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Response to the Letter to the Editor: Lack of association between classical HLA genes and asymptomatic SARS-CoV-2 infection.
HGG Adv
January 2025
Helix, San Mateo, CA, USA. Electronic address:
This letter highlights the crucial distinction between studying HLA alleles in unvaccinated individuals during the acute phase of primary SARS-CoV-2 infection versus any SARS-CoV-2 infection including re-infections, breakthrough infections, and primary infections in vaccinated individuals.
View Article and Find Full Text PDFWhole genome sequencing completes the molecular genetic testing workflow of patients with Lynch syndrome.
NPJ Genom Med
January 2025
Department of Molecular Genetics, National Institute of Oncology, Budapest, Hungary.
Multigene panel tests (MGPTs) revolutionized the diagnosis of Lynch syndrome (LS), however noncoding pathogenic variants (PVs) can only be detected by complementary methods including whole genome sequencing (WGS). Here we present a DNA-, RNA- and tumor tissue-based WGS prioritization workflow for patients with a suspicion of LS where MGPT detected no LS-related PV. Among the 100 enrolled patients, MGPT detected 28 simple PVs and an additional 3 complex PVs.
View Article and Find Full Text PDFIn silico functional analysis of the human, chimpanzee, and gorilla MHC-A repertoires.
Immunogenetics
January 2025
Theoretical Biology and Bioinformatics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands.
T cells recognize peptides displayed on the surface of cells on MHC molecules. Genetic variation in MHC genes alters their peptide-binding repertoire and thus influences the potential immune response generated against pathogens. Both gorillas and chimpanzees show reduced diversity at their MHC class I A (MHC-A) locus compared to humans, which has been suggested to be the result of a pathogen-mediated selective sweep.
View Article and Find Full Text PDFConcentration-Bias-Free Discrimination of Single Nucleotide Variants Using Isothermal Nucleic Acid Amplification and Mismatch-Guided DNA Assembly.
Anal Chem
January 2025
Key Laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu 610064, Sichuan, China.
Isothermal nucleic acid amplification techniques are promising alternatives to polymerase chain reaction (PCR) for amplifying and detecting nucleic acids under resource-limited conditions. While many isothermal amplification strategies, such as recombinase polymerase amplification (RPA), offer comparable sensitivity to PCR, they often lack the specificity and robustness for discriminating single nucleotide variants (SNVs), mainly due to the uncontrolled production of massive amplicons. Herein, we introduce a mismatch-guided DNA assembly (MGDA) approach capable of discriminating SNVs in the presence of high concentrations of wild-type (WT) interferences.
View Article and Find Full Text PDFNo evidence for sex-differential transcriptomes driving genome-wide sex-differential natural selection.
Am J Hum Genet
January 2025
Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA; Department of Population Health, University of Texas at Austin, Austin, TX, USA. Electronic address:
Sex differences in human transcriptomes have been argued to drive sex-differential selection (SDS). Here, we show that previous evidence supporting this hypothesis has been largely unfounded. We develop a method to test for a genome-wide relationship between sex differences in expression and selection on expression-influencing alleles (expression quantitative trait loci [eQTLs]).
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