[From an optimal management of bone tissue samples to a quality patients' care in 2022 : A new paradigm]. / D'une gestion optimale des échantillons osseux à une prise en charge de qualité des malades en 2022 : un nouveau paradigme.

Bone tissue can be involved by primitive or metastatic tumors and requires a specific processing both at the department of pathology and during multidisciplinary meetings. The development of fine-needle percutaneous biopsies and of molecular techniques in bone tumor pathology requires a specific management. Moreover, decalcification of samples is crucial but can be deleterious if not controlled or not appropriate. The aim of this review is to provide recommendations for management and decalcification of bone tumor samples.

Patterns of brachyury expression in chordomas.

INTRODUCTION: Chordomas are rare malignant midline tumors, presumed to arise from notochordal remnants. This was further suggested by the discovery of the brachyury in chordomas pathogenesis. Its immunohistochemical expression has become the principal adjunct in the diagnosis of chordomas. However, studies about brachyury expression in chordomas are not fully comparable, mainly because they use different primary antibodies. Thus, the aim of this study is to investigate the expression of brachyury expression in a series of chordomas in conjunction to clinicopathological characteristics and to review the relevant literature providing all the details needed in the immunohistochemical study of brachyury. MATERIALS AND METHODS: This is a retrospective study of 62 chordomas, diagnosed over a 22-year period. No dedifferentiated or poorly differentiated cases were included. A monoclonal primary antibody (clone A-4) was used and brachyury expression was evaluated by the H-score. Clinicopathological parameters studied were age, sex, tumor localization, decalcification status and tissue age. Fetal notochords were used for comparison. RESULTS: Mean H-score of nuclear brachyury expression was 129.8. The tissue age significantly influenced brachyury expression, the older samples expressing less brachyury. Decalcification demonstrated a trend to weaken brachyury expression. Clinical characteristics were not correlated with the patterns of brachyury expression. Notochords were negative. Literature review reveals several polyclonal antibodies used and a positivity of 75%-100% in chordomas with even more variable results in notochords. CONCLUSION: In chordomas, as in other tumor types, an uniformization of studies about brachyury expression is needed, by considering the clone used, and the decalcification and the age of the sample, given the growing importance of brachyury in diagnosis and therapeutic steps.

Effect of decalcification protocols on immunohistochemistry and molecular analyses of bone samples.

Diagnosis of osteocartilaginous pathologies depends on morphological examination and immunohistochemical and molecular biology analyses. Decalcification is required before tissue processing, but available protocols often lead to altered proteins and nucleic acids, and thus compromise the diagnosis. The objective of this study was to compare the effect of different methods of decalcification on histomolecular analyses required for diagnosis and to recommend an optimal protocol for processing these samples in routine practice. We prospectively submitted 35 tissue samples to different decalcification procedures with hydrochloric acid, formic acid, and EDTA, in short, overnight and long cycles for 1 to >10 cycles. Preservation of protein integrity was examined by immunohistochemistry, and quality of nucleic acids was estimated after extraction (DNA and RNA concentrations, 260/280 ratios, PCR cycle thresholds), analysis of DNA mutations (high-resolution melting) or amplifications (PCR, in situ hybridization), and detection of fusion transcripts (RT-PCR, in situ hybridization). Hydrochloric acid- and long-term formic acid-based decalcification induced false-negative results on immunohistochemistry and molecular analysis. EDTA and short-term formic acid-based decalcification (<5 cycles of 6 h each) did not alter antigenicity and allowed for detection of gene mutations, amplifications or even fusion transcripts. EDTA showed superiority for in situ hybridization techniques. According to these results and our institutional experience, we propose recommendations for decalcification of bone samples, from biopsies to surgical specimens.

Optimization of immunohistochemical detection of collagen type II in osteochondral sections by comparing decalcification and antigen retrieval agent combinations.

