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Fazzini F, Lamina C, Raftopoulou A, Koller A, Fuchsberger C, Pattaro C, Del Greco FM, Döttelmayer P, Fendt L, Fritz J, Meiselbach H, Schönherr S, Forer L, Weissensteiner H, Pramstaller PP, Eckardt K, Hicks AA, Kronenberg F. Association of mitochondrial DNA copy number with metabolic syndrome and type 2 diabetes in 14 176 individuals. J Intern Med 2021; 290:190-202. [PMID: 33453124 PMCID: PMC8359248 DOI: 10.1111/joim.13242] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 11/24/2020] [Accepted: 12/14/2020] [Indexed: 12/14/2022]
Abstract
BACKGROUND Mitochondria play an important role in cellular metabolism, and their dysfunction is postulated to be involved in metabolic disturbances. Mitochondrial DNA is present in multiple copies per cell. The quantification of mitochondrial DNA copy number (mtDNA-CN) might be used to assess mitochondrial dysfunction. OBJECTIVES We aimed to investigate the cross-sectional association of mtDNA-CN with type 2 diabetes and the potential mediating role of metabolic syndrome. METHODS We examined 4812 patients from the German Chronic Kidney Disease (GCKD) study and 9364 individuals from the Cooperative Health Research in South Tyrol (CHRIS) study. MtDNA-CN was measured in whole blood using a plasmid-normalized qPCR-based assay. RESULTS In both studies, mtDNA-CN showed a significant correlation with most metabolic syndrome parameters: mtDNA-CN decreased with increasing number of metabolic syndrome components. Furthermore, individuals with low mtDNA-CN had significantly higher odds of metabolic syndrome (OR = 1.025; 95% CI = 1.011-1.039, P = 3.19 × 10-4 , for each decrease of 10 mtDNA copies) and type 2 diabetes (OR = 1.027; 95% CI = 1.012-1.041; P = 2.84 × 10-4 ) in a model adjusted for age, sex, smoking and kidney function in the meta-analysis of both studies. Mediation analysis revealed that the association of mtDNA-CN with type 2 diabetes was mainly mediated by waist circumference in the GCKD study (66%) and by several metabolic syndrome parameters, especially body mass index and triglycerides, in the CHRIS study (41%). CONCLUSIONS Our data show an inverse association of mtDNA-CN with higher risk of metabolic syndrome and type 2 diabetes. A major part of the total effect of mtDNA-CN on type 2 diabetes is mediated by obesity parameters.
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Affiliation(s)
- F. Fazzini
- From theDepartment of Genetics and PharmacologyInstitute of Genetic EpidemiologyMedical University of InnsbruckInnsbruckAustria
| | - C. Lamina
- From theDepartment of Genetics and PharmacologyInstitute of Genetic EpidemiologyMedical University of InnsbruckInnsbruckAustria
| | - A. Raftopoulou
- Eurac ResearchInstitute for BiomedicineAffiliated Institute of the University of LübeckBolzanoItaly
| | - A. Koller
- From theDepartment of Genetics and PharmacologyInstitute of Genetic EpidemiologyMedical University of InnsbruckInnsbruckAustria
| | - C. Fuchsberger
- Eurac ResearchInstitute for BiomedicineAffiliated Institute of the University of LübeckBolzanoItaly
| | - C. Pattaro
- Eurac ResearchInstitute for BiomedicineAffiliated Institute of the University of LübeckBolzanoItaly
| | - F. M. Del Greco
- Eurac ResearchInstitute for BiomedicineAffiliated Institute of the University of LübeckBolzanoItaly
| | - P. Döttelmayer
- From theDepartment of Genetics and PharmacologyInstitute of Genetic EpidemiologyMedical University of InnsbruckInnsbruckAustria
| | - L. Fendt
- From theDepartment of Genetics and PharmacologyInstitute of Genetic EpidemiologyMedical University of InnsbruckInnsbruckAustria
| | - J. Fritz
- Department of Medical StatisticsInformatics and Health EconomicsMedical University of InnsbruckInnsbruckAustria
- Department of Integrative PhysiologyUniversity of Colorado BoulderBoulderCOUSA
| | - H. Meiselbach
- Department of Nephrology and HypertensionFriedrich‐Alexander Universität Erlangen‐Nürnberg (FAU)ErlangenGermany
| | - S. Schönherr
- From theDepartment of Genetics and PharmacologyInstitute of Genetic EpidemiologyMedical University of InnsbruckInnsbruckAustria
| | - L. Forer
- From theDepartment of Genetics and PharmacologyInstitute of Genetic EpidemiologyMedical University of InnsbruckInnsbruckAustria
| | - H. Weissensteiner
- From theDepartment of Genetics and PharmacologyInstitute of Genetic EpidemiologyMedical University of InnsbruckInnsbruckAustria
| | - P. P. Pramstaller
- Eurac ResearchInstitute for BiomedicineAffiliated Institute of the University of LübeckBolzanoItaly
| | - K.‐U. Eckardt
- Department of Nephrology and HypertensionFriedrich‐Alexander Universität Erlangen‐Nürnberg (FAU)ErlangenGermany
- Department of Nephrology and Medical Intensive CareCharité – Universitätsmedizin BerlinBerlinGermany
| | - A. A. Hicks
- Eurac ResearchInstitute for BiomedicineAffiliated Institute of the University of LübeckBolzanoItaly
