Biology subjects

Xiao, C.

Publications and source records attributed to Xiao, C..

At least 55 records · Page 3Linked to original sources

bioRxiv2024

msCNVS: medium throughput single cell copy number variation sequencing with barcoded library construction free of preamplification toward clinical implementation

Single cell copy number variation sequencing (scCNV-seq) is valuable for genomic analysis of a variety of health and disease systems, yet the available methods either depend on either preamplification of the whole genome of each cell, special devices or untracable, which hinder scCNV-seq practice in clinics. Here we provide scalable multiplex scCNV-seq (msCNVS) that allows direct medium-throughput library construction for single cells, which are barcoded individually with Tn5 transposome in a microplate and immediately pooled for downstream processes, elevating the efficiency by orders of magnitude. An algorithm is developed on the distribution of segmented normalized read count density to identify the major peaks associating with integer copy numbers, further improving the accuracy for objective CNV calling. Here msCNVS faithfully distinguishes the unique CNV patterns of 5 cell lines. The individual msCNVS profiles of 70 individual K562 cells highly correlate with the profile of K562 bulk cells (R=0.90-0.98), and the triplicates of HeLa3 bulk cells correlated nearly perfect (R=0.99). The msCNVS CNV profiles of primary cell cultures of amniotic fluid are confirmed by G-banding karyotype analysis and chromosomal microarray analysis. Additionally, the coverage uniformity of msCNVS is superior to that of MDA and MALBAC and approaches what eMDA and DOP-PCR achieves. Furthermore, msCNVS detects CNV deletions in 2 stunted, abnormal blastocysts, one with CNV mosaicism, and uncovered variants of CNVs in circulated tumor cells, cancerous pleural effusion cells, and patient-derived xenograft nuclei. Thus, msCNVS promises a robust, reliable and highly efficient approach to genomic testing of precious and rare cells like those typically obtained in reproductive and cancer clinics. One-Sentence SummaryBy early pooling of multiple single cells individually barcoded with Tn5 transposome, msCNVS enables efficient CNV profiling of rare clinic samples

genomics↗

bioRxiv2024

A hemagglutinin and neuraminidase biased immunological memory shapes the dynamics of antibody responses to Influenza A virus

Influenza A virus (IAV) infection establishes a more diverse immunological memory to different viral proteins compared to vaccination. We hypothesized that the relative abundance of pre-existing immune memory to different viral antigens could skew post-infection antibody responses. To explore this, we generated mouse models with either an IAV hemagglutinin (HA)- or neuraminidase (NA)-biased immunological memory. We inoculated groups of mice with cocktails of isogenic viruses bearing antigenically-distinct HA (H3v) or NA (N2v) chosen to span the IAV H3N2 human circulation history. We challenged the mice with two H3N2 strains of opposing virulence and antigenic distance (AD) and examined the post-infection antibody landscapes. In both challenges, immune-naive mice seroconverted to both HA and NA whereas in primed mice, antibody response was detected to the antigen for which there is no pre-existing memory. In cases where the homologous antibody response was blunted, there was diversification on the breadth of response to antigenically-related strains with low baseline titers. Our findings clarifies the concept of "original antigenic sin" and demonstrate a mechanism by which the dynamics of antibody responses to HA and NA after infection can be altered by pre-existing immunity.

immunology↗

bioRxiv2024

Considerations for reporting variants in novel candidate genes identified during clinical genomic testing

Since the first novel gene discovery for a Mendelian condition was made via exome sequencing (ES), the rapid increase in the number of genes known to underlie Mendelian conditions coupled with the adoption of exome (and more recently, genome) sequencing by diagnostic testing labs has changed the landscape of genomic testing for rare disease. Specifically, many individuals suspected to have a Mendelian condition are now routinely offered clinical ES. This commonly results in a precise genetic diagnosis but frequently overlooks the identification of novel candidate genes. Such candidates are also less likely to be identified in the absence of large-scale gene discovery research programs. Accordingly, clinical laboratories have both the opportunity, and some might argue a responsibility, to contribute to novel gene discovery which should in turn increase the diagnostic yield for many conditions. However, clinical diagnostic laboratories must necessarily balance priorities for throughput, turnaround time, cost efficiency, clinician preferences, and regulatory constraints, and often do not have the infrastructure or resources to effectively participate in either clinical translational or basic genome science research efforts. For these and other reasons, many laboratories have historically refrained from broadly sharing potentially pathogenic variants in novel genes via networks like Matchmaker Exchange, much less reporting such results to ordering providers. Efforts to report such results are further complicated by a lack of guidelines for clinical reporting and interpretation of variants in novel candidate genes. Nevertheless, there are myriad benefits for many stakeholders, including patients/families, clinicians, researchers, if clinical laboratories systematically and routinely identify, share, and report novel candidate genes. To facilitate this change in practice, we developed criteria for triaging, sharing, and reporting novel candidate genes that are most likely to be promptly validated as underlying a Mendelian condition and translated to use in clinical settings.

