Biology subjects

Park, P. J.

Publications and source records attributed to Park, P. J..

At least 19 recordsLinked to original sources

bioRxiv2026

Complete timing of copy-number amplification histories reveals whole-genome duplication dynamics and coincident oncogene amplification bursts

Copy-number amplifications drive cancer evolution through increased oncogene dosage. Mutations acquired before a gain are co-amplified, so their multiplicity places successive gains on a molecular timescale. This principle has been used to time individual gains and whole-genome duplication (WGD), but possible gain histories multiply rapidly with copy number, confining existing methods to low copy-number states or predefined scenarios and leaving oncogene-bearing amplifications unresolved. Here we describe a mathematical framework to systematically enumerate every allele-specific gain route to a copy-number state and derive an analytical timing for each gain, implemented in a method called Tau. Across pan-cancer genomes, punctuated multichromosomal events account for roughly three-quarters of clonal gains. Most are WGD, acquired early and often repeated within a doubling-prone subset, but a distinct, predominantly monoallelic class recurs on tumor-type-specific chromosomes, representing a coordinated mode separate from doubling. Strikingly, the highest copy-number states are reached not gradually but in abrupt bursts that cluster around WGD and contain more gains than doubling alone can produce, recurring at oncogenes. WGD is therefore not a passive doubling but a window in which localized oncogene amplification becomes far more frequent. By resolving the order of gains and the mutational processes shifting between them, Tau establishes punctuated amplification as a pervasive mode of cancer genome evolution.

bioinformatics↗

bioRxiv2026

Somatic mutations and single-nucleus transcriptomics reveal uniquely human properties of neuronal aging

Human brain aging is frequently studied in model mammals that rarely show the natural age-related neurodegenerative conditions that afflict humans, yet little is known about how genomic stability compares across species during aging. Although somatic single nucleotide variant (SNV) and short insertion/deletion (Indel) mutations accumulate at rates that inversely scale to lifespan in colon cells - leaving diverse mammals with similar end-of-life burdens of mutations - here we show that cerebral cortical neurons accumulate SNVs at annual rates that are remarkably similar across six mammalian species (human, chimpanzee, rhesus macaque, marmoset, ferret, mouse) resulting in >12-fold more mutations in human neurons at the end of life compared to mouse neurons. Despite the conservation of overall annual mutation accumulation rates, mutational patterns--and hence likely mutagenic mechanisms--show sharp differences between species, with a nucleotide substitution pattern linked to neurodegenerative diseases accumulating almost exclusively in humans during aging. Coinciding with their higher mutational burden, single-nucleus transcriptomic analyses reveal pervasive age-associated proteostasis and mitochondrial dysregulation in human neurons that is far less pronounced in aged chimpanzees and rhesus macaques. These findings show that the pervasive effects of human neuronal aging might be linked to our long lifespan and are therefore not evident in animal models.

neuroscience↗

bioRxiv2026

Correlation-aware discovery of co-occurring mutational signatures in cancer

Somatic mutations in cancer genomes record the activities of diverse mutational processes. Mutational signature analysis has advanced mechanistic understanding of mutagenesis and informed clinical decision-making, yet existing methods assume independence among signatures--an unrealistic assumption that can produce composite or contaminated signatures, reduce detection power, and yield inconsistent results. Here we present Cornet (CORrelated NMF ExTraction), a framework for mutational signature discovery that explicitly models co-occurring processes and jointly infers signatures and their correlation structure. Benchmarking on simulated data shows Cornet more accurately recovers distinct signatures under strong correlations. Applied to cancer genomes, Cornet enables unsupervised discovery of the colibactin-associated signature SBS88 in oral cancers and identifies the tobacco smoking signature SBS4 in bladder cancer, where it was previously thought absent. Cornet also uncovers a novel mutational process implicated in early-onset colorectal cancer and a signature arising from the interplay between tobacco smoking and ERCC2-mutation-driven nucleotide-excision repair deficiency. Together, these results demonstrate that modeling correlations among mutational processes is essential for high-resolution signature discovery and dissecting the mutational etiology of human cancer.

