Evaluation of Forensic Genetic Parameters of 24 STR Loci and Y indel in a Southern Region Saudi Population Sample Using GlobalFiler™ PCR Amplification Kit

The last three decades have seen rapid advances in the field of short tandem repeats (STRs) genotyping technology. Autosomal STRs have emerged as a powerful tool in forensic identification and paternity investigations. The indigenous population of Saudi Arabia is irregularly distributed and has historically been organized into geographically distinct groups or tribes of patrilineal descent. So far, there has been no detailed investigation of the southern region Saudi population to assist in the interpretation of DNA-based forensic evidence and in the construction of DNA database. The objective of this study is to investigate the genetic structure in 154 unrelated healthy Saudi subjects within three generations from the southern Saudi regions using a GlobalFiler™ PCR Amplification kit. Intra- and Inter-population genetic diversity as well as the forensic genetics parameters were analyzed. Our results showed that SE33 and TPOX loci were the most and the least polymorphic loci, respectively. The PIC, PE, TPI, Ho and He varied from 0.56116 (TPOX) to 0.94393 (SE33), 0.26638 (TPOX) to 0.83859 (SE33), 1.1875 (TPOX) to 6.33333 (SE33), 0.57894 (TPOX) to 0.92105 (SE33) and 0.6169 (TPOX) to 0.952 (SE33), respectively. The highest PM was observed for D22S1045 (0.223944) and the highest PD for SE33 (0.98935). The combined PD was 99.99999999% and the combined PM was equal to 3.19021E-25. Phylogenetic parameters showed that the southern region Saudi population had the closest genetic relationship with the Saudi, Emirati, Kuwaiti, and Bahraini populations. The study offers some important insights into the southern region Saudi population structure using GlobalFiler™ PCR Amplification kit.

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Fingernail, as an Alternative Source of DNA for Forensic Investigations and Medical Diagnostics A new technique to obtain template DNA in critical situations

Acta geneticae medicae et gemellologiae twin research ◽

10.1017/s0001566000001525 ◽

1996 ◽

Vol 45 (1-2) ◽

pp. 301-302

Author(s):

U. Ricci ◽

M.L. Giovannucci Uzielli

Keyword(s):

Tandem Repeats ◽

Dna Analysis ◽

Dna Typing ◽

Pcr Amplification ◽

Medical Diagnostics ◽

Personal Identification ◽

Forensic Identification ◽

Alternative Source ◽

Chelex 100

The use of PCR (polymerase chain reaction) is having a profound impact on forensic science and medical diagnostics.Limited amounts of biological material and/or degraded low molecular weight DNA can be anticipated for forensic identification and often also for diagnostic investigations in fetuses, stillbirths and children with birth defects.In vitro amplification of DNA, via PCR, represents an important tool for overcoming some of the limitations. Nevertheless, the problem of availability of biological samples as DNA source is often critic.In order to obtain a useful and rapid procedure of DNA analysis in such difficult situations, we have recently developed a simple DNA extraction method using Chelex 100 and a PCR based amplification technique, and using fingernail as an alternative source of DNA.Chelex 100 procedures result in denaturated DNA samples, not suitable for RFLPS analysis. Nevertheless we demonstrated that no differences are detectable between the genotypes obtained by PCR amplification using the conventional phenol-chlorophorm or saline extraction and the Chelex based procedure.A DNA sample of 3-5 micrograms weight was easily obtained from fingernail clippings, and enabled us to perform several tests by using DNA typing methodologies, both for personal identification (in various forensic, medical and social situations) and in disputed parentage.Our laboratory uses as polymorphic markers a set of several VNTRs (variable number of tandem repeats) and, more recently, a series of unlinked STRs (short tandem repeats). The use of DNA typing with STR loci provides an accurate, highly sensitive and rapid assay for parentage testing, forensic identification and medical applications.