| | - F. Kronenberg
- From theDepartment of Genetics and PharmacologyInstitute of Genetic EpidemiologyMedical University of InnsbruckInnsbruckAustria
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Weissensteiner H, Forer L, Fendt L, Kheirkhah A, Salas A, Kronenberg F, Schoenherr S. Contamination detection in sequencing studies using the mitochondrial phylogeny. Genome Res 2021; 31:309-316. [PMID: 33452015 PMCID: PMC7849411 DOI: 10.1101/gr.256545.119] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 11/30/2020] [Indexed: 01/14/2023]
Abstract
Within-species contamination is a major issue in sequencing studies, especially for mitochondrial studies. Contamination can be detected by analyzing the nuclear genome or by inspecting polymorphic sites in the mitochondrial genome (mtDNA). Existing methods using the nuclear genome are computationally expensive, and no appropriate tool for detecting sample contamination in large-scale mtDNA data sets is available. Here we present haplocheck, a tool that requires only the mtDNA to detect contamination in both targeted mitochondrial and whole-genome sequencing studies. Our in silico simulations and amplicon mixture experiments indicate that haplocheck detects mtDNA contamination accurately and is independent of the phylogenetic distance within a sample mixture. By applying haplocheck to The 1000 Genomes Project Consortium data, we further evaluate the application of haplocheck as a fast proxy tool for nDNA-based contamination detection using the mtDNA and identify the mitochondrial copy number within a mixture as a critical component for the overall accuracy. The haplocheck tool is available both as a command-line tool and as a cloud web service producing interactive reports that facilitates the navigation through the phylogeny of contaminated samples.
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Affiliation(s)
- Hansi Weissensteiner
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Lukas Forer
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Liane Fendt
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Azin Kheirkhah
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Antonio Salas
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Sanitarias (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15782, Galicia, Spain
| | - Florian Kronenberg
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Sebastian Schoenherr
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, 6020 Innsbruck, Austria
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Fazzini F, Fendt L, Schönherr S, Forer L, Schöpf B, Streiter G, Losso JL, Kloss-Brandstätter A, Kronenberg F, Weissensteiner H. Analyzing Low-Level mtDNA Heteroplasmy-Pitfalls and Challenges from Bench to Benchmarking. Int J Mol Sci 2021; 22:ijms22020935. [PMID: 33477827 PMCID: PMC7832847 DOI: 10.3390/ijms22020935] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 01/05/2021] [Accepted: 01/15/2021] [Indexed: 12/27/2022] Open
Abstract
Massive parallel sequencing technologies are promising a highly sensitive detection of low-level mutations, especially in mitochondrial DNA (mtDNA) studies. However, processes from DNA extraction and library construction to bioinformatic analysis include several varying tasks. Further, there is no validated recommendation for the comprehensive procedure. In this study, we examined potential pitfalls on the sequencing results based on two-person mtDNA mixtures. Therefore, we compared three DNA polymerases, six different variant callers in five mixtures between 50% and 0.5% variant allele frequencies generated with two different amplification protocols. In total, 48 samples were sequenced on Illumina MiSeq. Low-level variant calling at the 1% variant level and below was performed by comparing trimming and PCR duplicate removal as well as six different variant callers. The results indicate that sensitivity, specificity, and precision highly depend on the investigated polymerase but also vary based on the analysis tools. Our data highlight the advantage of prior standardization and validation of the individual laboratory setup with a DNA mixture model. Finally, we provide an artificial heteroplasmy benchmark dataset that can help improve somatic variant callers or pipelines, which may be of great interest for research related to cancer and aging.
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Affiliation(s)
- Federica Fazzini
- Department of Genetics and Pharmacology, Institute of Genetic Epidemiology, Medical University of Innsbruck, A-6020 Innsbruck, Austria; (F.F.); (L.F.); (S.S.); (L.F.); (B.S.); (G.S.); (J.L.L.); (A.K.-B.); (F.K.)
| | - Liane Fendt
- Department of Genetics and Pharmacology, Institute of Genetic Epidemiology, Medical University of Innsbruck, A-6020 Innsbruck, Austria; (F.F.); (L.F.); (S.S.); (L.F.); (B.S.); (G.S.); (J.L.L.); (A.K.-B.); (F.K.)
