Assessing the Utility of Soil DNA Extraction Kits for Increasing DNA Yields and Eliminating PCR Inhibitors from Buried Skeletal Remains

DNA identification of human remains is often necessary when decedents are skeletonized; however, poor DNA recovery and polymerase chain reaction (PCR) inhibition are frequently encountered, a situation exacerbated by burial. In this research, the utility of integrating soil DNA isolation kits into buried skeletal DNA analysis was evaluated and compared to a standard human DNA extraction kit and organic extraction. The soil kits successfully extracted skeletal DNA at quantities similar to standard methods, although the two kits tested, which differ mechanistically, were not equivalent. Further, the PCR inhibitors calcium and humic acid were effectively removed using the soil kits, whereas collagen was less so. Finally, concordant control region sequences were obtained from human skeletal remains using all four methods. Based on these comparisons, soil DNA isolation kits, which quickened the extraction process, proved to be a viable extraction technique for skeletal remains that resulted in positive identification of a decedent.     

Modified Midi‐ and Mini‐Multiplex PCR Systems for Mitochondrial DNA Control Region Sequence Analysis in Degraded Samples

Two multiplex polymerase chain reaction (PCR) systems (Midiplex and Miniplex) were developed for the amplification of the mitochondrial DNA (mtDNA) control region, and the efficiencies of the multiplexes for amplifying degraded DNA were validated using old skeletal remains. The Midiplex system consisted of two multiplex PCRs to amplify six overlapping amplicons ranging in length from 227 to 267 bp. The Miniplex system consisted of three multiplex PCRs to amplify 10 overlapping short amplicons ranging in length from 142 to 185 bp. Most mtDNA control region sequences of several 60‐year‐old and 400–500‐year‐old skeletal remains were successfully obtained using both PCR systems and consistent with those previously obtained by monoplex amplification. The multiplex system consisting of smaller amplicons is effective for mtDNA sequence analyses of ancient and forensic degraded samples, saving time, cost, and the amount of DNA sample consumed during analysis.     

Nondestructive Methods for Recovery of Biological Material from Human Teeth for DNA Extraction

The extraction of DNA from human skeletal remains applied to forensic, and evolutionary studies do not exclude risks, which are to be evaluated when working with unique specimens that could be damaged or even destroyed. In the present study were evaluated several nondestructive methods for recovering DNA instead of the most currently used pulverization method. Three different procedures to access inside the dental pieces (occlusal perforation, cervical perforation, and cervical cut) have been compared with the aim of recovering as many cell remains as possible to carry out a DNA extraction. Given the DNA quantitation results, a method was proposed that consists of a cervical cut to facilitate the access to the pulp cavity and a subsequent filing of the root canals down to the apex of the dental root. This methodology allows the recovery of both mitochondrial and nuclear DNA, with the minimum deterioration for the dental pieces.     

The Correlation Between Skeletal Weathering and DNA Quality and Quantity*

Abstract: Mitochondrial DNA analysis of skeletal material is invaluable in forensic identification, although results can vary widely among remains. Previous studies have included bones of different ages, burial conditions, and even species. In the research presented, a collection of human remains that lacked major confounders such as burial age, interment style, and gross environmental conditions, while displaying a very broad range of skeletal degradation, were examined for both mitochondrial DNA (mtDNA) quality and quantity. Overall skeletal weathering, individual bone weathering, and bone variety were considered. Neither skeletal nor bone weathering influenced DNA quality or quantity, indicating that factors that degrade bone do not have the same effect on DNA. In contrast, bone variety, regardless of weathering level, was a significant element in DNA amplification success. Taken together, the results indicate that neither skeletal nor individual bone appearance are reliable indicators of subsequent mtDNA typing outcomes, while the type of bone assayed is.     

A review of the current understanding of burned bone as a source of DNA for human identification

Identification of incinerated human remains may rely on genetic analysis of burned bone which can prove far more challenging than fresh tissues. Severe thermal insult results in the destruction or denaturation of DNA in soft tissues, however genetic material may be preserved in the skeletal tissues. Considerations for DNA retrieval from these samples include low levels of exogenous DNA, the dense, mineralised nature of bone, and the presence of contamination, and qPCR inhibitors. This review collates current knowledge in three areas relating to optimising DNA recovery from burned bone: 1) impact of burning on bone and subsequent effects on sample collection, 2) difficulties of preparing burned samples for DNA extraction, and 3) protocols for bone decalcification and DNA extraction. Bone decalcification and various DNA extraction protocols have been tested and optimised for ancient bone, suggesting that prolonged EDTA (Ethylenediaminetetraacetic acid) demineralisation followed by solid-phased silica-based extraction techniques provide the greatest DNA yield. However, there is significantly less literature exploring the optimal protocol for incinerated bones. Although burned bone, like ancient and diagenetic bone, can be considered “low-copy”, the taphonomic processes occurring are likely different. As techniques developed for ancient samples are tailored to deal with bone that has been altered in a particular way, it is important to understand if burned bone undergoes similar or different changes. Currently the effects of burning on bone and the DNA within it is not fully understood. Future research should focus on increasing our understanding of the effects of heat on bone and on comparing the outcome of various DNA extraction protocols for these tissues.     