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Analysis of allele frequencies of the selected 15 autosomal STR markers in Tikrit population – Iraq with comparison to Middle Eastern, African, and Europeans

Asia Pacific Journal of Molecular Biology and Biotechnology ◽

10.35118/apjmbb.2021.029.2.08 ◽

2021 ◽

pp. 75-84

Author(s):

Maan Hasan Salih ◽

Akeel Hussain Ali Al-Assie ◽

Majeed Arsheed Sabbah

Keyword(s):

Tandem Repeats ◽

Human Genetics ◽

Forensic Genetics ◽

Middle Eastern ◽

Allele Frequencies ◽

Match Probability ◽

Discrimination Power ◽

Str Loci ◽

Dna Database ◽

Autosomal Str

Short tandem repeats (STRs) have been recommended as the highest polymorphic loci among the humana DNA regions. Therefore, STRs are agreeable to many genetic fields like forensic, population genetics and anthropological studies. The main aim of this research is to evaluate the autosomal STRs in Tikrit city-Iraq, to expand the human genetics database and forensic genetics analysis. The DNA database was obtained from 306 unrelated volunteers from native Tikrit population-Iraq, using 15 autosomal STR loci. The current study determined the allele frequencies in the Tikrit population and then compared them with other national Iraqi populations as well as with populations in the Middle East, Africa, and Europe. The highest level of heterozygosity was observed in D8S1179 and TH01 loci (0.797), while the less level was shown by CSF1PO (0.48). The departure from HWE Equilibrium was recorded in only 3 STR loci from a total of 15 loci analyzed (p<0.003). The Combined Match Probability (CMP) for 15 autosomal STR was 1 in 7.89208×10-19 and the Combined Discrimination Power (CDP) was 0.9999999997. The discrimination power (DP) was especially high in D2S1338, D18S51, D19S433 and D21S11. Based on the results observed in a Dendrogram, Tikrit population was clustered with other populations, likely reflecting the historical and geographical factors. D2S1338, D18S51, D19S433 and D21S11 markers were recognized as suitable for forensic genetics analysis in Tikrit population. Also, the 15 STRs markers provide information for the studies of genetic distances between the current study and other included populations to be compared with this study.

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Sexual Dimorphism of Selected Mandibular Anthropometric Parameters in Saudi Population Sample: Application in Forensic Identification

Ain Shams Journal of Forensic Medicine and Clinical Toxicology ◽

10.21608/ajfm.2014.18674 ◽

2014 ◽

Vol 23 (2) ◽

pp. 43-49

Author(s):

Sahar Moustafa

Keyword(s):

Sexual Dimorphism ◽

Population Sample ◽

Forensic Identification ◽

Saudi Population ◽

Anthropometric Parameters ◽

Sample Application

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Genetic diversity and haplotypic structure of a Saudi population sample using Investigator Argus X-12 amplification kit

10.1101/760819 ◽

2019 ◽

Cited By ~ 1

Author(s):

Safia A. Messaoudi ◽

Saranya R. Babu ◽

Abrar B. Alsaleh ◽

Mohamed Albajjah ◽

Noora AlSnan ◽

...

Keyword(s):

Population Sample ◽

Haplotype Diversity ◽

Turkish Population ◽

Female Offspring ◽

Fixation Index ◽

Saudi Population ◽

Linkage Groups ◽

Kinship Analysis ◽

Dna Database ◽

High Discrimination

AbstractX-chromosome short tandem repeat (X-STR) markers have shown a great capability in forensic identity investigations and paternity testing involving kinship analysis.In the current study, the distribution of 12 X-STR loci located in four linkage groups was evaluated using Investigator® Argus X-12 Amplification Kit in 200 unrelated healthy individuals (105 males and 95 females) from the central region of the Saudi Arabia in order to create a DNA database.Our results indicated that DXS10146 locus was the most informative with 21 alleles while DXS8378 locus was the least with five alleles. Forensic parameters showed that all X-STRs loci either as individual markers or as linkage groups provide genetic information with high discrimination that is appropriate for forensic purposes with Paternity Informed Consent (PIC), Power of exclusion (PE), and Paternity index (PI) varied from 0.61211 to 0.917979, 0.38722 to 0.842949, and 0.038416 to 0.16367, respectively. A significant Linkage disequilibrium (LD) with p-value after Bonferroni correction p ≤ 0.05/66= 0.0008 was observed for 17 pairs of loci in male samples and 4 pairs of loci in female. In the male group, LG3 showed relatively high values of Haplotype diversity. The pairwise genetic distance fixation index (Fst) results showed that the Saudi population is genetically close to the Egyptian and Emirati populations and distant to the Turkish population.The current study revealed that Investigator® Argus 12 X-STR kit would support forensic application, kinship testing involving female offspring, and human identification in Saudi populations.