| | - Sebastian Schönherr
- Department of Genetics and Pharmacology, Institute of Genetic Epidemiology, Medical University of Innsbruck, A-6020 Innsbruck, Austria; (F.F.); (L.F.); (S.S.); (L.F.); (B.S.); (G.S.); (J.L.L.); (A.K.-B.); (F.K.)
| | - Lukas Forer
- Department of Genetics and Pharmacology, Institute of Genetic Epidemiology, Medical University of Innsbruck, A-6020 Innsbruck, Austria; (F.F.); (L.F.); (S.S.); (L.F.); (B.S.); (G.S.); (J.L.L.); (A.K.-B.); (F.K.)
| | - Bernd Schöpf
- Department of Genetics and Pharmacology, Institute of Genetic Epidemiology, Medical University of Innsbruck, A-6020 Innsbruck, Austria; (F.F.); (L.F.); (S.S.); (L.F.); (B.S.); (G.S.); (J.L.L.); (A.K.-B.); (F.K.)
| | - Gertraud Streiter
- Department of Genetics and Pharmacology, Institute of Genetic Epidemiology, Medical University of Innsbruck, A-6020 Innsbruck, Austria; (F.F.); (L.F.); (S.S.); (L.F.); (B.S.); (G.S.); (J.L.L.); (A.K.-B.); (F.K.)
| | - Jamie Lee Losso
- Department of Genetics and Pharmacology, Institute of Genetic Epidemiology, Medical University of Innsbruck, A-6020 Innsbruck, Austria; (F.F.); (L.F.); (S.S.); (L.F.); (B.S.); (G.S.); (J.L.L.); (A.K.-B.); (F.K.)
| | - Anita Kloss-Brandstätter
- Department of Genetics and Pharmacology, Institute of Genetic Epidemiology, Medical University of Innsbruck, A-6020 Innsbruck, Austria; (F.F.); (L.F.); (S.S.); (L.F.); (B.S.); (G.S.); (J.L.L.); (A.K.-B.); (F.K.)
- Carinthia University of Applied Sciences, A-9524 Villach, Austria
| | - Florian Kronenberg
- Department of Genetics and Pharmacology, Institute of Genetic Epidemiology, Medical University of Innsbruck, A-6020 Innsbruck, Austria; (F.F.); (L.F.); (S.S.); (L.F.); (B.S.); (G.S.); (J.L.L.); (A.K.-B.); (F.K.)
| | - Hansi Weissensteiner
- Department of Genetics and Pharmacology, Institute of Genetic Epidemiology, Medical University of Innsbruck, A-6020 Innsbruck, Austria; (F.F.); (L.F.); (S.S.); (L.F.); (B.S.); (G.S.); (J.L.L.); (A.K.-B.); (F.K.)
- Correspondence: ; Tel.: +43-512-9003-70564
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Fendt L, Fazzini F, Weissensteiner H, Bruckmoser E, Schönherr S, Schäfer G, Losso JL, Streiter GA, Lamina C, Rasse M, Klocker H, Kofler B, Kloss-Brandstätter A, Huck CW, Kronenberg F, Laimer J. Profiling of Mitochondrial DNA Heteroplasmy in a Prospective Oral Squamous Cell Carcinoma Study. Cancers (Basel) 2020; 12:E1933. [PMID: 32708892 PMCID: PMC7409097 DOI: 10.3390/cancers12071933] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 07/13/2020] [Accepted: 07/15/2020] [Indexed: 01/25/2023] Open
Abstract
While a shift in energy metabolism is essential to cancers, the knowledge about the involvement of the mitochondrial genome in tumorigenesis and progression in oral squamous cell carcinoma (OSCC) is still very limited. In this study, we evaluated 37 OSCC tumors and the corresponding benign mucosa tissue pairs by deep sequencing of the complete mitochondrial DNA (mtDNA). After extensive quality control, we identified 287 variants, 137 in tumor and 150 in benign samples exceeding the 1% threshold. Variant heteroplasmy levels were significantly increased in cancer compared to benign tissues (p = 0.0002). Furthermore, pairwise high heteroplasmy frequency difference variants (∆HF% > 20) with potential functional impact were increased in the cancer tissues (p = 0.024). Fourteen mutations were identified in the protein-coding region, out of which thirteen were detected in cancer and only one in benign tissue. After eight years of follow-up, the risk of mortality was higher for patients who harbored at least one ∆HF% > 20 variant in mtDNA protein-coding regions relative to those with no mutations (HR = 4.6, (95%CI = 1.3-17); p = 0.019 in primary tumor carriers). Haplogroup affiliation showed an impact on survival time, which however needs confirmation in a larger study. In conclusion, we observed a significantly higher accumulation of somatic mutations in the cancer tissues associated with a worse prognosis.
