Biology subjects

Paten, B.

Publications and source records attributed to Paten, B..

At least 19 recordsLinked to original sources

bioRxiv2026

Pangenome alignment reveals global diversity and evolution of human centromeric regions

Centromeres play essential roles in chromosome segregation and genome stability, yet they remain among the least characterized regions of the human genome. Despite advances in long-read sequencing and complete genome assembly, the extreme repetitiveness and structural complexity of these regions still challenge population-scale analysis, obscuring their mutational dynamics. The Human Pangenome Reference Consortium has now accurately assembled over 6,000 centromeres, providing an opportunity to catalog global centromere variation. However, centromeric regions have been systematically excluded from pangenome alignments due to the technical challenge of aligning their highly repetitive tandem arrays and extreme structural variability. Here we introduce Centrolign, a graph-based multiple sequence alignment tool that combines a uniqueness-driven objective function with partial-order partial-order alignment to accurately align alpha satellite higher-order repeats. By prioritizing rare matches within tandem arrays and leveraging extended centromere-spanning haplotypes formed by suppressed recombination, Centrolign produces progressive multiple sequence alignments that preserve ancestral repeat organization. Applied across human centromeres, these alignments reveal the phylogenetic structure of similar satellite array haplotypes and enable precise estimation of variation rates, structural variant frequencies, and spatial patterns of mutation within satellite arrays. Integrating Centrolign graphs with repeat annotation tools and pangenome mapping algorithms allows accurate variant calling and genotyping from long reads without prior assembly. Moreover, we show that centromere haplotypes can be accurately subtyped with k-mers alone. Together, these advances establish a robust framework for incorporating centromeres into broader pangenomes, and population genomics in general, advancing our understanding of human genome evolution and diversity.

genomics↗

bioRxiv2026

GBZ-base and GAF-base: Indexed pangenome file formats

MotivationExisting pangenome file formats are designed for batch processing. Graphs must be loaded into memory, and alignment files must be read sequentially. Indexed file formats that can be used directly from disk would be more appropriate for interactive applications. ResultsWe propose GBZ-base and GAF-base -- SQLite-backed file formats comparable to GBZ and GAF. GBZ-base supports efficient extraction of local subgraphs, and GAF-base lets us extract all alignments to the subgraph. Additionally, GAF-base is smaller than any other file format for sequence-to-graph alignments. Availability and implementationFrom https://github.com/jltsiren/gbz-base and https://crates.io/crates/gbz-base under the MIT license.

bioinformatics↗

bioRxiv2026

Scalable and rare-variant aware genome inference across the 1kGP cohort

Pangenome graphs built from haplotype-resolved de novo assemblies enable accurate analysis of genetic variation. The short-read-based tool PanGenie efficiently genotypes variants discovered in a pangenome across large cohorts and outper-forms linear reference-based methods for structural variants (SVs). However, it cannot detect novel variants absent from the graph, missing many rare SVs (allele frequency < 1%) and was limited to graphs with 254 haplotypes. First, we introduce a haplotype sampling step that reduces the number of haplotypes using sample-specific k-mers before genotyping, decreasing runtime twelvefold and memory usage 1.4-fold at 30x coverage. Second, we present a polishing work-flow that corrects residual errors in haplotypes inferred from PanGenie genotypes and incorporates rare and private mutations. We genotype 3,202 samples from the 1000 Genomes Project and use low-coverage ONT data (967 samples) for polishing. We achieve a median QV of 46 and provide the 1,934 polished haplotype sequences as a community resource.

bioinformatics↗

bioRxiv2026

A Pan-pangenome illuminates complex structural variation and selection in humans, chimpanzees, and bonobos