genetics↗

bioRxiv2023

Single cell sequencing as a general variant interpretation assay

The human genome contains [~]70 million possible protein-altering variants, the vast majority of which are of uncertain clinical significance. Closing this gap is essential for accurate diagnosis of disease-causing variants and understanding their mechanisms of action. Towards this goal, we developed a pooled perturbation approach combining saturation mutagenesis with single cell RNA sequencing to map the effects of every single nucleotide variant in a gene. We sequenced [~]440,000 cells expressing variants in CDKN2A (p16INK4a), TP53, and SOD1, observing almost all possible protein-coding variants, with a mean of 61 cells per variant. Using single cell gene expression signatures, we show that each gene may contain multiple types of pathogenic variants that affect distinct downstream pathways. We demonstrate that single cell expression signatures outperform existing bulk experimental assays and computational models for predicting pathogenicity, and summarize both the utility and potential limitations of single cell sequencing as a general variant interpretation assay.

genomics↗

bioRxiv2023

Benchmarking multi-omics integration algorithms across single-cell RNA and ATAC data

Recent advancements in single-cell sequencing technologies have generated extensive omics data in various modalities and revolutionized cell research, especially in the single cell RNA and ATAC data. The joint analysis across scRNA-seq data and scATAC-seq data has paved the way to comprehending the cellular heterogeneity and complex cellular regulatory networks. Multi-omics integration is gaining attention as an important step in joint analysis, and the number of computational tools in this field is growing rapidly. In this paper, we benchmarked 12 multi-omics integration methods on three integration tasks via qualitative visualization and quantitative metrics, considering six main aspects that matter in multi-omics data analysis. Overall, we found that different methods have their own advantages on different aspects, while some methods outperformed other methods in most aspects. We therefore provided guidelines for selecting appropriate methods for specific scenarios and tasks to help obtain meaningful insights from multi-omics data integration.

bioinformatics↗

bioRxiv2023

Small variant benchmark from a complete assembly of X and Y chromosomes

The sex chromosomes contain complex, important genes impacting medical phenotypes, but differ from the autosomes in their ploidy and large repetitive regions. To evaluate variant detection on chromosomes X and Y, we created an 111,725 variant benchmark for the Genome in a Bottle HG002 reference material. We show how complete assemblies can expand benchmarks to difficult regions, but highlight remaining challenges benchmarking complex gene conversions, copy number variable gene arrays, and human satellites.

genomics↗

bioRxiv2023

The roles of DDR2 and substrate stiffness on cancer cell transcriptome and proliferation

The interactions between cancer cells and the ECM regulate carcinogenesis. The collagen receptor kinase DDR2 is dysregulated in certain cancer cells, but its precise role in these malignancies remains unclear. In this study, we perform RNA-seq to determine how DDR2 and the biomechanical environment regulate cancer cell behaviors. We show that DDR2 knockdown in SH-SY5Y neuroblastoma cells inhibits proliferation and promotes senescence by regulating relevant genes. Increasing substrate stiffness reduces proliferation and promotes cell spreading but does not change senescence or transcriptome. Furthermore, DDR2 knockdown modulates cellular responses to substrate stiffness changes, unraveling a crosstalk between DDR2 and mechanosensing. These findings indicate DDR2 and ECM biomechanics regulate cancer cell behavior through distinct mechanisms, providing new mechanistic insights of cancer progression.

