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  • 1
    In: BMC Cancer, Springer Science and Business Media LLC, Vol. 11, No. 1 ( 2011-12)
    Abstract: The availability of well-annotated prostate tissue samples through biobanks is key for research. Whereas fresh-frozen tissue is well suited for a broad spectrum of molecular analyses, its storage and handling is complex and cost-intensive. Formalin-fixed paraffin-embedded specimens (FFPE) are easy to handle and economic to store, but their applicability for molecular methods is restricted. The recently introduced Hepes-glutamic acid-buffer mediated Organic solvent Protection Effect (HOPE) is a promising alternative, which might have the potential to unite the benefits of FFPE and fresh-frozen specimen. Aim of the study was to compare HOPE-fixed, FFPE and fresh-frozen bio-specimens for their accessibility for diagnostic and research purposes. Methods 10 prostate cancer samples were each preserved with HOPE, formalin, and liquid nitrogen and studied with in-situ and molecular methods. Samples were H & E stained, and assessed by immunohistochemistry (i.e. PSA, GOLPH2, p63) and FISH (i.e. ERG rearrangement). We assessed DNA integrity by PCR, using control genes ranging from 100 to 600 bp amplicon size. RNA integrity was assessed through qRT-PCR on three housekeeping genes (TBP, GAPDH, β-actin). Protein expression was analysed by performing western blot analysis using GOLPH2 and PSA antibodies. Results Of the HOPE samples, morphologic quality of H & E sections, immunohistochemical staining, and the FISH assay was at least equal to FFPE tissue, and significantly better than the fresh-frozen specimens. DNA, RNA, and protein analysis of HOPE samples provided similar results as compared to fresh-frozen specimens. As expected, FFPE-samples were inferior for most of the molecular analyses. Conclusions This is the first study, comparatively assessing the suitability of these fixation methods for diagnostic and research utilization. Overall, HOPE-fixed bio-specimens combine the benefits of FFPE- and fresh-frozen samples. Results of this study have the potential to expand on contemporary prostate tissue biobanking approaches and can serve as a model for other organs and tumors.
    Type of Medium: Online Resource
    ISSN: 1471-2407
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2011
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  • 2
    In: Journal of Clinical Oncology, American Society of Clinical Oncology (ASCO), Vol. 35, No. 15_suppl ( 2017-05-20), p. e23146-e23146
    Abstract: e23146 Background: The importance and clinical use of liquid biopsies to identify somatic, targetable alterations in the plasma of cancer patients is steadily increasing. However, their concordance with alterations identified in cancer specimens tested in routine diagnostics is not being monitored. In a cohort of non-squamous cell lung cancer patients, our aim was to systematically compare alterations found by a massively parallel sequencing liquid biopsy assay covering 39 cancer related genes (NEOliquid) with alterations identified by routine diagnostics in a certified central pathology laboratory. Methods: Routine Diagnostics: DNA mutational analysis was performed using cobas or Sanger-Sequencing. Rearrangements were identified using immunohistochemistry or FISH. NEOliquid assay: Cell-free DNA from plasma was subjected to hybrid-capture based next-generation sequencing to detect point mutations, small insertions and deletions, copy number alterations and genomic translocations in 39 clinically relevant genes in a single assay. To evaluate and compare the performance of liquid biopsies, we applied the NEOliquid tests on blood samples of 82 non-squamous NSCLC patients and correlated them with results of routine diagnostics of matched tissue samples. Results: Routine diagnostics for lung cancer related oncogenes (EGFR, ALK, ROS1, KRAS, BRAF) identified a total of 50 somatic alterations of which 37 were point mutations, 11 InDels and 2 gene fusions. NEOliquid analysis of the corresponding plasma sample revealed a total of 34 alterations, including 21 targetable driver alterations. Overall, the concordance of mutation calls between routine diagnostic testing and NEOliquid was 97.6%, with a sensitivity of 〉 70% and a specificity of 100%. Importantly, NEOliquid identified additional clinically relevant genomic alterations, not covered by routine testing. Conclusions: We have shown high concordance of genomic alterations identified from liquid biopsies and tumor tissue specimens. The excellent specificity of actionable alterations identified by NEOliquid offers analytical performance for routine diagnostic use.
