MHC Class II haplotypes of Colombian Amerindian tribes

We analyzed 1041 individuals belonging to 17 Amerindian tribes of Colombia, Chimila, Bari and Tunebo (Chibcha linguistic family), Embera, Waunana (Choco linguistic family), Puinave and Nukak (Maku-Puinave linguistic families), Cubeo, Guanano, Tucano, Desano and Piratapuyo (Tukano linguistic family), Guahibo and Guayabero (Guayabero Linguistic Family), Curripaco and Piapoco (Arawak linguistic family) and Yucpa (Karib linguistic family). for MHC class II haplotypes (HLA-DRB1, DQA1, DQB1). Approximately 90% of the MHC class II haplotypes found among these tribes are haplotypes frequently encountered in other Amerindian tribes. Nonetheless, striking differences were observed among Chibcha and non-Chibcha speaking tribes. The DRB1*04:04, DRB1*04:11, DRB1*09:01 carrying haplotypes were frequently found among non-Chibcha speaking tribes, while the DRB1*04:07 haplotype showed significant frequencies among Chibcha speaking tribes, and only marginal frequencies among non-Chibcha speaking tribes. Our results suggest that the differences in MHC class II haplotype frequency found among Chibcha and non-Chibcha speaking tribes could be due to genetic differentiation in Mesoamerica of the ancestral Amerindian population into Chibcha and non-Chibcha speaking populations before they entered into South America

Origen geno-geográfico de haplotipos STR del cromosoma Y en una muestra caucásico-mestiza y afrodescendiente de Colombia

Introduction: Y chromosome STR haplotypes have been widely used in population studies to establish the origin of diverse populations.Objective: We analyzed Y chromosome STR haplotypes (8 loci) in 134 Caucasian-mestizo and 137 African-descent Colombian unrelated individuals to correlate the geographical origin with historical data as well as the genetic relationships and possible admixture patterns.Materials and methods: One hundred samples of African descent and 137 Caucasian-mestizo samples analyzed for Y chromosome STR haplotypes by PCR followed by acrylamide electrophoresis.Results: No evidence of population substructure was found for the African descent. Two point fiftynine per cent of the haplotypes were shared between the two groups with the possible existence of Caucasian gene flow towards Afro-descendants.Conclusion: The Caucasian-Mestizo Colombian population is grouped with other populations of the Iberian Peninsula and Europe, while the Afro-Colombian population is grouped with other African populations reported. doi: http://dx.doi.org/10.7705/biomedica.v33i3.807 Introducción. Los haplotipos STR de cromosoma Y han sido ampliamente utilizados en estudios de poblaciones para establecer el origen de diversas poblaciones.Objetivo. Se analizaron haplotipos STR del cromosoma Y (8 loci) en 134 afrodescendientes y caucásico-mestizos no relacionados de Colombia, para correlacionar el origen geográfico con los datos históricos, así como las relaciones genéticas y posibles patrones de mezcla.Materiales y métodos. Se analizaron los haplotipos STR del cromosoma Y mediante PCR seguidas de electroforesis en acrilamida, de 134 muestras de afrodescendientes y 137 muestras de caucásicos mestizos.Resultados. No se encontró evidencia de subestructuración de la población afrodescendiente. El 2,59 % de los haplotipos eran compartidos en los dos grupos analizados, con la posible existencia deflujo génico de caucásico-mestizos hacia los afrodescendientes.Conclusión. La población caucásico-mestiza colombiana se agrupa con otras poblaciones de la península Ibérica y Europa, mientras que la población afrodescendiente colombiana se agrupa conotras poblaciones africanas reportadas. doi: http://dx.doi.org/10.7705/biomedica.v33i3.80

Performance of non-invasive tests and histology for the prediction of clinical outcomes in patients with non-alcoholic fatty liver disease: an individual participant data meta-analysis

