Evaluation of 13 rapidly-mutating Y-STRs in endogamous Punjabi and Sindhi ethnic groups from Pakistan

Y-chromosomal short tandem repeats (Y-STRs) are commonly used to conclude population histories, discover ancestral relationships, and identify males for criminal justice purposes. Y-STRs being largely in forensic use have low haplotype diversity in some populations and fail to discriminate between male relatives. Rapidly mutating Y-STRs (RM Y-STRs) were breakthrough of this decade and have been paid much attention. A set of 13 rapidly-mutating (RM) Y-STRs (DYF387S1, DYF399S1, DYF403S1a/b1/b2, DYF404S1, DYS449, DYS518, DYS526I/II, DYS547, DYS570, DYS576, DYS612, DYS626, and DYS627) typically reveals higher haplotype diversities than the commercially available Y-STR sets and allows differentiating male relatives for which commercial Y-STR sets are usually not informative. Here, we amplified the 13 RM Y-STRs in 168 (37 Sindhi and 131 Punjabi) individuals from Pakistan, which is characterized by high rates of endogamy. The haplotype diversity and discrimination capacity were 1. Allelic frequencies ranged from 0.0060 to 0.5060, while gene diversity ranged from 0.6759 (DYS526a) to 0.9937 (DYF399S1). A total 319 unique alleles were observed. Results of our study showed that RM Y-STRs provided substantially stronger discriminatory power in Pakistani populations

Population genetic diversity in an Iraqi population and gene flow across the Arabian Peninsula

Abstract: Y-STRs have emerged as important forensic and population genetic markers for human identification and population differentiation studies. Therefore, population databases for these markers have been developed for almost all major populations around the world. The Iraqi population encompasses several ethnic groups that need to be genetically characterised and evaluated for possible substructures. Previous studies on the Iraqi population based on Y-STR markers were limited by a restricted number of markers. A larger database for Iraqi Arab population needed to be developed to help study and compare the population with other Middle Eastern populations. Twenty-three Y-STR loci included in the PowerPlex Y23 (Promega, Madison, WI, USA) were typed in 254 males from the Iraqi Arab population. Global and regional Y-STR analysis demonstrated regional genetic continuity among the populations of Iraq, the Arabian Peninsula and the Middle East. The Iraqi Arab haplotypes were used to allocate samples to their most likely haplogroups using Athey’s Haplogroup Predictor tool. Prediction indicated predominance (36.6%) of haplogroup J1 in Iraqi Arabs. The migration rate between other populations and the Iraqis was inferred using coalescence theory in the Migrate-n program. Y-STR data were used to test different out-of-Africa migration models as well as more recent migrations within the Arabian Peninsula. The migration models demonstrated that gene flow to Iraq began from East Africa, with the Levantine corridor the most probable passageway out of Africa. The data presented here will enrich our understanding of genetic diversity in the region and introduce a PowerPlex Y23 database to the forensic community

Hubungan Antara Pemakaian Sepatu Hak Tinggi Dengan Terjadinya Patellofemoral Pain Syndrome Dan Perubahan Sudut Quadriceps Pada Sales Promotion Girl Di Matahari Johar Plaza Kota Jember

Latar belakang :Timbulnya permasalahan patellofemoral pain syndrome dan perubahan sudut Quadriceps pada sales promotion girl disebabkan karena posisi bekerja berdiri statis dalam jangka waktu lama. Nyeri yang dialami akan menyebabkan perubahan posisi tumpuan pada lutut yang menyebabkan perubahan Sudut Quadriceps. Tujuan penelitian ini,untuk mengetahui hubungan antara pemakaian high heels dengan terjadinya Patellofemoral pain syndrome dan Perubahan Sudut Quadricep pada Sales Promotion Girls di Matahari Johar Plaza Kota Jember. Metode Penelitian: dengan metode survei/observasi Analitik dengan pendekatan cross sectional. Desain penelitian ini yaitu Point Time Approach artinya tiap subjek penelitian hanya diobsevasi sekali saja dan pengukuran dilakukan terhadap status karakter atau variabel subjek pada saat pemeriksaan. Pengambilan sample dengan metode total sampling. Uji Normalitas data dengan kolmogrov-smirnov, uji hubungan bivariat dengan chi square. Subjek berjumlah 30 orang. Hasil: hasil uji hubungan menunjukkan bahwa p-value <0,05 pada patellofemoral pain syndrom dan perubahan sudut Quadriceps. Kesimpulan: ada hubungan yang signifikan pemakaian heigh heels terhadap terjadinya patellofemoral pain syndrome dan perubahan sudut quadriceps

Internal validation of GlobalFilerTM kit using reduced reaction volume

For approximately two decades, Microsatellites or Short Tandem Repeat (STR) markers have been the backbone for human identification testing in the forensic field. The expansion of STR multiplex kits can improve global sharing of STR profiles, rapid DNA typing, and DNA typing Flores et al. (2014). GlobalFiler™ kit is highly sensitive and has extremely high power of discrimination. An internal validation of GlobalFiler™ Kit was carried out to test the robustness of this kit through a range of internal validation studies including half volume reaction, reproducibility, sensitivity, specificity, stability, mixture, analytical threshold, sensitivity & stochastic threshold, heterozygous balance & stutter threshold studies in accordance with SGWDAM guidelines Scientific Working Group on DNA . Reference and real casework samples previously tested using other autosomal STR kits from forensic cases were used during the validation. It was demonstrated that the GlobalFiler™ kit has enhanced discrimination power, is robust and extremely useful for forensic casework

The study of 95 identity SNPs for Qatari population using massively parallel sequencing (MPS)