bioinformatics↗

bioRxiv2026

Integrated map of somatic mosaicism across human tissues in 25 individuals

Although all cells in the body descend from one genome, they accumulate distinct genetic and epigenetic changes over a lifetime, producing a mosaic of somatic variation that can shape development, aging, and disease. This mosaicism is often studied in isolation, leaving unclear how these forms relate within and between individuals. Here, we present the first integrated analysis of the Somatic Mosaicism across Human Tissues (SMaHT) Network's production resource, profiling up to 20 tissues from 25 donors using short- and long-read, duplex, single-cell, transcriptomic, and epigenomic sequencing, alongside donor-specific near-telomere-to-telomere assemblies. Somatic mutation burden cannot be captured by a single data type or metric, as tissues accumulate distinct variant classes largely independently of one another. Long-read and single-cell data resolved cell-type-specific mutational processes, traced mobile element insertions to source loci, and revealed the developmental timing and functional consequences of individual mutations. Donor-specific assemblies uncovered elevated mutation rates within centromeres and segmental duplications inaccessible to standard reference genomes, while haplotype-resolved chromatin and methylation data showed that nongenetically-deterministic epigenetic states are pervasive across tissues. Together, these findings provide an integrated, multi-scale portrait of somatic mosaicism across the human body, establishing a baseline against which its contributions to aging and disease can be measured.

genomics↗

bioRxiv2026

Replication fork directionality reveals how structural variants arise under replication stress

Structural variants (SVs) in cancer are associated with defects in DNA repair and replication stress, but the mechanisms generating common SV types remain unresolved. We propose that large (>100 kb) tandem duplications originate through a novel sister-fork breakage-fusion mechanism. To capture replication-related context beyond breakpoints, we developed an algorithm to characterize replication timing, origin density, and fork direction across SV-spanned regions, features that refine and differentiate previously defined SV signatures. Large tandem duplications frequently overlap replication origins from which forks proceed bidirectionally; combined with independent evidence from APOBEC strand asymmetry, this pattern is compatible uniquely with the proposed mechanism. Although tandem duplications in CCNE1-amplified and CDK12-mutant cancers also concentrate around origins and highly transcribed genes, they display distinct contexts: CDK12-mutant SVs arise near later-firing origins, whereas those in CCNE1-amplified tumors often coincide with genes in specific strand configurations, suggesting different causes of fork stalling. Incorporating replication features into signature analysis enabled the discovery of new SV signatures, which we used to build SVIG, a multi-class classifier of SV phenotypes. SV signatures attributed to replication stress may help guide therapies targeting this vulnerability.

bioinformatics↗

bioRxiv2026

Topographical archetypes of somatic mutagenesis in cancer

The genome of every cancer cell carries a record of the mutational processes that have acted throughout its history. Mutational signature analysis, which infers the activity of mutagenic processes from their characteristic base-change patterns, has become an indispensable tool for interpreting somatic mutations. However, this framework captures only which types of mutations a process generates and not where in the genome they occur -- a distribution influenced by replication timing, chromatin organization, transcription, DNA secondary structure, and other genomic features. Here, we present a generative probabilistic framework (MuTopia) that jointly infers mutational spectra and their genome-wide topography as nonlinear functions of genomic and epigenomic state. Applied to whole-genome sequencing data from 15 tumor types, MuTopia reveals that mutational processes fall into eight conserved topographic archetypes, or topotypes, shaped primarily by replication timing and chromatin state. Diverse mutational processes converge upon this limited repertoire, indicating that the genomic distribution of mutagenesis is constrained less by the source of damage than by how that damage is processed. Individual mutational processes exhibit state-dependent variation in their genomic distributions: the same signature can adopt distinct topotypes depending on repair proficiency and replication stress. For instance, SBS8 shifts from a canonical late-replicating profile in homologous recombination-proficient tumors to an early-replicating, stress-associated topotype in HR-deficient tumors, and replication stress similarly reshapes the genomic distribution of APOBEC editing. Topotypes, therefore, provide a classification of mutagenesis distinct from spectral signatures, capturing aspects of tumor biology that spectra alone cannot resolve.

