Publications by authors named "Olga Chervova"

Importance: Exposure to war is associated with poor mental health outcomes. Adverse and traumatic experiences can lead to long-lasting DNA methylation changes, potentially mediating the link between adversity and mental health. To date, limited studies have investigated the impact of war on DNA methylation in children or adolescents, hampering our understanding of the biological impact of war exposure.

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Background: Lung adenocarcinoma (LUAD) with lymph node (LN) metastasis is linked to poor prognosis, yet the underlying mechanisms remain largely undefined. This study aimed to elucidate the immunogenomic landscape associated with LN metastasis in LUAD.

Methods: We employed broad-panel next-generation sequencing (NGS) on a cohort of 257 surgically treated LUAD patients to delineate the molecular landscape of primary tumors and identify actionable driver-gene alterations.

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Epigenetic clocks provide an accurate molecular readout of epigenetic age and epigenetic age acceleration (EAA) derived from DNA methylation data have shown promise as biomarkers of ageing. This systematic review synthesised research on associations between EAA measures and various physiological, cognitive, social, and environmental factors. A comprehensive search strategy identified 299 publications reporting 1050 unique EAA-factor associations based on 53 methylation clocks.

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Recently, DNA methylation clocks have been proven to be precise age predictors, and the application of these clocks in cancer tissue has revealed a global age acceleration in a majority of cancer subtypes when compared to normal tissue from the same individual. The polycomb repressor complex 2 plays a pivotal role in the aging process, and its targets have been shown to be enriched in CpG sites that gain methylation with age. This complex is further regulated by the chromatin remodeling complex SWItch/Sucrose Non-Fermentable and its core subunit, notably the tumor suppressor gene SMARCB1, which under physiological conditions inhibits the activity of the polycomb repressor complex 2.

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Article Synopsis
  • The study explores the link between epigenetic age acceleration (EAA) from DNA methylation and the risk of developing colorectal cancer (CRC) using data from 9,360 participants over 16 years.
  • Four measures of EAA (Horvath, Hannum, PhenoAge, and BLUP) were positively associated with increased CRC risk, with odds ratios significantly above 1 for each decile increase.
  • Two other EAA measures (Skin and Blood, and Elastic Net) showed a negative or minimal association with CRC risk, indicating the need for further research to understand these relationships better.
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Aberrant DNA methylation (DNAm) is known to be associated with the aetiology of cancer, including colorectal cancer (CRC). In the past, the availability of open access data has been the main driver of innovative method development and research training. However, this is increasingly being eroded by the move to controlled access, particularly of medical data, including cancer DNAm data.

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We report a personalized tumor-informed technology, Patient-specific pROgnostic and Potential tHErapeutic marker Tracking (PROPHET) using deep sequencing of 50 patient-specific variants to detect molecular residual disease (MRD) with a limit of detection of 0.004%. PROPHET and state-of-the-art fixed-panel assays were applied to 760 plasma samples from 181 prospectively enrolled early stage non-small cell lung cancer patients.

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SETD2-dependent H3 Lysine-36 trimethylation (H3K36me3) has been recently linked to the deposition of de-novo DNA methylation. SETD2 is frequently mutated in cancer, however, the functional impact of SETD2 loss and depletion on DNA methylation across cancer types and tumorigenesis is currently unknown. Here, we perform a pan-cancer analysis and show that both SETD2 mutation and reduced expression are associated with DNA methylation dysregulation across 21 out of the 24 cancer types tested.

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Background: The feasibility of DNA methylation-based assays in detecting minimal residual disease (MRD) and postoperative monitoring remains unestablished. We aim to investigate the dynamic characteristics of cancer-related methylation signals and the feasibility of methylation-based MRD detection in surgical lung cancer patients.

Methods: Matched tumor, tumor-adjacent tissues, and longitudinal blood samples from a cohort (MEDAL) were analyzed by ultra-deep targeted sequencing and bisulfite sequencing.

