Pan-cancer analysis of whole genomes

Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale(1-3). Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter(4); identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation(5,6); analyses timings and patterns of tumour evolution(7); describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity(8,9); and evaluates a range of more-specialized features of cancer genomes(8,10-18).Peer reviewe

Персонализированная терапия при солидных опухолях: результаты ретроспективного многоцентрового исследования клинической применимости теста FoundationOne® Medicine

Background. The use of targeted sequencing panels makes it possible to optimize and personalize the treatment strategy for cancer patients. Given the lack of a clear «portrait of the patient», the role of large panels (200 or more genes) in the treatment of a patient has not yet been determined.Aim. Assessment of the relationship between the results of targeted sequencing of tumor tissue or ctDNA and the treatment carried out after obtaining these data in patients with various solid tumors.Materials and methods. We retrospectively evaluated the NGS results and the treatments, provided to the 184 patients after NGS testing between 06.2016 and 06.2021. For analysis, one of two methods is used: a histological sample or the patient’s blood plasma. Evaluation of the results and determination of treatment tactics were carried out within the framework of a multidisciplinary commission. The frequency of detection of molecular disorders, the number of mutations in each sample, and the frequency of detection of targets for targeted therapy were assessed.Results. Molecular disorders were detected in 88.5 % (n = 163). The average number of mutations in one sample was 6. The maximum was detected in colorectal cancer patients; their average value was 8. The minimum was determined in non-small cell lung cancer and ovarian cancer patients, the average number of mutations was 3 in each localization. The average time from the moment the material was received by the laboratory to the generation of the report was 11 days. Targeted targets were identified in 25 (13.6 %) patients and therapy was started. Therapy with tyrosine kinase inhibitors of the first – third generations were performed in 12 (48 %) patients, PARP inhibitors – in 3 (24 %), BRAF and MEK inhibitors – in 2 (8 %), anti-HER2 therapy – in 1 (4 %). Targeted therapy within international clinical trials was initiated in 4 (16 %) patients. Immunotherapy was recommended in 3 (12 %) patients. In multivariate analysis, the chance of prescribing therapy based on the results of FM1 analysis was influenced by: mRAS (odds ratio 0.08; 95 % confidence interval 0.01–0.65; p = 0.018) and mEGFR (odds ratio 4.8; 95 % confidence interval 1.4–16.3; p = 0.012).Conclusion. The effectiveness of the FM1 test in real clinical practice in the Russian Federation corresponds to international data. In the presence of a mutation in the RAS genes, an additional FM1 test determines a low chance of detecting clinically significant disorders for which personalized treatment can be prescribed. The high frequency of prescription of therapy based on the results of blood plasma tests is due to the cohort of patients with non-small cell lung cancer and the detection of a mutation in the EGFR gene.Введение. Применение панелей таргетного секвенирования дает возможность оптимизировать и персонализировать стратегию лечения онкологических пациентов. Учитывая отсутствие четкого «портрета пациента», на сегодняшний день не определена роль больших панелей (200 и более генов).Цель исследования – оценка связи результатов таргетного секвенирования ткани опухоли или циркулирующей опухолевой ДНК и проведенного после получения этих данных лечения у больных с различными солидными опухолями.Материалы и методы. На базе 6 российских центров за период с июня 2016 г. по июнь 2021 г. было выполнено таргетное секвенирование FoundationOne® Medicine 184 пациентам с солидными опухолями. Для проведения анализа использовали 1 из 2 методов: гистологический образец или плазма крови пациента. Оценка результатов и определение тактики лечения проводились в рамках мультидисциплинарной комиссии. Оценивали частоту выявления молекулярных нарушений, число мутаций в каждом образце, частоту выявления мишеней для таргетной терапии.Результаты. Молекулярные нарушения выявлены у 88,5 % (n = 163). Среднее число мутаций в 1 образце – 6. Максимальное число выявлено при колоректальном раке, их среднее значение составило 8. Минимальное же число определялось при немелкоклеточном раке легкого и раке яичников, среднее число мутаций составило по 3 в каждой локализации. Среднее время с момента поступления материала в лабораторию до формирования отчета составило 11 дней. У 25 (13,6 %) пациентов выявлены таргетные мишени и начато лечение. Терапия ингибиторами тирозинкиназы I–III поколений проведена 12 (48 %) пациентам, PARP-ингибиторами – 3 (24 %), BRAF- и MEK-ингибиторами – 2 (8 %), анти-HER2 терапия – 1 (4 %). Таргетная терапия в рамках международных клинических исследований начата у 4 (16 %) пациентов. Иммунотерапия рекомендована 3 (12 %) пациентам. При многофакторном анализе на шанс назначения терапии по результатам анализа FM1 влияли mRAS (отношение шансов 0,08; 95 % доверительный интервал 0,01–0,65; р = 0,018) и mEGFR (отношение шансов 4,8; 95 % доверительный интервал 1,4–16,3; р = 0,012).Выводы. Эффективность применения теста FM1 в реальной клинической практике в РФ соответствует международным данным. При наличии мутации в генах RAS дополнительное проведение теста FM1 определяет низкий шанс выявления клинически значимых нарушений, к которым можно будет назначить персонализированное лечение. Высокая частота назначения терапии по результатам анализа плазмы крови обусловлена когортой пациентов с немелкоклеточным раком легкого и выявлением мутации в гене EGFR

Career Development and Gender in Latvia and Finland

Šī bakalaura mērķis ir noskaidrot dzimuma ietekmi uz karjeru Latvijā un Somijā. Darbā aplūkota dzimumu līdztiesības vēsturiskā attīstība abās valstīs, atšķirības mūsdienu darba tirgū, ģimeņu ar maziem bērniem vieta darba tirgū, izglītības ietekme uz karjeras izaugsmi, kā arī citi faktori, kas palīdz noteikt dzimuma ietekmi uz karjeru. Darba gaitā izmantoti Latvijā un Somijā līdz šim veiktie pētījumi, kuri iepriekš nav tikuši salīdzināti, abu valstu centrālo statistikas biroju sniegtie dati, kā arī valstu politikas dokumenti.The aim of bachelor thesis Career Development and Gender in Latvia and Finland is to research gender’s influence on career in Latvia and Finland. Some of the topics covered in the paper are historical development of gender equality, differences in labor market, the situation of families with small children in labor market, as well as influence of education on career development. Materials used in research include researches done till now in Latvia in Finland, whitch are not compared between themselves, the date provided by Central Statistical Bureaus of both countries and policy documents

Ab initio calculations of elastic properties of Ru1-xNixAl superalloys

Contains fulltext : 76051.pdf (publisher's version ) (Open Access)3 p

Electronic structure and anomalous physical properties of metastable Al-Si solid solutions

Al-Si solid solutions synthesized under high pressure demonstrate striking physical properties, such as enhanced superconductivity and peculiarities of low-temperature transport coefficients. In order to understand the connection of these effects to the electronic structure changes we have performed a first-principles study of the electronic spectra and Fermi surfaces of Al-Si solid solutions. We show that two electronic topological transitions (ETT's) lead to unusual concentration dependencies of the resistivity, thermoelectric power and Hall constant of the system while a variety of other interesting phenomena such as lattice instability and superconductivity enhancement may be a result of the nesting features appearing upon Si doping. We present also the results of our theoretical calculations of the thermodynamic and transport properties of Al-Si solid solutions which are in good agreement with experiment and reproduce nicely the experimentally observed peculiarities