Probing enzyme-dependent pseudouridylation using direct RNA sequencing to assess neuronal epitranscriptome plasticity

Chemical modifications in mRNAs such as pseudouridine (psi) can regulate gene expression, although our understanding of the functional impact of individual psi modifications, especially in neuronal cells, is limited. We apply nanopore direct RNA sequencing to investigate psi dynamics under cellular perturbations in SH-SY5Y cells. We assign sites to psi synthases using siRNA-based knockdown. A steady-state enzyme-substrate model reveals a strong correlation between psi synthase and mRNA substrate levels and psi modification frequencies. Next, we performed either differentiation or lead-exposure to SH-SY5Y cells and found that, upon lead exposure, not differentiation, the modification frequency is less dependent on enzyme levels suggesting translational control. Finally, we compared the plasticity of psi sites across cellular states and found that plastic sites can be condition-dependent or condition-independent; several of these sites fall within transcripts encoding proteins involved in neuronal processes. Our psi analysis and validation enable investigations into the dynamics and plasticity of RNA modifications.

Pangenome graph construction from genome alignments with Minigraph-Cactus

Pangenome references address biases of reference genomes by storing a representative set of diverse haplotypes and their alignment, usually as a graph. Alternate alleles determined by variant callers can be used to construct pangenome graphs, but advances in long-read sequencing are leading to widely available, high-quality phased assemblies. Constructing a pangenome graph directly from assemblies, as opposed to variant calls, leverages the graph's ability to represent variation at different scales. Here we present the Minigraph-Cactus pangenome pipeline, which creates pangenomes directly from whole-genome alignments, and demonstrate its ability to scale to 90 human haplotypes from the Human Pangenome Reference Consortium. The method builds graphs containing all forms of genetic variation while allowing use of current mapping and genotyping tools. We measure the effect of the quality and completeness of reference genomes used for analysis within the pangenomes and show that using the CHM13 reference from the Telomere-to-Telomere Consortium improves the accuracy of our methods. We also demonstrate construction of a Drosophila melanogaster pangenome.

Nanopore sequencing of 1000 Genomes Project samples to build a comprehensive catalog of human genetic variation

Less than half of individuals with a suspected Mendelian condition receive a precise molecular diagnosis after comprehensive clinical genetic testing. Improvements in data quality and costs have heightened interest in using long-read sequencing (LRS) to streamline clinical genomic testing, but the absence of control datasets for variant filtering and prioritization has made tertiary analysis of LRS data challenging. To address this, the 1000 Genomes Project ONT Sequencing Consortium aims to generate LRS data from at least 800 of the 1000 Genomes Project samples. Our goal is to use LRS to identify a broader spectrum of variation so we may improve our understanding of normal patterns of human variation. Here, we present data from analysis of the first 100 samples, representing all 5 superpopulations and 19 subpopulations. These samples, sequenced to an average depth of coverage of 37x and sequence read N50 of 54 kbp, have high concordance with previous studies for identifying single nucleotide and indel variants outside of homopolymer regions. Using multiple structural variant (SV) callers, we identify an average of 24,543 high-confidence SVs per genome, including shared and private SVs likely to disrupt gene function as well as pathogenic expansions within disease-associated repeats that were not detected using short reads. Evaluation of methylation signatures revealed expected patterns at known imprinted loci, samples with skewed X-inactivation patterns, and novel differentially methylated regions. All raw sequencing data, processed data, and summary statistics are publicly available, providing a valuable resource for the clinical genetics community to discover pathogenic SVs.

Multiparametric MRI and T2/FLAIR mismatch complements the World Health Organization 2021 classification for the diagnosis of IDH-mutant 1p/19q non-co-deleted/ATRX-mutant astrocytoma

AIM

To investigate whether T2-weighted imaging-fluid-attenuated inversion recovery (T2/FLAIR) mismatch, T2∗ dynamic susceptibility contrast (DSC) perfusion, and magnetic resonance spectroscopy (MRS) correlated with the histological diagnosis and grading of IDH (isocitrate dehydrogenase)-mutant, 1p/19q non-co-deleted/ATRX (alpha-thalassemia mental retardation X-linked)-mutant astrocytoma.