Extraction of DNA from Skeletonized Postcranial Remains: A Discussion of Protocols and Testing Modalities

This paper provides a retrospective of the DNA analysis performed by the Armed Forces Medical Examiner–Armed Forces DNA Identification Laboratory between 1990 and 2018. Over 13,000 postcranial osseous materials, comprised of wartime losses from World War II, the Korean War, and South‐East Asia, were examined by the following: mitochondrial DNA sequencing, a modified AmpFlSTR® Yfiler?, AmpFlSTR® MiniFiler?, PowerPlex® Fusion, or NGS. Four different DNA extraction protocols were used: incomplete demineralization coupled with an organic purification; complete demineralization with an organic purification; complete demineralization with an inorganic purification using QIAquick PCR Purification Kit; and a protocol designed specifically for use with next‐generation sequencing. In general, complete demineralization coupled with an organic purification was the optimal extraction protocol for sequencing of mitochondrial DNA, regardless of the osseous element tested. For STR testing, demineralization paired with an inorganic purification provided optimum results, regardless of kit used or osseous element tested.     

DNA Identification of Commingled Human Remains from the Cemetery Relocated by Flooding in Central Bosnia and Herzegovina

The floods in Bosnia and Herzegovina in May 2014 caused landslides all over the country. In the small village of ?eri?i, near the town of Zenica, a landslide destroyed the local cemetery, relocated graves, and commingled skeletal remains. As the use of other physical methods of identification (facial recognition, fingerprint analysis, dental analysis, etc.) was not possible, DNA analysis was applied. DNA was isolated from 20 skeletal remains (bone and tooth samples) and six reference samples (blood from living relatives) and amplified using PowerPlex^® Fusion and PowerPlex^®Y23 kits. DNA profiles were generated for all reference samples and 17 skeletal remains. A statistical analysis (calculation of paternity, maternity, and sibling indexes and matching probabilities) resulted in 10 positive identifications. In this study, 5 individuals were identified based on one reference sample. This has once again demonstrated the significance of DNA analysis in resolving the most complicated cases, such as the identification of commingled human skeletal remains.     

Getting Ahead: Extraction of DNA from Skeletonized Cranial Material and Teeth

Between 1990 and 2018, the Defense POW/MIA Accounting Agency submitted 2177 cranial elements and 1565 teeth to the Armed Forces Medical Examiner System—Armed Forces DNA Identification Laboratory for DNA testing. In an effort to identify missing United States service members, materials were recovered from wartime losses inclusive of World War II, the Korean War, and Southeast Asia. Using four different DNA extraction protocols, DNA testing was performed using mitochondrial DNA Sanger sequencing, modified AmpFlSTR^® Yfiler?, AmpFlSTR^® MiniFiler?, PowerPlex^® Fusion, or Next Generation Sequencing. This paper aims to provide optimal strategies for the DNA testing of skeletonized cranial materials. Cranial elements produced the most consistent results in Sanger sequencing using an organic purification; however, teeth were most successful for the same platform with an inorganic purification. The inverse is true for STR testing of cranial bones. Of the cranial elements, the temporal provided the most consistent results.     

Schmorl's nodes in an American military population: frequency, formation, and etiology

This research investigates the frequency of Schmorl's nodes in differing populations, with new data from a skeletal sample from the Central Identification Laboratory (CIL) at the Joint Prisoner of War/Missing in Action Accounting Command, while also reviewing the etiology of Schmorl's node formation. Processes implicated in Schmorl's node formation include trauma, old age, disease, intrinsic abnormalities, and biomechanical factors, and they correlate with Schmorl's node formation to varying degrees. A survey of research from the anthropology and medical literature revealed Schmorl's node population frequencies ranging from 8 to 80%. The current study consists of two samples, one derived from CIL case reports and one analyzing skeletal remains. The case report sample yielded a Schmorl's node frequency of 19.8%. The examined sample yielded a frequency of 73.7%. The disparate frequencies reported are likely due mainly to differences in completeness and observability. It is likely that trauma was a major factor in the formation of Schmorl's nodes in the CIL study.     