    Type of Medium: Online Resource
    ISSN: 0732-183X , 1527-7755
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    Language: English
    Publisher: American Society of Clinical Oncology (ASCO)
    Publication Date: 2017
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  • 3
    In: Science, American Association for the Advancement of Science (AAAS), Vol. 362, No. 6419 ( 2018-12-07), p. 1165-1170
    Abstract: Neuroblastoma is a pediatric tumor of the sympathetic nervous system. Its clinical course ranges from spontaneous tumor regression to fatal progression. To investigate the molecular features of the divergent tumor subtypes, we performed genome sequencing on 416 pretreatment neuroblastomas and assessed telomere maintenance mechanisms in 208 of these tumors. We found that patients whose tumors lacked telomere maintenance mechanisms had an excellent prognosis, whereas the prognosis of patients whose tumors harbored telomere maintenance mechanisms was substantially worse. Survival rates were lowest for neuroblastoma patients whose tumors harbored telomere maintenance mechanisms in combination with RAS and/or p53 pathway mutations. Spontaneous tumor regression occurred both in the presence and absence of these mutations in patients with telomere maintenance–negative tumors. On the basis of these data, we propose a mechanistic classification of neuroblastoma that may benefit the clinical management of patients.
    Type of Medium: Online Resource
    ISSN: 0036-8075 , 1095-9203
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    Language: English
    Publisher: American Association for the Advancement of Science (AAAS)
    Publication Date: 2018
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    SSG: 11
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  • 4
    In: Journal of Personalized Medicine, MDPI AG, Vol. 11, No. 8 ( 2021-07-22), p. 691-
    Abstract: For many years, the risk-based therapy stratification of children with neuroblastoma has relied on clinical and molecular covariates. In recent years, genome analysis has revealed further alterations defining risk, tumor biology, and therapeutic targets. The implementation of a robust and scalable method for analyzing traditional and new molecular markers in routine diagnostics is an urgent clinical need. Here, we investigated targeted panel sequencing as a diagnostic approach to analyze all relevant genomic neuroblastoma risk markers in one assay. Our “neuroblastoma hybrid capture sequencing panel” (NB-HCSP) assay employs a technology for the high-coverage sequencing ( 〉 1000×) of 55 selected genes and neuroblastoma-relevant genomic regions, which allows for the detection of single nucleotide changes, structural rearrangements, and copy number alterations. We validated our assay by analyzing 15 neuroblastoma cell lines and a cohort of 20 neuroblastomas, for which reference routine diagnostic data and genome sequencing data were available. We observed a high concordance for risk markers identified by the NB-HSCP assay, clinical routine diagnostics, and genome sequencing. Subsequently, we demonstrated clinical applicability of the NB-HCSP assay by analyzing routine clinical samples. We conclude that the NB-HCSP assay may be implemented into routine diagnostics as a single assay that covers all essential covariates for initial neuroblastoma classification, extended risk stratification, and targeted therapy selection.
    Type of Medium: Online Resource
    ISSN: 2075-4426
    Language: English
    Publisher: MDPI AG
    Publication Date: 2021
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  • 5
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 76, No. 14_Supplement ( 2016-07-15), p. 3190-3190
    Abstract: Background Salivary gland neoplasms represent a heterogeneous group of benign and malignant tumors that comprise 6% of all head and neck cancers. Due to their low incidence, these tumors are poorly understood and remain a diagnostic and therapeutic challenge. Methods Out of 182 analyzed salivary gland tumors with various histologies, eight were positive for ALK immunohistochemistry. The cut-off was 15% positive cells in either membranous, nuclear or cytoplasmic compartments. The ALK positive tumors were first subjected to FISH analysis. Subsequently, these tumors were analyzed using hybrid capture based next generation sequencing to confirm possible ALK gene fusions or copy number alterations, and to detect additional genomic alterations of clinical relevance. Results An in-depth genomic analysis of the samples resulted in the detection of inactivating mutations in BRAF (p.D594N) and TP53 (p.C238S), as well as amplifications of ERBB2 and ALK. Strikingly, a novel MYO18A (Exon1-40)-ALK (exon 20-29) gene fusion was detected in a patient with adenocarcinoma not otherwise specified. This tumor was FISH positive and 100% of cells showed strong membranous staining for ALK. MYO18A (Exon1-40)-ALK (exon 20-29) gene fusion resulted in the retention of the kinase domain of ALK and the coiled-coil domain of MYO18A. Similarly to other ALK fusions, we hypothesize that the coiled-coil domain of MYO18A mediates the dimerization and activation of MYO18A-ALK, thereby resulting in an overexpression of constantly activated ALK. Conclusion Using hybrid capture based next generation sequencing, we identified in salivary gland tumors numerous genomic alterations in therapeutically relevant genes and a novel gene fusion (MYO18A-ALK). Patients harboring this fusion may potentially benefit from treatment with ALK inhibitors. Citation Format: Hanna Majewska, Judith Müller, Sotirios Lakis, Piotr Czapiewski, Adam Gorczyński, Mariola Iliszko, Alena Skalova, Rafal Dziadziuszko, Jacek Jassem, Wojciech Biernat, Roopika Menon, Johannes M. Heuckmann, Lukas C. Heukamp. Genomic profiling of salivary gland tumors identifies novel and targetable alterations. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3190.
