Feng, B. N. | Search bioRxiv

bioRxiv2026

Assessing and Optimizing Low-Frequency Somatic Mutation Detection: A Multi-Platform High-Throughput Sequencing Perspective

The availability of multiple commercial short-read sequencing platforms necessitates systematic cross-platform performance comparisons, particularly for challenging applications such as low-frequency somatic mutation detection. Here, a large-scale targeted sequencing dataset from five Genome in a Bottle (GIAB) human genomic DNA reference standards, HG001 to HG005, alongside Twist Biosciences cfDNA reference standards featuring 1% variant allele frequency (VAF), was generated by six platforms (NovaSeq 6000, NovaSeq X, FASTASeq 300, GenoLab M, SURFSeq 5000, and MGISEQ-T7). To build a realistic benchmark while keeping authentic sequencing backgrounds, we developed PosMix, a simulating tool that generates position-specific VAFs. To overcome the limitations of conventional variant callers (high recall with poor precision for VarScan2, higher precision with lower recall for Strelka2/Mutect2), we developed SomaticXGB, a machine learning-based caller. In this study, SURFSeq 5000 consistently exhibited the lowest error rates and achieved superior accuracy for VAFs as low as 0.5%, outperforming all other sequencing platforms. On the other hand, SomaticXGB attained F1 scores of approximately 0.92 on simulated datasets with VAFs ranging from 0.5% to 1.5% and 0.89 on Twist 1% standards, substantially outperforming conventional methods. This work delivers a valuable rich multi-platform data resource, offering a standardized pipeline for performance benchmarking and a machine learning-based strategy for optimized somatic mutation detection.

bioinformatics↗

bioRxiv2025

Lubricin's Mucin Domain Has Strong Polyproline Type-II Helical Character

Lubricin is a glycoprotein that is crucial for maintaining joint health by preventing joint wear by reducing joint friction in the boundary mode. Lubricin was recently observed to hinder the formation of uric acid crystals in the joint and prevent a form of gouty arthritis. However, despite lubricins great physiological importance, our current understanding of the molecular origins of lubricins beneficial properties is limited by a lack of detailed structural information regarding its central mucin domain: lubricins large size (227.5 kDa) and numerous glycosylations pose a substantial obstacle to conventional experimental methods for solving protein structures. In this work, we employ a combination of physics-based replica exchange molecular dynamics (REMD) simulations and circular dichroism (CD) experiments to shed light on the structure of lubricins central mucin domain. Using REMD, we model [KEPAPTTP]2, an amino acid repeat found throughout the mucin domain, and find that the mucin domain is likely to exhibit polyproline type II (PPII) helices, which are further stabilized by O-linked oligosaccharide chains. Motivated by these simulation results, we performed circular dichroism spectroscopy on fragments of the mucin domain that also show clear polyproline-II helical character, corroborating our computational findings. Altogether, this work provides strong evidence of a lubricin mucin domain with significant polyproline type II content. As polyproline helices are often also found in other glycoproteins with antifreeze properties, this work may also explain the atomistic underpinnings of their interfacial functions, including lubrication and competition with crystal formation. SIGNIFICANCELubricin is a mucinous glycoprotein containing a central heavily glycosylated domain that plays a crucial role in the lubrication of joints. However, little is known about the structure of this large central mucin domain, which makes the development of related therapeutics or biomedical devices challenging. In this work, we provide strong evidence that lubricins mucin domain possesses polyproline type II (PPII) character that is enhanced by glycosylation upon the basis of a combination of molecular dynamics simulations and circular dichroism experiments. Lubricins PPII character provides a molecular basis for its lubricating properties, which may provide insights into related antifreeze glycoproteins (AFGP) and the development of new biocompatible lubricants and ryo-preservatives.

biophysics↗