Bone containing tissues such as osteochondral joint are resistant to routine tissue processing, therefore require decalcification. This technique causes removal of mineral salts, but in the process may macerate the organic tissue, hence the need for tissue fixation. Such severe processing demands careful antigen retrieval to necessitate optimal staining. The aim of our study was to compare five different antigen retrieval protocols (heat retrieval and protein digestion) following decalcification of rabbit knee joints using two different techniques (20% formic acid and 10% ethylenediamine-tetra acetic acid: EDTA). Osteochondral sections were compared based on time required for decalcification, ease of sectioning, morphological integrity using HE staining and antigen preservation (Collagen type II) using immunohistochemistry. The two decalcification solutions did not impair the tissue morphology and ease of sectioning. Joints processed with formic acid decalcified four times faster than EDTA. Among the five antigen retrieval approaches, maximal collagen II uptake with minimal nonspecific staining was found with protein digestion (pronase and hyaluronidase) in both formic acid and EDTA sections. For osteo-chondral sections, we recommend using 10% EDTA for decalcification and pronase plus hyaluronidase for antigen retrieval if maintaining tissue morphology is crucial, whereas if time is of the essence, 20% FA with pronase plus hyaluronidase is the faster option while still preserving structural integrity. Clin. Anat. 33:343-349, 2020. © 2019 Wiley Periodicals, Inc.

Decalcification can cause the failure of BRAF molecular analyses and anti-BRAFV600E VE1 immunohistochemistry.

BRAF mutation detection is worthwhile for the management of patients with some advanced cancers. The tumor samples are sometimes difficult to analyze using DNA-based molecular methods because of poor tumor DNA quality or quantity. Anti-BRAFV600E VE1 immunohistochemistry (IHC) has been proposed as a valuable ancillary tool to analyze some "molecularly challenging" tumor samples. In this technical study, we focused on its application in the field of decalcified tumor samples. We selected four patients with known BRAFV600E-mutated cancer (3 metastatic melanomas and 1 hairy cell leukemia) and paired non-decalcified/decalcified tumor samples. Molecular analyses failed in the four decalcified samples (3 bone metastases and 1 osteo-medullar biopsy) with non-contributive mutation status. Whereas non-decalcified tumor samples were all positive using anti-BRAFV600E VE1 IHC, the four decalcified samples were concluded negative. Because decalcified tumor samples are difficult to analyze from a molecular point of view, it is tempting to use IHC instead of DNA-based methods searching for BRAFV600E mutations in these samples. Nevertheless, the decalcification process may also cause false-negative results using VE1 IHC. Decalcified samples require specific and optimized IHC and molecular protocols and quality controls.

Periodontal ligament-like tissue regeneration with drilled porous decalcified dentin matrix sheet composite.

OBJECTIVE: In this study, we constructed a composite by combining the human dental follicle cell sheet and a manual drilled porous decalcified dentin matrix that was used to construct ectopic tissue-engineered periodontal ligament-like tissues in renal capsules of nude mice. MATERIALS AND METHODS: Human dental follicle cells were harvested from human lower third molars and then embedded into a temperature-sensitive culture dish. These cells were then placed into frozen porous decalcified dentin matrix sheets and induced by 50 g/ml ascorbic acid. This established a "sandwich structure" in vitro implant that was placed in nude mice under the renal capsule. The mice were sacrificed at 4 and 8 weeks after implantation, and the implants were assessed after haematoxylin-eosin staining, Masson staining and immunohistochemical staining. RESULTS: The experimental group showed a fibre structure between the dentin and HA-TCP after 4 weeks. After 8 weeks, the collagen fibres increased, and the direction was perpendicular to the dentin. Immunohistochemistry showed positive staining in the osteopontin and periostin. CONCLUSION: The composite can induce ectopic bone and fibre formation, and the fibre had a certain directionality. Besides, the composite can maintain the stability of the periodontal ligament width.

Influence of decalcification procedures on immunohistochemistry and molecular pathology in breast cancer.

Distant breast cancer metastases are nowadays routinely biopsied to reassess receptor status and to isolate DNA for sequencing of druggable targets. Bone metastases are the most frequent subgroup. Decalcification procedures may negatively affect antigenicity and DNA quality. We therefore evaluated the effect of several decalcification procedures on receptor status and DNA/RNA quality. In 23 prospectively collected breast tumors, we compared ERα, PR and HER2 status by immunohistochemistry in (non-decalcified) tissue routinely processed for diagnostic purposes and in parallel tissue decalcified in Christensen's buffer with and without microwave, EDTA and Formical-4. Furthermore, HER2 fluorescence in situ hybridization and DNA/RNA quantity and quality were assessed. We found that the percentage of ERα-positive cells were on average lower in EDTA (P=0.049) and Formical-4 (P=0.047) treated cases, compared with controls, and PR expression showed decreased antigenicity after Christensen's buffer treatment (P=0.041). Overall, a good concordance (weighted kappa) was seen for ERα, PR and HER2 immunohistochemistry when comparing the non-decalcified control tissues with the decalcified tissues. For two patients (9%), there was a potential influence on therapeutic decision making with regard to hormonal therapy or HER2-targeted therapy. HER2 fluorescence in situ hybridization interpretation was seriously hampered by Christensen's buffer and Formical-4, and DNA/RNA quantity and quality were decreased after all four decalcification procedures. Validation on paired primary breast tumor specimens and EDTA-treated bone metastases showed that immunohistochemistry and fluorescence in situ hybridization were well assessable and DNA and RNA yield and quality were sufficient. With this, we conclude that common decalcification procedures have only a modest negative influence on hormone and HER2 receptor immunohistochemistry in breast cancer. However, they may seriously affect DNA/RNA-based diagnostic procedures. Overall, EDTA-based decalcification is therefore to be preferred as it best allows fluorescence in situ hybridization and DNA/RNA isolation.