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
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    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2016
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    detail.hit.zdb_id: 1432-1
    detail.hit.zdb_id: 410466-3
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  • 6
    In: Molecular Cancer Therapeutics, American Association for Cancer Research (AACR), Vol. 14, No. 12_Supplement_2 ( 2015-12-01), p. B135-B135
    Abstract: Background: Research in the field of molecular cancer profiling has allowed for the detection of cell free tumor DNA to identify disease using patient blood. Therefore, liquid biopsies that can detect cancer specific driver mutations as well as emerging resistance mutations have the potential to revolutionize cancer treatment of the future. Methods: At NEO New Oncology AG (Cologne, Germany), we have developed a ctDNA-based assay called NEOLiquid®. NEOLiquid® is a hybrid-capture and next-generation based sequencing assay that covers clinically relevant genomic alterations, such as mutations, gene fusions and copy number alterations in more than 30 genes. Here we describe, a 50-year-old never-smoker who was diagnosed with metastatic lung adenocarcinoma harbouring an activating EGFR exon 19 deletion and no T790M resistance mutation in 2012. The disease remained in remission under Erlotinib for one year. In 2014, the patient was diagnosed with brain metastasis and was subjected to whole brain radiotherapy. The disease was stable under Afatinib treatment for 6 months, followed by progression. Results: Previous attempts to detect a T790M resistance mutation by sequencing in re-biopsied tumor material failed. Following consent, NEOLiquid® analysis was performed on the patient's plasma. A T790M mutation was found (allele frequency 39%), along with the previously described exon 19 deletion (allele frequency 28%). Based on the detection of the T790M resistance mutation, the patient was given AZD9291 on compassionate use. Within a few days, the patients' clinical condition improved. Further blood samples under AZD9291 therapy in intervals of 2 weeks were analysed using the NEOLiquid® technology, showing gradual decrease of the T790M allele frequency. After 6 weeks, the T790M mutation was detected at an allele frequency of only 0.03%, with no indication of the exon 19 deletion anymore. Currently, AZD9291 therapy is ongoing, tolerability is excellent, and there is no evidence of tumor progression. In summary, we describe the successful detection and monitoring of a T790M resistance mutation in a patient not suitable for biopsy, even at very low allele frequencies, using our sensitive and reliable NEOLiquid® assay. The ability to detect residual disease and resistance mutations, non-invasively, using liquid biopsies will greatly influence cancer treatment in the future. Citation Format: Roopika Menon, Oliver Gautschi, Frauke Leenders, Judith Müller, Matthias Ballhause, Stefan Aebi, Klaus Strobel, Joachim Diebold, Bernhard Schwizer, Petra Schneider, Christian Gloeckner, Johannes Heuckmann, Lukas Heukamp. Successful AZD9291 therapy based on NEOLiquid detection of circulating T790M in a liquid biopsy sample. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2015 Nov 5-9; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2015;14(12 Suppl 2):Abstract nr B135.
