AI Article Synopsis
Article Abstract
Summary: Mutational signatures are recurring DNA alteration patterns caused by distinct mutational events during the evolution of cancer. In recent years, several bioinformatics tools are available for mutational signature analysis. However, most of them focus on specific type of mutation or have limited scope of application. A pipeline tool for comprehensive mutational signature analysis is still lacking. Here we present Sigflow pipeline, which provides an one-stop solution for de novo signature extraction, reference signature fitting, signature stability analysis, sample clustering based on signature exposure in different types of genome DNA alterations including single base substitution, doublet base substitution, small insertion and deletion and copy number alteration. A Docker image is constructed to solve the complex and time-consuming installation issues, and this enables reproducible research by version control of all dependent tools along with their environments. Sigflow pipeline can be applied to both human and mouse genomes.
Availability And Implementation: Sigflow is an open source software under academic free license v3.0 and it is freely available at https://github.com/ShixiangWang/sigflow or https://hub.docker.com/r/shixiangwang/sigflow.
Supplementary Information: Supplementary data are available at Bioinformatics online.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8275980 | PMC |
| http://dx.doi.org/10.1093/bioinformatics/btaa895 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Defining 2 Biologically and Clinically Distinct Groups in Acute Leukemia with a Mixed Phenotype.
Blood
January 2025
Memorial Sloan Kettering Cancer Center, New York, New York, United States.
A mixed phenotype is characteristic of de novo Mixed Phenotype Acute Leukemia (MPAL) but can also be seen in other leukemias. It poses substantial classification and management dilemmas. Herein, we report a large cohort of acute leukemia with a mixed phenotype and define Acute Myeloid Leukemia with Mixed Phenotype (AML-MP) and MPAL as two distinct groups by characterizing the clinical, genetic, and transcriptomic features.
View Article and Find Full Text PDFMutations disrupting the kinase domain of IKKα lead to immunodeficiency and immune dysregulation in humans.
J Exp Med
February 2025
Laboratory of Immunogenetics of Pediatric Autoimmune Diseases, INSERM UMR 1163, Imagine Institute, University Paris Cité, Paris, France.
IKKα, encoded by CHUK, is crucial in the non-canonical NF-κB pathway and part of the IKK complex activating the canonical pathway alongside IKKβ. The absence of IKKα causes fetal encasement syndrome in humans, fatal in utero, while an impaired IKKα-NIK interaction was reported in a single patient and causes combined immunodeficiency. Here, we describe compound heterozygous variants in the kinase domain of IKKα in a female patient with hypogammaglobulinemia, recurrent lung infections, and Hay-Wells syndrome-like features.
View Article and Find Full Text PDFA Mitochondria-Related Signature in Diffuse Large B-Cell Lymphoma: Prognosis, Immune and Therapeutic Features.
Cancer Med
January 2025
Department of Pharmacology, College of Pharmacy, Jinan University, Guangzhou, China.
Background: Distinctive heterogeneity characterizes diffuse large B-cell lymphoma (DLBCL), one of the most frequent types of non-Hodgkin's lymphoma. Mitochondria have been demonstrated to be closely involved in tumorigenesis and progression, particularly in DLBCL.
Objective: The purposes of this study were to identify the prognostic mitochondria-related genes (MRGs) in DLBCL, and to develop a risk model based on MRGs and machine learning algorithms.
Genetic profiling of osteosarcoma in an adolescent using a next‑generation sequencing panel and Sanger sequencing: A case report and review of the literature.
Biomed Rep
March 2025
Circulating Biomarkers Laboratory, Pathology Department, Faculty of Medical Sciences, Rio de Janeiro State University, Rio de Janeiro 20550-170, Brazil.
Osteosarcoma (OS) is the most common malignant bone tumor affecting adolescents and young adults and it usually occurs in the long bones of the extremities. The detection of cancer-related genetic alterations has a growing effect in guiding diagnosis, prognosis and targeted therapies. However, little is known about the molecular aspects involved in the etiology and progression of OS, which limits options for targeted therapies.
View Article and Find Full Text PDFAlterations in cardiac function correlate with a disruption in fatty acid metabolism in a mouse model of SMA.
Hum Mol Genet
January 2025
Centre for Discovery Brain Sciences, Hugh Robson Building, George Square, University of Edinburgh, Edinburgh EH8 9XD, United Kingdom.
Spinal Muscular Atrophy is an autosomal dominant disease caused by mutations and deletions within the SMN1 gene, with predominantly childhood onset. Although primarily a motor neuron disease, defects in non-neuronal tissues are described in both patients and mouse models. Here, we have undertaken a detailed study of the heart in the Smn2B/- mouse models of SMA, and reveal a thinning of the ventriclar walls as previously described in more severe mouse models of SMA.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!