Cementoblastoma Solely Involving Maxillary Primary Teeth--A Rare Presentation.

Cementoblastoma is a rare benign neoplasm of odontogenic ectomesenchyme origin, involving the roots of any tooth, which occurs predominantly in second and third decade of life. Very few cases of cementoblastoma associated with a primary tooth or having a maxillary presentation have been reported in the past. Here, a rare case of a ten year old boy who presented to the department with a swelling in maxillary posterior region since one month is being discussed. The radiographic presentation was mimicking an odontoma. The final diagnosis was cementoblastoma. We have advocated the use of polarized microscopy to support the histopathological diagnosis with respect to its cemental origin. Cementoblastoma should be considered in the differential diagnosis of radio-opaque lesions in the transitional dentition.

Towards the lean lab: the industry challenge.

In anatomic pathology, the current state encompassing the pre-analytic processes of tissue collection, handling, examination, preparation, processing, and storage are largely uncontrolled, inconsistently performed, and/or not standardized according to the sound scientific data. Pre-analytic defects result in nearly three-quarters of the problems in laboratory diagnostics. This is evident in quality surveys from well-respected institutions that document high miss rates in the required basics of information related to patient and tissue identity, let alone parameters documenting quality aspects related to the surgical specimen and its preservation. This talk will describe the historical approach to tissue processing and identify gaps from worldwide observations in current laboratory practices. It will also offer potential methodological and technological solutions and process improvements that laboratories may consider in serving the ultimate users of pathology information: the clinician and the patient. It illustrates the need for scientifically validated specimen guidelines and a performance based, standardized and documented "chain of custody" of the pre-analytical steps from the patient's body through fixation. For thought leaders and professional standard setters, opportunities for optimizing molecular studies exist in specimen collection, transfer, grossing, fixation, and decalcification protocols. In this evolving era of molecular profiling and personalized therapeutic decision-making, a well-reasoned and coordinated focus on pre-analytic processes that optimizes specimens for subsequent testing will result in: Improved specimen quality for molecular testing Improved accuracy of diagnostic and molecular test results Reduced Turnaroundtimes for same-day diagnosis Enhanced satisfaction of clinicians and patients.

Rapid mandible margins for intraoperative assessment.

OBJECTIVES: To determine the feasibility of a rapid method of processing mandible bone margins for intraoperative histopathologic examination and to assess the relative value of fine, coarse, and core specimens in assessing bone margins. STUDY DESIGN: Prospective histologic controlled study. SETTING: A tertiary level academic medical center histopathology laboratory. SUBJECTS AND METHODS: Multiple bone samples were collected from fresh (<12 hours post-mortem) human cadaveric mandible using a 1) standard 4mm otolaryngologic cutting drill bit 2) diamond drill bit and 3) cutting core biopsy trocar. The specimens were placed in one of three decalcifying solutions (Decal A, Calex, EDTA Decal) from 15 to 75 minutes or control (fixation in 10% formalin). After each designated decalcification time period, specimens were cryosectioned or paraffin embedded and subsequently reviewed by a head and neck surgical pathologist. The specimens were assessed for overall quality, adequacy of decalcification, soft tissue quality, marrow quality, and presence of artifact. RESULTS: Bone margin specimens collected with a 4mm burr and processed with EDTA Decal for 30 minutes yielded the highest quality histopathologic slides compared to the other methods in a similar time frame. The adequacy of decalcification directly impacted the quality of histopathologic assessment. CONCLUSIONS: Mandible bone margins can be rapidly and safely prepared and adequately evaluated with only 30 minutes of decalcification. This method may provide acceptable intraoperative assessment of bone margins in patients with tumors which involve or approximate bone. We plan to examine this model in a prospective clinical study of patients with cancer invading mandibular bone.

