STR and mitochondrial DNA SNP typing of a bone marrow transplant recipient after death in a fire

Development of an epigenetic age predictor for costal cartilage with a simultaneous somatic tissue differentiation system

Age prediction from DNA has been a topic of interest in recent years due to the promising results obtained when using epigenetic markers. Since DNA methylation gradually changes across the individual's lifetime, prediction models have been developed accordingly for age estimation. The tissue-dependence for this biomarker usually necessitates the development of tissue-specific age prediction models, in this way, multiple models for age inference have been constructed for the most commonly encountered forensic tissues (blood, oral mucosa, semen). The analysis of skeletal remains has also been attempted and prediction models for bone have now been reported. Recently, the VISAGE Enhanced Tool was developed for the simultaneous DNA methylation analysis of 8 age-correlated loci using targeted high-throughput sequencing. It has been shown that this method is compatible with epigenetic age estimation models for blood, buccal cells, and bone. Since when dealing with decomposed cadavers or postmortem samples, cartilage samples are also an important biological source, an age prediction model for cartilage has been generated in the present study based on methylation data collected using the VISAGE Enhanced Tool. In this way, we have developed a forensic cartilage age prediction model using a training set composed of 109 samples (19-74 age range) based on DNA methylation levels from three CpGs in FHL2, TRIM59 and KLF14, using multivariate quantile regression which provides a mean absolute error (MAE) of ± 4.41 years. An independent testing set composed of 72 samples (19-75 age range) was also analyzed and provided an MAE of ± 4.26 years. In addition, we demonstrate that the 8 VISAGE markers, comprising EDARADD, TRIM59, ELOVL2, MIR29B2CHG, PDE4C, ASPA, FHL2 and KLF14, can be used as tissue prediction markers which provide reliable blood, buccal cells, bone, and cartilage differentiation using a developed multinomial logistic regression model. A training set composed of 392 samples (n = 87 blood, n = 86 buccal cells, n = 110 bone and n = 109 cartilage) was used for building the model (correct classifications: 98.72%, sensitivity: 0.988, specificity: 0.996) and validation was performed using a testing set composed of 192 samples (n = 38 blood, n = 36 buccal cells, n = 46 bone and n = 72 cartilage) showing similar predictive success to the training set (correct classifications: 97.4%, sensitivity: 0.968, specificity: 0.991). By developing both a new cartilage age model and a tissue differentiation model, our study significantly expands the use of the VISAGE Enhanced Tool while increasing the amount of DNA methylation-based information obtained from a single sample and a single forensic laboratory analysis. Both models have been placed in the open-access Snipper forensic classification website.

Cartilage Tissue in Forensic Science—State of the Art and Future Research Directions

Cartilage tissue performs many functions in the human body. The diseases and injuries affecting it are prevalent due to its slow regeneration rate. However, cartilage tissue is exceptionally important for its auspicious use in forensic medicine due to its slow postmortem degradation rate. The presented review summarizes the latest research on cartilage tissues and their current and potential applications in forensic science. It also describes the most important studies on using cartilage and its microscopic and macroscopic analyses to estimate the deceased age and determine postmortem interval (PMI) values and the crime weapon. Additionally, the review describes attempts to isolate DNA from cartilage tissue for individual identification. The review also mentions recent, less abundant studies on the cartilage in forensic toxicology and genetics. It points out further directions and prospects for research development on cartilage tissue and its promising use in forensic medicine

Filter mask as a new candidate of personal belonging used in cadaver identification – a case report

The case report presents an identification process based on DNA isolated from personal belongings, including a filter mask. In May 2021, an unidentified 65-year-old male corpse was revealed by the city’s outskirts road. Since it was impossible to use material from living relatives for comparative analysis, the samples of personal belongings of the alleged victim were used instead: clippings of the filtering face piece type 2 (FFP2) face mask (parts adhering to the nose and the earlobes, the central part of the mask), swabs from the razor (blade and shaft), toothbrush shaft, and toothbrush filaments clippings. The presented case indicates the need for collecting a wide range of samples for genetic analyses, including filter masks as an alternative item of personal belonging.

Costal cartilage ensures low degradation of DNA needed for genetic identification of human remains retrieved at different decomposition stages and different postmortem intervals

Introduction

The study aimed to evaluate if costal cartilage is a good source of DNA for genetic individual identification tests performed in forensic autopsies.