Complete, haplotype-resolved genome assemblies have provided unprecedented insight into the evolution of structurally complex, rapidly evolving regions of human genomes1-6; however, population-scale pangenome resources of our closest relatives, chimpanzees and bonobos (genus, Pan), are necessary to ascertain the origins and evolutionary context of these loci. Here, we sequence and assemble 58 haplotypes from four distinct Pan clades to high contiguity (median contig NG50=54 Mb), including eight near-T2T genomes. These genomes reveal previously intractable genetic variation increasing estimates of genome-wide genetic diversity 6-37% across populations compared to short-read estimates7. We identify recurrent structural polymorphisms across species impacting genes associated with immune response and host-pathogen interaction and find that structural variants (SVs) are 170- to 260-fold more likely than single nucleotide variants (SNVs) to exhibit high-impact effects across species. Contrasting SV patterns across primates we find that transposable element mutation rates differ by as much as threefold between species. We show that human disease-associated short tandem repeat (TR) loci have uniquely expanded in humans sensitizing our species to these TR-expansion disorders. Physically phased haplotypes enable reconstruction of genome-wide genealogical histories, uncovering ancient, functional genetic variation maintained by balancing selection, as well as signatures of recent adaptation in chimpanzee subspecies. Several malaria-associated loci exhibit ancient structural polymorphism, including the African great ape-specific glycophorin (GYP) gene expansion. We characterize the sequence, structure, and composition of diverse glycophorin haplotypes in humans and chimpanzees. We identify independent malaria-protective GYPA-B fusion events in humans and novel chimpanzee glycophorin genes resulting from both ancient and recent fusion events demonstrating parallel adaptations to pathogen resistance across hominins. Together, our resource highlights the critical importance of nonhuman primate population-scale pangenomics for understanding the evolution of complex genome structures and the biodiversity of our endangered closest living relatives.

evolutionary biology↗

bioRxiv2026

Population-scale Y chromosome assemblies reveal recurrent remodeling within constrained architectures

The human Y chromosome is among the most structurally dynamic chromosomes in the human genome, yet much of its diversity remains unresolved because of extensive palindromes, ampliconic gene families, satellite-rich heterochromatin and large segmental duplications. What remained unclear was how these diverse forms of variation fit together across the full chromosome, how often similar structures recur in different lineages, and which aspects of organization remain constrained despite rapid sequence turnover. Here, we generated and analyzed 142 nearly complete human Y chromosome assemblies from 17 major haplogroups spanning approximately 180,000 years of evolution, creating a population-scale resource for studying Y chromosome biology and diversity. These assemblies show that structural change on the Y chromosome is recurrent but constrained, even in its most repetitive regions. In the fertility-associated azoospermia factor c (AZFc) region, recurrent inversions, deletions, and complex rearrangements generate a limited repertoire of structural haplotypes. Multicopy ampliconic gene families follow distinct evolutionary paths: DAZ paralogues differ in structural constraint, RBMY evolves within a modular array, and TSPY copy number varies mainly through local expansion and contraction. The centromere and Yq12 heterochromatin vary greatly in size but retain a stable higher-order organization, including a single hypomethylated centromeric core and conserved Yq12 repeat composition and orientation. Methylation across palindromic and ampliconic regions is likewise structured by repeat class, copy order and local architecture. Together, these results provide a population-scale resource for the human Y chromosome and show that its rapid structural evolution is repeatedly funneled into a limited set of architectural outcomes.