BackgroundHistologically assessed liver fibrosis stage has prognostic significance in patients with non-alcoholic fatty liver disease (NAFLD) and is accepted as a surrogate endpoint in clinical trials for non-cirrhotic NAFLD. Our aim was to compare the prognostic performance of non-invasive tests with liver histology in patients with NAFLD.MethodsThis was an individual participant data meta-analysis of the prognostic performance of histologically assessed fibrosis stage (F0–4), liver stiffness measured by vibration-controlled transient elastography (LSM-VCTE), fibrosis-4 index (FIB-4), and NAFLD fibrosis score (NFS) in patients with NAFLD. The literature was searched for a previously published systematic review on the diagnostic accuracy of imaging and simple non-invasive tests and updated to Jan 12, 2022 for this study. Studies were identified through PubMed/MEDLINE, EMBASE, and CENTRAL, and authors were contacted for individual participant data, including outcome data, with a minimum of 12 months of follow-up. The primary outcome was a composite endpoint of all-cause mortality, hepatocellular carcinoma, liver transplantation, or cirrhosis complications (ie, ascites, variceal bleeding, hepatic encephalopathy, or progression to a MELD score ≥15). We calculated aggregated survival curves for trichotomised groups and compared them using stratified log-rank tests (histology: F0–2 vs F3 vs F4; LSM: 2·67; NFS: 0·676), calculated areas under the time-dependent receiver operating characteristic curves (tAUC), and performed Cox proportional-hazards regression to adjust for confounding. This study was registered with PROSPERO, CRD42022312226.FindingsOf 65 eligible studies, we included data on 2518 patients with biopsy-proven NAFLD from 25 studies (1126 [44·7%] were female, median age was 54 years [IQR 44–63), and 1161 [46·1%] had type 2 diabetes). After a median follow-up of 57 months [IQR 33–91], the composite endpoint was observed in 145 (5·8%) patients. Stratified log-rank tests showed significant differences between the trichotomised patient groups (p<0·0001 for all comparisons). The tAUC at 5 years were 0·72 (95% CI 0·62–0·81) for histology, 0·76 (0·70–0·83) for LSM-VCTE, 0·74 (0·64–0·82) for FIB-4, and 0·70 (0·63–0·80) for NFS. All index tests were significant predictors of the primary outcome after adjustment for confounders in the Cox regression.InterpretationSimple non-invasive tests performed as well as histologically assessed fibrosis in predicting clinical outcomes in patients with NAFLD and could be considered as alternatives to liver biopsy in some cases

Mitochondrial DNA (mtDNA) haplogroups in 1526 unrelated individuals from 11 Departments of Colombia

The frequencies of four mitochondrial Native American DNA haplogroups were determined in 1526 unrelated individuals from 11 Departments of Colombia and compared to the frequencies previously obtained for Amerindian and Afro-Colombian populations. Amerindian mtDNA haplogroups ranged from 74% to 97%. The lowest frequencies were found in Departments on the Caribbean coast and in the Pacific region, where the frequency of Afro-Colombians is higher, while the highest mtDNA Amerindian haplogroup frequencies were found in Departments that historically have a strong Amerindian heritage. Interestingly, all four mtDNA haplogroups were found in all Departments, in contrast to the complete absence of haplogroup D and high frequencies of haplogroup A in Amerindian populations in the Caribbean region of Colombia. Our results indicate that all four Native American mtDNA haplogroups were widely distributed in Colombia at the time of the Spanish conquest

Population Frequencies for CSF1PO, TPOX, TH01, F13A01, FES/FPS y VWA in Seven Amerindian Populations from Colombia

eng: While previous research has examined the STR variability among Caucasian and Afro-Colombian populations, few studies have focused on the STR variability among Amerindian tribes. In Colombia, Amerindians make up approximately 1.7 percent of the population and they are located primarily in the Amazonian/Orinoquian region, the Northeast, Southwest, and Pacific regions of the country. The F13A01, FES/FPS, VWA, CSF1PO, TPOX, and THO1 STR loci were amplified from DNA obtained from 7 Amerindian populations named Cubeo (N=49), Curripaco (N=32), Desano (N=28), Tucano (N=26), Embera (N=31), Puinabe (N=77), and Nukak (N=29). Under examination were the allele frequencies and other forensically important parameters. The data provide little evidence of deviation from independence within the populations studied. The complete dataset is available to any researcher via electronic mail from the corresponding author.spa: Mientras que investigaciones anteriores han examinado la variabilidad de los STR entre las poblaciones caucásicas y afrocolombianas, pocos estudios se han centrado en la variabilidad de los STR entre las tribus amerindias. En Colombia, los amerindios constituyen aproximadamente el 1,7 por ciento de la población y se localizan principalmente en la región amazónica/orinoquiana, el noreste, el suroeste y el Pacífico del país. Los loci STR F13A01, FES/FPS, VWA, CSF1PO, TPOX y THO1 fueron amplificados a partir de ADN obtenido de 7 poblaciones amerindias denominadas Cubeo (N=49), Curripaco (N=32), Desano (N=28), Tucano (N=26), Embera (N=31), Puinabe (N=77) y Nukak (N=29). Se examinaron las frecuencias alélicas y otros parámetros de importancia forense. Los datos proporcionan pocas pruebas de desviación de la independencia dentro de las poblaciones estudiadas. El conjunto de datos completo está a disposición de cualquier investigador a través del correo electrónico del autor correspondiente