bioinformatics↗

bioRxiv2025

Nanopore whole-genome sequencing reveals conserved chromosome-specific telomere architecture across tissues and populations

Telomeres are repetitive nucleoprotein structures that cap the ends of linear chromosomes and are essential for maintaining genomic stability. While individual chromosome ends maintain distinct telomere lengths, the extent of this conservation across tissues and populations remains unclear due to the difficulty of analyzing repetitive telomeric sequences. Here, we show that high-coverage whole-genome Nanopore sequencing enables robust measurement of telomere length at the level of individual chromosomes. Nanopore reads yield reproducible telomere length estimates across replicates, in contrast to PacBio HiFi reads. Across > 250 individuals from 1000 Genomes and the SMaHT projects, chromosome-specific telomere length patterns are conserved across individuals and tissues, with tissues from the same individual showing highly similar patterns. This conserved landscape suggests coordinated regulation, whose disruption may contribute to genomic instability. Nanopore sequencing also allows simultaneous detection of structural variants, including disruption of TERT and NHP2 that drive global telomere shortening. Furthermore, our quantification of telomere variant repeats in positional context indicates active telomerase-mediated elongation. Our integrated profiling of telomere length and structural variation enables inference of variant effects on chromosome-specific telomere dynamics and may uncover risk factors for short telomere syndromes and cancer. Importantly, positionally fully resolved telomeric variant repeat patterns may predict activated telomere maintenance mechanisms with high accuracy. SignificanceResolving chromosome-specific telomere length and variant-repeat architecture across tissues and individuals provides a framework to dissect coordinated telomere maintenance, its disruption by genetic variants, and how this shapes telomere mosaicism and disease risk.

genomics↗

bioRxiv2025

A comprehensive view of somatic mosaicism by single-cell DNA analysis

Single-cell DNA sequencing offers a powerful means of studying somatic mosaicism but requires careful analysis to mitigate DNA amplification-related artifacts. We performed primary template-directed amplification (PTA) and sequencing of 102 nuclei from postmortem lung and colon tissues of a 74-year-old male. Single-cell mutation burdens and spectra were validated by duplex sequencing and revealed heterogeneity across organs and cells, including signatures of APOBEC activity and tobacco exposure. Cells from both tissues exhibited chromosomal aneuploidies, loss of chromosome Y, and chromosomal rearrangements including rearrangements of the T-cell receptor loci indicative of T-cells. Shared embryonic mutations between cells enabled reconstruction of cellular ancestries from the zygote, which were validated by bulk sequencing. Collectively, we demonstrate a comprehensive approach for single-cell genomics that yields an expansive view of diverse somatic mutation types from development through aging across diverse tissues--insights that are obscured in bulk sequencing and only partially captured by other single-cell methods.

genomics↗

bioRxiv2025

Diploid donor-specific assembly enhances somatic structural variant detection in cancer genomes

Somatic structural variants (SVs) play a crucial role in tumor development and evolution, yet their identification remains challenging, partly due to limitations in current reference genomes. We present a systematic evaluation of diploid donor-specific assemblies (DSAs)--generated based on hybrid long-read sequencing data--as the reference genome for detecting somatic SVs. We analyzed six tumor-normal cell line pairs, using the EchoSV tool we developed to consolidate haplotype-based SVs into a single DSA-based set and to compare SVs across reference genomes. Across Illumina, PacBio HiFi, and Oxford Nanopore Technology (ONT) data, DSA-based analysis improved read-mapping quality, identified over 20% additional SVs compared to GRCh38 and CHM13, and reduced germline artifacts. Most DSA-specific SVs were isolated deletions or insertions in repetitive elements, especially in satellite regions. By tracking sequence-context differences, we identified scenarios in which DSAs enabled detection of SVs missed on GRCh38/CHM13, and confirmed their functional impact with RNA-seq. These results highlight the value of integrating diploid DSAs into somatic SV analysis.

