Filipino DNA variation at 12 X-chromosome short tandem repeat markers

Salvador, Jazelyn M.; Apaga, Dame Loveliness T.; Delfin, Frederick C.; Calacal, Gayvelline C.; Dennis, Sheila Estacio; Ungria, Maria Corazon A. De

doi:10.1016/j.fsigen.2018.06.008

Cited by 30 publications

(21 citation statements)

References 39 publications

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“…The evidentiary DNA profile is only meaningful when compared to a known or reference profile. Generally, the weight of the evidence depends on the rarity of the profile estimated from a reference database of the relevant population [ 31 , 32 ]. To avoid possible confirmation bias, interpretation of DNA typing results from the evidence should be done before any comparison to a known profile except those assumed to be already present in the mixture (e.g.…”

Section: An Integrated System For Dna Testing In Sexual Assault Casesmentioning

confidence: 99%

An integrated system for forensic DNA testing of sexual assault cases in the Philippines

Rodriguez

Laude

Ungria

2021

Forensic Science International: Synergy

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In the Philippines, more than 7000 cases of sexual assault are reported annually. DNA technology is a powerful tool in identifying assailants. However, it is not routinely used in sexual assault investigations due to insufficient government support to cover the high cost of DNA testing and the absence of a national system for sample collection, handling, storage, and DNA testing of biological evidence. In itself, the nature of sexual assault samples containing DNA mixtures presents challenges to laboratory methods and interpretation of results. The sample recovered from the victim may only contain trace amounts of the assailant’s DNA, may have degraded due to prolonged storage in ambient conditions which is warm and humid in the tropics, or contaminated with inhibitors, such as in anal swabs. Hence, a closer evaluation of the processes of evidence collection and DNA testing is needed to increase the likelihood of success in generating conclusive results. In this paper, we propose an integrated system for DNA testing of biological samples collected from sexual assault victims considering the limitations of resources and the prevailing warm climate. Recommendations in this work should provide basis for formulating national guidelines for DNA analysis in aid of criminal investigations. The proposed scheme can be adopted by forensic DNA laboratories in the Philippines and in other countries facing similar challenges.

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Section: An Integrated System For Dna Testing In Sexual Assault Casesmentioning

confidence: 99%

An integrated system for forensic DNA testing of sexual assault cases in the Philippines

Rodriguez

Laude

Ungria

2021

Forensic Science International: Synergy

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“…This situation changed in 2010 with the publication of a large empirical Y‐STR mutation rate study analyzing 186 Y‐STRs in nearly 2,000 DNA‐confirmed father–son pairs, which highlighted 13 Y‐STR markers with mutation rates > 10 −2 mutations per marker per meiosis termed rapidly mutating (RM) Y‐STRs (Ballantyne et al, 2010). Followed by the first empirical demonstrations of their suitability for male relative differentiation (Ballantyne et al, 2012, 2014), many subsequent studies provided increasing evidence on the value of RM Y‐STRs for differentiating related, including closely related, and also unrelated men (Adnan, Ralf, Rakha, Kousouri, & Kayser, 2016; Alghafri, Goodwin, & Hadi, 2013; Boattini et al, 2016, 2019; Lang et al, 2017; Niederstätter, Berger, Kayser, & Parson, 2016; Robino et al, 2015; Salvador et al, 2019; Turrina, Caratti, Ferrian, & De Leo, 2016; Westen et al, 2015; Zgonjanin, Alghafri, Antov et al, 2017). In genetic genealogy too, RM Y‐STRs are advantageous as they provide improved differentiation of unrelated individuals (Ballantyne et al, 2014) and they allow distinguishing closely related from more distantly related males by taking the number of observed mutations into account (Larmuseau et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

