A robust deep learning workflow to predict CD8 + T-cell epitopes
ConclusionsThis study presents a novel computational workflow for accurately predicting CD8 + T-cell epitopes to foster a better understanding of antigen-specific T-cell response and the development of effective clinical therapeutics. (Source: Genome Medicine)
Source: Genome Medicine - September 13, 2023 Category: Genetics & Stem Cells Source Type: research
SARS-CoV-2 infection induces a long-lived pro-inflammatory transcriptional profile
ConclusionsSARS-CoV-2 infection causes a prolonged increase in the pro-inflammatory transcriptional status that could predispose post-acute patients to the development of long-term health consequences, including autoimmune disease, reactivation of other viruses and disruption of the host immune system-microbiome ecosystem. (Source: Genome Medicine)
Source: Genome Medicine - September 12, 2023 Category: Genetics & Stem Cells Source Type: research
Transcriptional immunogenomic analysis reveals distinct immunological clusters in paediatric nervous system tumours
ConclusionsGiven the heterogeneity of immune infiltration within pedNST, our findings suggest personalized immunogenomic profiling is needed to guide selection of immunotherapeutic strategies. (Source: Genome Medicine)
Source: Genome Medicine - September 7, 2023 Category: Genetics & Stem Cells Source Type: research
ClinPrior: an algorithm for diagnosis and novel gene discovery by network-based prioritization
ConclusionsClinPrior is an algorithm that uses standardized phenotype information and interactome data to improve clinical genomic diagnosis. It helps in identifying atypical cases and efficiently predicts novel disease-causing genes. This leads to increasing diagnostic yield, shortening of the diagnostic Odysseys and advancing our understanding of human illnesses. (Source: Genome Medicine)
Source: Genome Medicine - September 7, 2023 Category: Genetics & Stem Cells Source Type: research
Revealing the developmental origin and lineage predilection of neural progenitors within human bone marrow via single-cell analysis: implications for regenerative medicine
ConclusionsThis study suggested BMSCs originating from truncal neural crest to be the source of cells within long bone marrow possessing neural differentiation potential. Unravelling the transcriptomic dynamics of BMSC-derived neural progenitors promises to enhance differentiation efficiency and safety towards clinical application in cell therapy and disease modelling. (Source: Genome Medicine)
Source: Genome Medicine - September 4, 2023 Category: Genetics & Stem Cells Source Type: research
Interplay of Mendelian and polygenic risk factors in Arab breast cancer patients
ConclusionsOverall, our study provides a framework to assess polygenic risk in an understudied population using lpWGS and identifies common variant risk as a factor independent of pathogenic variant carrier status for earlier age of onset of breast cancer among indigenous Arab breast cancer patients. (Source: Genome Medicine)
Source: Genome Medicine - September 1, 2023 Category: Genetics & Stem Cells Source Type: research
A machine learning classifier using 33 host immune response mRNAs accurately distinguishes viral and non-viral acute respiratory illnesses in nasal swab samples
ConclusionThis proof-of-concept signature has potential to be adapted as a clinical point-of-care test ( ‘RespVerity’) to improve the diagnosis of viral ARIs. (Source: Genome Medicine)
Source: Genome Medicine - August 28, 2023 Category: Genetics & Stem Cells Source Type: research
Long-read sequencing identifies a common transposition haplotype predisposing for CLCNKB deletions
ConclusionsThe presence of multiple different deletion alleles in our cohort suggests that largeCLCNKB gene deletions originated from many independently recurring genomic events clustered in a few hot spots. The uncovered associated sequence transposition haplotype apparently predisposes to these additional events.The spectrum ofCLCNKB deletion alleles is broader than expected and likely still incomplete, but represents an obvious candidate for future genotype/phenotype association studies.We suggest a sensitive and cost-efficient approach, consisting of indirect sequence capture and long-read sequencing, to analyse diseas...
Source: Genome Medicine - August 23, 2023 Category: Genetics & Stem Cells Source Type: research
Sequence dependencies and mutation rates of localized mutational processes in cancer
ConclusionsWe summarize our findings in a catalog of localized mutational processes, their sequence preferences, and their estimated mutation rates. (Source: Genome Medicine)
Source: Genome Medicine - August 17, 2023 Category: Genetics & Stem Cells Source Type: research
CCR2 macrophage response determines the functional outcome following cardiomyocyte transplantation
ConclusionsOur results demonstrate that the improved functional outcome following cardiomyocyte transplantation is dependent on a specific CCR2 macrophage response. This work highlights the need to study the role of the immune response for cardiomyocyte cell therapy for successful clinical translation. (Source: Genome Medicine)
Source: Genome Medicine - August 10, 2023 Category: Genetics & Stem Cells Source Type: research
Shared genetic architecture between irritable bowel syndrome and psychiatric disorders reveals molecular pathways of the gut-brain axis
ConclusionsWe found extensive polygenic overlap of IBS and psychiatric and gastrointestinal phenotypes beyond what was revealed with genetic correlations. Leveraging the overlap, we discovered genetic loci associated with IBS which implicate a wide range of biological pathways beyond the gut-brain axis. Genetic differences may underlie the clinical subtype of IBS. These results increase our understanding of the pathophysiology of IBS which may form the basis for the development of individualized interventions. (Source: Genome Medicine)
Source: Genome Medicine - August 1, 2023 Category: Genetics & Stem Cells Source Type: research
A meta-analysis of immune-cell fractions at high resolution reveals novel associations with common phenotypes and health outcomes
ConclusionsThis work contributes an extensively validated high-resolution DNAm reference matrix for blood, which is made freely available, and uses it to generate a comprehensive map of associations between immune-cell fractions and common phenotypes, including health outcomes. (Source: Genome Medicine)
Source: Genome Medicine - July 31, 2023 Category: Genetics & Stem Cells Source Type: research
Morphological and transcriptomic analyses of stem cell-derived cortical neurons reveal mechanisms underlying synaptic dysfunction in schizophrenia
ConclusionsTaken together, our findings in iPSC-derived cortical neurons recapitulate cell type-specific findings in postmortem studies in schizophrenia and have led to the identification of a specific isoform of NRXN3 that modulates synaptic deficits in schizophrenia neurons. (Source: Genome Medicine)
Source: Genome Medicine - July 28, 2023 Category: Genetics & Stem Cells Source Type: research
Prioritizing genes associated with brain disorders by leveraging enhancer-promoter interactions in diverse neural cells and tissues
ConclusionsOverall, our study characterized the gene-enhancer regulatory networks and genetic mechanisms in the human neural cells and tissues, and illustrated the value of reanalysis of publicly available genomic datasets. (Source: Genome Medicine)
Source: Genome Medicine - July 24, 2023 Category: Genetics & Stem Cells Source Type: research
Systematic genomic analysis of SARS-CoV-2 co-infections throughout the pandemic and segregation of the strains involved
ConclusionsCo-infection cases were identified throughout the pandemic, not just in the time periods when highly divergent lineages were co-circulating. Co-infections involving different lineages or strains from the same lineage were occurring in the same proportion. Most cases were mild, did not require medical assistance and were not vaccinated, and a large proportion were associated with the hospital environment. (Source: Genome Medicine)
Source: Genome Medicine - July 24, 2023 Category: Genetics & Stem Cells Source Type: research