biochemistry↗

bioRxiv2023

Adaptive Functions of Structural Variants in Human Brain Development

Quantifying the structural variants (SVs) in nonhuman primates could provide a niche to clarify the genetic backgrounds underlying human-specific traits, but such resource is largely lacking. Here, we report an accurate SV atlas in a population of 562 rhesus macaques, verified by two public SV benchmarks, an inhouse benchmark of eight macaque genomes with long-read sequencing and another inhouse benchmark of one macaque genome with whole-genome assembly. This accurate, quantitative SV map indicates stronger purifying selection on inversions, one type of poorly-clarified SVs to date, especially for those located on regulatory regions, suggesting a strategy for prioritizing inversions with the most important functions. Based on the distribution and the evolutionary features of these inversions in macaque population, we then identified 75 human-specific inversions, clarified their functional effects and prioritized them. Notably, the top-ranked inversions have substantially shaped the human transcriptome, through their dual-effects of reconfiguring the ancestral genomic architecture and introducing regional mutation hotspots at the inverted regions. As a proof-of-concept, we linked APCDD1, located on one of these inversions with the highest rank score and downregulated in human brains, to neuronal maturation. The accumulation of human-specific mutations on its promoter region, accelerated by the formation of the inversion, contributed to the decreased expression in humans. Notably, the overexpression of APCDD1 could accelerate the neuronal maturation, while its depletion in mice delays the neuronal maturation. This study thus highlights the contribution of SVs, especially the inversions, to the distinct features in human brain development.

evolutionary biology↗

bioRxiv2023

Microglia Regulate Sleep via Calcium-Dependent Modulation of Norepinephrine Transmission

Sleep interacts reciprocally with immune system activity, but its specific relationship with microglia - the resident immune cells in the brain - remains poorly understood. Here we show that microglia can regulate sleep through a mechanism involving Gi-coupled GPCRs, intracellular Ca2+ signaling, and suppression of norepinephrine transmission. Chemogenetic activation of microglia Gi signaling strongly promoted sleep, whereas pharmacological blockade of Gi-coupled P2Y12 receptors decreased sleep. Two-photon imaging showed that P2Y12/Gi activation elevated microglia intracellular Ca2+, and blockade of this Ca2+ elevation largely abolished the Gi-induced sleep increase. Microglia Ca2+ level also increased at natural wake-to-sleep transitions, caused partly by reduced norepinephrine. Furthermore, imaging of norepinephrine activity with its biosensor showed that microglia P2Y12/Gi activation significantly reduced norepinephrine, partly by increasing the adenosine concentration. Thus, microglia can regulate sleep through reciprocal interactions with norepinephrine transmission.

neuroscience↗

bioRxiv2023

Multiscale Model for Ion Transport in Cellular Media and Applications in Smooth Muscle Cells

Ion transport in biological tissues is crucial in the study of many biological and pathological problems. Some multi-cellular structures, like the smooth muscles on vessel walls, can be treated as periodic bi-domain structures consisting of the intracellular space (ICS) and extracellular space (ECS) with semipermeable membranes in between. In this work, we first use a multi-scale asymptotic method to derive a macroscopic homogenized bidomain model from the microscopic electro-neutral (EN) model with different diffusion coefficients and nonlinear interface conditions. Then, the obtained homogenized model is applied to study ion transportation and micro-circulation in multi-celluar tissues under the impact of agonists, an internal calcium source, and extracellular potassium. Our model serves as a useful bridge between existing ordinary differential equation models and partial differential models that take into consideration spatial variation. On the one hand, numerical results show that ECS variables are almost invariant in the first two scenarios and confirm the validity of existing single-domain models, which treat variables in the ECS as constants. On the other hand, only the bidomain model is applicable to consider the effect of local extracellular potassium. Finally, the membrane potential of syncytia formed by connected cells is found to play an important role in the propagation of oscillation from the stimulus region to the non-stimulus region. Author summarySmooth muscle cells (SMCs) play a vital role in neurovascular coupling, which is the mechanism by which changes in neural activity are linked to alterations in blood flow. Dysfunctional SMCs can have significant implications for human health. The activation of SMCs is primarily regulated by the intracellular concentration of calcium ions (Ca2+). A multi-scale model for ion transport in multicellular tissue with varying connectivity has been proposed to investigate SMC activation under different stimuli. The simulation results confirm the critical role of gap junctions in wave propagation and vasoconstriction in the vessel wall. The blockage of gap junctions prevents the spread of the wave. Furthermore, the propagation of membrane potential is the primary cause of wave propagation.

cell biology↗

bioRxiv2023

The potential of Senicapoc, a KCNN4 inhibitor, for the prevention and treatment of breast cancer

