for population-scale long-read assembly, thereby facilitating the construction of human pan-genomes, using Nanopore long read sequencing data.

Human Leukocyte Antigen (HLA)-G participates in several biological processes, including reproduction, vascular remodeling, immune tolerance, and hypoxia response. HLA-G is a potential candidate gene for high altitude adaptation since its expression is modulated in both micro and macro environment under hypoxia and constant cellular stress. Besides the promoter region, the HLA-G 3'untranslated region (UTR) influences HLA-G expression patterns through several post-transcriptional mechanisms. Currently, the 3'UTR genetic diversity in terms of altitude adaptation of Native American populations is still unexplored, particularly at high altitude ecoregions. Here, we evaluated 288 Native Americans from 9 communities located in the Andes [highland (HL); ≥2,500 m (range = 2,838-4,433 m)] and 8 populations located in lowland (LL) regions [2,500 m (range = 80-431 m); Amazonian tropical forest, Brazilian central plateau, and Chaco] of South America. In total, nine polymorphic sites and ten haplotypes were observed. The most frequent haplotypes (UTR-1, UTR-2, and UTR-3) accounted for ∼ 77% of haplotypes found in LL, while in the HL, the same haplotypes reach ∼ 93%. Also, a remarkable high frequency of putative ancestral UTR-5 haplotype was observed in LL (21.5%), while in HL UTR-2 reaches up to 47%. Further, UTR-2 frequency positively correlates with altitude-related variables, while a negative correlation for UTR-5 was observed. From an evolutionary perspective, we observed a tendency towards balancing selection in HL and LL populations thus suggesting that haplotypes of ancient and more derived alleles may have been co-opted for relatively recent adaptations such as those experienced by modern humans in the highland and lowland of South America. We also discuss how long-term balancing selection can be a reservoir of genetic variants that can be positively selected. Finally, our study provides some pieces of evidence that HLA-G 3'UTR haplotypes may have contributed to high altitude adaptation in the Andes.

Background: Preeclampsia is a multiorgan disorder associated with maternal and perinatal morbi-mortality. In Peru, incidence is 10% and accounts for 22% of maternal deaths. Genome and genetic epidemiological studies have found an association between preeclampsia and genetic polymorphisms. Objective: To determine the association of the vascular endothelial growth factor (VEGF) +936 C/T and +405 G/C, interleukine-6 (IL-6) -174 G/C, IL-1β-511 C/T, Apo A-1-75 G/A, Apo B-100 2488 C/T (Xbal) polymorphisms with preeclampsia in pregnant Peruvian women. Methods: Were included preeclamptic and healthy (control) pregnant women. Maternal blood samples were subjected to DNA extraction, and molecular genetic analysis was conducted using the PCR-RFLP technique and following a specific protocol for each gene. Allele and genotypic frequencies in the cases and controls were compared. Results: No association was found between the VEGF+936C/T and VEGF+405 polymorphisms and preeclampsia. The frequencies of the GG genotypes and the G allele of the -174 G/C polymorphism in the IL6 gene in preeclamptic and controls showed significant differences, with higher frequencies in cases. For the -511 C/T polymorphism of the IL-1β gene, no significant differences were found in the frequencies of TT genotypes compared with CT+CC. The genotypes and alleles of the Apo-A1-75 G/A and Apo-B100 Xbal variants showed no significant differences between cases and controls. Conclusion: No association was found between the studied genetic markers and preeclampsia. However, in the -174G/C polymorphism of the IL-6 gene, significant differences were found mainly in the GG genotype and G allele. Resumen Antecedentes: La preeclampsia es un trastorno multiorgánico asociado con la morbi-mortalidad materna y perinatal. En el Perú, su incidencia es del 10% y causa el 22% de las muertes maternas. Se encontró una asociación entre la preeclampsia y ciertos polimorfismos. Objetivo: Determinar asociación entre los polimorfismos genéticos del factor de crecimiento endotelial vascular (VEGF) +936 C/T y +405 G/C, interleucina-6 (IL-6) -174G/C, IL-1β -511 C/T, Apo A-1 -75 G/A, Apo B-100 2488 C/T (Xbal), y preeclampsia en gestantes peruanas. Métodos: Se incluyeron gestantes preeclámpticas y sanas (controles). Las muestras de sangre fueron procesadas para extracción del ADN, y el análisis se realizó con la técnica PCR-RFLP con protocolos específicos para cada gen y confirmación con secuenciamiento Sanger. Se compararon las frecuencias alélicas y genotípicas en los casos (preeclampsia) y los controles. Resultados: No se halló asociación entre los polimorfismos VEGF+936-C/T y VEGF+405 y la preeclampsia. Las frecuencias de los genotipos GG y el alelo G del polimorfismo -174-G/C en el gen IL6 en preeclámpticas y controles, mostraron diferencias significativas, con frecuencias más altas en los casos. Para el polimorfismo -511-C/T del gen IL-1β, no se encontraron diferencias significativas en las frecuencias de genotipos TT comparados con CT+CC. Los genotipos y alelos de las variantes Apo-A1-75-G/A y Apo-B100 Xbal no mostraron diferencias significativas entre los grupos Conclusión: No se encontró asociación entre los marcadores genéticos estudiados y la preeclampsia. Sin embargo, el polimorfismo -174-G/C en el gen IL6 mostró diferencias significativas principalmente en el genotipo GG y el alelo G.

