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Stanasiuk C, Milting H, Homm S, Persson J, Holtz L, Wittmer A, Fox H, Laser T, Knöll R, Pohl GM, Paluszkiewicz L, Jakob T, Bachmann-Mennenga B, Henzler D, Grautoff S, Veit G, Klingel K, Hori E, Kellner U, Karger B, Schlepper S, Pfeiffer H, Gummert J, Gärtner A, Tiesmeier J. Blood taken immediately after fatal resuscitation attempts yields higher quality DNA for genetic studies as compared to autopsy samples. Int J Legal Med 2023; 137:1569-1581. [PMID: 36773088 PMCID: PMC10421769 DOI: 10.1007/s00414-023-02966-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 02/03/2023] [Indexed: 02/12/2023]
Abstract
BACKGROUND The out-of-hospital cardiac arrest (OHCA) in the young may be associated with a genetic predisposition which is relevant even for genetic counseling of relatives. The identification of genetic variants depends on the availability of intact genomic DNA. DNA from autopsy may be not available due to low autopsy frequencies or not suitable for high-throughput DNA sequencing (NGS). The emergency medical service (EMS) plays an important role to save biomaterial for subsequent molecular autopsy. It is not known whether the DNA integrity of samples collected by the EMS is better suited for NGS than autopsy specimens. MATERIAL AND METHODS DNA integrity was analyzed by standardized protocols. Fourteen blood samples collected by the EMS and biomaterials from autopsy were compared. We collected 172 autopsy samples from different tissues and blood with postmortem intervals of 14-168 h. For comparison, DNA integrity derived from blood stored under experimental conditions was checked against autopsy blood after different time intervals. RESULTS DNA integrity and extraction yield were higher in EMS blood compared to any autopsy tissue. DNA stability in autopsy specimens was highly variable and had unpredictable quality. In contrast, collecting blood samples by the EMS is feasible and delivered comparably the highest DNA integrity. CONCLUSIONS Isolation yield and DNA integrity from blood samples collected by the EMS is superior in comparison to autopsy specimens. DNA from blood samples collected by the EMS on scene is stable at room temperature or even for days at 4 °C. We conclude that the EMS personnel should always save a blood sample of young fatal OHCA cases died on scene to enable subsequent genetic analysis.
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Affiliation(s)
- Caroline Stanasiuk
- Erich and Hanna Klessmann-Institute for Cardiovascular Research and Development, Heart- and Diabetes Center NRW, University Hospital of the Ruhr-University Bochum, Georgstr. 11, D-32545, Bad Oeynhausen, Germany
| | - Hendrik Milting
- Erich and Hanna Klessmann-Institute for Cardiovascular Research and Development, Heart- and Diabetes Center NRW, University Hospital of the Ruhr-University Bochum, Georgstr. 11, D-32545, Bad Oeynhausen, Germany.
| | - Sören Homm
- Institute for Anesthesiology, Intensive Care- and Emergency Medicine, Johannes Wesling Hospital Minden, MKK-Hospital, Campus OWL, Ruhr-University Bochum, Bochum, Germany
| | - Jan Persson
- Institute for Anesthesiology, Intensive Care- and Emergency Medicine, Johannes Wesling Hospital Minden, MKK-Hospital, Campus OWL, Ruhr-University Bochum, Bochum, Germany
| | - Lars Holtz
- Emergency Department, Herford Hospital, Campus OWL, Ruhr-University Bochum, Bochum, Germany
| | - Axel Wittmer
- Institute for Pathology, Herford Hospital, Campus OWL, Ruhr-University Bochum, Bochum, Germany
| | - Henrik Fox
- Clinic for Thoracic and Cardiovascular Surgery, Heart- and Diabetes Center NRW, D-32545 Bad Oeynhausen, University Hospital of the Ruhr-University Bochum, Bochum, Germany
| | - Thorsten Laser
- Center for Congenital Heart Diseases, Heart and Diabetes Center NRW, 32545 Bad Oeynhausen, University Hospital of the Ruhr-University Bochum, Bochum, Germany
| | - Ralph Knöll
- Karolinska Institute, University Hospital, Myocardial Genetic, 14157, Huddinge, Sweden
| | - Greta Marie Pohl
- Erich and Hanna Klessmann-Institute for Cardiovascular Research and Development, Heart- and Diabetes Center NRW, University Hospital of the Ruhr-University Bochum, Georgstr. 11, D-32545, Bad Oeynhausen, Germany
| | - Lech Paluszkiewicz
- Clinic for Thoracic and Cardiovascular Surgery, Heart- and Diabetes Center NRW, D-32545 Bad Oeynhausen, University Hospital of the Ruhr-University Bochum, Bochum, Germany
| | - Thomas Jakob
- Intensive Care and Emergency Medicine, Herford Hospital, Campus OWL, Ruhr-University Bochum, University Clinic for Anesthesiology, Bochum, Germany
- Present address: Clinic for Anesthesiology, Intensive Care Medicine, Emergency Medicine and Pain Medicine, Bielefeld Hospital, University Hospital Eastern Westphalia-Lippe, Bielefeld University, Bielefeld, Germany
| | - Bernd Bachmann-Mennenga
- Institute for Anesthesiology, Intensive Care- and Emergency Medicine, Johannes Wesling Hospital Minden, MKK-Hospital, Campus OWL, Ruhr-University Bochum, Bochum, Germany