MATERIALS

Imaging of 101 IDH-mutant diffuse glioma cases of histological grades 2-3 (2019-2021) were analysed retrospectively by two neuroradiologists blinded to the molecular diagnosis. T2/FLAIR mismatch sign is used for radio-phenotyping, and pre-biopsy multiparametric MRI images were assessed for grading purposes. Cut-off values pre-determined for radiologically high-grade lesions were relative cerebral blood volume (rCBV) ≥2, choline/creatine ratio (Cho/Cr) ≥1.5 (30 ms echo time [TE]), Cho/Cr ≥1.8 (135 ms TE).

RESULTS

Sixteen of the 101 cases showed T2/FLAIR mismatch, all of which were histogenetically confirmed IDH-mutant 1p/19q non-co-deleted/ATRX mutant astrocytomas; 50% were grade 3 (8/16) and 50% grade 2 (8/16). None showed contrast enhancement. Nine of the 16 had adequate multiparametric MRI for analysis. Any positive value by combining rCBV ≥2 with Cho/Cr ≥1.5 (30 ms TE) or Cho/Cr ≥1.8 (135 ms TE) predicted grade 3 histology with sensitivity, specificity, positive predictive value, negative predictive value, and accuracy of 100%.

CONCLUSION

The T2/FLAIR mismatch sign detected diffuse astrocytomas with 100% specificity. When combined with high Cho/Cr and raised rCBV, this predicted histological grading with high accuracy. The future direction for imaging should explore a similar integrated layered approach of 2021 classification of central nervous system (CNS) tumours combining radio-phenotyping and grading from structural and multiparametric imaging.

Assessing methylation detection for primary human tissue using Nanopore sequencing

DNA methylation most commonly occurs as 5-methylcytosine (5-mC) in the human genome and has been associated with human diseases. Recent developments in single-molecule sequencing technologies (Oxford Nanopore Technologies (ONT) and Pacific Biosciences) have enabled readouts of long, native DNA molecules, including cytosine methylation. ONT recently upgraded their Nanopore sequencing chemistry and kits from R9 to the R10 version, which yielded increased accuracy and sequencing throughput. However the effects on methylation detection have not yet been documented. Here we performed a series of computational analyses to characterize differences in Nanopore-based 5mC detection between the ONT R9 and R10 chemistries. We compared 5mC calls in R9 and R10 for three human genome datasets: a cell line, a frontal cortex brain sample, and a blood sample. We performed an in-depth analysis on CpG islands and homopolymer regions, and documented high concordance for methylation detection among sequencing technologies. The strongest correlation was observed between Nanopore R10 and Illumina bisulfite technologies for cell line-derived datasets. Subtle differences in methylation datasets between technologies can impact analysis tools such as differential methylation calling software. Our findings show that comparisons can be drawn between methylation data from different Nanopore chemistries using guided hypotheses. This work will facilitate comparison among Nanopore data cohorts derived using different chemistries from large scale sequencing efforts, such as the NIH CARD Long Read Initiative.

ECFS standards of care on CFTR-related disorders: Towards a comprehensive program for affected individuals

After three publications defining an updated guidance on the diagnostic criteria for people with cystic fibrosis transmembrane conductance regulator (CFTR)-related disorders (pwCFTR-RDs), establishing its relationship to CFTR-dysfunction and describing the individual disorders, this fourth and last paper in the series addresses some critical challenges facing health care providers and pwCFTR-RD. Topics included are: 1) benefits and obstacles to collect data from pwCFTR-RD are discussed, together with the opportunity to integrate them into established CF-registries; 2) the potential of infants designated CRMS/CFSPID to develop a CFTR-RD and how to communicate this information; 3) a description of the challenges in genetic counseling, with particular regard to phenotypic variability, unknown long-term evolution, CFTR testing and pregnancy termination 4) a proposal for the assessment of potential barriers to the implementation and dissemination of the produced documents to health care professionals involved in the care of pwCFTR-RD and a process to monitor the implementation of the CFTR-RD recommendations; 5) clinical trials investigating the efficacy of CFTR modulators in CFTR-RD and how endpoints and outcomes might be adapted to the heterogeneity of these disorders.

