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Currently, autosomal Short Tandem Repeat (STR) markers represent the method of election in forensic human identification. Commercial kits of most common use nowadays –e.g. PowerPlex ® Fusion, Promega Corp.; AmpFlSTR GlobalFiler, Thermofisher scientific; Investigator 24Plex QS,Qiagen-, allow the co-amplification of 23 highly polymorphic STR loci providing a high discrimination power in human identity testing. However, in complex kinship analysis and familial database searches involving distant relationships, additional DNA typing is often required in order to achieve well-founded conclusions. The recently developed kit Investigator ® HDplex (Qiagen) co-amplify twelve autosomal STRs markers (D7S1517, D3S1744, D12S391, D2S1360, D6S474, D4S2366, D8S1132, D5S2500, D18S51, D21S2055, D10S2325, SE33), nine of which are not present in the above mentioned kits, providing a set of efficient supplementary markers for human identification purposes. In this study we genotyped a sample of 980 individuals from urban areas of ten Argentinean provinces using the Investigator ® HDplex kit, aiming to provide forensic estimates for use in forensic casework and parentage testing in Argentina. We report reference allelic frequency databases for each of the provinces studied as well as for the combined samples. No deviation of Hardy-Weinberg equilibrium was observed. A reasonable discrimination capacity and power of exclusion was estimated which allowed predicting an acceptable forensic behavior of this kit, either to be used as the main STR panel for simple cases or as an auxiliary tool in complex cases. Additionally, population comparison tests showed that the studied samples are relatively homogeneous across the country for these STR set. [ABSTRACT FROM AUTHOR]

Y haplogroups, defined by Y-SNPs, allow the reconstruction of the human Y chromosome genealogy, which is important for population, evolutionary and forensic genetics. In this study, Y-SNPs were typed and haplogroups inferred with the MPS Ion AmpliSeq™ HID Y-SNP Research Panel v1, as a high-throughput approach. Firstly, the performance of the panel was evaluated with different DNA input amounts, reagent volumes and cycle numbers. DNA-inputs from 0.5 to 1 ng generated the most balanced read depth. Combined with full reagent and 19 cycles, this offered the highest number of amplicons with a sequencing read depth of at least 20 reads. Secondly, the sub-haplogroups of 182 admixed South Americans and Greenlanders belonging to haplogroup Q were inferred and tested for potential improvement in resolution. Most samples were assigned to lineage Q-M3 with some samples assigned to lineages upstream (Q-M346, L56, L57; Q-L331, L53; Q-L54; Q-CTS11969, CTS11970) or parallel (Q-L330, L334; Q-Z780/M971) to Q-M3. Only one sample was assigned to a downstream lineage (Q-Z35615, Z35616). Most individuals of haplogroup Q with NAM ancestry could neither be distinguished from each other, nor from half of the Greenlandic samples. Typing additional, known SNPs within lineage Q-M3, Z19483 and SA05, increased the resolution of predicted haplogroups. The search for novel variants in the sequenced regions allowed the detection of 42 variants and the subdivision of lineage Q-M3 into new subclades. The variants found in six of these subclades were exclusive to certain South American countries. In light of the limited differentiation of haplogroup Q samples, the additional information on known or novel SNPs disclosed in this study when using MPS Ion AmpliSeq™ HID Y-SNP Research Panel v1 should be included in the Yleaf software, to increase the differentiation of lineage Q-M3. • The performance of the MPS Ion AmpliSeq™ HID Y-SNP Research Panel was tested. • Haplogroup Q distribution of admixed South Americans and Greenlanders was explored. • 85% of all samples were assigned to male lineage Q-M3. • The addition of SNPs, Z19483 and SA05, increased the resolution of lineage Q-M3. • Within lineage Q-M3, additional 10 annotated SNPs and 32 novel variants were found. [ABSTRACT FROM AUTHOR]