Diaphonization: a recipe to study teeth.

AIM: There are various techniques to study root canal morphology and diaphonization is one of them. There are various methods of decalcification and diaphonization, cited in literature and the main aim of this paper was to give a brief account of the various techniques and share our experience of the technique at a teaching institution in Karachi, Pakistan. MATERIALS AND METHODS: Diaphonization is one of the oldest methods and is based on decalcification of teeth followed by clearing and dye penetration. The specimen is later studied under microscope without sectioning. RESULTS: After the process of clearing a three-dimensional (3D) structure of the internal canal anatomy was visible with naked eye. CONCLUSION: This paper entails a detailed historical background as well as the author's technique including percentages of various chemicals used and the timing of immersion of teeth into these agents. CLINICAL SIGNIFICANCE: The read out is simple and can be subjected to interpretation by direct observation under microscope and can be helpful for students undertaking research in not only the discipline of dentistry but also in other fields such as botany and zoology.

Long-term follow-up after reimplantation of tumorous mandible bone treated with combination of decalcification and lyophilization.

Mandibular resection requires reconstruction, with often unsatisfactory morphofunctional results. Reimplantation of the resected mandible itself is one of ideal solutions to this problem. However, both devitalization of tumor cells involved in resected bone and preservation of osteoinductive activity are required for successful results. Lyophilization appears to enable devitalization of tumor cells, and decalcified bone implants are likely to have osteoinductive potential. Accordingly, we speculated that decalcification and lyophilization of resected bone would be an appropriate method for mandibular reconstruction. However, there is no study on the reimplantation of mandibles treated with these methods to date. The purpose of this study was to estimate the long-term follow-up of reimplanted mandibles treated with decalcification and lyophilization. Presented here are 2 patients of reimplanted mandibles treated by decalcification and lyophilization who were followed up for 8 and 9 years. We observed a good incorporation of the graft in 1 case, but severe absorption in the other. Our results suggest that treatment with decalcification and lyophilization is 1 strategy for reimplantation of the resected bone in mandibular reconstruction, but further study is needed to prevent absorption of the reimplanted bone over the long term.

Effect of "apical clearing" and "apical foramen widening" on apical ramifications and bacterial load in root canals.

The purpose of the study was to determine the effect of apical clearing and apical foramen widening in reducing apical ramifications and bacterial load in the apical third of root canals. The mesio-buccal roots of 21 maxillary first molar teeth were inoculated with Enterococcus faecalis suspension using a sterile pipette. Samples were incubated at 37°C for 72 hrs and divided into 3 groups: Group A, control group (n=5), no preparation; Group B (n=8) conventional preparation alone; and Group C (n=8), apical clearing and foramen widening in addition to conventional preparation. Bacterial counts were semi-quantitatively analyzed pre- and post-preparation. Samples were demineralized with 5% nitric acid after injection of India ink. Cross sections were obtained at every 0.5 mm from the apex to 3 mm of the root using a vibratome and viewed under a stereomicroscope at 64×magnification to locate any debris or apical ramifications. The Kruskal-Wallis and Mann-Whitney U tests were used for the statistical analysis. A statistically significant difference was observed (p value 0.006) in the number of ramifications among the 3 groups. Group C had a lower average number of ramifications (1) than Group B (2.5) or A (4). The debris score was analyzed at each level (0.5-3 mm). A statistically significant difference was observed at 0.5 mm and 1 mm between Group A and C (p=0.0041) and Group B and C (p=0.0050), whereas no difference was found between Group A and B (p>0.05). These results indicate that there was less debris and fewer apical ramifications in Group C. The microbiological study revealed a lower number of colony forming units (10(2) -10(3)) in Group B or C than in Group A (>10(5)). These results suggest that apical widening and clearing facilitates removal of apical ramifications and bacterial load within root canals.

[Introduction of a decalcification method for bone marrow biopsy tissue].