genomics↗

bioRxiv2025

Timing the onset of homologous recombination deficiency before cancer diagnosis

Mutations in BRCA1 and BRCA2 genes, whether inherited or somatically acquired, cause homologous recombination deficiency (HRD) in tumor cells. The timing of HRD onset in the emerging tumor lineage is unknown. Here, we present HRDTimer, an algorithm to infer the onset of HRD-driven mutagenesis prior to cancer diagnosis. We estimate that HRD arises at 34% of SBS1-based molecular time---corresponding to a median of 8.3 years (IQR 7.1--10.4) prior to diagnosis in triple-negative breast cancers, and 15.0 years (IQR 12.0--20.6) in ER-positive breast cancers. Bulk sequencing reveals accelerated SBS1 accumulation following neoplastic transformation compared to normal tissue, influencing the estimated age of HRD onset. Single-cell duplex sequencing confirms SBS1 acceleration in tumors and further shows that non-tumor cells largely lack the HRD signature, indicating that HRD is rare in pre-malignant cells, even in BRCA1/2 mutation carriers. Together, our analysis pinpoints the onset of HRD before diagnosis, defining a window for detection and potential interception.

genomics↗

bioRxiv2025

Comprehensive benchmarking of somatic single-nucleotide variant and indel detection at ultra-low allele fractions using short- and long-read data

Mosaic mutations in normal tissues occur at low variant allele fractions (VAFs), complicating detection. To benchmark strategies, the SMaHT Network created a cell-line mixture (1:49) and produced ultra-deep whole-genome sequencing using short and long reads (five centers, 180-500x each). We assembled a reference of 44,008 mosaic SNVs and 2,059 Indels, cross-validation between platforms to expose limits of short-read analysis. We also partitioned the genome by mappability to examine the impact of genomic context, added a negative reference set, and accounted for culture-derived mutations. When seven institutions applied eleven algorithms to mixture data, call sets were largely discordant across tools and replicates, partly reflecting stochastic presence of low-VAF mutations in biological replicants. For >2% VAF SNVs, sensitivity and precision approached [~]80% at [≥]300x, with little gain from additional sequencing. This work provides a comprehensive framework for reliable detection of low-VAF mutations in non-cancer tissues and a valuable resource for the community.

bioinformatics↗

bioRxiv2025

Tissue specificity and chromosomal alterations shape divergent immune programs in HRD tumors

Homologous recombination deficiency (HRD) activates pro-inflammatory cGAS/STING signaling, positioning it as a biomarker for combining immune checkpoint blockade (ICB) and PARP inhibition (PARPi). However, the consequences of HRD on the immune landscape across cancers remain unclear. Here, we applied a pan-cancer HRD classifier to >10,000 tumors from The Cancer Genome Atlas and uncovered striking heterogeneity in immune activity. Compared to HR-proficient tumors, HRD tumors showed elevated inflammation in breast, ovarian, and endometrial cancers. These tumors exhibited robust activation of innate and adaptive immune pathways (IFN, NF-{kappa}B) and transcriptional hallmarks of senescence, angiogenesis, and adenosine signaling. In contrast, lung, head and neck, and melanoma HRD tumors displayed suppressed inflammation and evidence of immune escape through large-scale loss-of-heterozygosity (LOH) at IFNA/B, STING, and other loci. These tumors also frequently presented HLA LOH and oncogene amplifications, suggesting selection under immune pressure and replication stress. Together, our study resolves HRD tumors into two immune archetypes, immune-inflamed and immune-evasive, linked to chromosomal instability and lineage, informing biomarker-driven evaluation of immune checkpoint blockade/PARPi combinatorial therapies.