BackgroundGenome-wide association studies have identified a breast cancer risk locus at 19q13.31. The candidate causal variants at this locus are located in the first exon of KCNN4. KCNN4, which regulates membrane potential and Ca2+ signaling, is a good candidate for drug repositioning because its inhibitor, Senicapoc, has been shown to be well tolerated in Phase-II and -III clinical trials for asthma and sickle cell anemia. MethodsWe evaluated public mRNA expression data to determine whether the allele at 19q13.31 associated with increased breast cancer risk was associated with KCNN4 expression. We also used immunohistochemistry to evaluate the relationship between KCNN4 protein expression and breast cancer survival. We then used Senicapoc in two murine mammary tumor models to determine if it would delay tumor development. We also treated mice bearing 4T1 mammary tumors with Senicapoc, by subcutaneous injection and by oral gavage. Finally we used gene editing to make deletions within Kcnn4 in 4T1 to determine whether Senicapoc had off-target effects on tumor growth. ResultsAnalysis of the Genotype-Tissue Expression Project showed that the allele at 19q13.31 associated with increased breast cancer risk is associated with increased KCNN4 expression, suggesting that inhibiting KCNN4 might reduce breast cancer risk. Using immunohistochemistry in a large breast cancer cohort, we found that membrane and cytoplasmic expression is a marker of poor prognosis in triple negative breast cancer. We then tested the efficacy of Senicapoc to prevent and treat breast cancer. This showed that it delays the development of mammary tumors in two murine models, and slows growth of a syngeneic (4T1) model of triple negative breast cancer. Senicapoc monotherapy showed similar efficacy to anthracycline/taxane-based chemotherapy in these studies, with a stronger effect when they were combined. ConclusionsThese results provide a rationale for clinical testing of Senicapoc for treating, and even preventing, breast cancer.

cancer biology↗

bioRxiv2023

6mA-Sniper: Quantifying 6mA Sites in Eukaryotes at Single-Nucleotide Resolution

While N6-methyldeoxyadenine (6mA) modification has been linked to fundamental regulatory processes in prokaryotes, its prevalence and functional implications in eukaryotes are controversial. Here, we report 6mA-Sniper to quantify 6mA sites in eukaryotes at single-nucleotide resolution. With 6mA-Sniper, we delineated an accurate 6mA profile in C. elegans with 2,034 sites, significantly enriched on sequences of [GC]GAG motif. Twenty-six of 39 6mA events with MnlI restriction endonuclease sites were experimentally verified, demonstrating the feasibility of this method. Notably, the enrichment of these 6mA sites on a specific sequence motif, their within-population conservation and the combinatorial patterns, and the selective constrains on them jointly support an active model for the shaping of the profile by some undiscovered methyltransferases. In a joint study (Cell Research, in revision), Ma et al. reported METL-9 as a new methyltransferase in shaping the basal and stress-dependent 6mA profile in C. elegans. Notably, with the 6mA profile identified by 6mA-Sniper at single-nucleotide resolution, we found that the levels of 6mAs are significantly decreased in strains with the removal of METL-9 (METL-9 KO-OP50), while generally increased after P. aeruginosa infection, further verified the efficiency of 6mA-Sniper in accurately pinpointing 6mA sites. Moreover, for the regions marked by 998 6mA sites emerged specifically after the infection, we identified an enrichment of the upregulated genes after the infection. The gene upregulations are likely mediated through a mutual exclusive crosstalk between 6mA and H3K27me3 modification, as supported by their co-occurrence, and the signal of increased H3K27me3 at regions marked by 6mAs depleted in METL-9 KO-OP50 strains. Notably, in different C. elegans strains, the cross-strain genetic variants removing 6mA sites are associated with the decreased expression of their host genes, and the removal of two randomly-selected 6mA events with genome editing directly decreased the expression of their host genes. We thus highlight 6mA regulation as a previously-neglected regulator of transcriptome in eukaryotes.

genomics↗

bioRxiv2022

Towards increased accuracy and reproducibility in SARS-CoV-2 next generation sequence analysis for public health surveillance