Background According to history, in the pre-Hispanic period, during the conquest and Inka expansion in Ecuador, many Andean families of the Cañar region would have been displaced to several places of Tawantinsuyu, including Kañaris, a Quechua-speaking community located at the highlands of the Province of Ferreñafe, Lambayeque (Peru). Other families were probably taken from the Central Andes to a place close to Kañaris, named Inkawasi. Evidence of this migration comes from the presence near the Kañaris–Inkawasi communities of a village, a former Inka camp, which persists until the present day. This scenario could explain these toponyms, but it is still controversial. To clarify this historical question, the study presented here focused on the inference of the genetic relationship between ‘Cañaris’ populations, particularly of Cañar and Ferreñafe, compared to other highland populations. We analysed native patrilineal Y chromosome haplotypes composed of 15 short tandem repeats, a set of SNPs, and maternal mitochondrial DNA haplotypes of control region sequences. Results After the genetic comparisons of local populations—three from Ecuador and seven from Peru—, Y chromosome analyses (n = 376) indicated that individuals from the Cañar region do not share Y haplotypes with the Kañaris, or even with those of the Inkawasi. However, some Y haplotypes of Ecuadorian ‘Cañaris’ were associated with haplotypes of the Peruvian populations of Cajamarca, Chivay (Arequipa), Cusco and Lake Titicaca, an observation that is congruent with colonial records. Within the Kañaris and Inkawasi communities there are at least five clans in which several individuals share haplotypes, indicating that they have recent common ancestors. Despite their relative isolation, most individuals of both communities are related to those of the Cajamarca and Chachapoyas in Peru, consistent with the spoken Quechua and their geographic proximity. With respect to mitochondrial DNA haplotypes (n = 379), with the exception of a shared haplotype of the D1 lineage between the Cañar and Kañaris, there are no genetic affinities. Conclusion Although there is no close genetic relationship between the Peruvian Kañaris (including Inkawasi) and Ecuadorian Cañar populations, our results showed some congruence with historical records.

Summary There are many unanswered questions about the population history of the Central and South Central Andes, particularly regarding the impact of large-scale societies, such as the Moche, Wari, Tiwanaku, and Inca. We assembled genome-wide data on 89 individuals dating from ∼9,000-500 years ago (BP), with a particular focus on the period of the rise and fall of state societies. Today’s genetic structure began to develop by 5,800 BP, followed by bi-directional gene flow between the North and South Highlands, and between the Highlands and Coast. We detect minimal admixture among neighboring groups between ∼2,000–500 BP, although we do detect cosmopolitanism (people of diverse ancestries living side-by-side) in the heartlands of the Tiwanaku and Inca polities. We also highlight cases of long-range mobility connecting the Andes to Argentina and the Northwest Andes to the Amazon Basin. Video Abstract, Graphical Abstract, Highlights • Ancient DNA transect reveals north-south substructure of Andean highlands by 5,800 BP • After 5,800 BP, gene flow mixed highland people with their neighbors • After 2,000 BP, striking genetic continuity through rise and fall of major cultures, Genome-wide data from 89 ancient humans illuminates the changes to the genetic landscape in the Central Andes over 9,000 years, revealing large-scale gene flow and cosmopolitan societies in the Tiwanaku and Inca polities.