A phenome-wide association study of methylated GC-rich repeats identifies a GCC repeat expansion in AFF3 as a significant cause of intellectual disability

GC-rich tandem repeat expansions (TREs) are often associated with DNA methylation, gene silencing and folate-sensitive fragile sites and underlie several congenital and late-onset disorders. Through a combination of DNA methylation profiling and tandem repeat genotyping, we identified 24 methylated TREs and investigated their effects on human traits using PheWAS in 168,641 individuals from the UK Biobank, identifying 156 significant TRE:trait associations involving 17 different TREs. Of these, a GCC expansion in the promoter of AFF3 was linked with a 2.4-fold reduced probability of completing secondary education, an effect size comparable to several recurrent pathogenic microdeletions. In a cohort of 6,371 probands with neurodevelopmental problems of suspected genetic etiology, we observed a significant enrichment of AFF3 expansions compared to controls. With a population prevalence that is at least 5-fold higher than the TRE that causes fragile X syndrome, AFF3 expansions represent a significant cause of neurodevelopmental delay.

Profiling of repetitive RNA sequences in the blood plasma of patients with cancer

Liquid biopsies provide a means for the profiling of cell-free RNAs secreted by cells throughout the body. Although well-annotated coding and non-coding transcripts in blood are readily detectable and can serve as biomarkers of disease, the overall diagnostic utility of the cell-free transcriptome remains unclear. Here we show that RNAs derived from transposable elements and other repeat elements are enriched in the cell-free transcriptome of patients with cancer, and that they serve as signatures for the accurate classification of the disease. We used repeat-element-aware liquid-biopsy technology and single-molecule nanopore sequencing to profile the cell-free transcriptome in plasma from patients with cancer and to examine millions of genomic features comprising all annotated genes and repeat elements throughout the genome. By aggregating individual repeat elements to the subfamily level, we found that samples with pancreatic cancer are enriched with specific Alu subfamilies, whereas other cancers have their own characteristic cell-free RNA profile. Our findings show that repetitive RNA sequences are abundant in blood and can be used as disease-specific diagnostic biomarkers.

Microbial isolation and characterization from two flex lines from the urine processor assembly onboard the international space station

Urine, humidity condensate, and other sources of non-potable water are processed onboard the International Space Station (ISS) by the Water Recovery System (WRS) yielding potable water. While some means of microbial control are in place, including a phosphoric acid/hexavalent chromium urine pretreatment solution, many areas within the WRS are not available for routine microbial monitoring. Due to refurbishment needs, two flex lines from the Urine Processor Assembly (UPA) within the WRS were removed and returned to Earth. The water from within these lines, as well as flush water, was microbially evaluated. Culture and culture-independent analysis revealed the presence of Burkholderia, Paraburkholderia, and Leifsonia. Fungal culture also identified Fusarium and Lecythophora. Hybrid de novo genome analysis of the five distinct Burkholderia isolates identified them as B. contaminans, while the two Paraburkholderia isolates were identified as P. fungorum. Chromate-resistance gene clusters were identified through pangenomic analysis that differentiated these genomes from previously studied isolates recovered from the point-of-use potable water dispenser and/or current NCBI references, indicating that unique populations exist within distinct niches in the WRS. Beyond genomic analysis, fixed samples directly from the lines were imaged by environmental scanning electron microscopy, which detailed networks of fungal-bacterial biofilms. This is the first evidence of biofilm formation within flex lines from the UPA onboard the ISS. For all bacteria isolated, biofilm potential was further characterized, with the B. contaminans isolates demonstrating the most considerable biofilm formation. Moreover, the genomes of the B. contaminans revealed secondary metabolite gene clusters associated with quorum sensing, biofilm formation, antifungal compounds, and hemolysins. The potential production of these gene cluster metabolites was phenotypically evaluated through biofilm, bacterial-fungal interaction, and hemolytic assays. Collectively, these data identify the UPA flex lines as a unique ecological niche and novel area of biofilm growth within the WRS. Further investigation of these organisms and their resistance profiles will enable engineering controls directed toward biofilm prevention in future space station water systems.

Scalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation

Long-read sequencing technologies substantially overcome the limitations of short-reads but have not been considered as a feasible replacement for population-scale projects, being a combination of too expensive, not scalable enough or too error-prone. Here we develop an efficient and scalable wet lab and computational protocol, Napu, for Oxford Nanopore Technologies long-read sequencing that seeks to address those limitations. We applied our protocol to cell lines and brain tissue samples as part of a pilot project for the National Institutes of Health Center for Alzheimer's and Related Dementias. Using a single PromethION flow cell, we can detect single nucleotide polymorphisms with F1-score comparable to Illumina short-read sequencing. Small indel calling remains difficult within homopolymers and tandem repeats, but achieves good concordance to Illumina indel calls elsewhere. Further, we can discover structural variants with F1-score on par with state-of-the-art de novo assembly methods. Our protocol phases small and structural variants at megabase scales and produces highly accurate, haplotype-specific methylation calls.

Local read haplotagging enables accurate long-read small variant calling

Long-read sequencing technology has enabled variant detection in difficult-to-map regions of the genome and enabled rapid genetic diagnosis in clinical settings. Rapidly evolving third-generation sequencing platforms like Pacific Biosciences (PacBio) and Oxford nanopore technologies (ONT) are introducing newer platforms and data types. It has been demonstrated that variant calling methods based on deep neural networks can use local haplotyping information with long-reads to improve the genotyping accuracy. However, using local haplotype information creates an overhead as variant calling needs to be performed multiple times which ultimately makes it difficult to extend to new data types and platforms as they get introduced. In this work, we have developed a local haplotype approximate method that enables state-of-the-art variant calling performance with multiple sequencing platforms including PacBio Revio system, ONT R10.4 simplex and duplex data. This addition of local haplotype approximation makes DeepVariant a universal variant calling solution for long-read sequencing platforms.

The complete sequence of a human Y chromosome

The human Y chromosome has been notoriously difficult to sequence and assemble because of its complex repeat structure that includes long palindromes, tandem repeats and segmental duplications1-3. As a result, more than half of the Y chromosome is missing from the GRCh38 reference sequence and it remains the last human chromosome to be finished4,5. Here, the Telomere-to-Telomere (T2T) consortium presents the complete 62,460,029-base-pair sequence of a human Y chromosome from the HG002 genome (T2T-Y) that corrects multiple errors in GRCh38-Y and adds over 30 million base pairs of sequence to the reference, showing the complete ampliconic structures of gene families TSPY, DAZ and RBMY; 41 additional protein-coding genes, mostly from the TSPY family; and an alternating pattern of human satellite 1 and 3 blocks in the heterochromatic Yq12 region. We have combined T2T-Y with a previous assembly of the CHM13 genome4 and mapped available population variation, clinical variants and functional genomics data to produce a complete and comprehensive reference sequence for all 24 human chromosomes.

Inhaled mRNA therapy for treatment of cystic fibrosis: Interim results of a randomized, double-blind, placebo-controlled phase 1/2 clinical study

BACKGROUND

MRT5005, a codon-optimized CFTR mRNA, delivered by aerosol in lipid nanoparticles, was designed as a genotype-agnostic treatment for CF lung disease.