genomics↗

bioRxiv2026

A Complete Genome for the Common Marmoset

The common marmoset is a New World monkey (NWM) commonly used as a model organism to investigate questions in primate evolution and human disease, including Alzheimers and other neurodegenerative diseases, as well as neuropsychiatric disorders. Here we present the first telomere-to-telomere (T2T) reference genome for the common marmoset, adding over 88 Mb of sequence and resolving challenging genomic regions. An additional near-T2T assembly from a second unrelated individual yields a total of four high-quality haplotypes for analysis. The improved contiguity and accuracy of these assemblies enable unprecedented insights into complex and rapidly evolving genomic regions such as centromeres, sex chromosomes, ribosomal DNA (rDNA) structure, and the major histocompatibility complex (MHC). We fully resolved all marmoset centromeres, uncovering dimeric alpha satellites with chromosomal specificity and stratified inactive layers documenting ancestral centromere turnover. We assembled six acrocentric autosomes with gene-poor, satellite-rich short arms and provide evidence that most of them can harbor rDNA and all of them share large pseudo-homologous regions (PHRs). The Y chromosome, but not the X chromosome, carries active rDNA and PHRs, and the rDNA copy number is sexually dimorphic. Chromosomes that share PHRs also share closely related centromeric satellite DNA, supporting a model of ongoing recombinational exchange between heterologous chromosomes facilitated by rDNA. We discovered multiple novel, marmoset-specific MHC genes that are predicted to protect against pathogens encountered in its environment. Leveraging this complete reference, we further identified over 500 transcribed genes with transcript models or expansions specific to the marmoset lineage. Together with additional long-read marmoset assemblies, these genomes were used to construct a marmoset pangenome, providing a robust reference framework for short-read mapping across diverse individuals. This resource will improve the utility of the common marmoset as a biomedical model organism and fill key gaps in our understanding of primate evolution.

genomics↗

bioRxiv2026

The complete genome of the KOLF2.1J reference iPSC line

While induced pluripotent stem cells (iPSCs) have gained popularity in studying neurodegenerative diseases, the heterogeneity of stem cells used across studies impacts cross-study comparison. The iPSC Neurodegenerative Disease Initiative (iNDI) selected the KOLF2.1J cell line and prioritized its use as a reference standard for studying the effects of pathogenic variants on cell biology due to its stability and neutral neurodegenerative disease genetic risk. This cell line, and its derivatives expressing over 100 variants related to Alzheimers disease, Parkinsons disease, and other neurological diseases, are available for academic and industry access. Current genomic data analyses are limited by the use of a human reference genome that does not capture the complete genetic background of a given iPSC line. While in the future this issue may be partially mitigated by the creation of a comprehensive human pangenome, previous work has shown that generating custom genomes is of value both to characterize the variation present and to serve as a more appropriate genomic reference. Here, we generated and characterized a custom complete genome assembly from KOLF2.1J. Mapping of sequencing reads to a personalized diploid assembly results in more comprehensive mapping compared to traditional linear references (i.e GRCh38). In addition, we provide a comprehensive custom gene annotation along with isoform expression and differential methylation analyses across multiple cell types. The assembly and all additional data is browsable and publicly available. This resource will enable more accurate investigation of the KOLF2.1J cell line and any genomics data generated compared to using traditional generalized references, while also serving as a foundational approach for establishing custom reference assemblies for other high-value iPSC lines.

genomics↗

bioRxiv2026

Evaluating genome assemblies with HMM-Flagger

HMM-Flagger is a reference-free tool for detecting structural errors in haplotype-resolved genome assemblies based upon the coverage of mapped reads. It models read coverage with a hidden Markov model augmented by a Gaussian autoregressive process, which enables classifying coverage anomalies as erroneous blocks, false duplications, or collapsed blocks. Trained and tested on synthetic misassemblies, it detected synthetic errors using Pacific Biosciences HiFi and Oxford Nanopore Technologies R10 data with F1 scores of 78.4% and 60.4% respectively. When applied to six HG002 assemblies it revealed multiple large misassemblies including false duplications and collapse events in human satellites. Applied to assemblies from the Human Pangenome Reference Consortium (HPRC), HMM-Flagger demonstrated substantial improvements from release 1 (0.94% error rate) to release 2 (0.38%), reflecting technological advances. HMM-Flagger also validated NOTCH2NL assemblies in HPRC release 2 and confirmed the correctness of three novel structural configurations.

