PURPOSEHigh throughput panel sequencing to tailor therapy in precision oncology promises to improve outcome in patients with metastatic breast cancer. However, data that clearly show any benefit from ...such an approach is still pending. MATERIALS AND METHODSWe performed a retrospective analysis of advanced breast cancer patients that underwent panel sequencing for suggestion of target related drugs. We aimed to (i) determine the frequency of actionable mutations per patient and to (ii) assess the clinical impact of results on treatment options. RESULTSA total of 52 patients underwent panel sequencing of archived tumor tissue. Every sample showed at least one affected gene, accounting for actionable mutations in 45 of 52 patients (87%). New treatment options that would not have been used as indicated by standard predictive markers (such as hormonal receptor status or HER2-status) were found in 22 of 52 patients (42%). We detected therapeutic relevant pathogenic germline variants in 9,6% (5/52) of the patients. CONCLUSIONSUsing a high throughput-panel sequencing approach to identify actionable mutations in patients with metastatic breast cancer, we identified potential target-related treatment options in a large proportion of our patients, some of which would not have been considered without this data. Prospective clinical trials with compounds targeting the identified actionable mutations are needed to determine which treatments can indeed improve survival or quality of life by limiting exposure to ineffective drugs in advanced breast cancer.
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312
Background: Data on intratumoral heterogeneity of small intestine neuroendocrine tumors (SI-NETs) and related liver metastasis is limited. Further investigation might have impact on ...development of targeted therapy regimens. The aim of the study was to characterize genetic heterogeneity of 5 patients suffering from SI-NETs. Methods: Formalin-fixed, paraffin-embedded tissues samples of primary and metastatic lesion as well as benign liver of five patients with synchronously metastasized, well or moderately differentiated SI-NETs were analyzed with whole exome sequencing. For one patient, chip based 850k whole DNA methylome analysis was performed of primary and metastatic tumor tissue as well as control tissue. Alterations that occurred only in one tumor site were defined as private, whereas mutations present in both metastasis and primary lesion were regarded as common. Results: 156 single nucleotide variants (SNVs) in 150 genes were identified and amount of mutations/per sample ranged from 9-34 (mean 22). The degree of common (0-94%) and private mutations/per sample was strongly varying (6-100%). In all patients, copy number variations (CNV) were found and the degree of intratumoral heterogeneity of CNVs corresponded to SNV analysis. DNA methylation analysis of a patient without common SNVs revealed are large overlap of common methylated CpG sites. Conclusions: SI-NET primary and metastatic lesions show a highly varying degree of intratumoral heterogeneity. Driver events might not be detectable with exome analysis.
Background
The development of Precision Medicine strategies requires high-dimensional phenotypic and genomic data, both of which are highly privacy-sensitive data types. Conventional data management ...systems lack the capabilities to sufficiently handle the expected large quantities of such sensitive data in a secure manner. PROMISE is a genetic data management concept that implements a highly secure platform for data exchange while preserving patient interests, privacy, and autonomy.
Methods
The concept of PROMISE to democratize genetic data was developed by an interdisciplinary team. It integrates a sophisticated cryptographic concept that allows only the patient to grant selective access to defined parts of his genetic information with single DNA base-pair resolution cryptography. The PROMISE system was developed for research purposes to evaluate the concept in a pilot study with nineteen cardiomyopathy patients undergoing genotyping, questionnaires, and longitudinal follow-up.
Results
The safety of genetic data was very important to 79%, and patients generally regarded the data as highly sensitive. More than half the patients reported that their attitude towards the handling of genetic data has changed after using the PROMISE app for 4 months (median). The patients reported higher confidence in data security and willingness to share their data with commercial third parties, including pharmaceutical companies (increase from 5 to 32%).
Conclusion
PROMISE democratizes genomic data by a transparent, secure, and patient-centric approach. This clinical pilot study evaluating a genetic data infrastructure is unique and shows that patient’s acceptance of data sharing can be increased by patient-centric decision-making.
Graphic abstract
BRAF and MEK inhibitors significantly improved the prognosis of metastatic melanoma. Nevertheless, initial treatment response may be only temporary. Liquid biopsies (LB) offer a possibility to ...monitor patients by measuring circulating tumor DNA (ctDNA). We sought to find out whether ctDNA can be used to reliably determine progressive disease under targeted therapy. In addition, we wanted to check whether ctDNA may represent a possible prognostic marker for survival.
We included 19 melanoma patients with BRAF and MEK inhibitor therapy. For each patient, a 710 gene panel was analyzed on the latest available tumor tissue before the start of therapy. Repetitive LB were collected in which BRAF V600E/K mutations were monitored using digital droplet PCR (ddPCR). We correlated radiological staging results and overall survival with ctDNA results.
In 13 patients, ctDNA was detectable when starting targeted therapy, whereas in six patients, ddPCR was always negative, which we confirmed with ultra-deep sequencing. All patients with initially detectable ctDNA had ctDNA values declining to zero during follow-up, increasing again at the time of extracerebral progression or even slightly before detection by imaging. Survival was significantly worse for patients with elevated LDH (p=0.034) or detectable ctDNA (p=0.008) at the start of targeted therapy.
Therapy monitoring by ctDNA seems to be a reliable method for detecting extracranial progression, even more sensitive and specific than LDH or S100B. However, due to the small number of cases in our study, further studies are necessary.