METHODS

This was a randomized, double-blind, placebo-controlled Phase 1/2 study performed in the US. Adults with 2 severe class I and/or II CFTR mutations and baseline ppFEV1 values between 50 and 90% were randomized 3:1 (MRT5005: placebo). Six dose levels of MRT5005 (4, 8, 12, 16, 20, and 24 mg) or placebo (0.9% Sodium Chloride) were administered by nebulization. The single ascending dose cohort was treated over a range from 8 to 24 mg; the multiple ascending dose cohort received five weekly doses (range 8-20 mg); and the daily dosing cohort received five daily doses (4 mg).

RESULTS

A total of 42 subjects were assigned to MRT5005 [31] or placebo [11]. A total of 14 febrile reactions were observed in 10 MRT5005-treated participants, which were mild [3] or moderate [11] in severity; two subjects discontinued related to these events. Additionally, two MRT5005-treated patients experienced hypersensitivity reactions, which were managed conservatively. The most common treatment emergent adverse events were cough and headache. No consistent effects on FEV1 were noted.

CONCLUSIONS

MRT5005 was generally safe and well tolerated through 28 days of follow-up after the last dose, though febrile and hypersensitivity reactions were noted. The majority of these reactions resolved within 1-2 days with supportive care allowing continued treatment with MRT5005 and careful monitoring. In this small first-in-human study, FEV1 remained stable after treatment, but no beneficial effects on FEV1 were observed.

A draft human pangenome reference

Here the Human Pangenome Reference Consortium presents a first draft of the human pangenome reference. The pangenome contains 47 phased, diploid assemblies from a cohort of genetically diverse individuals1. These assemblies cover more than 99% of the expected sequence in each genome and are more than 99% accurate at the structural and base pair levels. Based on alignments of the assemblies, we generate a draft pangenome that captures known variants and haplotypes and reveals new alleles at structurally complex loci. We also add 119 million base pairs of euchromatic polymorphic sequences and 1,115 gene duplications relative to the existing reference GRCh38. Roughly 90 million of the additional base pairs are derived from structural variation. Using our draft pangenome to analyse short-read data reduced small variant discovery errors by 34% and increased the number of structural variants detected per haplotype by 104% compared with GRCh38-based workflows, which enabled the typing of the vast majority of structural variant alleles per sample.

Multicellular, IVT-derived, unmodified human transcriptome for nanopore direct RNA analysis

Nanopore direct RNA sequencing (DRS) enables measurements of native RNA modifications. Modification-free transcripts are an important control for DRS. Additionally, it is advantageous to have canonical transcripts from multiple cell lines to better account for human transcriptome variation. Here we generated and analyzed Nanopore DRS datasets for five human cell lines using in vitro transcribed (IVT) RNA. We compared performance statistics amongst biological replicates. We also documented nucleotide and ionic current level variation across cell lines. These data will serve as a resource to the community for RNA modification analysis.

Scalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation

Long-read sequencing technologies substantially overcome the limitations of short-reads but to date have not been considered as feasible replacement at scale due to a combination of being too expensive, not scalable enough, or too error-prone. Here, we develop an efficient and scalable wet lab and computational protocol for Oxford Nanopore Technologies (ONT) long-read sequencing that seeks to provide a genuine alternative to short-reads for large-scale genomics projects. We applied our protocol to cell lines and brain tissue samples as part of a pilot project for the NIH Center for Alzheimer's and Related Dementias (CARD). Using a single PromethION flow cell, we can detect SNPs with F1-score better than Illumina short-read sequencing. Small indel calling remains to be difficult inside homopolymers and tandem repeats, but is comparable to Illumina calls elsewhere. Further, we can discover structural variants with F1-score comparable to state-of the-art methods involving Pacific Biosciences HiFi sequencing and trio information (but at a lower cost and greater throughput). Using ONT based phasing, we can then combine and phase small and structural variants at megabase scales. Our protocol also produces highly accurate, haplotype-specific methylation calls. Overall, this makes large-scale long-read sequencing projects feasible; the protocol is currently being used to sequence thousands of brain-based genomes as a part of the NIH CARD initiative. We provide the protocol and software as open-source integrated pipelines for generating phased variant calls and assemblies.

