Biology subjects

Choi, H. W.

Publications and source records attributed to Choi, H. W..

4 recordsLinked to original sources

bioRxiv2026

Quantitative Optimization of Sensitivity and Specificity in Targeted and Whole-Exome Sequencing Using Reference-Standard DNA Mixtures

BackgroundWe previously developed a benchmarking strategy using mixtures of homozygote and heterozygote DNAs as reference standards to simultaneously assess sensitivity and false positive (FP) error rates in targeted next-generation sequencing (T-NGS) and whole-exome sequencing (WES), revealing substantial variability across commercial platforms. However, optimal analytic conditions for clinical application remain undefined. MethodsWe systematically evaluated multiple sequencing kits and bioinformatics pipelines across various variant allele fraction (VAF) thresholds to identify conditions that maximize both sensitivity and specificity. Recurrent error-prone alleles were defined and filtered to enhance specificity. ResultsOptimal performance was achieved using the DRAGEN pipeline with recurrent FP allele filtering. For T-NGS, a 1% VAF cutoff yielded a 95% detection threshold of 2.99% and 1.21 FPs per megabase (FP/Mb); for WES, a 2% cutoff yielded a 95% threshold of 5.02% and 1.15 FP/Mb. These settings improved sensitivity >3-fold and reduced FP rates >96% versus suboptimal pipelines. Notably, VAF thresholds flattened sensitivity differences across platforms, obscuring key performance disparities--challenging assumptions that T-NGS is inherently more sensitive than WES. In-house and conventional pipelines undercalled up to 10% of true variants. Restricting reporting of 1-4% VAF variants to [~]1,000 predefined actionable sites enabled recovery of clinically relevant mutations while reducing FP risk >99%. ConclusionsThis study provides a quantitative framework for optimizing NGS performance. Our findings support actionable strategies to improve diagnostic accuracy in clinical genomics through tailored pipeline selection, VAF thresholding, and artifact filtering.

bioinformatics↗

bioRxiv2025

Asymmetric distribution of mitochondrial Ca2+ regulators specifies compartment-specific mitochondrial function and neuronal development

Neuronal polarization is essential for functional compartmentalization, enabling dendritic synaptic integration and axonal action potential generation. While structural differences in mitochondria across compartments have been identified, their functional distinctions remain unclear. Here, we uncovered compartment-specific mitochondrial Ca2+ dynamics and their molecular determinants. In axonal mitochondria, Ca2+ uptake through MCU occurs independently of ER-stored Ca2+ release, with faster matrix Ca2+ clearance than dendritic mitochondria, where Ca2+ uptake predominantly originates from ER Ca2+. The ER-independent mitochondrial Ca2+ uptake in axonal mitochondria is mediated by enriched MCU-regulating proteins, MICU1 and MICU2, while higher NCLX expression facilitates rapid Ca2+ clearance. Moreover, NCLX knockdown, which functionally mimics a mental retardation-associated mutation, caused more significant axonal branching defects compared to dendrites in vivo, aligning with its enrichment in axons. These findings highlight fundamental Ca2+-modulating features and developmental importance of neuronal mitochondria in a compartment-specific manner and reveal the key underlying molecular mechanisms.

neuroscience↗

bioRxiv2024

Evaluation of false positive and false negative errors in targeted next generation sequencing

BackgroundAlthough next generation sequencing (NGS) has been adopted as an essential diagnostic tool in various diseases, NGS errors have been the most serious problem in clinical implementation. Especially in cancers, low level mutations have not been easy to analyze, due to the contaminating normal cells and tumor heterozygosity. ResultsIn targeted NGS (T-NGS) analyses for reference-standard samples containing mixtures of homozygote H. mole DNA with blood genomic DNA at various ratios from four certified NGS service providers, large differences in the lower detection limit of variants (16.3 times, 1.51[~]24.66%) and the false positive (FP) error rate (4280 times, 5.814 x 10-4 [~]1.359 x 10-7) were found. Employment of the commercially available Dragen system for bioinformatic analyses reduced FP errors in the results from companies BB and CC, but the errors originating from the NGS raw data persisted. Bioinformatic conditional adjustment to increase sensitivity (less than 2 times) led to a much higher FP error rate (610[~]8200 times). In addition, problems such as biased preferential reference base calls during bioinformatic analysis and high-rate FN errors in HLA regions were found in the NGS analysis. ConclusionT-NGS results from certified NGS service providers can be quite various in their sensitivity and FP error rate, suggesting the necessity of further quality controls for clinical implementation of T-NGS. The present study also suggests that mixtures of homozygote and heterozygote DNAs can be easily employed as excellent reference-standard materials for quality control of T-NGS.

genomics↗

bioRxiv2017

Members of the abscisic acid co-receptor PP2C protein family mediate salicylic acid-abscisic acid crosstalk

The interplay between abscisic acid (ABA) and salicylic acid (SA) influences plant responses to various (a)biotic stresses; however, the underlying mechanism(s) for this crosstalk is largely unknown. Here we report that type 2C protein phosphatases (PP2Cs), some of which are negative regulators of ABA signaling, bind SA. SA binding suppressed the ABA-enhanced interaction between these PP2Cs and various ABA receptors belonging to the PYR/PYL/RCAR protein family. Additionally, SA suppressed ABA-enhanced degradation of PP2Cs and ABA-induced stabilization of SnRK2s. Supporting SAs role as a negative regulator of ABA signaling, exogenous SA suppressed ABA-induced gene expression, whereas SA-deficient sid2-1 mutants displayed heightened PP2C degradation and hypersensitivity to ABA-induced suppression of seed germination. Together, these results suggest a new molecular mechanism through which SA antagonizes ABA signaling. A better understanding of the crosstalk between these hormones is important for improving the sustainability of agriculture in the face of climate change.

plant biology↗