This study focuses on the descendants of the royal Inka family. The Inkas ruled Tawantinsuyu, the largest pre-Columbian empire in South America, which extended from southern Colombia to central Chile. The origin of the royal Inkas is currently unknown. While the mummies of the Inka rulers could have been informative, most were destroyed by Spaniards and the few remaining disappeared without a trace. Moreover, no genetic studies have been conducted on present-day descendants of the Inka rulers. In the present study, we analysed uniparental DNA markers in 18 individuals predominantly from the districts of San Sebastian and San Jerónimo in Cusco (Peru), who belong to 12 families of putative patrilineal descent of Inka rulers, according to documented registries. We used single-nucleotide polymorphisms and short tandem repeat (STR) markers of the Y chromosome (Y-STRs), as well as mitochondrial DNA D-loop sequences, to investigate the paternal and maternal descent of the 18 alleged Inka descendants. Two Q-M3* Y-STR clusters descending from different male founders were identified. The first cluster, named AWKI-1, was associated with five families (eight individuals). By contrast, the second cluster, named AWKI-2, was represented by a single individual; AWKI-2 was part of the Q-Z19483 sub-lineage that was likely associated with a recent male expansion in the Andes, which probably occurred during the Late Intermediate Period (1000–1450 AD), overlapping the Inka period. Concerning the maternal descent, different mtDNA lineages associated with each family were identified, suggesting a high maternal gene flow among Andean populations, probably due to changes in the last 1000 years. Electronic supplementary material The online version of this article (10.1007/s00438-018-1427-4) contains supplementary material, which is available to authorised users.

Studies of Native South American genetic diversity have helped to shed light on the peopling and differentiation of the continent, but available data are sparse for the major ecogeographic domains. These include the Pacific Coast, a potential early migration route; the Andes, home to the most expansive complex societies and to one of the most widely spoken indigenous language families of the continent (Quechua); and Amazonia, with its understudied population structure and rich cultural diversity. Here, we explore the genetic structure of 176 individuals from these three domains, genotyped with the Affymetrix Human Origins array. We infer multiple sources of ancestry within the Native American ancestry component; one with clear predominance on the Coast and in the Andes, and at least two distinct substrates in neighboring Amazonia, including a previously undetected ancestry characteristic of northern Ecuador and Colombia. Amazonian populations are also involved in recent gene-flow with each other and across ecogeographic domains, which does not accord with the traditional view of small, isolated groups. Long-distance genetic connections between speakers of the same language family suggest that indigenous languages here were spread not by cultural contact alone. Finally, Native American populations admixed with post-Columbian European and African sources at different times, with few cases of prolonged isolation. With our results we emphasize the importance of including understudied regions of the continent in high-resolution genetic studies, and we illustrate the potential of SNP chip arrays for informative regional-scale analysis.

Studies of Native South American genetic diversity have helped to shed light on the peopling and differentiation of the continent, but available data are sparse for the major ecogeographic domains. These include the Pacific Coast, a potential early migration route; the Andes, home to the most expansive complex societies and to one of the most spoken indigenous language families of the continent (Quechua); and Amazonia, with its understudied population structure and rich cultural diversity. Here we explore the genetic structure of 177 individuals from these three domains, genotyped with the Affymetrix Human Origins array. We infer multiple sources of ancestry within the Native American ancestry component; one with clear predominance on the Coast and in the Andes, and at least two distinct substrates in neighboring Amazonia, with a previously undetected ancestry characteristic of northern Ecuador and Colombia. Amazonian populations are also involved in recent gene-flow with each other and across ecogeographic domains, which does not accord with the traditional view of small, isolated groups. Long distance genetic connections between speakers of the same language family suggest that languages had spread not by cultural contact alone. Finally, Native American populations admixed with post-Columbian European and African sources at different times, with few cases of prolonged isolation. With our results we emphasize the importance of including under-studied regions of the continent in high-resolution genetic studies, and we illustrate the potential of SNP chip arrays for informative regional scale analysis.