    Type of Medium: Online Resource
    ISSN: 1535-7163 , 1538-8514
    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2015
    detail.hit.zdb_id: 2062135-8
    SSG: 12
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  • 7
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 75, No. 15_Supplement ( 2015-08-01), p. LB-210-LB-210
    Abstract: Neuroblastoma is a malignant pediatric tumor of the sympathetic nervous system. While roughly half of these tumors regress spontaneously or are cured by limited therapy, high-risk neuroblastomas have an unfavorable clinical course, despite intensive multimodal treatment. The genetic basis of the various clinical subtypes of the disease has remained largely elusive. To gain a better understanding of the genetic events that may drive neuroblastoma tumorigenesis, we here performed whole-genome sequencing of 42 primary neuroblastomas (high-risk, n = 25; low-risk, n = 17). We identified genomic rearrangements affecting chromosome 5p15.22 in a 50 kb region centromeric of the human telomerase reverse transcriptase gene (TERT) in 8 tumors. The rearrangements occurred only in high-risk neuroblastomas (8/25, 32%) in mutually exclusive fashion with MYCN amplifications and ATRX mutations, which are known genetic events in this tumor type. In an Independent validation cohort of 14 high-risk neuroblastomas, we detected rearrangements of the TERT locus in 4 additional samples. The structure of the rearrangements varied greatly, including balanced translocations, low-level copy number gains, focal amplifications and chromothripsis. Independent of the copy number at this region, all alterations consistently induced massive transcriptional up-regulation of TERT and of three additional genes located in close proximity to the chromosomal breakpoint. By contrast, MYCN-amplified tumors showed only up-regulation of TERT itself, suggesting that both MYCN amplification and TERT rearrangements converge on TERT activation. Supporting a functional role of TERT, both MYCN-amplified neuroblastoma cell lines and cell lines bearing TERT rearrangements exhibited elevated TERT expression and enzymatic telomerase activity in comparison to cell lines without these aberrations. Our findings show that remodeling of the genomic context abrogates transcriptional silencing of TERT in high-risk neuroblastoma, and places telomerase activation in the center of transformation in a large fraction of these tumors. More broadly, our findings provide a mechanistic basis for molecular diagnosis and therapy of this deadly pediatric tumor entity. Citation Format: Martin Peifer, Frederik Roels, Falk Hertwig, Roopika Menon, Andrea Kraemer, Reinhard Buettner, Sven Perner, Alexander Schramm, Johannes H. Schulte, Frank Westermann, Roman K. Thomas, Matthias Fischer. Telomerase activation by genomic rearrangements in high-risk neuroblastoma. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr LB-210. doi:10.1158/1538-7445.AM2015-LB-210
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
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    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2015
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    detail.hit.zdb_id: 1432-1
    detail.hit.zdb_id: 410466-3
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  • 8
    Online Resource
    Online Resource
    American Association for Cancer Research (AACR) ; 2014
    In:  Cancer Research Vol. 74, No. 19_Supplement ( 2014-10-01), p. 2373-2373
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 74, No. 19_Supplement ( 2014-10-01), p. 2373-2373
    Abstract: Patient derived xenograft (PDX) samples are powerful tools to analyze tumor biology and drug sensitivity of primary tumors in animal models. However, sequencing studies on those samples face the challenge of mouse stromal contamination, which varies in each of the explanted tumor specimen. Thus, without applying mouse and human specific filters on sequencing data, species specific genomic alterations and differences in expression are impossible to detect. To allow mouse and human specific transcriptome/genome analyses, we adapted our NGS data analysis pipelines to filter for mouse and human specific reads. By applying the analysis algorithms on hybrid-capture and transcriptome sequencing data from 60 lung cancer PDX samples, we were able to generate a comprehensive overview on tumor specific alterations, including point mutations, deletions and insertions, copy number alterations, gene fusions and isoform specific expression levels, as well as species specific genomic alterations and transcriptome wide expression levels. From 5781 nonsynonymous substitutions which were detected by hybrid-capture sequencing of 333 cancer relevant genes (CAGE-Rx Scanner), 863 human specific nonsynonymous substitutions were detected after filtering for mouse specific