| | - Dietrich Henzler
- Intensive Care and Emergency Medicine, Herford Hospital, Campus OWL, Ruhr-University Bochum, University Clinic for Anesthesiology, Bochum, Germany
| | - Steffen Grautoff
- Emergency Department, Herford Hospital, Campus OWL, Ruhr-University Bochum, Bochum, Germany
| | - Gunter Veit
- Institute for Anesthesiology, Intensive Care- and Emergency Medicine, Johannes Wesling Hospital Minden, MKK-Hospital, Campus OWL, Ruhr-University Bochum, Bochum, Germany
| | - Karin Klingel
- Institute for Pathology and Neuropathology, University Hospital Tuebingen, D-72076, Tuebingen, Germany
| | - Erika Hori
- Institute for Pathology, Johannes Wesling Hospital Minden, MKK-Hospital, D-32429 Minden, Campus OWL, Ruhr-University Bochum, Bochum, Germany
| | - Udo Kellner
- Institute for Pathology, Johannes Wesling Hospital Minden, MKK-Hospital, D-32429 Minden, Campus OWL, Ruhr-University Bochum, Bochum, Germany
| | - Bernd Karger
- Institute for Forensic Medicine, University Hospital, Wilhelms-University Muenster, Muenster, Germany
| | - Stefanie Schlepper
- Institute for Forensic Medicine, University Hospital, Wilhelms-University Muenster, Muenster, Germany
| | - Heidi Pfeiffer
- Institute for Forensic Medicine, University Hospital, Wilhelms-University Muenster, Muenster, Germany
| | - Jan Gummert
- Clinic for Thoracic and Cardiovascular Surgery, Heart- and Diabetes Center NRW, D-32545 Bad Oeynhausen, University Hospital of the Ruhr-University Bochum, Bochum, Germany
| | - Anna Gärtner
- Erich and Hanna Klessmann-Institute for Cardiovascular Research and Development, Heart- and Diabetes Center NRW, University Hospital of the Ruhr-University Bochum, Georgstr. 11, D-32545, Bad Oeynhausen, Germany
| | - Jens Tiesmeier
- Erich and Hanna Klessmann-Institute for Cardiovascular Research and Development, Heart- and Diabetes Center NRW, University Hospital of the Ruhr-University Bochum, Georgstr. 11, D-32545, Bad Oeynhausen, Germany
- Institute for Anesthesiology, Intensive Care- and Emergency Medicine, Luebbecke MKK-Hospital, Campus OWL, Ruhr-University Bochum, Bochum, Germany
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Wu X, Deng J, Zhang N, Liu X, Zheng X, Yan T, Ye W, Gong Y. Pedigree investigation, clinical characteristics, and prognosis analysis of haematological disease patients with germline TET2 mutation. BMC Cancer 2022; 22:262. [PMID: 35279121 PMCID: PMC8917718 DOI: 10.1186/s12885-022-09347-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 02/28/2022] [Indexed: 12/18/2022] Open
Abstract
Background Increasing germline gene mutations have been discovered in haematological malignancies with the development of next-generation sequencing (NGS), which is critical for proper clinical management and long-term follow-up of affected individuals. Tet methylcytosine dioxygenase 2 (TET2) is one of the most common mutations in haematological neoplasms. We aimed to compare the clinical characteristics of patients with germline and somatic TET2 mutations in haematological diseases and to analyse whether germline TET2 mutations have a family aggregation and tumour predisposition. Methods Out of 612 patients who underwent NGS of 34 recurrently mutated genes in haematological diseases, 100 haematological patients with TET2 mutations were selected for further study. Somatic mutations were detected by NGS in bone marrow/peripheral blood genomic DNA (gDNA). Germline TET2 mutations were validated in nail/hair gDNA by Sanger sequencing. Digital data were extracted from the haematology department of the West China Hospital of Sichuan University. TET2 mutation results were analysed by referencing online public databases (COSMIC and ClinVar). Results One hundred patients were studied, including 33 patients with germline and 67 patients with somatic TET2 mutations. For germline TET2 mutations, the variant allele frequency (VAF) was more stable (50.58% [40.5–55], P < 0.0001), and mutation sites recurrently occurred in three sites, unlike somatic TET2 mutations. Patients with germline TET2 mutations were younger (median age 48, 16–82 years) (P = 0.0058) and mainly suffered from myelodysplastic syndromes (MDS) (n = 13, 39.4%), while patients with somatic TET2 mutations were mainly affected by acute myeloid leukemia (AML) (n = 26, 38.8%) (P = 0.0004). Germline TET2 mutation affected the distribution of cell counts in the peripheral blood and bone marrow (P < 0.05); it was a poor prognostic factor for MDS patients via univariate analysis (HR = 5.3, 95% CI: 0.89–32.2, P = 0.0209) but not in multivariate analysis using the Cox regression model (P = 0.062). Conclusions Germline TET2 mutation might have a family aggregation, and TET2 may be a predisposition gene for haematological malignancy under the other gene mutations as the second hit. Germline TET2 mutation may play a role in the proportion of blood and bone marrow cells and, most importantly, may be an adverse factor for MDS patients. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-022-09347-0.