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335
Background: No personalized therapy regimens could demonstrate a benefit in survival in intrahepatic cholangiocarcinoma (iCCA). Since genetic heterogeneity might influence single ...biopsy based targeted therapy or the outcome of clinical trials, aim of the present study was to investigate intratumoral heterogeneity of iCCA by whole exome sequencing. Methods: Samples from tumor center and tumor periphery of large iCCA lesions as well as a control from healthy liver tissue were obtained from 4 patients and whole exome sequencing was performed. Mutations that occurred only in the tumor center or periphery were defined as private, whereas mutations present in both samples were regarded as common. Results: A mean of 3 non-synonymous private mutations (range 0-13) per sample compared to 31.8 common mutations per sample (range 23-39) was identified. Mean percentage of non-synonymous private mutations per sample was 12% (range 0-57). In all samples of patient 1-3 as well as the central sample of patient 4 ≤ 10% private mutations were found, whereas 57% of private mutations were identified in the peripheral sample of patient 4. In this sample, a private mutation in the DNA mismatch repair protein MSH6 as well as a spatial loss of expression of MSH6 could be identified most likely causing the high amount of private mutations. No substantial intratumoral heterogeneity was found in copy number variation analysis apart from a heterozygous duplication of chromosome 6p of patient 4. Conclusions: iCCA show a small but distinct intratumoral heterogeneity. Somatic mutations in mismatch repair proteins might contribute significantly to increased spatial tumor burden and thereby can have crucial impact on clinical management.
The analysis of expression quantitative trait locus (eQTL) data is a challenging scientific endeavor, involving the processing of very large, heterogeneous and complex data. Typical eQTL analyses ...involve three types of data: sequence-based data reflecting the genotypic variations, gene expression data and meta-data describing the phenotype. Based on these, certain genotypes can be connected with specific phenotypic outcomes to infer causal associations of genetic variation, expression and disease. To this end, statistical methods are used to find significant associations between single nucleotide polymorphisms (SNPs) or pairs of SNPs and gene expression. A major challenge lies in summarizing the large amount of data as well as statistical results and to generate informative, interactive visualizations.
We present Reveal, our visual analytics approach to this challenge. We introduce a graph-based visualization of associations between SNPs and gene expression and a detailed genotype view relating summarized patient cohort genotypes with data from individual patients and statistical analyses.
Reveal is included in Mayday, our framework for visual exploration and analysis. It is available at http://it.inf.uni-tuebingen.de/software/reveal/.
guenter.jaeger@uni-tuebingen.de.
Tools aiding in collaborative data analysis are becoming ever more important as researchers work together over long distances. We present an extension to the Gaggle framework, which has been widely ...adopted as a tool to enable data exchange between different analysis programs on one computer.
Our program, GaggleBridge, transparently extends this functionality to allow data exchange between Gaggle users at different geographic locations using network communication. GaggleBridge can automatically set up SSH tunnels to traverse firewalls while adding some security features to the Gaggle communication.
GaggleBridge is available as open-source software implemented in the Java language at http://it.inf.uni-tuebingen.de/gb.
florian.battke@uni-tuebingen.de
Supplementary data are available at Bioinformatics online.
An individual’s genetic information is possibly the most valuable personal information. While knowledge of a person’s DNA sequence can facilitate the diagnosis of several heritable diseases and allow ...personalized treatment, its exposure comes with significant threats to the patient’s privacy. Currently known solutions for privacy-respecting computation require the owner of the DNA to either be heavily involved in the execution of a cryptographic protocol or to completely outsource the access control to a third party. This motivates the demand for cryptographic protocols which enable computation over encrypted genomic data while keeping the owner of the genome in full control. We envision a scenario where data owners can exercise arbitrary and dynamic access policies, depending on the intended use of the analysis results and on the credentials of who is conducting the analysis. At the same time, data owners are not required to maintain a local copy of their entire genetic data and do not need to exhaust their computational resources in an expensive cryptographic protocol.
In this work, we present METIS, a system that assists the computation over encrypted data stored in the cloud while leaving the decision on admissible computations to the data owner. It is based on garbled circuits and supports any polynomially-computable function. A critical feature of our system is that the data owner is free from computational overload and her communication complexity is independent of the size of the input data and only linear in the size of the circuit’s output. We demonstrate the practicality of our approach with an implementation and an evaluation of several functions over real datasets.
GlnK is an important nitrogen sensor protein in
Streptomyces coelicolor.
Deletion of
glnK
results in a medium-dependent failure of aerial mycelium and spore formation and loss of antibiotic ...production. Thus, GlnK is not only a regulator of nitrogen metabolism but also of morphological differentiation and secondary metabolite production. Through a comparative transcriptomic approach between the
S. coelicolor
wild-type and a
S. coelicolor glnK
mutant strain, 142 genes were identified that are differentially regulated in both strains. Among these are genes of the
ram
and
rag
operon, which are involved in
S. coelicolor
morphogenesis, as well as genes involved in gas vesicle biosynthesis and ectoine biosynthesis. Surprisingly, no relevant nitrogen genes were found to be differentially regulated, revealing that GlnK is not an important nitrogen sensor under the tested conditions.
Celotno besedilo
Dostopno za:
CEKLJ, DOBA, EMUNI, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SBMB, SBNM, UILJ, UKNU, UL, UM, UPUK
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