Only a few genetic studies have been carried out to date in Bolivia. However, some of the most important (pre)historical enclaves of South America were located in these territories. Thus, the (sub)-Andean region of Bolivia was part of the Inca Empire, the largest state in Pre-Columbian America. We have genotyped the first hypervariable region (HVS-I) of 720 samples representing the main regions in Bolivia, and these data have been analyzed in the context of other pan-American samples (>19,000 HVS-I mtDNAs). Entire mtDNA genome sequencing was also undertaken on selected Native American lineages. Additionally, a panel of 46 Ancestry Informative Markers (AIMs) was genotyped in a sub-set of samples. The vast majority of the Bolivian mtDNAs (98.4%) were found to belong to the main Native American haplogroups (A: 14.3%, B: 52.6%, C: 21.9%, D: 9.6%), with little indication of sub-Saharan and/or European lineages; however, marked patterns of haplogroup frequencies between main regions exist (e.g. haplogroup B: Andean [71%], Sub-Andean [61%], Llanos [32%]). Analysis of entire genomes unraveled the phylogenetic characteristics of three Native haplogroups: the pan-American haplogroup B2b (originated ∼21.4 thousand years ago [kya]), A2ah (∼5.2 kya), and B2o (∼2.6 kya). The data suggest that B2b could have arisen in North California (an origin even in the north most region of the American continent cannot be disregarded), moved southward following the Pacific coastline and crossed Meso-America. Then, it most likely spread into South America following two routes: the Pacific path towards Peru and Bolivia (arriving here at about ∼15.2 kya), and the Amazonian route of Venezuela and Brazil southwards. In contrast to the mtDNA, Ancestry Informative Markers (AIMs) reveal a higher (although geographically variable) European introgression in Bolivians (25%). Bolivia shows a decreasing autosomal molecular diversity pattern along the longitudinal axis, from the Altiplano to the lowlands. Both autosomes and mtDNA revealed a low impact (1–2%) of a sub-Saharan component in Bolivians. [ABSTRACT FROM AUTHOR]

Abstract: The use of miniSTR markers is a valuable tool in the forensic laboratory since it allows high-quality genetic profiles to be obtained on low copy number (LCN) or degraded DNA taken from different samples, such as cadaveric material, paraffin-embedded tissue, chewing gum, traces of saliva, pieces of cloth, cigarette butts, bone samples, etc. In addition, it is useful to have additional STR loci to solve paternity cases with one or more inconsistencies or to increase the amount of genetic information for incomplete family studies, where the genetic profile of the alleged father has to be reconstructed. Genetic frequencies and forensic parameters were calculated for 12 non-CODIS miniSTR loci (D20S480, D6S2439, D6S1056, D9S1118, D4S2639, D17S1290, D10S1248, D14S1434, D22S1045, D4S2364, D2S441 and D1S1677) from a total of 506 unrelated individuals from various provinces in the central region of Argentina (Cordoba, Buenos Aires, Salta, Entre Rios and Santa Fe). The application of these miniSTR markers allowed LR>1000 values to be obtained in kinship cases with incomplete families whose results had not been significant when using commercial kits. In conclusion, a database with Argentine population frequencies from these 12 miniSTR markers may be very useful in adding supplementary information for the forensic genetic laboratory. [Copyright &y& Elsevier]

Abstract: Allele frequencies and forensic parameters for twelve miniSTR autosomal loci (D10S1248, D14S1434, D22S1045, D4S2364, D2S441, D1S1677, D20S480, D6S2439, D6S1056, D9S1118, D4S2639 and D17S1290) were calculated from a sample of 506 unrelated individuals from the Central-East Region of Argentina. No significant deviations from Hardy–Weinberg expectations were found. Furthermore, comparisons with other previously studied populations were made. These twelve miniSTR markers may help forensic laboratories in solving parentage testing as well as in typing degraded DNA samples. [Copyright &y& Elsevier]

Abstract: The allelic distribution of seventeen short tandem repeat (STR) loci, together with some parameters of forensic interest were estimated from a sample set of unrelated healthy individuals from six provinces in Argentina (Buenos Aires, Córdoba, Santa Fe, Salta, Entre Ríos and Chaco). All loci of the sample were in agreement with Hardy–Weinberg equilibrium, after Bonferroni correction. The combined discrimination power for these 17 STRs was 0.999999999999999999997, whereas the combined probability of exclusion was 0.99999993. Furthermore, this population was compared to other previously published samples from Argentina, showing significant values in the population differentiation tests. [Copyright &y& Elsevier]