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Affiliation(s)
- Liane Fendt
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, A-6020 Innsbruck, Austria; (L.F.); (F.F.); (H.W.); (S.S.); (J.L.L.); (G.A.S.); (C.L.); (A.K.-B.); (F.K.)
| | - Federica Fazzini
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, A-6020 Innsbruck, Austria; (L.F.); (F.F.); (H.W.); (S.S.); (J.L.L.); (G.A.S.); (C.L.); (A.K.-B.); (F.K.)
| | - Hansi Weissensteiner
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, A-6020 Innsbruck, Austria; (L.F.); (F.F.); (H.W.); (S.S.); (J.L.L.); (G.A.S.); (C.L.); (A.K.-B.); (F.K.)
| | - Emanuel Bruckmoser
- Oral and Maxillofacial Surgeon, Private Practice, A-5020 Salzburg, Austria;
| | - Sebastian Schönherr
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, A-6020 Innsbruck, Austria; (L.F.); (F.F.); (H.W.); (S.S.); (J.L.L.); (G.A.S.); (C.L.); (A.K.-B.); (F.K.)
| | - Georg Schäfer
- Institute for Pathology, Neuropathology and Molecular Pathology, Medical University of Innsbruck, A-6020 Innsbruck, Austria;
| | - Jamie Lee Losso
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, A-6020 Innsbruck, Austria; (L.F.); (F.F.); (H.W.); (S.S.); (J.L.L.); (G.A.S.); (C.L.); (A.K.-B.); (F.K.)
| | - Gertraud A. Streiter
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, A-6020 Innsbruck, Austria; (L.F.); (F.F.); (H.W.); (S.S.); (J.L.L.); (G.A.S.); (C.L.); (A.K.-B.); (F.K.)
| | - Claudia Lamina
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, A-6020 Innsbruck, Austria; (L.F.); (F.F.); (H.W.); (S.S.); (J.L.L.); (G.A.S.); (C.L.); (A.K.-B.); (F.K.)
| | - Michael Rasse
- University Hospital for Craniomaxillofacial and Oral Surgery, Medical University of Innsbruck, A-6020 Innsbruck, Austria;
- Clinic for Maxillofacial Surgery, Sechenov University, Trubetskaya Str. 8 b.2, 119992 Moscow, Russia
| | - Helmut Klocker
- Division of Experimental Urology, Department of Urology, Medical University of Innsbruck, A-6020 Innsbruck, Austria;
| | - Barbara Kofler
- Department of Otorhinolaryngology, Medical University of Innsbruck, Anichstrasse 35, A-6020 Innsbruck, Austria;
| | - Anita Kloss-Brandstätter
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, A-6020 Innsbruck, Austria; (L.F.); (F.F.); (H.W.); (S.S.); (J.L.L.); (G.A.S.); (C.L.); (A.K.-B.); (F.K.)
- Carinthia University of Applied Sciences, A-9524 Villach, Austria
| | - Christian W. Huck
- Institute of Analytical Chemistry and Radiochemistry, CCB-Center for Chemistry and Biomedicine, Leopold Franzens University Innsbruck, A-6020 Innsbruck, Austria;
| | - Florian Kronenberg
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, A-6020 Innsbruck, Austria; (L.F.); (F.F.); (H.W.); (S.S.); (J.L.L.); (G.A.S.); (C.L.); (A.K.-B.); (F.K.)
| | - Johannes Laimer
- University Hospital for Craniomaxillofacial and Oral Surgery, Medical University of Innsbruck, A-6020 Innsbruck, Austria;
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Fazzini F, Lamina C, Fendt L, Schultheiss UT, Kotsis F, Hicks AA, Meiselbach H, Weissensteiner H, Forer L, Krane V, Eckardt KU, Köttgen A, Kronenberg F. Mitochondrial DNA copy number is associated with mortality and infections in a large cohort of patients with chronic kidney disease. Kidney Int 2019; 96:480-488. [PMID: 31248648 DOI: 10.1016/j.kint.2019.04.021] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 03/29/2019] [Accepted: 04/05/2019] [Indexed: 12/16/2022]
Abstract
Damage of mitochondrial DNA (mtDNA) with reduction in copy number has been proposed as a biomarker for mitochondrial dysfunction and oxidative stress. Chronic kidney disease (CKD) is associated with increased mortality and risk of cardiovascular disease, but the underlying mechanisms remain incompletely understood. Here we investigated the prognostic role of mtDNA copy number for cause-specific mortality in 4812 patients from the German Chronic Kidney Disease study, an ongoing prospective observational national cohort study of patients with CKD stage G3 and A1-3 or G1-2 with overt proteinuria (A3) at enrollment. MtDNA was quantified in whole blood using a plasmid-normalized PCR-based assay. At baseline, 1235 patients had prevalent cardiovascular disease. These patients had a significantly lower mtDNA copy number than patients without cardiovascular disease (fully-adjusted model: odds ratio 1.03, 95% confidence interval [CI] 1.01-1.05 per 10 mtDNA copies decrease). After four years of follow-up, we observed a significant inverse association between mtDNA copy number and all-cause mortality, adjusted for kidney function and cardiovascular disease risk factors (hazard ratio 1.37, 95% CI 1.09-1.73 for quartile 1 compared to quartiles 2-4). When grouped by causes of death, estimates pointed in the same direction for all causes but in a fully-adjusted model decreased copy numbers were significantly lower only in infection-related death (hazard ratio 1.82, 95% CI 1.08-3.08). A similar association was observed for hospitalizations due to infections in 644 patients (hazard ratio 1.19, 95% CI 1.00-1.42 in the fully-adjusted model). Thus, our data support a role of mitochondrial dysfunction in increased cardiovascular disease and mortality risks as well as susceptibility to infections in patients with CKD.