The Americas were the last inhabitable continents to be occupied by humans, with a growing multidisciplinary consensus for entry 15-25 thousand years ago (kya) from northeast Asia via the former Beringia land bridge [1-4]. Autosomal DNA analyses have dated the separation of Native American ancestors from the Asian gene pool to 23 kya or later [5, 6] and mtDNA analyses to ∼25 kya [7], followed by isolation ("Beringian Standstill" [8, 9]) for 2.4-9 ky and then a rapid expansion throughout the Americas. Here, we present a calibrated sequence-based analysis of 222 Native American and relevant Eurasian Y chromosomes (24 new) from haplogroups Q and C [10], with four major conclusions. First, we identify three to four independent lineages as autochthonous and likely founders: the major Q-M3 and rarer Q-CTS1780 present throughout the Americas, the very rare C3-MPB373 in South America, and possibly the C3-P39/Z30536 in North America. Second, from the divergence times and Eurasian/American distribution of lineages, we estimate a Beringian Standstill duration of 2.7 ky or 4.6 ky, according to alternative models, and entry south of the ice sheet after 19.5 kya. Third, we describe the star-like expansion of Q-M848 (within Q-M3) starting at 15 kya [11] in the Americas, followed by establishment of substantial spatial structure in South America by 12 kya. Fourth, the deep branches of the Q-CTS1780 lineage present at low frequencies throughout the Americas today [12] may reflect a separate out-of-Beringia dispersal after the melting of the glaciers at the end of the Pleistocene. ispartof: CURRENT BIOLOGY vol:29 issue:1 pages:149-+ ispartof: location:England status: published

The Inca Empire is claimed to have driven massive population movements in western South America, and to have spread Quechua, the most widely-spoken language family of the indigenous Americas. A test-case is the Chachapoyas region of northern Peru, reported as a focal point of Inca population displacements. Chachapoyas also spans the environmental, cultural and demographic divides between Amazonia and the Andes, and stands along the lowest-altitude corridor from the rainforest to the Pacific coast. Following a sampling strategy informed by linguistic data, we collected 119 samples, analysed for full mtDNA genomes and Y-chromosome STRs. We report a high indigenous component, which stands apart from the network of intense genetic exchange in the core central zone of Andean civilization, and is also distinct from neighbouring populations. This unique genetic profile challenges the routine assumption of large-scale population relocations by the Incas. Furthermore, speakers of Chachapoyas Quechua are found to share no particular genetic similarity or gene-flow with Quechua speakers elsewhere, suggesting that here the language spread primarily by cultural diffusion, not migration. Our results demonstrate how population genetics, when fully guided by the archaeological, historical and linguistic records, can inform multiple disciplines within anthropology.

In order to investigate the underlying genetic structure and genomic ancestry proportions of Peruvian subpopulations, we analyzed 551 human samples of 25 localities from the Andean, Amazonian, and Coastal regions of Peru with a set of 40 ancestry informative insertion–deletion polymorphisms. Using genotypes of reference populations from different continents for comparison, our analysis indicated that populations from all 25 Peruvian locations had predominantly Amerindian genetic ancestry. Among populations from the Titicaca Lake islands of Taquile, Amantani, Anapia, and Uros, and the Yanque locality from the southern Peruvian Andes, there was no significant proportion of non-autochthonous genomes, indicating that their genetic background is effectively derived from the first settlers of South America. However, the Andean populations from San Marcos, Cajamarca, Characato and Chogo, and coastal populations from Lambayeque and Lima displayed a low but significant European ancestry proportion. Furthermore, Amazonian localities of Pucallpa, Lamas, Chachapoyas, and Andean localities of Ayacucho and Huancayo displayed intermediate levels of non-autochthonous ancestry, mostly from Europe. These results are in close agreement with the documented history of post-Columbian immigrations in Peru and with several reports suggesting a larger effective size of indigenous inhabitants during the formation of the current country’s population. FAPEMIG y CNPq de Brasil