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Assessment of QIAGEN™ Investigator® 24plex GO! kit workflow for autosomal STR profiling of forensic reference samples

Egyptian Journal of Forensic Sciences ◽

10.1186/s41935-020-00203-5 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Hashom Mohd Hakim ◽

Hussein Omar Khan ◽

Siti Afifah Ismail ◽

Nurul Hazirah Mat Lazim ◽

Japareng Lalung ◽

...

Keyword(s):

Pcr Amplification ◽

Dna Profiling ◽

Buccal Swab ◽

Forensic Dna ◽

Str Typing ◽

Str Analysis ◽

Dna Database ◽

Autosomal Str ◽

Dna Template ◽

Reference Samples

Abstract Background DNA profiling has proven to be a valuable technique for identification of individuals in crime. Currently, the technique targets several short tandem repeat (STR) regions in human genome. However, increasing number of samples submitted for STR analysis may lead to delays due to the limited number of experienced analysts who might be available at any given moment and the time taken to complete lengthy DNA profiling procedures. This study was conducted to test the specificity, repeatability, reproducibility and robustness of Investigator® 24plex GO! kit for genotyping of reference samples submitted to the Royal Malaysian Police Forensic DNA Laboratory for DNA database. Material and methods In this study, Investigator® 24plex GO! kit was used to directly amplify STR loci from buccal swab cell of reference samples that had previously been STR typed using GlobalFiler™ Express kit. Capillary electrophoresis was carried out on a 3500xL Genetic Analyser using POP-4® Polymer. Amplified products were assigned to particular STR alleles using the GeneMapper ID-X version 1.4 software. Results Our study shows that STR profiles generated using Investigator® 24plex GO! gave concordance results with those previously obtained using the GlobalFiler™ Express kit. In addition, quality sensors included in the kit are of particular importance for determining the effectiveness of the PCR reaction and help to indicate the nature and quantity of DNA template for PCR amplification. Conclusion The Investigator® 24plex GO! kit is reliable for STR typing of reference samples.

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Comparison of the Allelic Alterations between InDel and STR Markers in Tumoral Tissues Used for Forensic Purposes

Medicina ◽

10.3390/medicina57030226 ◽

2021 ◽

Vol 57 (3) ◽

pp. 226

Author(s):

Pamela Tozzo ◽

Arianna Delicati ◽

Anna Chiara Frigo ◽

Luciana Caenazzo

Keyword(s):

Colorectal Cancer ◽

Genomic Instability ◽

Tandem Repeats ◽

Forensic Genetics ◽

Tumor Type ◽

Forensic Dna ◽

Dna Identification ◽

Human Dna ◽

Tumor Transformation ◽

Paternity Tests

Background and objectives: Over the last two decades, human DNA identification and kinship tests have been conducted mainly through the analysis of short tandem repeats (STRs). However, other types of markers, such as insertion/deletion polymorphisms (InDels), may be required when DNA is highly degraded. In forensic genetics, tumor samples may sometimes be used in some cases of human DNA identification and in paternity tests. Nevertheless, tumor genomic instability related to forensic DNA markers should be considered in forensic analyses since it can compromise genotype attribution. Therefore, it is useful to know what impact tumor transformation may have on the forensic interpretation of the results obtained from the analysis of these polymorphisms. Materials and Methods: The aim of this study was to investigate the genomic instability of InDels and STRs through the analysis of 55 markers in healthy tissue and tumor samples (hepatic, gastric, breast, and colorectal cancer) in 66 patients. The evaluation of genomic instability was performed comparing InDel and STR genotypes of tumor samples with those of their healthy counterparts. Results: With regard to STRs, colorectal cancer was found to be the tumor type affected by the highest number of mutations, whereas in the case of InDels the amount of genetic mutations turned out to be independent of the tumor type. However, the phenomena of genomic instability, such as loss of heterozygosity (LOH) and microsatellite instability (MSI), seem to affect InDels more than STRs hampering genotype attribution. Conclusion: We suggest that the use of STRs rather than InDels could be more suitable in forensic genotyping analyses given that InDels seem to be more affected than STRs by mutation events capable of compromising genotype attribution.