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Affiliation(s)
- Federica Fazzini
- Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Claudia Lamina
- Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Liane Fendt
- Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Ulla T Schultheiss
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany; Renal Division, Department of Medicine IV, Medical Center-University of Freiburg, Faculty of Medicine, Freiburg, Germany
| | - Fruzsina Kotsis
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Andrew A Hicks
- Institute for Biomedicine, EURAC Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy
| | - Heike Meiselbach
- Department of Nephrology and Hypertension, Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Hansi Weissensteiner
- Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Lukas Forer
- Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Vera Krane
- Division of Nephrology, Department of Internal Medicine I, Division of Nephrology and Comprehensive Heart Failure Centre, University Hospital Würzburg, Würzburg, Germany
| | - Kai-Uwe Eckardt
- Department of Nephrology and Hypertension, Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), Erlangen, Germany; Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Anna Köttgen
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Florian Kronenberg
- Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Innsbruck, Austria.
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Kloss-Brandstätter A, Weissensteiner H, Erhart G, Schäfer G, Forer L, Schönherr S, Pacher D, Seifarth C, Stöckl A, Fendt L, Sottsas I, Klocker H, Huck CW, Rasse M, Kronenberg F, Kloss FR. Validation of Next-Generation Sequencing of Entire Mitochondrial Genomes and the Diversity of Mitochondrial DNA Mutations in Oral Squamous Cell Carcinoma. PLoS One 2015; 10:e0135643. [PMID: 26262956 PMCID: PMC4532422 DOI: 10.1371/journal.pone.0135643] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 07/23/2015] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Oral squamous cell carcinoma (OSCC) is mainly caused by smoking and alcohol abuse and shows a five-year survival rate of ~50%. We aimed to explore the variation of somatic mitochondrial DNA (mtDNA) mutations in primary oral tumors, recurrences and metastases. METHODS We performed an in-depth validation of mtDNA next-generation sequencing (NGS) on an Illumina HiSeq 2500 platform for its application to cancer tissues, with the goal to detect low-level heteroplasmies and to avoid artifacts. Therefore we genotyped the mitochondrial genome (16.6 kb) from 85 tissue samples (tumors, recurrences, resection edges, metastases and blood) collected from 28 prospectively recruited OSCC patients applying both Sanger sequencing and high-coverage NGS (~35,000 reads per base). RESULTS We observed a strong correlation between Sanger sequencing and NGS in estimating the mixture ratio of heteroplasmies (r = 0.99; p<0.001). Non-synonymous heteroplasmic variants were enriched among cancerous tissues. The proportions of somatic and inherited variants in a given gene region were strongly correlated (r = 0.85; p<0.001). Half of the patients shared mutations between benign and cancerous tissue samples. Low level heteroplasmies (<10%) were more frequent in benign samples compared to tumor samples, where heteroplasmies >10% were predominant. Four out of six patients who developed a local tumor recurrence showed mutations in the recurrence that had also been observed in the primary tumor. Three out of five patients, who had tumor metastases in the lymph nodes of their necks, shared mtDNA mutations between primary tumors and lymph node metastases. The percentage of mutation heteroplasmy increased from the primary tumor to lymph node metastases. CONCLUSIONS We conclude that Sanger sequencing is valid for heteroplasmy quantification for heteroplasmies ≥10% and that NGS is capable of reliably detecting and quantifying heteroplasmies down to the 1%-level. The finding of shared mutations between primary tumors, recurrences and metastasis indicates a clonal origin of malignant cells in oral cancer.