Objectives: To determine genetic differences between agriculturalist and hunter-gatherer southern Native American populations for selected metabolism-related markers and to test whether Neel's thrifty genotype hypothesis (TGH) could explain the genetic patterns observed in these populations. Materials and Methods: 375 Native South American individuals from 17 populations were genotyped using six markers (APOE rs429358 and rs7412; APOA2 rs5082; CD36 rs3211883; TCF7L2 rs11196205; and IGF2BP2 rs11705701). Additionally, APOE genotypes from 39 individuals were obtained from the literature. AMOVA, main effects, and gene-gene interaction tests were performed. Results: We observed differences in allele distribution patterns between agriculturalists and hunter-gatherers for some markers. For instance, between-groups component of genetic variance (FCT) for APOE rs429358 showed strong differences in allelic distributions between hunter-gatherers and agriculturalists (p = 0.00196). Gene-gene interaction analysis indicated that the APOE E4/CD36 TT and APOE E4/IGF2BP2 A carrier combinations occur at a higher frequency in hunter-gatherers, but this combination is not replicated in archaic (Neanderthal and Denisovan) and ancient (Anzick, Saqqaq, Ust-Ishim, Mal'ta) hunter-gatherer individuals. Discussion: A complex scenario explains the observed frequencies of the tested markers in hunter-gatherers. Different factors, such as pleotropic alleles, rainforest selective pressures, and population dynamics, may be collectively shaping the observed genetic patterns. We conclude that although TGH seems a plausible hypothesis to explain part of the data, other factors may be important in our tested populations. Fil: Reales, Guillermo. Universidade Federal do Rio Grande do Sul; Brasil Fil: Rovaris, Diego L.. Universidade Federal do Rio Grande do Sul; Brasil Fil: Jacovas, Vanessa C.. Universidade Federal do Rio Grande do Sul; Brasil Fil: Hünemeier, Tábita. Universidade de Sao Paulo; Brasil Fil: Sandoval, José R.. Universidad de San Martín de Porres. Facultad de Medicina Humana; Perú Fil: Salazar Granara, Alcibiades. Universidad de San Martín de Porres. Facultad de Medicina Humana; Perú Fil: Demarchi, Dario. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Antropología de Córdoba. Universidad Nacional de Córdoba. Facultad de Filosofía y Humanidades. Instituto de Antropología de Córdoba; Argentina Fil: Tarazona Santos, Eduardo. Universidade Federal de Minas Gerais; Brasil Fil: Felkl, Aline B.. Universidade Federal do Rio Grande do Sul; Brasil Fil: Serafini, Michele A.. Universidade Federal do Rio Grande do Sul; Brasil Fil: Salzano, Francisco M.. Universidade Federal do Rio Grande do Sul; Brasil Fil: Bisso Machado, Rafael. Universidad de la República; Uruguay Fil: Comas, David. Universitat Pompeu Fabra; España Fil: Paixão Côrtes, Vanessa R.. Universidade Federal da Bahia; Brasil Fil: Bortolini, Maria Catira. Universidade Federal do Rio Grande do Sul; Brasil

N-acetyltransferase 2 (NAT2) is responsible for metabolizing xenobiotics; NAT2 polymorphisms lead to three phenotypes: rapid, intermediate and slow acetylators. We aimed to investigate NAT2 diversity in Native Americans. NAT2 exon 2 was sequenced for 286 individuals from 21 populations (Native American and American Mestizos). Excluding the basal/rapid haplotype NAT2*4, the most frequent haplotypes are NAT2*5B (35.95%) in hunter-gatherers and NAT2*7B (20.61%) and NAT2*5B (19.08%) in agriculturalists that were related to the slow phenotype. A new haplotype was identified in two Amerindians. Data from the ~ 44 kb region surrounding NAT2 in 819 individuals from Africa, East-Asia, Europe and America were used in additional analyses. No significant differences in the acetylator NAT2 haplotype and phenotype distributions were found between Native American populations practicing farming and/or herding and those practicing hunting and gathering, probably because of the absence or weakness of selection pressures and presence of demographic and random processes preventing detection of any selection signal. Fil: Bisso Machado, R.. Universidade Federal do Rio Grande do Sul; Brasil Fil: Ramallo, Virginia. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Paixão Côrtes, V. R.. Universidade Federal do Rio Grande do Sul; Brasil Fil: Acuña Alonzo, V.. Escuela Nacional de Antropología e Historia; México Fil: Demarchi, Dario. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Córdoba. Instituto de Antropología de Córdoba; Argentina. Universidad Nacional de Córdoba; Argentina Fil: Sandoval, J. R. S.. Universidad de San Martin de Porres; Perú Fil: Granara, A. A. S.. Universidad de San Martin de Porres; Perú Fil: Salzano, F. M.. Universidade Federal do Rio Grande do Sul; Brasil Fil: Hünemeier, T.. Universidade de Sao Paulo; Brasil Fil: Bortolini, M. C.. Universidade Federal do Rio Grande do Sul; Brasil