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Inkret J, Podovšovnik E, Zupanc T, Pajnič IZ. Nails as a primary sample type for molecular genetic identification of highly decomposed human remains. Int J Legal Med 2020; 134:1629-1638. [PMID: 32372234 DOI: 10.1007/s00414-020-02289-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 03/30/2020] [Indexed: 11/30/2022]
Abstract
For identification of badly preserved cadavers, only a few tissues can be used as a source of DNA, mostly bones and teeth, from which sampling and DNA extraction are difficult and time-consuming. In most highly decomposed remains, the nails are preserved. The aim of this study was to evaluate nails as an alternative source of DNA instead of bones and teeth in demanding routine identification cases. An automated extraction method was optimized on nails obtained from 33 cadavers with a post-mortem interval (PMI) up to 5 years. The commercially available EZ1 Investigator Kit (Qiagen) was used for extraction, and the G2 buffer included in the kit was replaced with TNCa buffer, and DTT was added for digestion of 5 mg of nail. The DNA was purified in a Biorobot EZ1 device (Qiagen), quantified using the PowerQuant System (Promega), and STR typing was performed with the NGM kit (TFS). From 0.3 to 270 μg DNA/g of nail was obtained from the samples analyzed, with an average yield of 36 μg DNA/g of nail. Full STR profiles were obtained from all nails except one. The optimized extraction method proved to be fast and highly efficient in the removal of PCR inhibitors, and it yields high amounts of DNA for successful STR typing. Nails were implemented as the primary sample type for obtaining DNA from highly decomposed and partially skeletonized cadavers in routine forensic identification cases in our laboratory.
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Affiliation(s)
- Jezerka Inkret
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000, Ljubljana, Slovenia
| | - Eva Podovšovnik
- Faculty of Tourism Studies - Turistica, University of Primorska, Portorož, Slovenia
| | - Tomaž Zupanc
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000, Ljubljana, Slovenia
| | - Irena Zupanič Pajnič
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000, Ljubljana, Slovenia.
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Lee J, Axilbund J, Dalton WB, Laheru D, Watkins S, Chu D, Cravero K, Button B, Kyker-Snowman K, Waters I, Gocke CD, Lauring J, Park BH. A Polycythemia Vera JAK2 Mutation Masquerading as a Duodenal Cancer Mutation. J Natl Compr Canc Netw 2017; 14:1495-1498. [PMID: 27956534 DOI: 10.6004/jnccn.2016.0161] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 08/11/2016] [Indexed: 11/17/2022]
Abstract
Next-generation sequencing (NGS) is increasingly being used in cancer care to identify both somatic tumor driver mutations that can be targeted for therapy, and heritable mutations in the germline associated with increased cancer risk. This report presents a case of a JAK2 V617F mutation falsely identified as a duodenal cancer mutation via NGS. The patient was found to have a history of polycythemia vera, a disorder with a high incidence of JAK2 somatic mutations. Buccal cell DNA showed heterozygosity for the mutation, suggesting that it was potentially germline. However, subsequent resequencing of tumor, adjacent normal tissue, and fingernail DNA confirmed the mutation was somatic, and its presence in tumor and buccal cells resulted from contaminating blood cells. This report highlights important nuances of NGS that can lead to misinterpretation of results with potential clinical implications.
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Affiliation(s)
- Justin Lee
- From The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, and The Whiting School of Engineering, Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, Maryland
| | - Jennifer Axilbund
- From The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, and The Whiting School of Engineering, Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, Maryland
| | - W Brian Dalton
- From The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, and The Whiting School of Engineering, Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, Maryland
| | - Daniel Laheru
- From The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, and The Whiting School of Engineering, Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, Maryland
| | - Stanley Watkins
- From The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, and The Whiting School of Engineering, Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, Maryland
| | - David Chu
- From The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, and The Whiting School of Engineering, Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, Maryland
| | - Karen Cravero
- From The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, and The Whiting School of Engineering, Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, Maryland
| | - Berry Button
- From The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, and The Whiting School of Engineering, Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, Maryland
| | - Kelly Kyker-Snowman
- From The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, and The Whiting School of Engineering, Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, Maryland
| | - Ian Waters
- From The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, and The Whiting School of Engineering, Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, Maryland
| | - Christopher D Gocke
- From The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, and The Whiting School of Engineering, Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, Maryland
| | - Josh Lauring
- From The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, and The Whiting School of Engineering, Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, Maryland
| | - Ben Ho Park
- From The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, and The Whiting School of Engineering, Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, Maryland.,From The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, and The Whiting School of Engineering, Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, Maryland
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