Identification and characterization of novel rapidly mutating Y‐chromosomal short tandem repeat markers

et al. 2020

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Short tandem repeat polymorphisms on the male‐specific part of the human Y‐chromosome (Y‐STRs) are valuable tools in many areas of human genetics. Although their paternal inheritance and moderate mutation rate (~10−3 mutations per marker per meiosis) allow detecting paternal relationships, they typically fail to separate male relatives. Previously, we identified 13 Y‐STR markers with untypically high mutation rates (>10−2), termed rapidly mutating (RM) Y‐STRs, and showed that they improved male relative differentiation over standard Y‐STRs. By applying a newly developed in silico search approach to the Y‐chromosome reference sequence, we identified 27 novel RM Y‐STR candidates. Genotyping them in 1,616 DNA‐confirmed father–son pairs for mutation rate estimation empirically highlighted 12 novel RM Y‐STRs. Their capacity to differentiate males related by 1, 2, and 3 meioses was 27%, 47%, and 61%, respectively, while for all 25 currently known RM Y‐STRs, it was 44%, 69%, and 83%. Of the 647 Y‐STR mutations observed in total, almost all were single repeat changes, repeat gains, and losses were well balanced; allele length and fathers' age were positively correlated with mutation rate. We expect these new RM Y‐STRs, together with the previously known ones, to significantly improving male relative differentiation in future human genetic applications.

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“…Interpopulation pairwise genetic distances based on Fst between the population of Bahrain and the rest of populations extracted from the literature that included Saudi, 15 Filipino, 16 Emiratis, 17 Bengali, 18 Egyptian, 19 Turkish, 20 Indian, 21 Algerian, 22 and Jewish 23 were calculated using POPTREE2 software 24 and represented by a nonmetric multidimensional scaling (NM-MDS) analysis using IBM SPSS Statistics v21.0 software to investigate the populations' structure between Bahraini population and the already mentioned populations based on Fst's genetic distances. Phylogenetic tree was constructed from allele frequency data by using the neighbor-joining (NJ) method 25 via MEGA X: Molecular Evolutionary Genetics Analysis.…”

Section: Discussionmentioning

confidence: 99%

Population Genetic Analysis of 12 X-Chromosomal Short Tandem Repeats in a Bahraini Population Sample

Al-Snan

Messaoudi

Mansoor³

et al. 2021

Forensic Genomics

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Background: Recently, there are few genetic studies on the Kingdom of Bahrain, which is a small archipelago positioned in the Arabian Gulf. There are several tools used in population genetics and human identification. One of them is the X-chromosomal short tandem repeats (X-STRs). Methods: For this study, 156 buccal swabs were collected using cotton swabs from nonrelated Bahraini males. QIAsymphony SP instrument was used for genomic DNA extraction and purification and Investigator Quantiplex HYres Kit was used for DNA quantification in the 7500 Real-Time PCR System. ABI 3500xl Genetic Analyzer was used for detection. Analysis was done using multiple statistical software to obtain allele and haplotypes' frequencies based upon the available four clusters of linkage groups as well as different forensic and population parameters. Results: Results indicated the diversity of the Bahraini population in terms of high power of discrimination (PD) and probability of match (PM) values. The combined values of each forensic parameter such as combined PD in males (cPD M ), mean exclusion chance (cMEC) Krüger, cMEC Kishida, and cMEC Desmarais as well as cMEC Desmarais Duo were 0.9999983, 9999979, 0.9999939, 0.9999996, and 0.9999514, respectively, based on the allele and haplotype frequencies. No shared profiles were observed. The number of nonstandard alleles and null alleles was obtained, and more profoundly in locus DXS10148. We have constructed a phylogeny of these data as well as a multidimensional scale to analyze the interpopulation diversity between Bahraini population and other neighboring populations, and our findings reflected the geographical and social background of the region. Overall, the results confirmed the importance of X-STRs in discriminating between individuals among Bahraini population and in establishing DNA databases for forensic and kinship studies.

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Filipino DNA variation at 12 X-chromosome short tandem repeat markers

Cited by 30 publications

References 39 publications

An integrated system for forensic DNA testing of sexual assault cases in the Philippines

An integrated system for forensic DNA testing of sexual assault cases in the Philippines

Identification and characterization of novel rapidly mutating Y‐chromosomal short tandem repeat markers

Population Genetic Analysis of 12 X-Chromosomal Short Tandem Repeats in a Bahraini Population Sample

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