El cromosoma Y humano contiene marcadores altamente informativos para hacer inferencias históricas sobre el poblamiento precolombino de América. Sin embargo, la escasez de estos marcadores ha limitado su uso en la inferencia de ascendencia compartida y las migraciones pasadas pertinentes al origen de las diversidades cultural y biológica nativos americanos. Para identificar nuevos polimorfismos de nucleótido único (SNP) y aumentar la resolución filogenética del haplogrupo Q importante encontrado en las Américas, hemos realizado una búsqueda de nuevos polimorfismos basados en la secuenciación de los cromosomas Y divergentes identificados por análisis de haplotipos de microsatélites. Con este enfoque, un nuevo Y-SNP (SA01) ha sido identificado en las poblaciones andinas de América del Sur, lo que permite la detección de una nueva sublinaje de Q1a3a. Este sublinaje muestra una red filogeográfico menos complejo de microsatélites asociados y presencia geográfica más restringida, y se le da la designación Q1a3a4. Este resultado indica que nuestro enfoque puede ser utilizado con éxito para identificar sublinajes de interés en una región específica, que permiten la investigación de historias particulares de las poblaciones humanas. The human Y chromosome contains highly informative markers for making historical inferences about the pre-Columbian peopling of Americas. However, the scarcity of these markers has limited its use in the inference of shared ancestry and past migrations relevant to the origin of the culturally and biologically diverse Native Americans. To identify new single nucleotide polymorphisms (SNPs) and increase the phylogenetic resolution of the major haplogroup Q found in the Americas, we have performed a search for new polymorphisms based on sequencing divergent Y chromosomes identified by microsatellite haplotype analysis. Using this approach, a new Y-SNP (SA01) has been identified in the Andean populations of South America, allowing for the detection of a new sublineage of Q1a3a. This sublineage displays a less complex phylogeographic network of associated microsatellites and more restricted geographic occurrence, and is given the designation Q1a3a4. This result indicates that our approach can be successfully used to identify sublineages of interest in a specific region that allow the investigation of particular histories of human populations.

Correction to: Journal of Human Genetics (2016) 61, 593–603; doi:10.1038/jhg.2016.26; published online 31 March 2016 After online publication of this article, an error was identified in the list of authors. This error has been rectified and the corrected article appears in this issue. The html and online pdf versions have also been rectified.

Anales de la Facultad de Medicina es una publicación de la Universidad Nacional Mayor de San Marcos. El polimorfismo -511 citosina/timina (-511 C/T) en la región promotora del gen interleuquina 1 beta (IL1β) está implicado en la producción diferencial de la citoquina y por tanto puede estar asociado a la respuesta inmuno-inflamatoria en obesidad, dislipidemias, cardiopatías, cáncer, infecciones, y el tratamiento con nutrientes y fármacos. Objetivos: Establecer la distribución de frecuencias de los genotipos y alelos del polimorfismo -511 C/T del gen IL1β en diferentes subpoblaciones peruanas. Diseño: Estudio descriptivo, observacional, transversal. Instituciones: Centro de Investigación de Bioquímica y Nutrición e Instituto de Medicina Tropical D.A. Carrión, Facultad de Medicina, UNMSM y Centro de Genética y Biología Molecular, Facultad de Medicina, USMP, Lima, Perú. Participantes: Pobladores peruanos. Intervenciones: Extracción de ADN genómico a partir de muestras sanguíneas o epitelio bucal según metodología estándar, de 168 individuos de 9 grupos subpoblacionales: 23 mestizos de Lima, 33 amazónicos (20 de Pucallpa y 13 de Amazonas) y 112 andinos (12 de Ancash, 10 de Cajamarca, 18 de Huarochirí-Lima, 25 de Puno-Taquile, 25 de Puno-Uros y 22 de Puno-Anapia). Análisis del polimorfismo -511 C/T mediante la técnica de PCR/RFLP, con primers específicos y digestión con la enzima de restricción AvaI, detectándose los fragmentos por electroforesis en geles de agarosa al 2% y tinción con bromuro de etidio. Principales medidas de resultados: Frecuencias genotípicas y alélicas del gen IL1β. Resultados: Se encontró las siguientes frecuencias genotípicas CC=0,024; CT=0,369 y TT=0,607, consistentes con el equilibrio de Hardy-Weinberg; y las frecuencias alélicas fueron alelo C=0,208 y aleloT= 0,792. La frecuencia del alelo T, considerado el mutante, fue muy alta en los Uros de Puno (0,940) y más baja en los mestizos de Lima (0,609). La comparación de las frecuencias genotípicas (TT versus CT+CC) y alélicas (T versus C) mostraron diferencias significativas (p

