Biology subjects

Kristin, A.

Publications and source records attributed to Kristin, A..

3 recordsLinked to original sources

bioRxiv2025

A Universal Duplex Sequencing Approach for Accurate Detection of Somatic Mutations

Ultra-accurate detection of rare somatic mutations is critical for understanding mutational processes in human disease, aging, and environmental exposures, yet current methods are limited by error rates, restricted genome coverage, and high DNA input. We present UDSeq, a duplex sequencing protocol combining random fragmentation, efficient UMI ligation, and quantitative input control to achieve near-complete genome/exome representation from as little as 100 pg DNA. Benchmarking in human sperm estimates a UDSeq error rate of [~]2.5x10-9 per base pair. UDSeq captures mutational signatures from heterogeneous populations without clonal expansion, reproduces exposure-specific patterns in cell lines and rodent models, and enables cross-species profiling. Compared with prior duplex methods, UDSeq yields up to fourfold more usable duplex molecules, improves library conversion, and remains cost-effective. We include a step-by-step protocol with quality-control checkpoints for fragment size, ligation yield, library conversion, and duplication rate. UDSeq provides a scalable, low-input platform for accurate profiling of somatic mutagenesis.

genomics↗

bioRxiv2025

Improved Mutation Detection in Duplex Sequencing Data with Sample-Specific Error Profiles

Duplex sequencing enables highly accurate detection of rare somatic mutations, but existing variant callers often rely on protocol-specific heuristics that limit sensitivity, reproducibility, and cross-study comparability. We present DupCaller, a probabilistic variant caller that builds sample-specific error profiles and applies a strand-aware statistical model for mutation detection. Across 50 synthetic datasets, DupCaller identified 1.25-fold more single-base substitutions (SBSs) and 1.41-fold more indels than a state-of-the-art method, while exhibiting equal or better precision. In three duplex-sequenced cell lines treated with aristolochic acid, it recovered expected mutational signatures while detecting 3.5-fold more SBSs and 2.8-fold more indels. In 93 tissue samples-- including neurons, cord blood, sperm, saliva, and blood--DupCaller showed consistent gains, detecting 1.21- to 2.7-fold more mutations. Sensitivity scaled with sample duplication rate, yielding approximately 1.5-fold more mutations under optimal conditions and over 3-fold more in low-duplication samples where other tools falter. These results establish DupCaller as a robust and scalable solution for somatic mutation profiling in duplex sequencing across diverse biological and technical contexts.

bioinformatics↗

bioRxiv2024

Improving biodiversity in Central and Eastern European domestic gardens needs regionally scaled strategies

Amid ongoing urbanisation and increasing anthropogenic activities, domestic gardens, while they cannot replace undisturbed habitats, play a valuable role in enhancing urban biodiversity by supplementing green areas and improving landscape connectivity. Moreover, biodiversity-friendly gardens also improve human well-being and foster connections between nature and people. To study these benefits, we distributed an online questionnaire between 2022 and 2023, and used a scoring system to evaluate the ecological value of gardens, garden owners motivations, and pesticide use habits. We used machine learning to explore how these indices interact and what sociodemographic factors drive them across nine Central and Eastern European (CEE) countries. Additionally, we explored the differences and similarities between the ecological values of gardens and gardening practices in building high biodiversity. Our findings reveal significant variability both between and within countries, across all three indices with Romania faring low and Czechia reaching high scores in all three indices. Domestic pesticide use was ubiquitous across all CEE and largely unaffected by sociodemographic factors. However, increased time spent with gardening was associated with reduced pesticide use and a greater potential for fostering high biodiversity. Garden owners over 55 tended to follow and uphold longstanding conventional practices and thus lowered both pesticide and garden index scores. The local-scale differences we observed emphasise the need for regionally tailored guidelines for biodiversity-friendly gardening over standardized regulations across Europe. Optimal strategies for effective environmental educational and community programs can be developed based on local biodiversity and the three indices used in this study. To maximize their impact and meet local needs, these programs should educate garden owners about the environmental and health effects of pesticides and offer comprehensive biodiversity-related information across all regions and social strata. This is particularly crucial in Central and Eastern Europe (CEE), where such initiatives are currently underrepresented. HighlightsO_LIDomestic gardens can enhance biodiversity and support human well-being. C_LIO_LIStudy conducted across nine Central and Eastern European countries. C_LIO_LISignificant variability both between and within countries in gardening practices. C_LIO_LIImproving biodiversity in domestic gardens needs regionally scaled strategies. C_LIO_LIReducing pesticide use and increasing awareness are key. C_LI

ecology↗