•No technical bias between fresh frozen and FFPE samples.•A high fraction of adenocarcinoma patients with activating KRAS mutations.•Mutations in TP53, STK11 and SMARCA4 linked to poor prognosis in ...adenocarcinoma.•Mutations in CSMD3 linked to better prognosis in squamous cell carcinoma.•Co-mutations in TP53 or STK11 confer poor prognosis in KRAS positive patients.
Non-small cell lung cancer (NSCLC) is a heterogeneous disease with unique combinations of somatic molecular alterations in individual patients, as well as significant differences in populations across the world with regard to mutation spectra and mutation frequencies. Here we aim to describe mutational patterns and linked clinical parameters in a population-based NSCLC cohort.
Using targeted resequencing the mutational status of 82 genes was evaluated in a consecutive Swedish surgical NSCLC cohort, consisting of 352 patient samples from either fresh frozen or formalin fixed paraffin embedded (FFPE) tissues. The panel covers all exons of the 82 genes and utilizes reduced target fragment length and two-strand capture making it compatible with degraded FFPE samples.
We obtained a uniform sequencing coverage and mutation load across the fresh frozen and FFPE samples by adaption of sequencing depth and bioinformatic pipeline, thereby avoiding a technical bias between these two sample types. At large, the mutation frequencies resembled the frequencies seen in other western populations, except for a high frequency of KRAS hotspot mutations (43%) in adenocarcinoma patients. Worse overall survival was observed for adenocarcinoma patients with a mutation in either TP53, STK11 or SMARCA4. In the adenocarcinoma KRAS-mutated group poor survival appeared to be linked to concomitant TP53 or STK11 mutations, and not to KRAS mutation as a single aberration. Similar results were seen in the analysis of publicly available data from the cBioPortal. In squamous cell carcinoma a worse prognosis could be observed for patients with MLL2 mutations, while CSMD3 mutations were linked to a better prognosis.
Here we have evaluated the mutational status of a NSCLC cohort. We could not confirm any survival impact of isolated driver mutations. Instead, concurrent mutations in TP53 and STK11 were shown to confer poor survival in the KRAS-positive adenocarcinoma subgroup.
Abstract
Background
In recent years, nucleotide sequencing has become increasingly instrumental in both research and clinical settings. This has led to an explosive growth in sequencing data produced ...worldwide. As the amount of data increases, so does the need for automated solutions for data processing and analysis. The concept of workflows has gained favour in the bioinformatics community, but there is little in the scientific literature describing end-to-end automation systems. Arteria is an automation system that aims at providing a solution to the data-related operational challenges that face sequencing core facilities.
Findings
Arteria is built on existing open source technologies, with a modular design allowing for a community-driven effort to create plug-and-play micro-services. In this article we describe the system, elaborate on the underlying conceptual framework, and present an example implementation. Arteria can be reduced to 3 conceptual levels: orchestration (using an event-based model of automation), process (the steps involved in processing sequencing data, modelled as workflows), and execution (using a series of RESTful micro-services). This creates a system that is both flexible and scalable. Arteria-based systems have been successfully deployed at 3 sequencing core facilities. The Arteria Project code, written largely in Python, is available as open source software, and more information can be found at https://arteria-project.github.io/
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Conclusions
We describe the Arteria system and the underlying conceptual framework, demonstrating how this model can be used to automate data handling and analysis in the context of a sequencing core facility.
Twenty-four plant lignans were analyzed by high-performance liquid chromatography−tandem mass spectrometry in bran extracts of 16 cereal species, in four nut species, and in two oilseed species ...(sesame seeds and linseeds). Eighteen of these were lignans previously unidentified in these species, and of these, 16 were identified in the analyzed samples. Four different extraction methods were applied as follows: alkaline extraction, mild acid extraction, a combination of alkaline and mild acid extraction, or accelerated solvent extraction. The extraction method was of great importance for the lignan yield. 7-Hydroxymatairesinol, which has not previously been detected in cereals because of destructive extraction methods, was the dominant lignan in wheat, triticale, oat, barley, millet, corn bran, and amaranth whole grain. Syringaresinol was the other dominant cereal lignan. Wheat and rye bran had the highest lignan content of all cereals; however, linseeds and sesame seeds were by far the most lignan-rich of the studied species. Keywords: 7-Hydroxymatairesinol; syringaresinol; lignans; cereals; rye bran; wheat bran; HPLC-MS/MS; accelerated solvent extraction
► Cloudberry seeds are the third most lignan-rich dietary source known. ► Several berry species are more lignan-rich than cereal brans. ► The lignans are concentrated in the seeds of berries and in ...the hull of oilseeds. ► Berry and seed extracts contain usually both enantiomers of the major lignans. ► Berries and seeds contain todolactol and the novel lignan 7′-hydroxylariciresinol.
In seed extracts of five oilseed species, in bran extracts of three cereal species, and in seed and/or whole berry extracts of 10 berry species, the concentrations of a large number of lignans and the enantiomeric composition of selected lignans were determined. In the case of sesame and hemp seeds, the lignan content and composition of the whole seeds was compared to that of the hulled seeds. The results showed that cloudberry seeds are the third most lignan-rich food source after linseeds and whole sesame seeds, and that most of the berry species analysed were more lignan-rich than the cereal brans. The lignans are concentrated in the hull of the oilseeds and in the seeds of the berries. In most samples, secoisolarici-, pino-, medio-, and syringaresinol were present as a mixture of two enantiomers.
The main aim of this study was to chemically characterise the polymeric fraction of birch pulp extractives. We showed that 70–96% of the material in extracts of fully bleached birch kraft elemental ...chlorine-free (ECF) pulp from three Finnish mills consists of compounds that are undetectable by conventional gas chromatography (GC) analysis, i.e. high-molar mass (HM) material. There were small variations in the extractive content and composition between the three mills, but the overall trend was the same. The HM material was present mainly in the acetone extracts, and the molar mass was shown to range between ca. 1000 and 10 000 Da. Alkaline hydrolysis of the hexane and acetone extracts released fatty acids (FAs) especially, but also sterols and triterpenoids. The dominating FAs were palmitic and stearic acids. Pyrolysis and thermally assisted hydrolysis and methylation (THM)-GC-mass spectrometry (MS) analyses confirmed that the HM material consists mainly of FA units, and additionally of sterol, triterpenoid and aromatic units. Nuclear magnetic resonance (NMR) analysis further confirmed the presence of FAs containing aromatic groups, but also glycerol units. The FA chains seemed to be linked to each other by ester linkages mainly, although ether linkages were also present. The FA oligomers and polymers may have a suberin-like structure.
Stilbenes are plant polyphenols that have shown beneficial pharmacological activities in a variety of diseases. The considerable amount of stilbene glucosides in spruce inner bark encouraged us to ...develop a straightforward and simple method of extraction with high recovery and yield. Stilbene glucosides from fresh inner bark of Norway spruce were extracted in one simple step with acetone at 20 °C. After three weeks of soaking in acetone, the extracts were dried and the composition was determined by GC-FID using a short and a long column (HP-5) and GC-MS (HP-1). The amount of the extracted compounds was also compared with a similar extract from air dried inner bark samples. The extracts from the fresh sample contained 30–50% of stilbene glucosides and the average yield 0.185 g extract/g bark was as good as or slightly better than in previously reported works. However, no drying, milling, or sequential extractions with different solvents in elevated temperatures were needed. Moreover, this study revealed that the drying process can decrease the amount of extractable stilbenes significantly. Therefore, this method can be considered as an alternative for preparative isolation of stilbene glucosides, especially isorhapontin and astringin from inner bark of Norway spruce.
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