During the COVID-19 pandemic, SARS-CoV-2 surveillance efforts integrated genome sequencing of clinical samples to identify emergent viral variants and to support rapid experimental examination of genome-informed vaccine and therapeutic designs. Given the broad range of methods applied to generate new viral genomes, it is critical that consensus and variant calling tools yield consistent results across disparate pipelines. Here we examine the impact of sequencing technologies (Illumina and Oxford Nanopore) and 7 different downstream bioinformatic protocols on SARS-CoV-2 variant calling as part of the NIH Accelerating COVID-19 Therapeutic Interventions and Vaccines (ACTIV) Tracking Resistance and Coronavirus Evolution (TRACE) initiative, a public-private partnership established to address the COVID-19 outbreak. Our results indicate that bioinformatic workflows can yield consensus genomes with different single nucleotide polymorphisms, insertions, and/or deletions even when using the same raw sequence input datasets. We introduce the use of a specific suite of parameters and protocols that greatly improves the agreement among pipelines developed by diverse organizations. Such consistency among bioinformatic pipelines is fundamental to SARS-CoV-2 and future pathogen surveillance efforts. The application of analysis standards is necessary to more accurately document phylogenomic trends and support data-driven public health responses.

bioinformatics↗

bioRxiv2022

GenSLMs: Genome-scale language models reveal SARS-CoV-2 evolutionary dynamics.

We seek to transform how new and emergent variants of pandemiccausing viruses, specifically SARS-CoV-2, are identified and classified. By adapting large language models (LLMs) for genomic data, we build genome-scale language models (GenSLMs) which can learn the evolutionary landscape of SARS-CoV-2 genomes. By pretraining on over 110 million prokaryotic gene sequences and finetuning a SARS-CoV-2-specific model on 1.5 million genomes, we show that GenSLMs can accurately and rapidly identify variants of concern. Thus, to our knowledge, GenSLMs represents one of the first whole genome scale foundation models which can generalize to other prediction tasks. We demonstrate scaling of GenSLMs on GPU-based supercomputers and AI-hardware accelerators utilizing 1.63 Zettaflops in training runs with a sustained performance of 121 PFLOPS in mixed precision and peak of 850 PFLOPS. We present initial scientific insights from examining GenSLMs in tracking evolutionary dynamics of SARS-CoV-2, paving the path to realizing this on large biological data.

bioinformatics↗

bioRxiv2022

Beneficial Effects of Moderate Hepatic Activin A Expression on Metabolic pathways, Inflammation, and Atherosclerosis

BACKGROUNDAtherosclerosis is an inflammatory vascular disease marked by hyperlipidemia and hematopoietic stem cell (HSC) expansion. Activin A, a member of the Activin/GDF/TGF{beta}/BMP family is broadly expressed and increases in human atherosclerosis, but its functional effects in vivo in this context remain unclear. METHODSWe studied LDLR-/- mice on a Western diet for 12 weeks and used adeno-associated viral vectors with a liver-specific thyroxine binding globulin (TBG) promoter to express Activin A or GFP (control). Atherosclerotic lesions were analyzed by oil red staining. Blood lipid profiling was performed by HPLC (High Performance Liquid Chromatography), and immune cells were evaluated by flow cytometry. Liver RNA-sequencing was performed to explore the underlying mechanisms. RESULTSActivin A expression decreased in both livers and aortae from LDLR-/- mice fed a Western diet compared with chow. AAV-TBG-Activin A increased Activin A hepatic expression ([~]10-fold at 12-weeks, p<0.0001) and circulating Activin A levels ([~]2000pg/ml vs [~]50pg/ml, p<0.001, compared with controls). Hepatic Activin A expression decreased plasma total and low-density lipoprotein (LDL) cholesterol ([~]60% and [~]40%, respectively), reduced inflammatory cells in aortae and proliferating hematopoietic stem cells (HSC) in bone marrow, and reduced atherosclerotic lesion area in the aortic arch by [~]60%. Activin A also attenuated liver steatosis and expression of the lipogenesis genes, Srebp1 and Srebp2. RNA sequencing revealed Activin A not only blocked expression of genes involved in hepatic de novo lipogenesis but also fatty acid uptake, and liver inflammation. In addition, Activin A expressed in the liver also reduced white fat tissue accumulation, decreased adipocyte size, and improved glucose tolerance. CONCLUSIONSOur studies reveal hepatic Activin A expression reduces inflammation, HSC expansion, liver steatosis, circulating cholesterol, and fat accumulation, which likely all contribute to the observed protection against atherosclerosis. The reduced Activin A observed in LDLR-/- mice on a Western diet appears maladaptive and deleterious for atherogenesis.