Objetivos: Avanzar en el conocimiento del origen de las poblaciones peruanas estudiadas en un contexto filogeográfico. Diseño: Estudio genético poblacional. Instituciones: Laboratorio de Genética Humana, Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, e Instituto de Genética y Biología Molecular, Facultad de Medicina, Universidad San Martín de Porras, Lima, Perú. Participantes: Siete poblaciones peruanas. Metodología: Análisis comparativo de los resultados a partir del estudio del mtDNA y el gen nuclear MBL de siete poblaciones peruanas, procesados de manera separada y luego combinados, utilizando el programa PHYLYP 3.65, para obtener valores FST de diferenciación genética y la construcción de árboles de distancias por aplicación del algorritmo UPGMA y el análisis subsecuente de los agrupamientos (clusters) generados. Principales medidas de resultados: Árboles genéticos generados. Resultados: De manera separada, los árboles generados para cada marcador genético tuvieron topologías propias y diferentes entre sí. Procesados de manera combinada, el árbol resultante demostró que los mayores valores de diferenciación genética se hallaron en las Islas del Lago Titicaca (Puno, Perú) conocidas -Taquile, Amantani y Anapia-, que fue calificada como muy alta, porque mostró valores de FST de 0.3113, 0.2949 y 0.3348 respecto de las poblaciones estudiadas, tanto fuera del Departamento de Puno -como Chachapoyas, Pucallpa y Chiclayo, respectivamente-, así como a la de los Uro del mismo Puno y del mismo Lago Titicaca (0.2837). Fuera de Puno, el par de poblaciones Chachapoyas-Pucallpa fue el menos divergente, al alcanzar entre ellas un valor de FST de 0.0108, calificándosele de pequeña. Conclusiones: El árbol obtenido del procesamiento de los marcadores vía una matriz combinada demostró que las poblaciones que habitan las islas de Taquile, Amantani y Anapia, divergen notablemente de las restantes cuatro procesadas del Perú, incluyendo la más próxima a ellas dentro del mismo Lago Titicaca, como es la de los Uro. Explicar estos hallazgos será el siguiente objetivo de nuestras investigaciones, en principio, mediante la ampliación de los marcadores genéticos empleados y del número de poblaciones analizadas a nivel del Perú. Objectives: To advance in the knowledge of Peruvian populations’ origin in a phylogeographical context. Design: Population genetics study. Setting: Human Genetics Laboratory, Biological Sciences Faculty, Universidad Nacional Mayor de San Marcos, and Genetics and Molecular Biology Institute, Faculty of Medicine, Universidad San Martin de Porras, Lima, Peru. Participants: Seven Peruvian populations. Methods: Comparative analysis of mtDNA and MBL nuclear gene study results in seven Peruvian populations processed separately and then combined using PHYLYP 3.65 Program in order to obtain FST values of genetic differentiation; construction of distance trees by applying UPGMA algorithm and subsequent generated clusters’ analysis. Main outcome measures: Genetic trees. Results: Trees generated for each genetic marker had proper and distinct topologies among them. Combined processing resulted in a tree with higher values of genetic differentiation in Lago Titicaca Islands (Puno, Peru) Taquile, Amantani y Anapia, graded as very high because they showed 0.3113, 0.2949 y 0.3348 FST values with respect to the populations studied outside of Puno Department -like Chachapoyas, Pucallpa and Chiclayo-, as well as those of both Uro’s in same Puno and Lago Titicaca’s populations (0.2837). Out of Puno, the pair Chachapoyas-Pucallpa population was the least divergent with 0.0108 FST value between them, classifying as small. Conclusions: The tree obtained from markers by a combined matrix process determined that populations inhabiting in Taquile, Amantani y Anapia islands possess notable genetic divergence respect to the four remainders studied in Peru, including the Uro’s population geographically very close to them and within the same Lago Titicaca. Our next objective will be to explain these findings initially by increasing genetic markers and number of populations analyzed in Peru.

