Malaria genomic surveillance often estimates parasite genetic relatedness using metrics such as Identity-By-Decent (IBD). Yet, strong positive selection stemming from antimalarial drug resistance or other interventions may bias IBD-based estimates. In this study, we utilized simulations, a true IBD inference algorithm, and empirical datasets from different malaria transmission settings to investigate the extent of such bias and explore potential correction strategies. We analyzed whole genome sequence data generated from 640 new and 4,026 publicly available clinical isolates. Our findings demonstrated that positive selection distorts IBD distributions, leading to underestimated effective population size and blurred population structure. Additionally, we discovered that the removal of IBD peak regions partially restored the accuracy of IBD-based inferences, with this effect contingent on the population's background genetic relatedness. Consequently, we advocate for selection correction for parasite populations undergoing strong, recent positive selection, particularly in high malaria transmission settings.

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10370022PMC
http://dx.doi.org/10.1101/2023.07.14.549114DOI Listing

Publication Analysis

Top Keywords

positive selection
16
strong positive
12
population structure
8
genetic relatedness
8
malaria transmission
8
transmission settings
8
selection
5
selection biases
4
biases identity-by-descent-based
4
identity-by-descent-based inferences
4

Similar Publications

The association between multilingual experience factors and cognitive functioning in older adults: A Lifelines study.

J Gerontol B Psychol Sci Soc Sci

January 2025

Linguistics and English as a Second Language, Faculty of Arts, University of Groningen, Groningen, the Netherlands.

Objectives: The complex life experience of speaking two or more languages has been suggested to preserve cognition in older adulthood. This study aimed to investigate this further by examining the relationship between multilingual experience variables and cognitive functioning in a large cohort of older adults in the diversely multilingual north of the Netherlands.

Method: 11,332 older individuals participating in the Lifelines Cohort Study completed a language experience questionnaire.

View Article and Find Full Text PDF

Stroke is the second-leading global cause of death. The damage attributed to the immune storm triggered by ischemia-reperfusion injury (IRI) post-stroke is substantial. However, data on the transcriptomic dynamics of pyroptosis in IRI are limited.

View Article and Find Full Text PDF

Nitrogen doped Carbon Quantum Dots (NCQDs) have been synthesized using most economical and easiest hydrothermal process. Here, N-phenyl orthophenylenediamine and citric acid were utilised as a source of nitrogen and carbon for the preparation of NCQDs. The synthesized NCQDs were characterized using experimental techniques like UV - Vis absorption, FT-IR, transmission electron microscopy (TEM), X-ray Diffraction (XRD), EDX, dynamic light scattering (DLS), fluorimeter and time resolved fluorescence spectroscopy.

View Article and Find Full Text PDF

Subclavian Ansae Stimulation on Cardiac Hemodynamics and Electrophysiology in Atrial Fibrillation: A Target for Sympathetic Neuromodulation.

JACC Clin Electrophysiol

December 2024

St Bartholomew's Hospital, Barts Health NHS Trust, London, United Kingdom; William Harvey Research Institute, Queen Mary University of London, London, United Kingdom. Electronic address:

Background: The sympathetic autonomic nervous system plays a major role in arrhythmia development and maintenance. Historical preclinical studies describe preferential increases in cardiac sympathetic tone upon selective stimulation of the subclavian ansae (SA), a nerve cord encircling the subclavian artery.

Objectives: This study sought to define, for the first time, the functional anatomy and physiology of the SA in humans using a percutaneous approach.

View Article and Find Full Text PDF

Copper Chelate Targeting Externalized Phosphatidylserine Inhibits PD-L1 Expression and Enhances Cancer Immunotherapy.

J Am Chem Soc

January 2025

Department of Pharmacy, The First Affiliated Hospital of USTC; Division of Life Sciences and Medicine, University of Science and Technology of China, Anhui Provincial Key Laboratory of Precision Pharmaceutical Preparation and Clinical Pharmacy, Hefei, Anhui 230026, China.

Inhibitors of the PD-1/PD-L1 immune checkpoint have revolutionized cancer treatment. However, the clinical response remains limited, with only 20% of patients benefiting from treatment and approximately 60% of PD-L1-positive patients exhibiting resistance. One key factor contributing to resistance is the externalization of phosphatidylserine (PS) on the surface of cancer cells, which suppresses immune responses and promotes PD-L1 expression, further hindering the efficacy of PD-L1 blockade therapies.

View Article and Find Full Text PDF

Want 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!