The application of miniplex primer sets in the analysis of degraded DNA from human skeletal remains

A new set of multiplexed PCR primers has been applied to the analysis of human skeletal remains to determine their efficacy in analyzing degraded DNA. These primer sets, known as Miniplexes, produce shorter amplicons (50-280 base pairs (bp)) than standard short tandem repeat (STR) kits, but still utilize the 13 CODIS STR loci, providing results that are searchable on national DNA databases. In this study, a set of 31 different human remains were exposed to a variety of environmental conditions, extracted, and amplified with commercial and Miniplex DNA typing kits. The amplification efficiency of the Miniplex sets was then compared with the Promega PowerPlex 16 system. Sixty-four percent of the samples generated full profiles when amplified with the Miniplexes, while only 16% of the samples generated full profiles with the Powerplex 16 kit. Complete profiles were obtained for 11 of the 12 Miniplex loci with amplicon sizes less than 200 bp. These data suggest smaller PCR amplicons may provide a useful alternative to mitochondrial DNA for anthropological and forensic analysis of degraded DNA from human skeletal remains.     

DNA typing from skeletal remains using GlobalFiler™ PCR amplification and Investigator® 24plex QS kits

Since the beginning of our work in 2003 our laboratory has focused exclusively on STR DNA from bone, a powerful tool in missing person cases. In cases such as mass disasters or missing persons, human remains are challenging to identify as they may be fragmented, burnt, recovered from water, degraded, and/or contain inhibitory substances. To address these challenges, this study has evaluated the performance of relatively new STR kits Investigator® 24plex QS kit (Qiagen) and GlobalFiler™ PCR Amplification kit (Thermo Fisher Scientific) by comparing it with current uses of the AmpFLSTR® Identifiler® Plus kit (Applied Biosystems) to obtain genetic information from skeletal remains. We analyzed 20 bone samples of skeletal remains from routine casework submitted for body identifications by law enforcement corresponding using Investigator® 24plex QS kit and GlobalFiler™ PCR Amplification kit, previously analysed AmpFLSTR® Identifiler® Plus kit (Thermo Fisher Scientific). The data indicates that the STR profiles obtained using the GlobalFiler™ and Investigator® 24plex QS kit for analysis of skeletal remains has shown results in an increased number of reportable genetic loci, and provide greater power of discrimination in comparison to the Identifiler® Plus Kit. Advanced extraction and purification techniques, together with more sensitive and robust new amplification kits allowed us to overcome the challenges associated with processing compromised skeletal remains and ultimately obtain full STR DNA profiles in 99% of the bones.     

法医DNA实验室的DNA污染和防范

DNA污染是产生DNA鉴定结论错误的重要因素,法医DNA实验室要努力去解决这一问题。DNA污染有自身污染、交叉污染、PCR污染3种。法医DNA实验室要采取实验室分区、严格检验操作步骤、对试剂及消耗材料进行质量控制等方法防止发生DNA污染,采取设置对照样本、核查DNA结果、建立DNA排查数据库等方法监测和发现DNA污染。     

清代遗骸Y-STR检验1例

法医学实践中经常遇到对骨骼DNA检验的案例,但对保存超过100年的骨骼样本的检验报道较少。本文成功提取到150年前土埋遗骸的骨骼DNA,采用Y—filer试剂盒在9700型扩增仪上进行扩增,3130XL型遗传分析仪进行检测,得到遗骸Y—STR分型,并与对照样本比对,确认了遗骸身份。     

Forensic mitochondrial DNA analysis of 116 casework skeletal samples

Between February 1999 and May 2005, 116 DNA extractions were completed on skeletal remains from routine casework. Overall, at least a partial mitochondrial DNA (mtDNA) profile was obtained on 83.6% of samples. Skeletal remains fell into two general categories: (1) samples for body identifications submitted by law enforcement and (2) samples submitted to answer historical or family identity questions. Body identification cases were more likely to yield full mtDNA profiles, whereas historical cases were more likely to result in partial profiles. Overall, the ability to obtain a full or partial profile primarily reflects the difference in the average age and condition of the samples in these two categories and thus, difference in the quantity and quality of the DNA. Cremated remains were uniformly unsuccessful, whereas infant/fetal remains were uniformly successful. Heteroplasmy in skeletal remains was observed at a rate similar to that in hair ( approximately 10%). For body identification cases, skeletal remains had the same mtDNA profile as the accompanying reference sample in 50% of cases.     

A Method for Estimating Sex Using Metric Analysis of the Scapula*

Abstract: The most accurate and precise methods for the assessment of age and stature often require knowledge of sex. Thus, being able to correctly identify sex from skeletal remains is critical in the forensic context. The presence of the os coxae or skull can never be guaranteed, making the development of reliable methods of sex estimation using other skeletal elements necessary. Using a 724 individual calibration sample from the Hamann‐Todd collection, this study identifies sexual dimorphism in the human scapula, and presents a new five‐variable discriminant function for sex estimation. The overall accuracy of this method proved to be 95.7% on the cross‐validated calibration sample, 92.5% on an 80 individual test sample from the Hamann‐Todd collection, and 84.4% on a 32 individual test sample from the skeletal collection of the Wichita State University Biological Anthropology Laboratory. Additionally, a slightly less accurate two‐variable model was developed and has cross‐validated accuracy of 91.3%.     

