ABSTRACT
In recent years, probabilistic genotyping software has been adapted for the analysis of massively parallel sequencing (MPS) forensic data. Likelihood ratios (LR) are based on allele frequencies selected from populations of interest. This study provides an outline of sequence-based (SB) allele frequencies for autosomal short tandem repeats (aSTRs) and identity single nucleotide polymorphisms (iSNPs) in 371 individuals from Southern Norway. 27 aSTRs and 94 iSNPs were previously analysed with the ForenSeq™ DNA Signature Prep Kit (Verogen). The number of alleles with frequencies less than 0.05 for sequenced-based alleles was 4.6 times higher than for length-based alleles. Consistent with previous studies, it was observed that sequence-based data (both with and without flanks) exhibited higher allele diversity compared to length-based (LB) data; random match probabilities were lower for SB alleles confirming their advantage to discriminate between individuals. Two alleles in markers D22S1045 and Penta D were observed with SNPs in the 3´ flanking region, which have not been reported before. Also, a novel SNP with a minor allele frequency (MAF) of 0.001, was found in marker TH01. The impact of the sample size on minor allele frequency (MAF) values was studied in 88 iSNPs from Southern Norway (n = 371). The findings were then compared to a larger Norwegian population dataset (n = 15,769). The results showed that the smaller Southern Norway dataset provided similar results, and it was a representative sample. Population structure was analyzed for regions within Southern Norway; FST estimates for aSTR and iSNPs did not indicate any genetic structure. Finally, we investigated the genetic differences between Southern Norway and two other populations: Northern Norway and Denmark. Allele frequencies between these populations were compared, and we found no significant frequency differences (p-values > 0.0001). We also calculated the pairwise FST values per marker and comparisons between Southern and Northern Norway showed small differences. In contrast, the comparisons between Southern Norway and Denmark showed higher FST values for some markers, possibly driven by distinct alleles that were present in only one of the populations. In summary, we propose that allele frequencies from each population considered in this study could be used interchangeably to calculate genotype probabilities.
Subject(s)
DNA Fingerprinting , Gene Frequency , Genetics, Population , High-Throughput Nucleotide Sequencing , Microsatellite Repeats , Polymorphism, Single Nucleotide , Humans , Norway , Sequence Analysis, DNA , Likelihood Functions , GenotypeABSTRACT
Interpretation of DNA evidence involving mixtures is challenging when alleles from minor contributors coincide with stutters from major contributors. To accommodate this, it is important to have a good understanding of stutter sequence formation trends. Here, multiple stutter types were characterized based on massively parallel sequencing (MPS) data from 387 single source samples, using the Verogen ForenSeq™ DNA Signature Prep kit. A beta regression model was used to investigate the relationship between the stutter proportion and candidate explanatory variables. In the final model, stutter proportions were explained by the length of the parental uninterrupted stretch (PTUS), which is comparable to block length of the missing motif (BLMM). Also, different stutter types (n+1, n-1, n+2, n-2, n0) were analyzed separately per locus. The fitted stutter models were then integrated into an extended probabilistic genotyping model based on EuroForMix (MPSproto). An illustrative minor/major mock mixture example is discussed. Evaluation of multiple types of stutters on a per locus basis improved the probabilistic genotyping result compared to the conventional EuroForMix model, using the LUS+ nomenclature.
Subject(s)
DNA Fingerprinting , Microsatellite Repeats , Alleles , Artifacts , DNA/genetics , High-Throughput Nucleotide Sequencing , Humans , Sequence Analysis, DNAABSTRACT
Fundamentación: un 90 porciento de los pacientes con la infección por el virus de inmunodeficiencia humana tendrá una manifestación bucal en algún momento durante el curso de la enfermedad. El tipo y frecuencia de ellas varía con el estadio de la enfermedad y el grado de inmunosupresión. Estas pueden ser indicadores para el diagnóstico de infección por virus de inmunodeficiencia humana, cambiar la clasificación del estado de infección y predictor de la progresión de la enfermedad. Objetivo: caracterizar el estado de salud bucal de los pacientes seropositivos del área centro, Municipio Sancti Spíritus. Metodología: se realizó un estudio epidemiológico observacional descriptivo de corte transversal de febrero a marzo del 2012. El universo lo constituyó la población seropositiva del área centro y la muestra, obtenida de forma aleatoria simple, fue de 13 pacientes. Se tuvieron en cuenta variables como edad, sexo, clasificación clínico epidemiológica. Resultados: el grupo etáreo de 19-59 años fue el de mayor incidencia, el sexo masculino el más representativo. La mayoría de los pacientes ingieren los antirretrovirales y presenta periodontopatías. Conclusiones: las periodontopatías no asociadas a la infección por el virus de inmunodeficiencia humana fueron las manifestaciones bucales que prevalecieron y la estomatitis aftosa fue la lesión predominante(AU)