Bone marrow biopsy is one of the important means of hematopathological diagnosis, which has decisive diagnostic significance for various benign and malignant lymphohematopoietic system diseases. Its diagnostic value includes morphological observation, immunohistochemistry, genetics, and molecular biology testing. Owing to the unique nature of bone marrow biopsy, decalcification is an essential step in the pre-treatment process. Its purpose is to remove calcium from bone tissue, preserve intact collagen fiber components, facilitate tissue sectioning, and prevent tissue detachment during staining. If bone marrow biopsy lacks sufficient decalcification, preparing a section is difficult. Conversely, if decalcification is excessive, it can seriously disrupt tissue antigen activity. Therefore, a decalcification method with high decalcification efficiency and mild antigen damage is essential for bone marrow biopsy. This article introduces a bone marrow biopsy tissue decalcification method with high efficiency and less antigen loss: decalcification is performed at room temperature with 12% formic acid and 8% hydrochloric acid decalcification solution on a shaker.

Hypertonic saline- and detergent-accelerated EDTA-based decalcification better preserves mRNA of bones.

Ethylenediaminetetraacetic acid (EDTA), a classically used chelating agent of decalcification, maintains good morphological details, but its slow decalcification limits its wider applications. Many procedures have been reported to accelerate EDTA-based decalcification, involving temperature, concentration, sonication, agitation, vacuum, microwave, or combination. However, these procedures, concentrating on purely tissue-outside physical factors to increase the chemical diffusion, do not enable EDTA to exert its full capacity due to tissue intrinsic chemical resistances around the diffusion passage. The resistances, such as tissue inner lipids and electric charges, impede the penetration of EDTA. We hypothesized that delipidation and shielding electric charges would accelerate EDTA-based penetration and the subsequent decalcification. The hypothesis was verified by the observation of speedy penetration of EDTA with additives of detergents and hypertonic saline, testing on tissue-mimicking gels of collagen and adult mouse bones. Using a 26% EDTA mixture with the additives at 45°C, a conventional 7-day decalcification of adult mouse ankle joints could be completed within 24 h while the tissue morphological structure, antigenicity, enzymes, and DNA were well preserved, and mRNA better retained compared to using 15% EDTA at room temperature. The addition of hypertonic saline and detergents to EDTA decalcification is a simple, rapid, and inexpensive method that doesn't disrupt the current histological workflow. This method is equally or even more effective than the currently most used decalcification methods in preserving the morphological details of tissues. It can be highly beneficial for the related community.

Reconstruction of orbital defects by implantation of antigen-free bovine cancellous bone scaffold combined with bone marrow mesenchymal stem cells in rats.

BACKGROUND: Tissue-engineering approach can result in significant bone regeneration. We aimed to reconstruct the segmental orbital rim defects with antigen-free bovine cancellous bone (BCB) scaffolds combined with bone marrow mesenchymal stem cells (BMSCs) in rats. METHODS: BCB was prepared by degreasing, deproteinization and partly decalcification. BMSCs isolated from green fluorescent protein (GFP) transgenic rats were osteogenically induced and seeded onto BCB scaffolds to construct induced BMSCs/BCB composites. An 8-mm full-thickness defect on the rat inferior-orbit rim was established. Induced BMSCs/BCB composites cultured for 5 days were implanted into the orbital defects as the experimental group. Noninduced BMSCs/BCB group, BCB group and exclusive group were set. General condition, spiral CT, 3D orbital reconstruction, histological and histomorphometric analysis were performed after implantation. RESULTS: BCB presented reticular porous structure. GFP-BMSCs adhering to BCB appeared bright green fluorescence and grew vigorously. Infection and graft dislocation were not observed. In induced BMSCs/BCB group, CT and 3D reconstruction showed perfect orbital repair situation. Histological analysis indicated BCB was mostly biodegraded; newly formed bone and complete synostosis were observed. The percentage of newly formed bone was (57.12 ± 6.28) %. In contrast, more residual BCB, less newly formed bone and nonunion were observed in the noninduced BMSCs/BCB group. Slowly absorbed BCB enwrapped by fibrous connective tissue and a small amount of new bone occurred in BCB group. Fibrous connective tissue appeared in exclusive group. CONCLUSIONS: Antigen-free bovine cancellous bone that retains natural bone porous structure and moderate mechanical strength with elimination of antigen is the ideal carrier for mesenchymal stem cells in vitro. BCB combined with BMSCs is a promising composite for tissue engineering, and can effectively reconstruct the orbit rim defects in rats.

Analysis of the effect of various decalcification agents on the quantity and quality of nucleic acid (DNA and RNA) recovered from bone biopsies.

