Mutation Rate Analysis of RM Y-STRs in Deep-Rooted Multi-Generational Punjabi Pedigrees from Pakistan.

Y chromosome short tandem repeat polymorphisms (Y-STRs) are important in many areas of human genetics. Y chromosomal STRs, being normally utilized in the field of forensics, exhibit low haplotype diversity in consanguineous populations and fail to discriminate among male relatives from the same pedigree. Rapidly mutating Y-STRs (RM Y-STRs) have received much attention in the past decade. These 13 RM Y-STRs have high mutation rates (>10−2) and have considerably higher haplotype diversity and discrimination capacity than conventionally used Y-STRs, showing remarkable power when it comes to differentiation in paternal lineages in endogamous populations. Previously, we analyzed two to four generations of 99 pedigrees with 1568 pairs of men covering one to six meioses from all over Pakistan and 216 male relatives from 18 deep-rooted endogamous Sindhi pedigrees covering one to seven meioses. Here, we present 861 pairs of men from 62 endogamous pedigrees covering one to six meioses from the Punjabi population of Punjab, Pakistan. Mutations were frequently observed at DYF399 and DYF403, while no mutation was observed at DYS526a/b. The rate of differentiation ranged from 29.70% (first meiosis) to 80.95% (fifth meiosis), while overall (first to sixth meiosis) differentiation was 59.46%. Combining previously published data with newly generated data, the overall differentiation rate was 38.79% based on 5176 pairs of men related by 1−20 meioses, while Yfiler differentiation was 9.24% based on 3864 pairs. Using father−son pair data from the present and previous studies, we also provide updated RM Y-STR mutation rates.

Design and development of novel single multiplex system incorporating 26 rapidly mutating Y-STRs; 26 RM Yplex.

This article details the development of a single multiplex system amplifying 26 rapidly mutating Y-STR markers. A sequenced allelic ladder, constructed for calling alleles of all loci, is introduced. The multiplex system shows the ability to address the limitations of Y-STRs commercial kits in differentiating closely related males. The multiplex performed well in the prevalidation tests and showed great potential to be used in forensic casework.

The genomic history of the Middle East.

The Middle East region is important to understand human evolution and migrations but is underrepresented in genomic studies. Here, we generated 137 high-coverage physically phased genome sequences from eight Middle Eastern populations using linked-read sequencing. We found no genetic traces of early expansions out-of-Africa in present-day populations but found Arabians have elevated Basal Eurasian ancestry that dilutes their Neanderthal ancestry. Population sizes within the region started diverging 15-20 kya, when Levantines expanded while Arabians maintained smaller populations that derived ancestry from local hunter-gatherers. Arabians suffered a population bottleneck around the aridification of Arabia 6 kya, while Levantines had a distinct bottleneck overlapping the 4.2 kya aridification event. We found an association between movement and admixture of populations in the region and the spread of Semitic languages. Finally, we identify variants that show evidence of selection, including polygenic selection. Our results provide detailed insights into the genomic and selective histories of the Middle East.

First confirmed detection of SARS-COV-2 in untreated municipal and aircraft wastewater in Dubai, UAE: The use of wastewater based epidemiology as an early warning tool to monitor the prevalence of COVID-19.

Severe Acute Respiratory Syndrome - Coronavirus 2 (SARS-CoV-2) emerged in Wuhan, China and spread to more than 114 countries resulting in a pandemic, which was declared by the WHO in March 2020. Tracking the spread of the virus raised a main concern in every country. Many researches proved the presence of SARS-CoV-2 in stool samples of patients, where the genes of this virus gave a positive signal several days prior to the occurrence of symptoms. The fact of viral shedding in stools provides an advantage in utilizing wastewater systems as a tool to monitor the viral prevalence. We tested more than 2900 municipal wastewater samples coming from 49 distinctive area in Dubai, where 28.6% showed positive results. We also looked into the wastewater samples from 198 commercial aircrafts arriving at Dubai Airport, giving a positive result percentage of 13.6%. The presence of SARS-CoV-2 genes was confirmed using TaqPath™ Covid-19 RT-PCR kit, which targets ORF1ab, N gene and S gene. This project shows the significance of utilizing wastewater-based epidemiology (WBE) in monitoring the prevalence of various infectious diseases such as SARS-CoV-2, which can assist the decision makers to determine the level of precautionary measures according to the areas of the outbreak. With this in mind, pricewise, WBE is considered cost-effective when comparing to clinical nasal swabs.

Allelic and haplotype diversity of 12 X-STRs in the United Arab Emirates.

X-chromosomal short tandem repeats (X-STRs) are used to complement autosomal and Y-STRs in complex kinship testing, and can be of potential value when determining trace female DNA in male background. We analyzed extracted and directly-amplified samples of 501 males from the United Arab Emirates and report the forensic statistical parameters of 12 X-STRs and haplotypes of the four previously defined linkage groups using the Investigator Argus X-12 QS kit. Combined PDM, PDF, MEC Desmarais Trio and MEC Desmarais Duo based on allele (and haplotype) frequencies were 0.9999999997 (0.999999996), >0.9999999999 (>0.999999999), 0.999999999 (0.999999996) and 0.9999997 (0.99999994) respectively. No shared profile was observed, and significant linkage disequilibrium was detected only within the four linkage groups. We calculated pairwise genetic distance (FST) between our Emirati sample and 35 populations and find they generally mirror biogeography and historical relationships. We identified 20 distinct off-ladder alleles in seven loci, the majority of which at DXS10148 and DXS10134. Our analysis reveals that the 12 loci are informative and discriminatory in the Emirati population.