Materials and Methods

The study included samples of costal cartilage collected from 80 cadavers retrieved from different environments: indoors (flat/hospital), outdoors (primarily in the forest), a coal mine, a fire site, uninhabited buildings, a basement, bodies of fresh water, exhumation sites, and unknown locations. After isolation of DNA chondrocytes, T. Large autosomal chromosome (214 bp), T. Small autosomal chromosome (80 bp), and the Y chromosome (75 bp; for male cadavers), sequences were amplified using real-time PCR. Additionally, 23 autosomal short tandem repeat (STR) loci and 16 Y chromosome STR loci were amplified using multiplex PCR. Forensic DNA typing was done using capillary electrophoresis and all results were analyzed.

Results

There was no statistically significant difference in DNA concentration after T. Large, T. Small autosomal chromosome and the Y chromosome amplification between samples collected from cadavers retrieved from different environments. The DNA degradation index was the same regardless of the postmortem interval. The results show that it is possible to generate a full genetic profile from costal cartilage samples collected from cadavers retrieved from different environments and at different times elapsed after death.

Conclusions

The results suggest that costal cartilage can be routinely collected during forensic autopsies, especially from cadavers at the advanced decomposition stage.

Extraordinary claims require extraordinary evidence in asserted mtDNA biparental inheritance

A breakthrough article published in PNAS by Luo et al. challenges a central dogma in biology which states that the mitochondrial DNA (mtDNA) in humans is inherited exclusively from the mother. We re-analyzed original FASTQ files and results reported by Luo et al. to investigate methodological issues (e.g. nuclear mitochondrial DNA or NUMTs, DNA rearrangements) that could lead to biological misinterpretations. A comprehensive analysis of their data reveals several methodological and analytical issues that must be carefully addressed before challenging the current paradigm. We first show that the probability of the findings described by the authors is extremely small (most likely below 10^-37). The sequencing replicates from the same donors show aberrations in the variants detected that need further investigation to exclude contributions from other sources or methodological artifacts. Applying the principle of reductio ad absurdum, we demonstrate that the nuclear factor invoked by the authors to explain the phenomenon would need to be extraordinarily complex and precise to preclude linear accumulation of mtDNA lineages across generations, which would make the appearance of mixed haplotypes a much more frequent event in the population. We discuss alternate scenarios that explain findings of the same nature as reported by Luo et al., in the context of in-vitro fertilization and therapeutic mtDNA replacement ooplasmic transplantation.

Evaluation of reliability on STR typing at leukemic patients used for forensic purposes

Over the past decades, main advances in the field of molecular biology, coupled with benefits in genomic technologies, have led to detailed molecular investigations in the genetic diversity generated by researchers. Short tandem repeat (STR) loci are polymorphic loci found throughout all eukaryotic genome. DNA profiling identification, parental testing and kinship analysis by analysis of STR loci have been widely used in forensic sciences since 1993. Malignant tissues may sometimes be the source of biological material for forensic analysis, including identification of individuals or paternity testing. There are a number of studies on microsatellite instability in different types of tumors by comparing the STR profiles of malignant and healthy tissues on the same individuals. Defects in DNA repair pathways (non-repair or mis-repair) and metabolism lead to an accumulation of microsatellite alterations in genomic DNA of various cancer types that result genomic instabilities on forensic analyses. Common forms of genomic instability are loss of heterozygosity (LOH) and microsatellite instability (MSI). In this study, the applicability of autosomal STR markers, which are routinely used in forensic analysis, were investigated in order to detect genotypes in blood samples collected from leukemic patients to estimate the reliability of the results when malignant tissues are used as a source of forensic individual identification. Specimens were collected from 90 acute and 10 chronic leukemia volunteers with oral swabs as well as their paired peripheral blood samples from the Oncology Centre of the Department of Hematology at Istanbul University, during the years 2010-2011. Specimens were tested and compared with 16 somatic STR loci (CSFIPO, THO1, TPOX, vWA, D2S1338, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D19S433, D21S11 and FGA) widely used in forensic identification and kinship. Only two STR instabilities were encountered among 100 specimens. An MSI in the FGA loci and a LOH in the D2S1338 loci were determined in two individuals separately. Our results demonstrate that the use of the biological samples from leukemia patients in forensic identification and kinship testing is questionable, especially if known microsatellite instability is available. Genetic instabilities may alter the STR polymorphism, leading to potential errors on forensic identification of individuals. Therefore, typing of autosomal STRs from leukemia patients should be performed with both healthy and malignant tissue samples of individual as references.