genomics↗

bioRxiv2025

Multi-platform framework for mapping somatic retrotransposition in human tissues

Mobile element insertions (MEI) shape the human genome in both germline and somatic tissues. While inherited MEIs are well characterized, mapping somatic MEIs (sMEI) in non-cancer tissues remains challenging due to their low allelic fraction and repetitive nature. We established an integrative framework for sMEI analysis leveraging modern sequencing technologies and analytical innovations. We first benchmarked sMEI detection and demonstrated advantages of long-read and MEI-targeted sequencing for ultra-low-frequency events using a mixture of well-established cell lines. We then showed that haplotype phasing and donor-specific assemblies refine sMEI detection, effectively distinguishing from germline and false signals in in-silico tumor-normal mixtures. We further developed a source-tracing strategy based on internal sequence variation, expanding the catalogue of active source elements beyond traditional transduction-based methods. Applying this framework to donor tissues, we identified 18 rare somatic L1 insertions, revealing structural and source diversity. Our work provides a foundational framework and biological insight into sMEIs.

genomics↗

bioRxiv2025

A recurrent sequencing artifact on Illumina sequencers with two-color fluorescent dye chemistry and its impact on somatic variant detection

BackgroundThe sequencing-by-synthesis technology by Illumina, Inc. enables efficient and scalable readouts of mutations from genomic data. To enhance sequencing speed and efficiency, Illumina has shifted from the four-color base calling chemistry of the HiSeq series to a two-color fluorescent dye chemistry in the NovaSeq series. Benchmarking sequencing artifacts due to biases in the newer chemistry is important to evaluate the quality of identified mutations. ResultsWe re-analyzed a series of whole-genome sequencing experiments in which the same samples were sequenced on the NovaSeq 6000 (two-color) and HiSeq X10 (four-color) platforms by independent groups. In several samples, we observed a higher frequency of T-to-G and A-to-C substitutions ("T>G") at the read level for NovaSeq 6000 versus HiSeq X10. As the per-base error rate is still low, the artifactual substitutions have a negligible effect in identifying germline or high variant allele frequency (VAF) somatic mutations. However, such errors can confound the detection of low-VAF somatic variants in high-depth sequencing samples, particularly in studies of mosaic mutations in normal tissues, where variants have low read support and are called without a matched normal. The artifactual T>G variant calls disproportionately occur at NT[TG] trinucleotides, and we leveraged this observation to bioinformatically reduce the T>G excess in somatic mutation callsets. ConclusionsWe identified a recurrent artifact specific to the Illumina two-color chemistry platform on the NovaSeq 6000 with the potential to contaminate low-VAF somatic mutation calls. Thus, an unexpected enrichment of T>G mutations in mosaicism studies warrants caution.

genomics↗

bioRxiv2025

Comprehensive benchmarking of somatic structural variant detection at ultra-low allele fractions

Postzygotic mosaicism gives rise to somatic structural variants (SVs) at ultra-low variant allele fractions (VAFs), which pose challenges for detection due to the high-coverage sequencing required and noise introduced by sequencing artifacts. Although somatic SV detection has been extensively studied in cancer, these studies are not directly applicable to the study of tissue mosaicism, as they rely on matched normals, target higher VAF ranges, and are enriched for different types of SVs. We present comprehensive benchmark data and best practices for non-cancer somatic SV detection. We created a synthetic mosaic sample by combining six HapMap individuals at varying proportions, generating allele fractions as low as 0.25%. This sample was sequenced to [~]2,300x total coverage using Illumina, PacBio, and Nanopore technologies across multiple sequencing centers. A high-confidence benchmark SV set containing over 21,000 pseudo-somatic insertions and deletions [≥]50bp was derived from haplotype-resolved assemblies. We evaluated 12 SV discovery pipelines and identified caller-specific strengths and sequencing platform-specific shortcomings. We find that short read-based approaches show reduced recall for insertions and repeat-associated SVs, whereas long-read sequencing achieves high accuracy throughout the genome, increasing linearly with coverage. The best algorithms sensitivity exceeded 80% for VAFs [≥]4% and 15% for VAFs of 0.5-1% with 60x coverage. The publicly available benchmarking data and comparative analysis of current methods provide a foundation for robust discovery of SV mosaicism in non-cancer tissues..