bioinformatics↗

bioRxiv2025

Origin and evolution of acrocentric chromosomes in human and great apes

The short arms of human acrocentric chromosomes are characterized by nucleolar organizer regions essential for ribosome biogenesis, but their highly repetitive nature has hindered genomic analysis. Leveraging the recently completed genomes of all major ape lineages, we identified recurrent features of their acrocentrics, including enriched repeat classes, centromere repositioning by whole-arm inversion, interchromosomal sequence exchange, and birth-and-death evolution of multiple gene families. Together, these processes have enabled the repeated amplification and diversification of the FRG1 gene family over 25 million years of ape evolution, and, in gorilla, the formation and amplification of a novel IGSF3-GGT fusion gene under positive selection. Similar evolutionary events also explain the distribution of segmental duplications and heterochromatin in the modern human genome, predisposing it to karyotypic abnormalities such as Robertsonian translocations. Our findings highlight acrocentric chromosomes as key drivers of evolution in the great apes, with implications for speciation, adaptation, and clinical genomics.

genomics↗

bioRxiv2025

Complete genomes of a multi-generational pedigree to expand studies of genetic and epigenetic inheritance

Pedigree analysis remains the gold standard for rare disease diagnostics, yet whole genome sequencing studies typically omit critical regions like centromeres, telomeres, and acrocentric chromosome p-arms. Here, we present telomere-to-telomere (T2T) reference genomes for four self-identified African American individuals of admixed ancestry spanning three generations. Our parent-of-origin assigned, chromosome-level assemblies revealed precise meiotic recombination breakpoints in previously inaccessible regions, including recombination events across acrocentric and subtelomeric sequences. Centromeric regions were highly stable, with multi-megabase arrays inherited intact across three generations, while the position of kinetochore assembly sites remained consistent and predominantly associated with the p-arm proximal region. The relative lengths of telomeres on individual chromosomes were maintained across generations. Using a targeted rDNA assembly approach, we reconstructed a complete megabase-scale ribosomal DNA (rDNA) array corresponding to the paternal chromosome 14. This openly available pedigree provides a benchmark dataset for studying recombination and genetic and epigenetic variation across the complete genome.

genomics↗

bioRxiv2025

Rapid, accurate long- and short-read mapping to large pangenome graphs with vg Giraffe

1We previously introduced Giraffe, a short-read-to-pangenome graph mapper available in the vg pangenomics toolkit. Giraffe was fast and accurate for mapping short reads to human-scale pangenomes, but struggled with long reads. Long reads present a unique challenge to pangenome mapping algorithms due to their length and error profile, which allow them to take more topologically complex paths through the pangenome graph and increase the possible search space for the algorithm. We present updates to Giraffe that allow it to quickly and accurately map long reads to pangenome graphs. For both short and long reads, Giraffe mapping to a pangenome containing data from more than 450 human haplotypes, generated by the Human Pangenome Reference Consortium, is comparable in speed to linear mappers to human reference genomes; Giraffe is also over an order of magnitude faster than GraphAligner, the current state-of-the-art long-read-to-pangenome mapper. Its alignments produce similar or improved small and structural variant calling results, compared to those from commonly used graph-based and linear mappers. We additionally demonstrate using Giraffes long read alignments in a pangenome-guided assembly workflow, which is capable of producing more contiguous local assemblies than Hifiasm in our test regions.

bioinformatics↗

bioRxiv2025

An Efficient Graph Algorithm for Diploid Local Ancestry Inference

In this paper, we present diploid sequence graphs, graphs whose paths encode pairs of haplotypes. We describe an efficient algorithm for creating a diploid graph from a directed acyclic (haploid) sequence graph, such that the diploid graph represents all the possible pairings of haplotypes present in the sequence graph and their similarity relationships. Starting with the sequence graph, our method uses a graph decomposition approach based on an extension of the SPQR-tree to systematically identify structural patterns that reduce redundancy while preserving genetic variation. We develop a polynomial-time algorithm that parsimoniously enumerates all disjoint paths with shared endpoints in two-terminal directed acyclic graphs. In the future, we envisage that diploid graphs may enable more accurate modeling of recombination, phasing, and variation-aware alignment in diploid genomes.

bioinformatics↗

bioRxiv2025

Haplotype-Resolved DNA Methylation at the APOE Locus identifies Allele-Specific Epigenetic Signatures Relevant to Alzheimer's Disease Risk