Introducción: La farmacogenética tiene utilidad clínica para evaluar los efectos de los fármacos según perfil genético y aporta a la medicina poblacional y personalizada. La diabetes mellitus tipo 2 (DMT2) es una enfermedad prevalente en el Perú y el mundo. Para su tratamiento existen varios fármacos, entre ellos la metformina. La respuesta individual puede estar influenciada por el polimorfismo Val/Met en el gen octT1 y las frecuencias varían según grupo étnico. Se ha relacionado al alelo Met con una menor respuesta a la metformina. Objetivo: Evaluar la distribución del polimorfismo Val/Met en el gen OCT1 en muestras de sangre de sujetos de Lima y Puno, e inferir su impacto en la farmacogenética de la DMT2. Diseño: Estudio descriptivo, transversal. Lugar: Facultades de Farmacia y Bioquímica, Medicina, Universidad Nacional Mayor de San Marcos, Lima, Perú; Centro de Genética y Biología Molecular, Facultad de Medicina, Universidad de San Martín de Porres, Lima, Perú. Participantes: 56 individuos de Puno y 57 de Lima-ciudad. Intervenciones: Análisis del polimorfismo Val/Met en el gen OCT1 con la técnica PCR-RFLP. Principales medidas de resultados: Frecuencias genotípicas y alélicas. Resultados: Las frecuencias de los genotipos, en general, fueron: Val/Val=85,0% y Val/Met=15,0%. La frecuencia del alelo Val, en general, fue mayor al 93%; el alelo Met, asociado con una menor respuesta a metformina, se encontró presente en Amantaní (8,3%) y Lima (9,6%), y ausente en Taquile. Conclusiones: Para el alelo Val del gen OCT1, se ha encontrado la más alta frecuencia registrada en el mundo. Respecto al alelo Met, aunque es menos frecuente, existen diferencias entre las subpoblaciones peruanas evaluadas, y ese conocimiento puede ayudar en la farmacogenética y la toma de decisiones en el tratamiento con los antidiabéticos orales como la metformina., Introduction: Pharmacogenetics can be used in clinical analysis to assess the efficiency of drugs according to the patient’s genetic profile, and it is becoming important for population genetics and precision medicine. The type 2 diabetes mellitus (T2DM) is highly prevalent all over the world, including Peru. Among the different drugs for T2DM, metformin is used the most and patient’s response to it can be influenced by the Val/Met polymorphism of the OCT1 (SLC22) gene, where Met is associated with a lower response. The frequencies of these polymorphisms vary according to ethnic origin. Objective: To evaluate the distribution of the Val/Met polymorphism in the OCT1 gene in samples of Lima and Puno, and to assess their impact on pharmacogenetics of T2DM. Design: Descriptive, cross-sectional study. Settings: Faculties of Pharmacy and Biochemistry, and Medicine, Universidad Nacional Mayor de San Marcos, Lima, Peru; Centro de Genética y Biología Molecular, Facultad de Medicina, Universidad de San Martín de Porres, Lima, Peru. Participants: DNA samples of 56 non-selected subjects from Puno and 57 from Lima regions. Interventions: Analysis of the Val/Met polymorphism in OCT1 gene using the PCR-RFLP technique. Main outcome measures: Phenotypic and allelic frequencies. Results: Genotype frequencies were Val/Val=85,0% and Val/Met=15,0%. The Val allele frequency was higher than 93%, the Met allele was associated with a lower response to metformin and was present in Amantaní (8.3%) and in Lima (9.6%), and absent in Taquile. Conclusions: We found the highest Val allele frequency in the world. Regarding the Met allele, less frequent, we found differences among the Peruvian subpopulations tested, and this knowledge can help in the pharmacogenetics and decision making about oral treatment of metformin against diabetes.