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ISOLASI FRAGMEN GEN PENYANDI PUTRESIN N-METILTRANSFERASE DAN QUINOLINAT FOSFORIBOSILTRANSFERASE ASAL TEMBAKAU LOKAL TEMANGGUNG (Nicotiana tabacum)

Jurnal Penelitian Tanaman Industri ◽

10.21082/jlittri.v17n3.2011.109-117 ◽

2020 ◽

Vol 17 (3) ◽

pp. 109 ◽

Cited By ~ 1

Author(s):

SESANTI BASUKI ◽

NURHAJATI AA MATTJIK ◽

SUWARSO SUWARSO ◽

DESTA WIRNAS ◽

SUDARSONO SUDARSONO

Keyword(s):

Dna Sequences ◽

Pcr Amplification ◽

Data Bank ◽

Degenerate Primer ◽

Gene Encoding ◽

Methyl Transferase ◽

Dna Database ◽

Genes Encoding ◽

Tobacco Cultivar ◽

Dna Template

ABSTRAKUpaya untuk menurunkan kandungan nikotin merupakan salah satuprioritas utama penelitian tembakau. Nikotin adalah senyawa alkaloidutama berpotensi dikonversi menjadi senyawa nor-nikotin yang bersifatkarsinogen. Gen PMT sebagai penyandi enzim putresin n-metiltransferase(PMT) dan gen QPT - penyandi enzim quinolinat fosforibosiltransferase(QPT) merupakan dua gen kunci yang berperan penting pada proses bio-sintesis nikotin. Penelitian ini bertujuan untuk mengisolasi potongan genPMT dan QPT asal tembakau lokal Indonesia, mengkarakterisasi danmenganalisis runutan DNA-nya. Tahapan penelitian dimulai dengan me-rancang primer degenerate berdasarkan informasi yang ada di pangkalandata Bank Gen NCBI (National Centre for Biotechnology Information),mengamplifikasi PCR menggunakan templat DNA genomik tembakaulokal cv. Sindoro1, mengklon potongan DNA hasil PCR dan menentukanrunutan DNA-nya. Hasil penelitian menunjukkan dari dua belas pasangprimer degenerate yang dirancang, hanya dua pasang primer yang meng-hasilkan potongan DNA hasil amplifikasi PCR, yaitu pasangan primerPMt-7 (F & R) untuk gen PMT dan primer QPt-3 (F & R) untuk gen QPT.Setelah dilakukan penentuan runutan DNA-nya, amplikon yang didapatdari hasil PCR dengan pasangan primer PMt-7 sebesar 1418 bp, sedangkanuntuk primer QPt-3 sebesar 205 bp. Runutan DNA gen PMT dan gen QPTasal tembakau lokal cv. Sindoro1 mempunyai tingkat kesamaan yang ting-gi dengan gen PMT dan gen QPT asal tembakau lainnya yang ada dipangkalan data Bank Gen NCBI.Kata kunci : Gen PMT, gen QPT, lintasan biosintesis nikotin, perunutanDNA, amplifikasi PCR, primer degenerateABSTRACTIsolation of Genes encoding Putrescine N-Methyl-transferase and Quinolinat Phosphoribosyl transferasederived from Temanggung Tobacco Cultivar (Nicotianatabacum)Reduction of nicotine content is one of the major objective intobacco research. Nicotine is the main alcaloid compound that potentiallycould be converted into a carcinogenic compound (nor-nicotine). The PMTgene encoding putrescine N-methyl transferase (PMT) and the QPT gene -encoding quinolinate phosphoribosyl transferase (QPT) are the two keyenzymes involved in nicotine biosynthesis. The objectives of this researchwere to isolate PMT and QPT gene fragments originated from Indonesianlocal tobacco, to characterize, and to analyze their DNA sequences. Theresearch activities included: degenerate primer design based oninformation available in the GenBank DNA Database NCBI (NationalCentre for Biotechnology Information), PCR amplification usingdegenerate primer and genomic DNA template of a local tobacco cv.Sindoro1, clone the PCR amplified products, and determine their DNAnucleotide sequences. Results of the experiment indicated that from 12degenerate primer pairs synthesized, only two were able to yield positivePCR amplified products. These primer pairs were PMt-7 (F & R primers)for PMT and QPt-3 (F & R primers) for QPT. After DNA sequencing, theamplified DNA product amplified using PMt-7 degenerate primer pairswere 1418 bp, while that using QPt-3 primer pairs were only 205 bp.Nucleotide sequences of PMT or QPT gene fragments originated fromlocal tobacco cv. Sindoro1 showed a high nucleotide sequences identity ascompared to that of the respective genes from other tobacco species thatwere available in the GenBank DNA Database NCBI.Key words: PMT gene, QPT gene, nicotine biosynthetic pathways, DNAsequencing, PCR amplification, degenerate primer