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Affiliation(s)
| | - Hansi Weissensteiner
- Division of Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria
- Department of Database and Information Systems, Institute of Computer Science, Leopold-Franzens University of Innsbruck, Innsbruck, Austria
| | - Gertraud Erhart
- Division of Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Georg Schäfer
- Department of Urology, Medical University of Innsbruck, Innsbruck, Austria
| | - Lukas Forer
- Division of Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria
- Department of Database and Information Systems, Institute of Computer Science, Leopold-Franzens University of Innsbruck, Innsbruck, Austria
| | - Sebastian Schönherr
- Division of Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria
- Department of Database and Information Systems, Institute of Computer Science, Leopold-Franzens University of Innsbruck, Innsbruck, Austria
| | - Dominic Pacher
- Division of Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria
- Department of Database and Information Systems, Institute of Computer Science, Leopold-Franzens University of Innsbruck, Innsbruck, Austria
| | - Christof Seifarth
- Department of Urology, Medical University of Innsbruck, Innsbruck, Austria
| | - Andrea Stöckl
- Division of Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Liane Fendt
- Division of Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Irma Sottsas
- Department of Urology, Medical University of Innsbruck, Innsbruck, Austria
| | - Helmut Klocker
- Department of Urology, Medical University of Innsbruck, Innsbruck, Austria
| | - Christian W. Huck
- Institute of Analytical Chemistry and Radiochemistry, Leopold-Franzens University of Innsbruck, Innsbruck, Austria
| | - Michael Rasse
- Department for Cranio-, Maxillofacial and Oral Surgery, Medical University of Innsbruck, Innsbruck, Austria
| | - Florian Kronenberg
- Division of Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Frank R. Kloss
- Department for Cranio-, Maxillofacial and Oral Surgery, Medical University of Innsbruck, Innsbruck, Austria
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Just RS, Scheible MK, Fast SA, Sturk-Andreaggi K, Röck AW, Bush JM, Higginbotham JL, Peck MA, Ring JD, Huber GE, Xavier C, Strobl C, Lyons EA, Diegoli TM, Bodner M, Fendt L, Kralj P, Nagl S, Niederwieser D, Zimmermann B, Parson W, Irwin JA. Full mtGenome reference data: Development and characterization of 588 forensic-quality haplotypes representing three U.S. populations. Forensic Sci Int Genet 2015; 14:141-55. [DOI: 10.1016/j.fsigen.2014.09.021] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 09/08/2014] [Accepted: 09/26/2014] [Indexed: 11/26/2022]
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Parson W, Strobl C, Huber G, Zimmermann B, Gomes SM, Souto L, Fendt L, Delport R, Langit R, Wootton S, Lagaceé R, Irwin J. WITHDRAWN: Erratum to "Evaluation of next generation mtGenome sequencing using the Ion Torrent Personal Genome Machine (PGM)" [Forensic Sci. Int.: Genet. 7 (2013) 543-549]. Forensic Sci Int Genet 2014:S1872-4973(13)00179-8. [PMID: 26898381 DOI: 10.1016/j.fsigen.2013.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The Publisher regrets that this article is an accidental duplication of an article that has already been published, http://dx.doi.org/10.1016/j.fsigen.2013.09.007. The duplicate article has therefore been withdrawn. The full Elsevier Policy on Article Withdrawal can be found at http://www.elsevier.com/locate/withdrawalpolicy.
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Affiliation(s)
- Walther Parson
- Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria; Penn State Eberly College of Science, University Park, PA, USA.
| | - Christina Strobl
- Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria
| | - Gabriela Huber
- Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria
| | - Bettina Zimmermann
- Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria
| | - Sibylle M Gomes
- Department of Biology, University of Aveiro, Campus de Santiago, Aveiro, Portugal
| | - Luis Souto
- Department of Biology, University of Aveiro, Campus de Santiago, Aveiro, Portugal
| | - Liane Fendt
- Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria; Division of Human Genetics, Innsbruck Medical University, Innsbruck, Austria
| | - Rhena Delport
- Department of Chemical Pathology, School of Medicine, University of Pretoria, South Africa
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Parson W, Strobl C, Huber G, Zimmermann B, Gomes SM, Souto L, Fendt L, Delport R, Langit R, Wootton S, Lagacé R, Irwin J. Reprint of: Evaluation of next generation mtGenome sequencing using the Ion Torrent Personal Genome Machine (PGM). Forensic Sci Int Genet 2013; 7:632-639. [PMID: 24119954 DOI: 10.1016/j.fsigen.2013.09.007] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Insights into the human mitochondrial phylogeny have been primarily achieved by sequencing full mitochondrial genomes (mtGenomes). In forensic genetics (partial) mtGenome information can be used to assign haplotypes to their phylogenetic backgrounds, which may, in turn, have characteristic geographic distributions that would offer useful information in a forensic case. In addition and perhaps even more relevant in the forensic context, haplogroup-specific patterns of mutations form the basis for quality control of mtDNA sequences. The current method for establishing (partial) mtDNA haplotypes is Sanger-type sequencing (STS), which is laborious, time-consuming, and expensive. With the emergence of Next Generation Sequencing (NGS) technologies, the body of available mtDNA data can potentially be extended much more quickly and cost-efficiently. Customized chemistries, laboratory workflows and data analysis packages could support the community and increase the utility of mtDNA analysis in forensics. We have evaluated the performance of mtGenome sequencing using the Personal Genome Machine (PGM) and compared the resulting haplotypes directly with conventional Sanger-type sequencing. A total of 64mtGenomes (>1 million bases) were established that yielded high concordance with the corresponding STS haplotypes (<0.02% differences). About two-thirds of the differences were observed in or around homopolymeric sequence stretches. In addition, the sequence alignment algorithm employed to align NGS reads played a significant role in the analysis of the data and the resulting mtDNA haplotypes. Further development of alignment software would be desirable to facilitate the application of NGS in mtDNA forensic genetics.
