The Successful Recovery of Low Copy Number and Degraded DNA from Bones Exposed to Seawater Suitable for Generating a DNA STR Profile

Nails as optimal source of DNA for molecular identification of 5 decomposed bodies recovered from seawater: from Y-ancestry to personal identification

Molecular identification of extremely compromised human remains in forensic field is usually performed from DNA typing of bones, which are a difficult sample to work with. Moreover, autosomal STR profiles do not always result in the identification of the donor due to lack of comparisons or non-hit throughout database searching. An attempt to overcome these issues is represented by fingernails as an alternative DNA source and Y-STRs typing to infer both geographical and familial ancestry of the unknown donor. In this study, we analyzed both 24 autosomal and 27 Y-chromosome STRs from unidentified human remains (UHRs) of five males recovered from the water near the southwestern coast of Sardinia by the Italian Harbor Master's Office. Nail clippings provided an optimal source of autologous DNA for molecular identification in a very short time, producing complete autosomal and Y-STR profiles even under conditions of high body degradation. Unfortunately, no match neither compatibility occurred using autosomal STRs (aSTRs), initially. Upon analyzing the Y-haplotypes, we found out they had already been observed in northern Africa, providing us important investigative leads. This prompted the International Criminal Police Organization (INTERPOL) to provide us with references of alleged relatives that were then confirmed to be related. The use of fingernails represents an excellent DNA source especially for genetic identification of decomposed bodies recovered in seawater environment. Notably, DNA extracted from nails gave high-quality Y-STR haplotypes by which predicting paternal ancestry of the unidentified donors may result fundamental in the forensic investigative context.

Dead migrants in the Mediterranean: genetic analysis of bone samples exposed to seawater

In April 2015, a fishing boat that departed from Libya with about 1,000 migrants on board sank in the Mediterranean Sea. Most of the migrants were packed in the hull of the boat and drowned in the shipwreck. After fifteen months, the ship was recovered from the seabed and brought to a Sicilian naval area for forensic investigations. Skeletal remains belonging to more than 700 people were retrieved. A selected sample composed of 80 victims was considered in order to evaluate the possibility of achieving genetic profiles useful for a positive identification from these challenging specimens. The molecular features of the DNA recovered from a significant number of real casework samples exposed to seawater for long periods of time were described for the first time. Three different DNA extraction protocols and three different commercial kits were employed in order to generate genetic profiles based on the characterization of 21 autosomal STR loci. The combination of multiple DNA extractions and the cross-checking of multiple PCR amplifications with different kits allowed to obtain reliable genetic profiles characterized by at least 16 STR markers in more than 70% of the samples. The factors that could have affected the different quality of the genetic profiles were investigated and the bone preservation was examined through microscopic and macroscopic analyses. The approach presented in this study could be useful in the management of the genetic analysis of bone samples collected in other similar DVI scenarios. The genetic profiles recovered from the bone samples will be compared in kinship analysis to putative relatives of the victims collected in Africa in order to obtain positive identifications.

Sweet tooth: DNA profiling of a cranium from an isolated retained root fragment

Sampling of healthy multi‐rooted teeth is recommended for the genetic identification of human skeletal remains. However, this may not always be possible, as in the reported case consisting of an isolated human cranium found in an aggregate crushing and processing plant in Piedmont, Northwest Italy. The cranium displayed significant weathering, suggesting a post‐mortem interval of several years, and was edentulous with the exception of the apical root fragment of the upper left canine, consequence of an antemortem horizontal fracture. Prolonged decalcification of the root fragment followed by powder‐free DNA extraction from ~10 mg of root tip tissue led to the recovery of >10 ng of high molecular weight human DNA, in comparison with ~0.01 ng of DNA per mg of bone powder obtained from the petrous portion of the temporal bone. Quantity and quality of DNA isolated from apical tooth tissue enabled multiple genotyping, including a reportable female STR profile, mitochondrial DNA analysis, and ancestry‐informative insertion/deletion polymorphisms. Although the cranium remained unidentified after DNA comparisons, our findings confirm that apical tooth tissue is a promising source of DNA, easily obtained through a powder‐free extraction protocol. Results also indicate that root tips should not be overlooked in challenging identification cases, even in the presence of compromised tooth specimens.