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We explored the relationship between the copy number of mitochondrial DNA (mtDNA-CN) and all-cause natural mortality. We examined a random population sample in 2003/2005 ( = 9360, men/women, 45-69, the HAPIEE project) and followed up for 15 years. Using a nested case-control design, we selected non-external deaths among those free from baseline cardiovascular diseases (CVD) and cancer ( = 371), and a sex- and age-stratified control ( = 785).

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Epithelioid sarcoma is a rare and aggressive mesenchymal tumour, the genetic hallmark of which is the loss of expression of SMARCB1, a key member of the SWItch/Sucrose Non-Fermentable (SWI/SNF) chromatin remodelling complex. Hampered by its rarity, epithelioid sarcoma has received little research attention and therapeutic options for this disease remain limited. SMARCB1-deficient tumours also include malignant rhabdoid tumour, atypical teratoid and rhabdoid tumour, epithelioid malignant peripheral nerve sheath tumour, and poorly differentiated chordoma.

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Article Synopsis
  • Mosquito-borne diseases cause about a million deaths each year, prompting the need for new ways to control transmission, especially as mosquitoes develop resistance to current insecticides.
  • Researchers have developed a novel methodology using machine learning to analyze mosquito flight patterns, allowing for the identification of male, female, and mating couples through trajectory analysis.
  • This approach has the potential to enhance genetic control strategies for mosquitoes by providing insights into their mating behaviors, achieving a balanced accuracy of 64.5% and an ROC AUC score of 68.4% in field tests.
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Background: Liquid biopsy is a promising non-invasive alternative for cancer screening and minimal residual disease (MRD) detection, although there are some concerns regarding its clinical applications. We aimed to develop an accurate detection platform based on liquid biopsy for both cancer screening and MRD detection in patients with lung cancer (LC), which is also applicable to clinical use.

Methods: We applied a modified whole-genome sequencing (WGS) -based High-performance Infrastructure For MultIomics (HIFI) method for LC screening and postoperative MRD detection by combining the hyper-co-methylated read approach and the circulating single-molecule amplification and resequencing technology (cSMART2.

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We evaluated associations between nine epigenetic age acceleration (EAA) scores and 18 cardiometabolic phenotypes using an Eastern European ageing population cohort richly annotated for a diverse set of phenotypes (subsample, = 306; aged 45-69 years). This was implemented by splitting the data into groups with positive and negative EAAs. We observed strong association between all EAA scores and sex, suggesting that any analysis of EAAs should be adjusted by sex.

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We investigated the relationship between 'epigenetic age' (EA) derived from DNA methylation (DNAm) and myocardial infarction (MI)/acute coronary syndrome (ACS). A random population sample was examined in 2003/2005 ( = 9360, 45-69, the HAPIEE project) and followed up for 15 years. From this cohort, incident MI/ACS (cases, = 129) and age- and sex-stratified controls ( = 177) were selected for a nested case-control study.

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Article Synopsis
  • There has been a surge in whole genome sequencing data from research projects and consumer services, but a gap exists for free tools that simplify data interpretation for users.
  • GenomeChronicler was created by the Personal Genome Project UK to fill this gap, generating reports on genetic variants, ancestry, and traits based on open-access genomic data.
  • Reports can highlight beneficial and harmful variants using data from sources like SNPedia and ClinVar, and the tool can operate offline, ensuring privacy while offering flexible use for individual or batch sample analysis.
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Article Synopsis
  • Integrative analysis of multi-omics data helps to understand biological processes, but accessing raw sequencing data is often challenging due to restricted availability.* -
  • The Personal Genome Project UK (PGP-UK) offers openly accessible multi-omics data from ten different types of biological samples, ensuring participant consent and data integrity through strict quality control.* -
  • The PGP-UK dataset can be easily downloaded via a REST API and is hosted on cloud platforms, making it a valuable resource for researchers in personal and medical genomics.*
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