Biology subjects

Hain, C.

Publications and source records attributed to Hain, C..

4 recordsLinked to original sources

bioRxiv2026

HORoSCOPE: Decoding human centromere architecture from short reads using k-mer signatures

Centromeres safeguard genome integrity, yet their roles in human disease remain understudied because of their repetitive sequence. We present HOROSCOPE, a k-mer-based framework that infers centromere architecture and generates centromere length estimates directly from short-read data. Using a reference atlas of 11,836 centromeres from telomere-to-telomere haplotypes, we derive diagnostic k-mer signatures that classify chromosome-specific architectures with 98.2% precision and 99.1% recall. Applied to 4,029 genomes from 80 populations, HOROSCOPE uncovers continental centromeric structure and African-enriched rare architectures. Across 1,359 cancer genomes, HOROSCOPE reveals a dependency of chromosomal rearrangement locations on the kinetochore attachment site position.

genomics↗

bioRxiv2024

Long-read sequencing and structural variant characterization in 1,019 samples from the 1000 Genomes Project

Structural variants (SVs) contribute significantly to human genetic diversity and disease1-4. Previously, SVs have remained incompletely resolved by population genomics, with short-read sequencing facing limitations in capturing the whole spectrum of SVs at nucleotide resolution5-7. Here we leveraged nanopore sequencing8 to construct an intermediate coverage resource of 1,019 long-read genomes sampled within 26 human populations from the 1000 Genomes Project. By integrating linear and graph-based approaches for SV analysis via pangenome graph-augmentation, we uncover 167,291 sequence-resolved SVs in these samples, considerably advancing SV characterization compared to population-wide short-read sequencing studies3,4. Our analysis details diverse SV classes--deletions, duplications, insertions, and inversions--at population-scale. LINE-1 and SVA retrotransposition activities frequently mediate transductions9,10 of unique sequences, with both mobile element classes transducing sequences at either the 3'- or 5'-end, depending on the source element locus. Furthermore, analyses of SV breakpoint junctions suggest a continuum of homology-mediated rearrangement processes are integral to SV formation, and highlight evidence for SV recurrence involving repeat sequences. Our open-access dataset underscores the transformative impact of long-read sequencing in advancing the characterisation of polymorphic genomic architectures, and provides a resource for guiding variant prioritisation in future long-read sequencing-based disease studies.

genomics↗

bioRxiv2023

Long-read Sequencing Shows Complex Structural Variants in Tumor-stage Mycosis Fungoides

Mycosis fungoides is the most common cutaneous T-cell lymphoma. Recurrent copy-number variations are the main unifying mutations in this disease, but to date, a comprehensive analysis of occurrence and type of structural variants responsible for these copy-number variations remains elusive. In this study, we used Oxford Nanopore Technologies long-read sequencing to elucidate the highly rearranged genomic landscape of five mycosis fungoides samples. We show the occurrence of multiple classes of simple and complex SV and analyze the extend of tumor suppressor gene deletion by complex SVs. Furthermore, leveraging long-read data, we inferred the genomic structure of a chromothripsis event. Our findings highlight the potential of long-read sequencing as a powerful tool for comprehensive genomic analysis in mycosis fungoides.

genomics↗

bioRxiv2021

Global distribution of the rooting zone water storage capacity reflects plant adaptation to the environment

The rooting zone water storage capacity (S0) extends from the soil surface to the weathered bedrock (the Critical Zone) and determines land-atmosphere exchange during dry periods. Despite its importance to land-surface modeling, variations of S0 across space are largely unknown as they cannot be observed directly. We developed a method to diagnose global variations of S0 from the relationship between vegetation activity (measured by sun-induced fluorescence and by the evaporative fraction) and the cumulative water deficit (CWD). We then show that spatial variations in S0 can be predicted from the assumption that plants are adapted to sustain CWD extremes occurring with a return period that is related to the life form of dominant plants and the large-scale topographical setting. Predicted biome-level S0 distributions, translated to an apparent rooting depth (zr) by accounting for soil texture, are consistent with observations from a comprehensive zr dataset. Large spatial variations in S0 across the globe reflect adaptation of zr to the hydroclimate and topography and implies large heterogeneity in the sensitivity of vegetation activity to drought. The magnitude of S0 inferred for most of the Earths vegetated regions and particularly for those with a large seasonality in their hydroclimate indicates an important role for plant access to water stored at depth - beyond the soil layers commonly considered in land-surface models.

ecology↗