bioinformatics↗

bioRxiv2025

Efficient near telomere-to-telomere assembly of Nanopore Simplex reads

Telomere-to-telomere (T2T) assembly is the ultimate goal for de novo genome assembly. Existing algorithms capable of near T2T assembly all require Oxford Nanopore Technologies (ONT) ultra-long reads which are costly and experimentally challenging to obtain and are thus often unavailable for samples without established cell lines. Here, we introduce hifiasm (ONT), the first algorithm that can produce near T2T assemblies from standard ONT Simplex reads, eliminating the need for ultra-long sequencing. Compared to existing methods, hifiasm (ONT) reduces the computational demands by an order of magnitude and reconstructs more chromosomes from telomere to telomere on the same datasets. This advancement substantially broadens the feasibility of T2T assembly for applications previously limited by the high cost and experimental requirement of ultra-long reads.

bioinformatics↗

bioRxiv2025

Recurrent patterns of widespread neuronal genomic damage shared by major neurodegenerative disorders

Amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD), and Alzheimers disease (AD) represent two major categories of neurodegenerative disorders--TDP-43 and tau proteinopathies--for which the mechanisms driving neuronal death remain unclear. Single-cell whole-genome sequencing of 469 neurons from C9ORF72 ALS, C9ORF72 FTD, AD, and control brains revealed increased somatic single nucleotide variants (sSNVs) and insertions/deletions (sIndels) in all three diseases. Mutational signature analysis identified a disease-associated sSNV signature consistent with oxidative damage and an sIndel process affecting 22% of ALS, 76% of FTD, and 61% of AD neurons--but only 2% of control neurons--resembling signature ID4, previously linked to topoisomerase 1 (TOP1)-mediated mutagenesis. Rapid Approach to DNA Adduct Recovery (RADAR) assays confirmed increased TOP1-DNA covalent complexes and duplex sequencing confirmed the increased sIndels and identified single-strand events as likely precursor lesions. TOP1-associated sIndel mutagenesis and genome instability thus represents a mechanism shared by both TDP-43 and tau neurodegeneration.

genomics↗

bioRxiv2024

Perinatal Reduction of Genetically Aberrant Neurons from Human Cerebral Cortex

Human neurons are postmitotic and long-lived, requiring precise genomic regulation to maintain function over a lifetime. Normal neuronal function is highly dependent on gene dosage, with copy number variants (CNVs) and heterozygous point mutations associated with a host of neurodevelopmental and neuropsychiatric conditions [1-5]. Here, we investigated the landscape of somatic CNVs arising in fetal human brains, and how they change over development, to understand the processes that generate normal neuronal genomes. We sequenced 2,158 single neurons from human postmortem brain using two distinct single cell whole genome sequencing (scWGS) approaches. Tn5-transposase based (TbA) scWGS of 1,327 neurons from 16 individuals ranging in age from gestational week 14 to 90 years old resulted in 8,765 CNVs. Primary template amplification (PTA) was used to assess for CNV from 831 neurons from 12 individuals. Up to 46% of neurons in prenatal cortex showed aberrant genomes, characterized by widespread CNVs of multiple chromosomes, but this proportion reduces by 4-5 fold after birth across the two scWGS approaches (p=7.5x10-6, Fisher meta-analysis). We identified micronuclei in the developing cortex in situ, reflecting chromosomal material missegregated during neurodevelopment [6-8]. Neurons with widespread CNVs were eliminated in the perinatal period, while neurons with smaller CNV burden slowly declined during postnatal aging. CNVs in surviving neurons were depleted for genes that are dosage-sensitive or involved in neurodevelopmental disorders (p<0.05), suggesting selective elimination of neurons with CNVs involving these critical genes. We surveyed 44,861 nuclei with 10X Genomics scATAC/RNAseq and determined that neurons with high CNV burdens also showed abnormal expression of synaptic gene sets, suggesting that abnormal synaptic gene regulation contributes to neuronal elimination. Elimination of defective neuronal genomes during synaptogenesis may represent a critical process of genome quality control and a vulnerable target of factors that contribute to neurodevelopmental disease.

neuroscience↗