Evaluation of Parameters for Estimating the Postmortem Interval of Skeletal Remains Using Bovine Femurs: A Pilot Study

The postmortem interval (PMI) of victims is a key parameter in criminal investigations. However, effective methods for estimating the PMI of skeletal remains have not been established because it is determined by various factors, including environmental conditions. To identify effective parameters for estimating the PMI of skeletal remains, we investigated the change in bone focusing on the amount of DNA, element concentrations, and bone density that occurred in the bone samples of bovine femurs, each maintained under one of five simulated environmental conditions (seawater, freshwater, underground, outdoors, and indoors) for 1 year. The amount of extracted mitochondrial DNA (mtDNA; 404 bp fragment) decreased over time, and significant DNA degradation (p < 0.01), as estimated by a comparison with amplification results for a shorter fragment (128 bp), was detected between 1 month and 3 months. Eleven of 30 elements were detected in samples by inductively coupled plasma optical emission spectrometry, and Na and Ba showed significant quantitative differences in terms of environmental conditions and time (p < 0.01). This preliminary study suggests that the level of DNA degradation determined by real-time polymerase chain reaction and element concentrations determined by inductively coupled plasma optical emission may be useful indices for estimating the PMI of victims under a wide range of environmental conditions. However, this study is a limited experimental research and not applicable to forensic cases as it is. Further studies of human bone with longer observation periods are required to verify these findings and to establish effective methods for PMI estimation.

Human DNA extraction from highly degraded skeletal remains: How to find a suitable method?

Retrieving DNA from highly degraded human skeletal remains is still a challenge due to low concentration and fragmentation, which makes it difficult to extract and purify. Recent works showed that silica-based methods allow better DNA recovery and this fact may be attributed to the type of bones and the quality of the preserved tissue. However, more systematic studies are needed to evaluate the efficiency of the different silica-based extraction methods considering the type of bones. The main goal of the present study is to establish the best extraction method and the type of bone that can maximize the recovery of PCR-amplifiable DNA and the subsequent retrieval of mitochondrial and nuclear genetic information. Five individuals were selected from an archaeological site located in Catalonia-Spain dating from 5th to 11th centuries AD. For each individual, five samples from different skeletal regions were collected: petrous bone, pulp cavity and cementum of tooth, and rib and limb bones. Four extraction methods were tested, three silica-based (silica in-suspension, HE column and XS plasma column) and the classical method based on phenol-chloroform. Silica in-suspension method from petrous bone and pulp cavity showed the best results. However, the remains preservation will ultimately be the key to the molecular result success.

A first for forensic genetics in Africa: successful identification of skeletal remains from the marine environment using massively parallel sequencing

In unrelated circumstances, two young adult males allegedly went missing off the coast of Cape Town, South Africa, within two months of each other. Weeks after the second disappearance, a decomposed human lower limb was recovered from a beach in Cape Town, followed by a washed-up decomposed hand three days later. An item of female clothing was found with the remains, and preliminary analysis of the skeleton indicated a female, leading to confusion regarding the possible identity of the decedent. Consequently, DNA analyses were requested to determine the biological sex of the remains, and whether the two sets of remains originated from the same individual. Various samples were collected, including bone, nails and swabs of soft tissue. DNA quantity and quality varied between sample types, with better results obtained from metacarpal bone and swab lysates. DNA profiling revealed a male sex, which suggests cognitive bias may have played a role in initial sex estimations. In addition, massively parallel sequencing confidently matched the two sets of remains (random match probability: 1 in 2.70 x 10³¹). These results were a first for Africa where massively parallel sequencing was successfully used and assisted in the identification of human remains, thus, affording closure to the next-of-kin. Moreover, this constitutes the first global report where soft tissue lysates from a marine decomposition case yielded full DNA profiles with a massively parallel sequencing approach.

Improved resolution of mixed STR profiles using a fully automated differential cell lysis/DNA extraction method

Sexual assault evidence often contains sperm cells, which are typically separated from nonsperm cells using manual differential lysis procedures. The goal of this study was to evaluate the automated QIAGEN QIAcube for this purpose and to compare it to manual QIAGEN and manual organic differential methods using DNA yields and STR profile data for assessment. DNA yields were determined by qPCR, followed by multiplex STR amplification, CE analysis, and mixture interpretation. The automated method was capable of effective cell separation, producing DNA yields sufficient for STR amplification. Further, sperm fraction human:male DNA ratios from the QIAcube samples were consistently closer to the desired 1:1 and STR profiles were less likely to result in mixtures, with 6-8× fewer female alleles detected (median 1.5 alleles). Ultimately, using the QIAcube for automated differential processing of semen-containing mixtures reduces the need for downstream mixture interpretation and improves STR profile quality with substantially less hands-on time.

A Concentrated Hydrochloric Acid-based Method for Complete Recovery of DNA from Bone

The successful extraction of DNA from historical or ancient animal bone is important for the analysis of discriminating genetic markers. Methods used currently rely on the digestion of bone with EDTA and proteinase K, followed by purification with phenol/chloroform and silica bed binding. We have developed a simple concentrated hydrochloric acid-based method that precludes the use of phenol/chloroform purification and can lead to a several-fold increase in DNA yield when compared to other commonly used methods. Concentrated hydrochloric acid was shown to dissolve most of the undigested bone and allowed the efficient recovery of DNA fragments <100 bases in length. This method should prove useful for the recovery of DNAs from highly degraded animal bone, such as that found in historical or ancient samples.