Phased nanopore assembly with Shasta and modular graph phasing with GFAse

As a step towards simplifying and reducing the cost of haplotype resolved de novo assembly, we describe new methods for accurately phasing nanopore data with the Shasta genome assembler and a modular tool for extending phasing to the chromosome scale called GFAse. We test using new variants of Oxford Nanopore Technologies' (ONT) PromethION sequencing, including those using proximity ligation and show that newer, higher accuracy ONT reads substantially improve assembly quality.

Semi-automated assembly of high-quality diploid human reference genomes

The current human reference genome, GRCh38, represents over 20 years of effort to generate a high-quality assembly, which has benefitted society1,2. However, it still has many gaps and errors, and does not represent a biological genome as it is a blend of multiple individuals3,4. Recently, a high-quality telomere-to-telomere reference, CHM13, was generated with the latest long-read technologies, but it was derived from a hydatidiform mole cell line with a nearly homozygous genome5. To address these limitations, the Human Pangenome Reference Consortium formed with the goal of creating high-quality, cost-effective, diploid genome assemblies for a pangenome reference that represents human genetic diversity6. Here, in our first scientific report, we determined which combination of current genome sequencing and assembly approaches yield the most complete and accurate diploid genome assembly with minimal manual curation. Approaches that used highly accurate long reads and parent-child data with graph-based haplotype phasing during assembly outperformed those that did not. Developing a combination of the top-performing methods, we generated our first high-quality diploid reference assembly, containing only approximately four gaps per chromosome on average, with most chromosomes within ±1% of the length of CHM13. Nearly 48% of protein-coding genes have non-synonymous amino acid changes between haplotypes, and centromeric regions showed the highest diversity. Our findings serve as a foundation for assembling near-complete diploid human genomes at scale for a pangenome reference to capture global genetic variation from single nucleotides to structural rearrangements.

O-232 Art of fibroid removal in patients with infertility

Aim of myomectomy in infertile patient is to preserve and improve fertility, minimising excessive bleeding and pain. Relation ship of myoma and fertility remains debatable moreover removal of all myomas may not be helpful in improving fertility outcome thus it becomes important to decide which fibroid should be removed and which one shouldn’t be touched. Principle of minimal damage and complication should be kept in mind. Mapping of fibroid is an important step in planning the route of operation.Number and site of myoma decides the approach. A preoperative  meticulous TVS examination supplemented by TAS specially in large and multiple fibroids is extremely helpful in decision making. it is also important to preoperative differentiation of adenomyosis and fibroid to avoid a surprise element and excessive bleeding during removal. Use of colour flow may be helpful in differentiating. Use of 3-D is important specially in borderline sub mucous myoma. Extent of myoma in to uterine cavity is very important to decide the route of operation. various classifications have attempted to simplify the decision making but combining usg and hysteroscopy is the best way to decide. it is also important to diagnose a large intramural myoma touching the junctional zone. Instilling methylene blue before operation to outline the cavity during surgery in case of accidental entry is a good practice. using intraoperative ultrasound while tackling a large intracavitary fibroid having more than 75% extent in intra myometrial region may be helpful in complete removal.

The placement of the optical and secondary ports determines the degree of ergonomic surgery performance, time and difficulty of myoma enucleation, and the ease of suturing. reducing the bleeding during enucleation, dissection in the right plane, minimal use of cautery and proper suturing and closure avoiding any haematoma formation are key points for a successful myomectomy. Use of diluted vasopressin is very effective in making the surgery blood less. So also the use of bipolar in coagulating the large blood vessels. Using bipolar diathermy, a dissecting grasper, and a suction cannula, meticulous exploration of the dissection field can more efficiently detect and coagulate any actively bleeding vessels. Slow rotation of the bevelled morcellator and good control of the bag could reduce de novo myoma and endometriosis. The surgery outcome and the risk of intraoperative complications are highly dependent on trocar placement, finding of the correct cleavage plane, haemostasis, and suturing technique. Flap technique is an innovative approach for removing small fibroid near junctional zone. Good surgery with respect to minimal destruction and handling of the healthy tissue, avoiding unnecessary organ manipulation, controlled bleeding, minimal coagulation, and reasonable operating time remain the best ways to diminish the risk of adhesion formation.It is very important to preserve the cavity, minimal adhesion formation and perfect suturing avoiding dead spaces and haematoma formation for a successful out come in infertile patient.