Molecular studies are part of standard care for cancer patients. Bone, a common and sometimes sole site of metastasis, requires decalcification for morphological examination. Many commonly used decalcification agents contain strong acids that degrade nucleic acids. The paradigm shift in oncology, with biomarker targeted therapy and gene expression profiling analysis, requires sufficient nucleic acid recovery from bone biopsy specimens. We systematically studied the effects of a spectrum of decalcification agents on the quantity and quality of RNA and DNA recovered from bone biopsies. Multiple bone biopsies of similar size and cellularity were fixed in 10% neutral-buffered formalin, randomized to various decalcification agents for 2 hours then processed, and embedded. Tissue lysates were obtained from unstained sections and nucleic acid isolated. DNA and RNA were quantified. Assessment of DNA and RNA integrity was accomplished by comparison of the average cycle threshold by polymerase chain reaction of selected housekeeping genes for each agent. Results were then analyzed by 2-sample t test. There was a significant decrease in both DNA and RNA yield and integrity with strong acids (hydrochloric, nitric) vs 14% EDTA and formic acid. DNA yield was (mean nanograms) 6.15 vs 68.68 (P<.001) and RNA was (mean nanograms) 121.53 vs 288.89 (P=.003), respectively. DNA integrity (mean cycle threshold) was 35.79 vs 30.16 (P<.001), and RNA was 33.03 vs 26.5 (P<.001), respectively. Decalcification of bone biopsies with EDTA or formic acid agents was associated with a significant improvement in recovered nucleic acid quantity and quality.

Qualitative and quantitative evaluation of avian demineralized bone matrix in heterotopic beds.

OBJECTIVE: To evaluate the osteogenic potential of avian demineralized bone matrix (DBM) in the context of implant geometry. STUDY DESIGN: Experimental. ANIMALS: Rock pigeons (n = 24). METHODS: Tubular and chipped forms of DBM were prepared by acid demineralization of long bones from healthy allogeneic donors and implanted bilaterally into the pectoral region of 24 pigeons. After euthanasia at 1, 4, 6, 8, 10, and 12 weeks, explants were evaluated histologically and compared by means of quantitative (bone area) and semi quantitative measures (scores). RESULTS: All explants had new bone at retrieval with the exception of tubular implants at the end of week 1. The most reactive part in both implants was the interior region between the periosteal and endosteal surfaces followed by the area at the implant-muscle interface. Quantitative measurements demonstrated a significantly (P = .012) greater percentage of new bone formation induced by tubular implants (80.28 ± 8.94) compared with chip implants (57.64 ± 3.12). There was minimal inflammation. CONCLUSIONS: Avian DBM initiates heterotopic bone formation in allogeneic recipients with low grades of immunogenicity. Implant geometry affects this phenomenon as osteoconduction appeared to augment the magnitude of the effects in larger tubular implants.

[Decalcification in formic acid after fixation in zinc-ethanol-formaldehyde does not preclude identification of neuronal and glial markers].

The aim of this study was to determine the possibility of immunohistochemical demonstration of various tissue antigens in paraffin sections of zinc-ethanol-formaldehyde-fixed spinal cord, surrounded by the vertebral tissues and adjacent muscles, after decalcification in formic acid, in adult (n = 5) and newborn (n = 2) Wistar rats. In the present work, the antibodies used were against: glial fibrillary acidic protein, neurofilaments, neuronal specific nuclear protein, enzyme tyrosine hydroxylase, protein of synaptic vesicles--synaptophysin and the intermediate filament protein--vimentin. Combination of fixation in zinc-ethanol-formaldehyde and decalcification in 21% formic acid solution was shown to provide an optimal preservation of the antigens studied.

Comparison of three methods of DNA extraction from human bones with different degrees of degradation.

There is a necessity for deceased identification as a result of many accidents and sometimes bones are the only accessible source of DNA. So far, a universal method that allows for extraction of DNA from materials at different stages of degradation does not exist. The aims of this study were: the comparison of three methods of DNA extraction from bones with different degree of degradation and an evaluation of the usefulness of these methods in forensic genetics. The efficiency of DNA extraction, the degree of extract contamination by polymerase chain reaction (PCR) inhibitors and the possibility of determining the STR loci profile were especially being compared. Nuclear DNA from bones at different states of degradation was isolated using three methods: classical, organic phenol-chloroform extraction, DNA extraction from crystal aggregates and extraction by total demineralisation. Total demineralisation is the best method for most cases of DNA extraction from bones, although it does not provide pure DNA. DNA extraction from aggregates removes inhibitors much better and is also a good method of choice when identity determination of exhumed remains is necessary. In the case of not buried bones (remains found outside) total demineralisation or phenol-chloroform protocols are more efficient for successful DNA extraction.