For the last three decades, Short Tandem Repeat (STR) markers and capillary electrophoresis-based DNA sequencers have been the gold standard technology for human identification testing in the forensic field. All laboratories globally, including the Forensic Laboratory, have strategies in place for streamlined processing of high numbers of reference and casework samples, using instrumentation and technologies to maximize output using capillary electrophoresis (CE) based technology so far. Massoive Parallel Sequencing (MPS) technology has enabled sequencing of several types of genetic loci in one multiplex including single nucleotide polymorphisms (SNPs) and STRs. including the STRs using commonly in CE based flourescent multiplex kits. Therefore MPS has the potential to replace CE based technology. One hundred and fifty (150) reference samples from Qatari population were profiled using the ForenSeq™ DNA Signature kit. The data generated through MPS were analysed using ForenSeq™ Universal software and STRait Razor V3 for the primary, secondary and tertiary analyses. The average read depth was 20,000 reads for all sequencing runs. The analyses of the sequence of alleles in STRait Razor software were able to determine novel alleles in the Identntiy SNPs loci. The Qatari population has been a melting pot of various populations and this forensic study was the first of its kind to generate new data on the genetics of Qatari population. The 95 identity SNPs allele frequency data for 150 samples were analysed. The results have clearly demonstrated the potential use of MPS methods to study the genetics of Qatari population

The study of novel sequence alleles for Qatari population using ForenSeqTM DNA kit

For the last three decades, Short Tanddem Repeat (STR) markers and capillary electrophoresis-based DNA sequencers have been the gold standard technology for human identification testing in the forensic field. Massive Parallel Sequencing (MPS) technology has enabled sequencing of several types of genetic loci in one multiplex including single nucleotide polymorphisms (SNPs) and STRs. One hundred and fifty (150) reference samples were profiled using the ForenSeq™ DNA Signature kit. PCR Primer Mix B for this kit was used containing autosomal/Y/X STRs and AISNPS, iSNPs and pSNPs loci. The analyses of the sequence of STR alleles in STRait Razor software were able to determine novel alleles in the autosomal, Y and X STR as well as SNPs loci. This increased number of alleles had a clear advantage in forensic casework. Several of these sequenced-based alleles had not been reported earlier in the literature. This study also confirmed some of the previously determined alleles in several loci. The results have clearly demonstrated the potential use of MPS methods to study the genetics of Qatari population

A study of genetic analysis using novel rapidly mutating Y-STR multiplex for Qatari population

Differentiating male lineages using non-recombining Y-chromosomal genetic markers is highly informative for tracing human migration and for forensic studies. The aim of this study was to develop allelic frequency to evaluate the resolution power of Rapidly Mutating Y-STR (RMY-STR) on Qatar population in comparison to Worldwide population. In Qatari population the haplotype resolution of 100 % was achieved. The set of 13 RMY-STR markers showed remarkable haplotype resolution power in the Qatar population, high gene diversity and sufficient robustness. The novel multiplex PCR reaction wasused to type 250 samples from unrelated Qatari males. A total of 250 different haplotypes were det, with no shared haplotypes between individuals. The overall haplotype diversity (HD) was 100 %. It was found that the markers which contributed the most toward high HD were DYF399S1 and DYF403S1a/b. FST values were generated and AMOVA test performed between Qatar population and Middle Eastern/several worldwide population data sets were undertaken for FST values; geography was found to account considerably for the pattern of population sub structuring, although some discrepancies were observed in the relationship between geographical and genetic distance

Analysis of 55 Kidd ancestry SNPs in Qatari population using ForenSeq Universal software & STRUCTURE software

SNPs are good predictors of ethnicity and serval panels have been published [1]. The ForenSeq Signature kit (Illumina) offers coverage of 230 different markers including 55 ancestry SNPs (AISNPs). The ForenSeq Universal Analysis Software (UAS) brings the capability to analyse the sequencing data, represent results and accomplish statistical estimates of biogeographic ancestry. The ancestry prediction results in UAS are based on Principal Component Analysis (PCA) collected on several reference populations comprised in the 1000 Genomes project. This set does not include Qatari population. The data was analysed using STRUCTURE software. These data serves as an addition to the existing Middle Eastern population data for the 55 AISNPs. The Qatari population has been a melting pot of various populations and this forensic study was the first of its kind to generate new data on the genetics of Qatari population. The 55-ancestry marker allele frequency data for 150 samples were analysed and compared to 139 world populations using STRUCTURE software. FROG-kb analysis led to all Qatari samples being correctly assigned to Middle Eastern populations showing that the Illumina software needs to be enhanced by adding more databases from the Middle East. In conclusion, the results have clearly demonstrated the potential use of MPS methods to study the genetics of Qatari population

Optimisation of a reduced volume PCR amplification for PowerPlex® Fusion kit using FTA™ cards and generation of population genetic data for Brunei population

The commercial PowerPlex® Fusion kit is an autosomal STR multiplex kit that has high discrimination power and is more informative in forensic, paternity and relationship‐testing cases. Key features of this multiplex system are the possibility to direct amplify FTA™ card punches as well as non‐FTA cards and commonly used swabs; optimised inhibitor tolerance and high sensitivity generating full profiles from as little as 100 pg of human DNA. This study focused on the optimization of performance variables such as FTA™ punch sizes, reduced reaction volumes, and FTA™ purification reagent aiming to increase the analytical sensitivity, decrease the sample consumption and cost effectiveness. LOD and LOQ values demonstrated high sensitivity of the PowerPlex® Fusion system. In addition, population databases of Brunei Malay and Chinese from the Brunei Darussalam were established, and parameters of forensic importance were calculated. Overall, the forensic parameters indicated an enhanced utility of the PowerPlex® Fusion kit for forensic evidence analysis and paternity testing in Brunei Malay and Chinese populations