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The Trouble with Race in Forensic Identification

Science Technology & Human Values ◽

10.1177/0162243919899467 ◽

2020 ◽

Vol 45 (5) ◽

pp. 804-828 ◽

Cited By ~ 6

Author(s):

Amade M’charek ◽

Victor Toom ◽

Lisette Jong

Keyword(s):

Forensic Genetics ◽

Family Relations ◽

Interesting Case ◽

Forensic Identification ◽

Criminal Investigation ◽

Science And Society ◽

The Family ◽

Genetic Technologies ◽

The Individual ◽

Absent Presence

The capacity of contemporary forensic genetics has rendered “race” into an interesting tool to produce clues about the identity of an unknown suspect. Whereas the conventional use of DNA profiling was primarily aimed at the individual suspect, more recently a shift of interest in forensic genetics has taken place, in which the population and the family to whom an unknown suspect allegedly belongs, has moved center stage. Making inferences about the phenotype or the family relations of this unknown suspect produces suspect populations and families. We discuss the criminal investigation following the Marianne Vaatstra murder case in the Netherlands and the use of forensic (genetic) technologies therein. It is in many ways an interesting case, but in this paper, we focus on how race surfaced in science and society. We show that race materializes neither in the technologies used nor in the bodies at stake. Rather, race emerges through a material semiotic relation that surfaces in the translation that occurs as humans and things move across sites. We argue that race is enacted, firstly, in the context of legislation as biology reduced to bodily characteristics; secondly, in the forensic analyses as patterns of absent presence; and, thirdly, in society as a process of phenotypic othering.

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Genetic diversity of Mycoplasma hyopneumoniae isolates from conventional farrow-to-finish pig farms in Serbia

Acta Veterinaria Hungarica ◽

10.1556/avet.58.2010.3.3 ◽

2010 ◽

Vol 58 (3) ◽

pp. 297-308 ◽

Cited By ~ 4

Author(s):

Bozidar Savic ◽

Vojin Ivetic ◽

Vesna Milicevic ◽

Ivan Pavlovic ◽

Milenko Zutic ◽

...

Keyword(s):

Tandem Repeats ◽

Genetic Relatedness ◽

Pcr Amplification ◽

Mycoplasma Hyopneumoniae ◽

Variable Number ◽

Repeat Motif ◽

Typing Method ◽

Pig Farms ◽

Different Ages ◽

Swine Population

Mycoplasma hyopneumoniaeis a primary agent associated with mycoplasma pneumonia and the porcine respiratory disease complex (PRDC). Various reports have indicated that different strains ofM. hyopneumoniaeare circulating in the swine population. Lysates from lung swabs from naturally infected pigs of different ages were tested according to a new variable number of tandem repeats (VNTR) genetic typing method based on the polyserine repeat motif of the P146 lipoproteoadhesin, which can be applied directly on clinical material without isolation ofM. hyopneumoniae. The aim was to determine the diversity ofM. hyopneumoniaeisolates from conventional farrow-to-finish pig farms located in different geographical areas of Serbia. PCR amplification was carried out usingM. hyopneumoniae-specific designed, conserved primers (p146MH — L and p146MH — R) flanking the region encoding the repeat motif, followed by sequencing and cluster analysis. Five groups ofM. hyopneumoniaewith thirteen to twenty-four serine repeats were observed. Analysis of three samples from each farm indicated that the specific isolate is ubiquitous in pigs of different ages. Furthermore, seven clusters were observed within 27 tested samples. The results indicated a considerable diversity amongM. hyopneumoniaefield isolates in the swine population from conventional farrow-to-finish farms in Serbia and suggest close genetic relatedness of the corresponding isolates.

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