The APOE gene encodes a key lipid transport protein and plays a central role in Alzheimers disease (AD) pathogenesis. Three common APOE alleles, {varepsilon}2 (rs7412(C>T), {varepsilon}3 (reference), and {varepsilon}4 (rs429358(T>C)), arise from two coding variants in exon 4 and confer distinct AD risk profiles, with {varepsilon}4 increasing risk and {varepsilon}2 providing protection. The {varepsilon}3-linked APOE variant rs769455[T] has also been associated with elevated AD risk in individuals of African ancestry carrying both rs769455[T] and {varepsilon}4 alleles. These single nucleotide variants (SNVs) reside in a cytosine-phosphate-guanine (CpG) island, which is a region with a higher frequency of CpG sites compared to the rest of the genome. CpG sites are subject to 5-methylcytosine (5mC) methylation by DNA methyltransferases which add a methyl group to the fifth carbon on the cytosine residue of a CpG site. The presence of SNVs can disrupt this process, making these regions prime targets for differential methylation; however, allele-specific methylation patterns in APOE remain poorly resolved due to technical limitations of conventional bisulfite and methylation array based methods, including degraded DNA quality, sparse CpG coverage, and lack of haplotype phasing. Here, we leverage high-accuracy long-read sequencing data to generate haplotype-resolved methylation profiles of the APOE locus in 332 postmortem brain samples from two ancestrally different cohorts. This includes 201 individuals of European ancestry from the North American Brain Expression Consortium (NABEC), comprising 402 haplotypes (48 {varepsilon}2 and 58 {varepsilon}4 alleles), and 131 individuals of African and African admixed ancestry from the Human Brain Core Collection (HBCC), comprising 262 haplotypes (25 {varepsilon}2, 64 {varepsilon}4, and 7 rs769455 alleles). A linear regression analysis identified 18 novel differentially methylated CpG sites (DMCs) associated with APOE {varepsilon}2, {varepsilon}4, and rs769455 within a gene cluster spanning TOMM40, APOE, APOC1, and APOC4-APOC2. This represents the most comprehensive haplotype-resolved methylation study of APOE in human brain tissue to date. Our results uncover distinct allele-specific methylation signatures and demonstrate the power of long-read sequencing for resolving epigenetic variation relevant to AD risk.

genomics↗

bioRxiv2025

Pangenome-aware DeepVariant

Population-scale genomics information provides valuable prior knowledge for various genomic analyses, especially variant calling. A notable example of such application is the human pangenome reference released by the Human Pangenome Reference Consortium, which has been shown to improve read mapping and structural variant genotyping. In this work, we introduce pangenome-aware DeepVariant, a variant caller that uses a pangenome reference alongside sample-specific read alignments. It generates pileup images of both reads and pangenome haplotypes near potential variants and uses a Convolutional Neural Network to infer genotypes. This approach allows directly using a pangenome for distinguishing true variant signals from sequencing or alignment noise. We assessed its performance on various short-read sequencing platforms and read mappers. Across all settings, pangenome-aware DeepVariant outperformed the linear-reference-based DeepVariant, reducing errors by up to 25.5%. We also show that Element reads with pangenome-aware DeepVariant can achieve 23.6% more accurate variant calling performance compared to existing methods.