POS1057 IMPACT OF RISANKIZUMAB ON ENTHESITIS AND ASSOCIATED PAIN: POOLED RESULTS FROM THE PHASE 3, RANDOMIZED, DOUBLE-BLIND KEEPsAKE 1 AND 2 TRIALS

Background

Controlling or improving musculoskeletal disease activity of psoriatic arthritis (PsA) (eg, enthesitis and associated pain) is a treatment priority for patients, rheumatologists, and dermatologists.1 Enthesitis is the cardinal lesion in PsA and is immunogenetically and experimentally linked to the interleukin-23 (IL-23) pathway.2 Risankizumab (RZB), a humanized immunoglobulin G1 monoclonal antibody that specifically inhibits IL-23 by binding to its p19 subunit, was studied in a phase 3 adult PsA program (KEEPsAKE clinical trials).3,4 Pooled analyses from the program demonstrated the efficacy of RZB to treat enthesitis and pain associated with PsA, and increase the proportion of patients whose enthesitis resolved compared with placebo (PBO) in those patients who had an inadequate response or intolerance to ≥1 conventional synthetic disease-modifying antirheumatic drugs (KEEPsAKE 1 and 2) and/or ≤ 2 biological therapies (KEEPsAKE 2).

Objectives

To investigate whether patients without enthesitis at baseline (BL) (Leeds Enthesitis Index [LEI] = 0 at BL) remained enthesitis-free through week (W) 52, patients with enthesitis at BL (LEI > 0 at BL) had resolution of enthesitis through W52, and if greater pain relief was achieved with RZB 150 mg in patients with enthesitis at BL vs PBO up to W24.

Methods

The study design and primary results of KEEPsAKE 1 (NCT03675308) and KEEPsAKE 2 (NCT03671148) have been previously reported.3,4 Briefly, patients were randomized to receive RZB 150 mg or PBO subcutaneously at weeks 0, 4, and 16 during a 24-week, double-blind treatment period; at W28 all patients received open label RZB 150 mg. For this post hoc analysis, the RZB 150 mg and PBO groups were pooled across the 2 studies. Pain reductions (as measured by change from BL in visual analogue scale [VAS] scores) were assessed at each time point through W24 among patients with enthesitis at BL (LEI > 0 at BL) using mixed-effect model repeated measurement analysis. Additional enthesitis analyses were calculated on the data as observed.

Results

Across the pooled population, over 60% of patients in each treatment group had enthesitis at BL (RZB=444/707 [63%]; PBO=448/700 [64%]). Conversely, 37% (263/707) and 36% (252/700) had no enthesitis (LEI=0) at BL among those randomized to RZB and PBO, respectively. Among enthesitis-free patients at BL (LEI=0 at BL), 84.7% on PBO and 90% on RZB remained free of enthesitis through W24; by W52, approximately 93% of patients in both groups (RZB and PBO to RZB) remained enthesitis free. A numerically higher proportion of patients with enthesitis at BL (LEI > 0 at BL) treated with RZB (52.1%) achieved an enthesitis-free state at W24 vs PBO (41.8%); similar proportions achieved an enthesitis-free state at W36 and W52 during open label treatment (Figure 1). Among patients with enthesitis at BL, a significantly greater improvement in VAS pain scores was observed in patients treated with RZB 150 mg vs PBO, as early as W4 (P < .01) and increased through W24 (Figure 1; P < .001).

Figure 1.