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Affiliation(s)
- Walther Parson
- Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria; Penn State Eberly College of Science, University Park, PA, USA.
| | - Christina Strobl
- Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria
| | - Gabriela Huber
- Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria
| | - Bettina Zimmermann
- Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria
| | - Sibylle M Gomes
- Department of Biology, University of Aveiro, Campus de Santiago, Aveiro, Portugal
| | - Luis Souto
- Department of Biology, University of Aveiro, Campus de Santiago, Aveiro, Portugal
| | - Liane Fendt
- Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria; Division of Human Genetics, Innsbruck Medical University, Innsbruck, Austria
| | - Rhena Delport
- Department of Chemical Pathology, School of Medicine, University of Pretoria, South Africa
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Fendt L, Röck A, Zimmermann B, Bodner M, Thye T, Tschentscher F, Owusu-Dabo E, Göbel TMK, Schneider PM, Parson W. MtDNA diversity of Ghana: a forensic and phylogeographic view. Forensic Sci Int Genet 2011; 6:244-9. [PMID: 21723214 PMCID: PMC3314991 DOI: 10.1016/j.fsigen.2011.05.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2011] [Revised: 05/13/2011] [Accepted: 05/26/2011] [Indexed: 11/03/2022]
Abstract
West Africa is characterized by a migration history spanning more than 150,000 years. Climate changes but also political circumstances were responsible for several early but also recent population movements that shaped the West African mitochondrial landscape. The aim of the study was to establish a Ghanaian mtDNA dataset for forensic purposes and to investigate the diversity of the Ghanaian population sample with respect to surrounding populations. We sequenced full mitochondrial control regions of 193 Akan people from Ghana and excluded two apparently close maternally related individuals due to preceding kinship testing. The remaining dataset comprising 191 sequences was applied as etalon for quasi-median network analysis and was subsequently combined with 99 additional control region sequences from surrounding West African countries. All sequences were incorporated into the EMPOP database enriching the severely underrepresented African mtDNA pool. For phylogeographic considerations, the Ghanaian haplotypes were compared to those of 19 neighboring populations comprising a total number of 6198 HVS1 haplotypes. We found extensive genetic admixture between the Ghanaian lineages and those from adjacent populations diminishing with geographical distance. The extent of genetic admixture reflects the long but also recent history of migration waves within West Africa mainly caused by changing environmental conditions. Also, evidence for potential socio-economical influences such as trade routes is provided by the occurrence of U6b and U6d sequences found in Dubai but also in Tunisia leading to the African West Coast via Mauritania and Senegal but also via Niger, Nigeria to Cameroon.
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Affiliation(s)
- Liane Fendt
- Institute of Legal Medicine, Innsbruck Medical University, Muellerstrasse 44, 6020 Innsbruck, Austria
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Fendt L, Niederstätter H, Huber G, Zelger B, Dünser M, Seifarth C, Röck A, Schäfer G, Klocker H, Parson W. Accumulation of mutations over the entire mitochondrial genome of breast cancer cells obtained by tissue microdissection. Breast Cancer Res Treat 2010. [PMID: 20697806 DOI: 10.1007/s10549‐010‐1092‐8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The occurrence of heteroplasmy and mixtures is technically challenging for the analysis of mitochondrial DNA. More than that, observed mutations need to be carefully interpreted in the light of the phylogeny as mitochondrial DNA is a uniparental marker reflecting human evolution. Earlier attempts to explain the role of mtDNA in cancerous tissues led to substantial confusion in medical genetics mainly due to the presentation of low sequence data quality and misinterpretation of mutations representing a particular haplogroup background rather than being cancer-specific. The focus of this study is to characterize the extent and level of mutations in breast cancer samples obtained by tissue microdissection by application of an evaluated full mtDNA genome sequencing protocol. We amplified and sequenced the complete mitochondrial genomes of microdissected breast cancer cells of 15 patients and compared the results to those obtained from paired non-cancerous breast tissue derived from the same patients. We observed differences in the heteroplasmic states of substitutions between cancerous and normal cells, one of which was affecting a position that has been previously reported in lung cancer and another one that has been identified in 16 epithelial ovarian tumors, possibly indicating functional relevance. In the coding region, we found full transitions in two cancerous mitochondrial genomes and 12 heteroplasmic substitutions as compared to the non-cancerous breast cells. We identified somatic mutations over the entire mtDNA of human breast cancer cells potentially impairing the mitochondrial OXPHOS system.