bioinformatics↗

bioRxiv2025

Lossless Pangenome Indexing Using Tag Arrays

Pangenome graphs represent the genomic variation by encoding multiple haplotypes within a unified graph structure. However, efficient and lossless indexing of such structures remains challenging due to the scale and complexity of pangenomic data. We present a practical and scalable indexing framework based on tag arrays, which annotate positions in the Burrows-Wheeler transform (BWT) with graph coordinates. Our method extends the FM-index with a run-length compressed tag structure that enables efficient retrieval of all unique graph locations where a query pattern appears. We introduce a novel construction algorithm that combines unique k-mers, graph-based extensions, and haplotype traversal to compute the tag array in a memory-efficient manner. To support large genomes, we process each chromosome independently and then merge the results into a unified index using properties of the multi-string BWT and r-index. Our evaluation on the HPRC graphs demonstrates that the tag array structure compresses effectively, scales well with added haplotypes, and preserves accurate mapping information across diverse regions of the genome. This indexing method enables lossless and haplotype-aware querying in complex pangenomes and offers a practical indexing layer to develop scalable aligners and downstream graph-based analysis tools. The index additionally supports efficient one-to-all coordinate translation, enabling any interval on a haplotype to be mapped to its corresponding intervals across all other haplotypes in the graph.

bioinformatics↗

bioRxiv2025

Diploid genome assembly of human fibroblast cell lines enables clone specific variant calling, improved read mapping and accurate phasing

Human cell lines are fundamental tools in biomedical research and are widely used in disease modeling, drug development, and many other domains. Here, we present chromosome-level, phased diploid genome assemblies of two popular human cell lines: the BJ foreskin fibroblast line and the IMR-90 fetal lung fibroblast line. Our high-quality assemblies, generated using long-read and Hi-C sequencing data, reveal substantial structural variation, including more than 50,000 insertions, deletions, duplications, and inversions compared to the recent T2T-CHM13v2.0 reference. Our assemblies provide detailed maps of genetic variation, enabling more accurate variant calling and the ability to phase reads when using newly generated or historical sequencing data on these cell lines or their derivatives. All assemblies and associated data have been made available as a resource for the research community. We envision that diploid genome assembly will become a cornerstone approach for personalized medicine in the near future.

genomics↗

bioRxiv2025

Genetic diversity and regulatory features of human-specific NOTCH2NL duplications

NOTCH2NL (NOTCH2-N-terminus-like) genes arose from ape-specific chromosome 1 segmental duplications implicated in human brain cortical expansion, including an incomplete NOTCH2 gene. Genetic characterization of these loci and their regulation is complicated because they are embedded in large, nearly identical duplications that predispose to recurrent microdeletion syndromes. Using near-complete long-read assemblies generated from 70 human and 12 ape haploid genomes, we show independent recurrent duplication among apes with protein-coding copies emerging in humans 2.2-3.7 million years ago. We distinguish NOTCH2NL paralogs present in every human haplotype (NOTCH2NLA) from copy number variable ones. We also characterize large-scale structural variation, including gene conversion, for 28% of haplotypes leading to a previously undescribed paralog, NOTCH2tv. Finally, we apply Fiber-seq and long-read transcript sequencing to human dorsal forebrain organoids to characterize the regulatory landscape and find that the most fixed paralogs, NOTCH2 and NOTCH2NLA, harbor the greatest number of paralog-specific elements potentially driving their regulation.

genomics↗

bioRxiv2025

Lancet2: Improved and accelerated somatic variant calling with joint multi-sample local assembly graph

Here, we present Lancet2, an open-source somatic variant caller designed to improve detection of small variants in short-read sequencing data. Lancet2 introduces significant enhancements, including: 1) Improved variant discovery and genotyping through partial order multiple sequence alignment of assembled haplotype contigs and re-alignment of sample reads to the best supporting allele. 2) Optimized somatic variant scoring with Explainable Machine Learning models leading to better somatic filtering throughout the sensitivity scale. 3) Integration with Sequence Tube Map for enhanced visualization of variants with aligned sample reads in graph space. When benchmarked against enhanced two-tech truth sets generated using high-coverage short-read (Illumina) and long-read (Oxford Nanopore) data from four well characterized matched tumor/normal cell lines, Lancet2 outperformed other industry-leading tools in variant calling performance, especially for InDels. In addition, significant runtime performance improvements compared to Lancet1 ([~]10x speedup and 50% less peak memory usage) and most other state of the art somatic variant callers (at least 2x speedup with 8 cores or more) make Lancet2 an ideal tool for accurate and efficient somatic variant calling.

bioinformatics↗