DNA Typing for the Identification of Old Skeletal Remains from Korean War Victims*

Abstract: The identification of missing casualties of the Korean War (1950–1953) has been performed using mitochondrial DNA (mtDNA) profiles, but recent advances in DNA extraction techniques and approaches using smaller amplicons have significantly increased the possibility of obtaining DNA profiles from highly degraded skeletal remains. Therefore, 21 skeletal remains of Korean War victims and 24 samples from biological relatives of the supposed victims were selected based on circumstantial evidence and/or mtDNA‐matching results and were analyzed to confirm the alleged relationship. Cumulative likelihood ratios were obtained from autosomal short tandem repeat, Y‐chromosomal STR, and mtDNA‐genotyping results, and mainly confirmed the alleged relationship with values over 10⁵. The present analysis emphasizes the value of mini‐ and Y‐STR systems as well as an efficient DNA extraction method in DNA testing for the identification of old skeletal remains.     

The Effects of Different Maceration Techniques on Nuclear DNA Amplification Using Human Bone

Abstract: Forensic anthropologists routinely macerate human bone for the purposes of identity and trauma analysis, but the heat and chemical treatments used can destroy genetic evidence. As a follow‐up to a previous study on nuclear DNA recovery that used pig ribs, this study utilizes human skeletal remains treated with various bone maceration techniques for nuclear DNA amplification using the standard Combined DNA Index System (CODIS) markers. DNA was extracted from 18 samples of human lower leg bones subjected to nine chemical and heat maceration techniques. Genotyping was carried out using the AmpF?STR^® COfiler^® and AmpF?STR^® Profiler Plus^® ID kits. Results showed that heat treatments via microwave or Biz/Na₂CO₃ in sub‐boiling water efficiently macerate bone and produce amplifiable nuclear DNA for genetic analysis. Long‐term use of chemicals such as hydrogen peroxide is discouraged as it results in poor bone quality and has deleterious effects on DNA amplification.     

A fast and safe non-bleaching method for forensic skeletal preparation

Over the last three decades, forensic anthropologists increasingly have consulted on fleshed human remains cases in which the examination of skeletal elements is critical in answering questions of identification and the circumstances of death. This was certainly the case at the Human Identification Laboratory in Tucson, Arizona. As the caseload increased, it became clear that a method for defleshing human remains was needed in order to expeditiously expose the osseous surfaces for analysis, yet at the same time, preserving the evidentiary nature of the material. As a result, a fast, safe and economical method for defleshing human remains and producing high quality, degreased skeletal elements was developed. This non-bleaching cooking method utilizes chemicals that are easily obtained and inexpensive standard household ingredients that can be purchased at most grocery stores.     

Knowledge on DNA Success Rates to Optimize the DNA Analysis Process: From Crime Scene to Laboratory

DNA analysis has become an essential intelligence tool in the criminal justice system for the identification of possible offenders. However, it appears that about half of the processed DNA samples contains too little DNA for analysis. This study looks at DNA success rates within 28 different categories of trace exhibits and relates the DNA concentration to the characteristics of the DNA profile. Data from 2260 analyzed crime samples show that cigarettes, bloodstains, and headwear have relatively high success rates. Cartridge cases, crowbars, and tie‐wraps are on the other end of the spectrum. These objective data can assist forensics in their selection process.The DNA success probability shows a positive relation with the DNA concentration. This finding enables the laboratory to set an evidence‐based threshold value in the DNA analysis process. For instance, 958 DNA extracts had a concentration value of 6 pg/μL or less. Only 46 of the 958 low‐level extracts provided meaningful DNA profiling data.     

Antemortem and Postmortem Nonapposite Data—A Multidisciplinary Identification Strategy

Identification of human remains is often achieved by comparing documented reference data with the same type of evidence obtained from the remains. We present a case of a decomposed unidentified body, whose identity was presumed but because of the low validity range of the available data, the identification process could not be completed. Antemortem radiographs of the teeth found in the house of the reputed victim could not be compared to the edentulous cadaver and the kinship between the victim and the only living relative that could provide DNA for comparison was too tenuous. Isolated teeth found at the scene, were neither a source of DNA reference information nor questioned data to be compared to the antemortem radiographs. The strategy implemented by the investigators to reallocate the status of the isolated teeth from the questioned source to the reference source of DNA to be compared with the cadaver is presented.