Improved autosomal STR typing of degraded femur samples extracted using a custom demineralization buffer and DNA IQ™.

Bone samples are utilized as a source of DNA in disaster victim identification and human remains investigations. However, DNA recovery from bones is time consuming and prone to contamination. A logical approach for postmortem identification is to validate efficient DNA extraction methods requiring less bone material using improved molecular kits with less hands-on time and workflows that facilitate faster turn-around time for processing.

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

Demands for solving complex kinship scenarios where only distant relatives are available for testing have risen in the past years. In these instances, other genetic markers such as X-chromosome short tandem repeat (X-STR) markers are employed to supplement autosomal and Y-chromosomal STR DNA typing. However, prior to use, the degree of STR polymorphism in the population requires evaluation through generation of an allele or haplotype frequency population database.

Comparison of Two Massively Parallel Sequencing Platforms using 83 Single Nucleotide Polymorphisms for Human Identification.

The potential of Massively Parallel Sequencing (MPS) technology to vastly expand the capabilities of human identification led to the emergence of different MPS platforms that use forensically relevant genetic markers. Two of the MPS platforms that are currently available are the MiSeq FGx™ Forensic Genomics System (Illumina) and the HID-Ion Personal Genome Machine (PGM)™ (Thermo Fisher Scientific). These are coupled with the ForenSeq™ DNA Signature Prep kit (Illumina) and the HID-Ion AmpliSeq™ Identity Panel (Thermo Fisher Scientific), respectively.

Comparing different post-mortem human samples as DNA sources for downstream genotyping and identification.

The capability of DNA laboratories to perform genotyping procedures from post-mortem remains, including those that had undergone putrefaction, continues to be a challenge in the Philippines, a country characterized by very humid and warm conditions all year round. These environmental conditions accelerate the decomposition of human remains that were recovered after a disaster and those that were left abandoned after a crime. When considerable tissue decomposition of human remains has taken place, there is no other option but to extract DNA from bone and/or teeth samples.

Allele frequencies of 23 autosomal short tandem repeat loci in the Philippine population.

We characterized diversity and forensic descriptive parameters of 23 autosomal STR loci (CSF1PO, D13S317, D16S539, D5S818, D7S820, TPOX, D18S51, D21S11, D3S1358, D8S1179, FGA, TH01, vWA, D1S1656, D10S1248, D12S391, D2S441, D22S1045, D19S433, D2S1338, D6S1043, Penta D and Penta E) among 167 unrelated Filipinos. The most variable autosomal STR loci observed is Penta E (observed heterozygosity: 0.9222, match probability: 0.

Complete mtDNA genomes of Filipino ethnolinguistic groups: a melting pot of recent and ancient lineages in the Asia-Pacific region.

The Philippines is a strategic point in the Asia-Pacific region for the study of human diversity, history and origins, as it is a cross-road for human migrations and consequently exhibits enormous ethnolinguistic diversity. Following on a previous in-depth study of Y-chromosome variation, here we provide new insights into the maternal genetic history of Filipino ethnolinguistic groups by surveying complete mitochondrial DNA (mtDNA) genomes from a total of 14 groups (11 groups in this study and 3 groups previously published) including previously published mtDNA hypervariable segment (HVS) data from Filipino regional center groups. Comparison of HVS data indicate genetic differences between ethnolinguistic and regional center groups.

Y-STR DNA analysis of 154 female child sexual assault cases in the Philippines.

The laboratory evaluated 154 sexual assault cases from four Child Protection Units in the Philippines involving female child victims aged from 2 years to 18 years old. All child victims sought medical attention within 72 h after sexual contact. In 130 cases, the child victim knew the alleged offender and identified them during the interview with the social worker.

The Y-chromosome landscape of the Philippines: extensive heterogeneity and varying genetic affinities of Negrito and non-Negrito groups.

The Philippines exhibits a rich diversity of people, languages, and culture, including so-called 'Negrito' groups that have for long fascinated anthropologists, yet little is known about their genetic diversity. We report here, a survey of Y-chromosome variation in 390 individuals from 16 Filipino ethnolinguistic groups, including six Negrito groups, from across the archipelago. We find extreme diversity in the Y-chromosome lineages of Filipino groups with heterogeneity seen in both Negrito and non-Negrito groups, which does not support a simple dichotomy of Filipino groups as Negrito vs non-Negrito.

Mapping human genetic diversity in Asia.

Asia harbors substantial cultural and linguistic diversity, but the geographic structure of genetic variation across the continent remains enigmatic. Here we report a large-scale survey of autosomal variation from a broad geographic sample of Asian human populations. Our results show that genetic ancestry is strongly correlated with linguistic affiliations as well as geography.

Allele frequencies for two pentanucleotide STR loci Penta D and Penta E in a Philippine population.

Allele frequencies for the pentanucleotide STR markers Penta D and Penta E were analyzed in 100 unrelated Filipinos from different regions of the Philippine archipelago. These markers were found to be highly polymorphic in the studied population.

Fungal DNA challenge in human STR typing of bone samples.

The present study focuses on possible cross-reaction of fungal DNA with human STR primers that may affect subsequent forensic DNA analysis of forensic samples. Specificity of human STR markers namely HUMAMEL, HUMCSF1PO, D8S306, HUMTH01, HUMvWA, HUMFES/FPS, HUMF13A01, HUMDHFRP2, HUMFGA and HUMTPOX was tested using DNA of 24 different filamentous fungal isolates obtained from exhumed bone samples. The specificity of these ten STR markers for human DNA was demonstrated.

Identification of exhumed remains of fire tragedy victims using conventional methods and autosomal/Y-chromosomal short tandem repeat DNA profiling.

In a fire tragedy in Manila in December 1998, one of the worst tragic incidents which resulted in the reported death of 23 children, identity could not be established initially resulting in the burial of still unidentified bodies. Underscoring the importance of identifying each of the human remains, the bodies were exhumed 3 months after the tragedy. We describe here our work, which was the first national case handled by local laboratories wherein conventional and molecular-based techniques were successfully applied in forensic identification.

Identification of two fire victims by comparative nuclear DNA typing of skeletal remains and stored umbilical tissues.

We describe here our collaborative efforts in identifying 2 fatalities of a fire disaster by using a variety of identification techniques. Postmortem findings in both cases were reinforced using Short Tandem Repeat (STR) DNA technology to establish with a high degree of certainty the identities of 2 child victims. STR markers used in the present study include HUMAMEL, HUMCSFIPO, HUMTHO1, HUMvWA, HUMFES/FPS, HUMF13A01, HUMFOLP23, D8S3O6, HUMFGA, and HUMTPOX.