pathology↗

bioRxiv2022

Endothelial Brg1 fine-tunes Notch signaling during zebrafish heart regeneration

Myocardial Brg1 is essential for heart regeneration in zebrafish, but it remains unknown whether and how endothelial Brg1 plays a role in heart regeneration. Here, we found that both brg1 mRNA and protein were induced in cardiac endothelial cells after ventricular resection, and endothelium-specific over-expression of dominant-negative Xenopus Brg1 (DN-xBrg1) inhibited myocardial proliferation and heart regeneration and increased cardiac fibrosis. RNA-seq and ChIP-seq analysis revealed that the endothelium-specific over-expression of DN-xBrg1 changed the levels of H3K4me3 modifications in the promoter regions of the zebrafish genome and induced abnormal activation of Notch family genes upon injury. Mechanistically, Brg1 interacted with lysine demethylase 7aa (Kdm7aa) to fine-tune the level of H3K4me3 within the promoter regions of Notch family genes and thus regulated Notch gene transcription. Together, this work demonstrates that the Brg1-Kdm7aa-Notch axis in cardiac endothelial cells, including the endocardium, regulates myocardial proliferation and regeneration via modulating the H3K4me3 of the Notch promoters in zebrafish.

developmental biology↗

bioRxiv2021

The edible seaweed Laminaria japonica contains cholesterol analogues that inhibit Lipid Peroxidation and Cyclooxygenase Enzymes

In this study, 5 sterols were isolated and purified from Laminaria japonica, commonly known as edible brown seaweed, and their structures were identified based on detailed chemical methods and spectroscopic analyses. Spectroscopic analyses characterized 5 sterols as 29-Hydroperoxy-stigmasta-5,24(28)-dien-3{beta}-ol, saringosterol (24-vinyl-cholest-5-ene-3{beta},24-diol), 24-methylenecholesterol, fucosterol (stigmasta-5,24-diene-3{beta}-ol), and 24-Hydroperoxy-24-vinyl-cholesterol. The bioactivities of these sterols were tested using lipid peroxidation (LPO) and cyclooxygenase (COX-1 and -2) enzyme inhibitory assays. Fucosterol exhibited the highest COX-1 and -2 enzyme inhibitory activities at 59 and 47%, respectively. Saringosterol, 24-methylenecholesterol and fucosterol showed higher LPO inhibitory activity at >50% than the other compounds. In addition, the results of molecular docking revealed that the 5 sterols were located in different pocket of COX-1 and -2 and fucosterol with tetracyclic skeletons and olefin methine achieved the highest binding energy (-7.85 and -9.02 kcal/mol) through hydrophobic interactions and hydrogen bond. Our results confirm the presence of 5 sterols in L. japonica and its significant anti-inflammatory and antioxidant activity. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=89 SRC="FIGDIR/small/463984v1_ufig1.gif" ALT="Figure 1"> View larger version (21K): org.highwire.dtl.DTLVardef@16c3f43org.highwire.dtl.DTLVardef@1ad7385org.highwire.dtl.DTLVardef@7b3c4borg.highwire.dtl.DTLVardef@b3675a_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LISterols 29-hydroperoxy-stigmasta-5,24(28)-dien-3{beta}-ol and 24-hydroperoxy-24-vinyl-cholesterol are identified for the first time in L. japonica. C_LIO_LISaringosterol, 24-methylenecholesterol and fucosterol showed strong LPO inhibitory activity. C_LIO_LIFucosterol showed highest binding affinity for COX-1 and -2 enzymes through hydrophobic interactions. C_LI

biochemistry↗

bioRxiv2021

A complete reference genome improves analysis of human genetic variation

Compared to its predecessors, the Telomere-to-Telomere CHM13 genome adds nearly 200 Mbp of sequence, corrects thousands of structural errors, and unlocks the most complex regions of the human genome to clinical and functional study. Here we demonstrate how the new reference universally improves read mapping and variant calling for 3,202 and 17 globally diverse samples sequenced with short and long reads, respectively. We identify hundreds of thousands of novel variants per sample--a new frontier for evolutionary and biomedical discovery. Simultaneously, the new reference eliminates tens of thousands of spurious variants per sample, including up to 12-fold reduction of false positives in 269 medically relevant genes. The vast improvement in variant discovery coupled with population and functional genomic resources position T2T-CHM13 to replace GRCh38 as the prevailing reference for human genetics. One Sentence SummaryThe T2T-CHM13 reference genome universally improves the analysis of human genetic variation.

genomics↗