variations. The mean sequencing coverage of the CAGE analysis across all targeted bases in all 60 samples was 662x. An integrated analysis of this data set and corresponding transcriptome sequencing data revealed TP53 and KRAS as the most frequently mutated genes which were expressed. As expected, due to the relative high tumor content in all samples (ranging from 30 to 90% with a median of 90% as determined by pathological review), 80% of all mutations called from transcriptome sequencing in an unfiltered fashion were human specific and called after species specific filtering. In addition, the detection of mouse specific transcriptome sequencing reads identified several growth factors expressed by tumor surrounding tissue, which would have been discarded as unmapped reads in the normal analysis setting. Thus, our analysis alorithms not only enable to remove mouse specific false positive single nucleotide variants (SNVs), but also a detailed analysis of mouse specific expression patterns which might strongly influence tumor growth via the tumor microenvironment. Citation Format: Roopika Menon, Petra Schneider, Martin Peifer, Frauke Leenders, Johannes M. Heuckmann. Deep computational analysis of human and mouse specific next-generation sequencing data generated from PDX specimen. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 2373. doi:10.1158/1538-7445.AM2014-2373
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
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    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2014
    detail.hit.zdb_id: 2036785-5
    detail.hit.zdb_id: 1432-1
    detail.hit.zdb_id: 410466-3
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  • 9
    In: Journal of Clinical Oncology, American Society of Clinical Oncology (ASCO), Vol. 34, No. 15_suppl ( 2016-05-20), p. e23181-e23181
    Type of Medium: Online Resource
    ISSN: 0732-183X , 1527-7755
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    Language: English
    Publisher: American Society of Clinical Oncology (ASCO)
    Publication Date: 2016
    detail.hit.zdb_id: 2005181-5
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  • 10
    In: Journal of Clinical Oncology, American Society of Clinical Oncology (ASCO), Vol. 35, No. 15_suppl ( 2017-05-20), p. 5555-5555
    Abstract: 5555 Background: Surgical outcome is an important prognostic factor in advanced high-grade serous ovarian cancer (HGOC). Intra-operative determination of residual disease may be prone to subjective bias. Methods: We prospectively collected and analyzed tumor tissue and plasma from 21 pts with FIGO IIIC-IV HGOC. All tumor specimen showed loss of TP53 in immunohistochemistry. Tumor DNA from tissue and peri-operative cell-free DNA at baseline (BL) and at d(ays) 1, d4 and d10 were subjected to comprehensive hybrid-capture based next-generation sequencing (NEO New Oncology GmbH, Cologne, Germany). Results: The initial cohort comprised 10 pts without (TR 〉 0) and 11 pts with complete resection TR0, with a total of 43 somatic genomic alterations. TP53 was mutated in 20/21 (95.2%) of tissue samples and in 15/21 (71.4%) corresponding plasma samples at BL. Therefore, TP53 mutations were used as a molecular marker of circulating tumor DNA levels post-surgery. In the remaining 5 BL cases the TP53 mutations were either not present in plasma (N= 3) or rested below the detection limit (N= 2). In d1, d4 and d10 post-surgical samples, the sample specific TP53 mutations were detected in 12 out of 15, 10 out of 14 and in 7 out of 13 cases, respectively. TP53variant allele frequency (VAF) did not differ among TR0 and TR 〉 0 at BL (mean= 1.91 versus 1.73, Mann-Whitney test p = 0.86) whereas it was significantly lower for TR0 at d1 (mean= 0.06 versus 2,06; p value= 0.002), d4 (mean= 0.07 versus 1.8; p= 0.04) and d10 (mean VAF= 0 versus 1.04; p= 0.008). Five out of 9 TR 〉 0 cases showed at least one increase in VAF between d0 and any additional time-point. In 8 out of 9 mutations remained detectable at d10 (VAF: 0.076 – 3.26). By contrast, TR0 cases showed consistent reduction in VAF throughout the follow-up period which maximized at d10. Conclusions: Liquid biopsycan efficiently detect somatic mutations in the cfDNA of pts with HGOC following debulking surgery. Variation of the TP53 VAF in sequential post-surgical samples appears to be restricted to TR 〉 0 cases, whereas in TR0 pts VAF progressively decreases. Liquid biopsy may hold promise as a tool for the objective determination of residual disease after debulking surgery.
    Type of Medium: Online Resource
    ISSN: 0732-183X , 1527-7755
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    Language: English
    Publisher: American Society of Clinical Oncology (ASCO)
    Publication Date: 2017
    detail.hit.zdb_id: 2005181-5
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