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Affiliation(s)
- Liane Fendt
- Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria
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Fendt L, Niederstätter H, Huber G, Zelger B, Dünser M, Seifarth C, Röck A, Schäfer G, Klocker H, Parson W. Accumulation of mutations over the entire mitochondrial genome of breast cancer cells obtained by tissue microdissection. Breast Cancer Res Treat 2010; 128:327-36. [PMID: 20697806 DOI: 10.1007/s10549-010-1092-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2010] [Accepted: 07/23/2010] [Indexed: 12/01/2022]
Abstract
The occurrence of heteroplasmy and mixtures is technically challenging for the analysis of mitochondrial DNA. More than that, observed mutations need to be carefully interpreted in the light of the phylogeny as mitochondrial DNA is a uniparental marker reflecting human evolution. Earlier attempts to explain the role of mtDNA in cancerous tissues led to substantial confusion in medical genetics mainly due to the presentation of low sequence data quality and misinterpretation of mutations representing a particular haplogroup background rather than being cancer-specific. The focus of this study is to characterize the extent and level of mutations in breast cancer samples obtained by tissue microdissection by application of an evaluated full mtDNA genome sequencing protocol. We amplified and sequenced the complete mitochondrial genomes of microdissected breast cancer cells of 15 patients and compared the results to those obtained from paired non-cancerous breast tissue derived from the same patients. We observed differences in the heteroplasmic states of substitutions between cancerous and normal cells, one of which was affecting a position that has been previously reported in lung cancer and another one that has been identified in 16 epithelial ovarian tumors, possibly indicating functional relevance. In the coding region, we found full transitions in two cancerous mitochondrial genomes and 12 heteroplasmic substitutions as compared to the non-cancerous breast cells. We identified somatic mutations over the entire mtDNA of human breast cancer cells potentially impairing the mitochondrial OXPHOS system.
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Affiliation(s)
- Liane Fendt
- Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria
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Mikkelsen M, Rockenbauer E, Wächter A, Fendt L, Zimmermann B, Parson W, Nielsen SA, Gilbert T, Willerslev E, Morling N. Application of full mitochondrial genome sequencing using 454 GS FLX pyrosequencing. Forensic Science International: Genetics Supplement Series 2009. [DOI: 10.1016/j.fsigss.2009.09.028] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Turchi C, Buscemi L, Giacchino E, Onofri V, Fendt L, Parson W, Tagliabracci A. Polymorphisms of mtDNA control region in Tunisian and Moroccan populations: An enrichment of forensic mtDNA databases with Northern Africa data. Forensic Sci Int Genet 2009; 3:166-72. [DOI: 10.1016/j.fsigen.2009.01.014] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Fendt L, Zimmermann B, Daniaux M, Parson W. Sequencing strategy for the whole mitochondrial genome resulting in high quality sequences. BMC Genomics 2009; 10:139. [PMID: 19331681 PMCID: PMC2669098 DOI: 10.1186/1471-2164-10-139] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2008] [Accepted: 03/30/2009] [Indexed: 11/18/2022] Open
Abstract
Background It has been demonstrated that a reliable and fail-safe sequencing strategy is mandatory for high-quality analysis of mitochondrial (mt) DNA, as the sequencing and base-calling process is prone to error. Here, we present a high quality, reliable and easy handling manual procedure for the sequencing of full mt genomes that is also appropriate for laboratories where fully automated processes are not available. Results We amplified whole mitochondrial genomes as two overlapping PCR-fragments comprising each about 8500 bases in length. We developed a set of 96 primers that can be applied to a (manual) 96 well-based technology, which resulted in at least double strand sequence coverage of the entire coding region (codR). Conclusion This elaborated sequencing strategy is straightforward and allows for an unambiguous sequence analysis and interpretation including sometimes challenging phenomena such as point and length heteroplasmy that are relevant for the investigation of forensic and clinical samples.
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Affiliation(s)
- Liane Fendt
- Institute of Legal Medicine, Innsbruck Medical University, Müllerstrasse 44, Austria.
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Parson W, Fendt L, Ballard D, Børsting C, Brinkmann B, Carracedo Á, Carvalho M, Coble MD, Real FC, Desmyter S, Dupuy BM, Harrison C, Hohoff C, Just R, Krämer T, Morling N, Salas A, Schmitter H, Schneider PM, Sonntag ML, Vallone PM, Brandstätter A. Identification of West Eurasian mitochondrial haplogroups by mtDNA SNP screening: Results of the 2006–2007 EDNAP collaborative exercise. Forensic Sci Int Genet 2008; 2:61-8. [DOI: 10.1016/j.fsigen.2007.08.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2007] [Accepted: 08/13/2007] [Indexed: 11/15/2022]
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Zimmerli L, Maier S, Glatzel T, Gnecco E, Pfeiffer O, Diederich F, Fendt L, Meyer E. Formation of molecular wires on nanostructured KBr. ACTA ACUST UNITED AC 2007. [DOI: 10.1088/1742-6596/61/1/268] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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