Aplicaciones de la genética molecular en la practica forense

Desde el desarrollo de las huellas digitales a finales del siglo XIX, la tipificación del ADN por VNTR, representa la innovación más poderosa que se haya desarrollado en las ciencias forenses durante el siglo XX. Con el descubrimiento en 1980 del polimorfismo del ADN en el genoma humano y con la subsecuente demostración de que tal hipervariabilidad esta ampliamente distribuida en los humanos, las ciencias forenses han reconocido el enorme potencial que ofrece la tipificación del ADN para la identificación de un individuo a partir de una muestra biológica dejada en la escena del crimen. La utilidad de la tipificación del ADN como herramienta forense recae no solo en su alto poder de discriminación entre los individuos de una población, sino también porque se pueden utilizar muchos materiales de origen biológico, en diferentes circunstancias, que de otra manera serian inútiles en las pruebas de tipificación tradicional. El debate actual sobre las pruebas de ADN pone de relieve la necesidad de imponer un mayor rigor ante las dificultades que aparecen cuando una tecnología científica bastante compleja se introduce como prueba ante un tribunal de justicia. Se discuten las ventajas y limitaciones sobre el uso del polimorfismo del ADN en la medicina forense. En Colombia se deben establecer criterios nacionales para que las pruebas forenses del ADN sirvan a los intereses de la justicia, bien sea para identificar a un criminal o para absolver a un inocente

Genetic differences between Chibcha and Non-Chibcha speaking tribes based on mitochondrial DNA (mtDNA) haplogroups from 21 Amerindian tribes from Colombia

We analyzed the frequency of four mitochondrial DNA haplogroups in 424 individuals from 21 Colombian Amerindian tribes. Our results showed a high degree of mtDNA diversity and genetic heterogeneity. Frequencies of mtDNA haplogroups A and C were high in the majority of populations studied. The distribution of these four mtDNA haplogroups from Amerindian populations was different in the northern region of the country compared to those in the south. Haplogroup A was more frequently found among Amerindian tribes in northern Colombia, while haplogroup D was more frequent among tribes in the south. Haplogroups A, C and D have clinal tendencies in Colombia and South America in general. Populations belonging to the Chibcha linguistic family of Colombia and other countries nearby showed a strong genetic differentiation from the other populations tested, thus corroborating previous findings. Genetically, the Ingano, Paez and Guambiano populations are more closely related to other groups of south eastern Colombia, as also inferred from other genetic markers and from archeological data. Strong evidence for a correspondence between geographical and linguistic classification was found, and this is consistent with evidence that gene flow and the exchange of customs and knowledge and language elements between groups is facilitated by close proximity

Polymorphic Human Specific Alu Insertions as Markers for Human Identification

Alu sequences represent the largest family of short interspersed repetitive elements (SINEs) in humans with 500 000 copies per genome. Recently, one Alu subfamily was found to be human specific (HS). We originally described the use of polymorphic HS Alu insertions as a tool in population studies and recently as tools in DNA fingerprinting and forensic analysis. In this report, we will use this simple polymerase chain reaction (PCR) base technique for the detection of HS Alu insertion polymorphisms. We will test the resolving power of this DNA profiling approach in both population genetics and paternity assessment. At the population level, we will describe the genotypic distribution of five polymorphic Alu insertions among 3 populations from the American continent, one of African origin, the other two Amerindians. Insight into their relationships will be provided. At the family level, we will examine one European American family of seven individuals and the same pedigree will also be characterized by way of the two systems currently and widely used to ascertain paternity: PCR‐sequence specific oligonucleotide probe hybridization (PCR‐SSO) and PCR‐restriction fragment length polymorphism (PCR‐RFLP) of human leucocyte antigen (HLA) class II molecules, and a standard RFLP protocol used in forensic casework and paternity studies. The importance and strengths of the method as well as its perspectives for future use in filiation studies will be evaluated

Polymorphic Alu Insertions and the Asian Origin of Native American Populations

A rapid PCR-based assay was used to study the distribution of 5 polymorphic Alu insertions in 895 unrelated individuals from 30 populations, 24 from North, Central, and South America. Although a significant level of interpopulation variability was detected, the variability was less than that observed in a worldwide population survey. This is consistent with the bottleneck effect and genetic drift forces that may have acted on the migrating founder groups. The results corroborate the Asian origin of native American populations but do not support the multiple-wave migration hypothesis supposedly responsible for the tripartite Eskaleut, Nadene, and Amerind linguistic groups. Instead, these populations exhibit three major identifiable clusters reflecting geographic distribution. Close similarity between the Chinese and native Americans suggests recent gene flow from Asia