Conclusion

Long-term maintenance of an enthesitis-free state (LEI = 0) was similar between the RZB 150 mg and PBO groups, with approximately 93% of patients remaining free of enthesitis at W52. For LEI > 0 patients, the RZB 150-mg group had numerically more patients whose enthesitis resolved at W24, and similar proportions were observed at W52 after the open label switch. Patients with enthesitis at BL treated with RZB 150 mg had statistically greater improvements in pain compared with patients taking PBO starting at W4 through to W24.

References

[1]Orbai A-M, et al. Ann Rheum Dis. 2017;76:673–680.

[2]Stavre Z, et al. Arthritis Res Ther. 2022;24(1):24.

[3]Kristensen LE, et al. Ann Rheum Dis. 2021;0:1–7.

[4]Östör A, et al. Ann Rheum Dis. 2021;0:1–8.

Acknowledgements

AbbVie Inc. participated in the study design; study research; collection, analysis, and interpretation of data; and writing, reviewing, and approving this abstract for submission. All authors had access to the data; participated in the development, review, and approval of the abstract; and agreed to submit this abstract to EULAR 2022 for consideration as a poster or oral presentation. No honoraria or payments were made for authorship. AbbVie and the authors thank all study investigators for their contributions and the patients who participated in this study. AbbVie funded the research for this study and provided writing support for this abstract. Medical writing assistance, funded by AbbVie, was provided by Kersten Reich, MPH, and Nancy Niguidula, DPH, of JB Ashtin.

Disclosure of Interests

Marina Magrey Consultant of: MM has received consulting fees from UCB, Novartis, Eli Lilly, Pfizer, and Janssen., Grant/research support from: MM received research grants from Amgen, AbbVie, and UCB Pharma, Manish Jain Consultant of: MJ received consulting fees from Amgen, Abbvie, Eli Lilly, Pfizer, and Novartis., Grant/research support from: MJ received research support from Amgen, Abbvie, Eli Lilly, Pfizer, and Novartis., R Ranza Speakers bureau: RR is a member of speaker bureaus for AbbVie, Janssen, Novartis, and Pfizer, Consultant of: RR is a consultant for AbbVie, Janssen, Novartis, and Pfizer, Jayne Stigler Shareholder of: JS may hold AbbVie stock or stock options., Employee of: JS is a full-time employee of AbbVie., Erin McDearmon-Blondell Shareholder of: EMB may hold AbbVie stock or stock options., Employee of: EMB is a full-time employee of AbbVie., Cuiyong Yue Shareholder of: CY may hold AbbVie stock or stock options., Employee of: CY is a full-time employee of AbbVie., Byron Padilla Shareholder of: BP may hold AbbVie stock or stock options., Employee of: BP is a full-time employee of AbbVie., Christian Kaufmann Shareholder of: CK may hold AbbVie stock or stock options., Employee of: CK is a full-time employee of AbbVie., Dennis McGonagle Speakers bureau: DM is a member of speaker bureaus for AbbVie, Janssen, Novartis, and Pfizer., Grant/research support from: DM received research grants from AbbVie, Janssen, Novartis, and Pfizer, UCB, BMS, Celgene.

POS0683 EFFICACY AND SAFETY OF UPADACITINIB IN TNFi-IR PATIENTS WITH RHEUMATOID ARTHRITIS FROM THREE PHASE 3 CLINICAL TRIALS

Background

For patients with RA who are refractory to biologic DMARDs (bDMARDs), such as tumor necrosis factor inhibitors (TNFis), optimal disease control is less likely to be achieved with subsequent therapy.1 In line with recommendations from EULAR and ACR, switching to a treatment with a different mechanism of action is appropriate for these patients.

Objectives

To describe the efficacy and safety of upadacitinib (UPA) 15 mg once daily in patients with RA and an inadequate response or intolerance to TNFis (TNFi-IR).

Methods

A post hoc subgroup analysis was conducted in TNFi-IR patients who were treated with UPA 15 mg once daily in three Phase 3 clinical trials: SELECT-BEYOND,2 -CHOICE,3 and -COMPARE.4 For COMPARE, only patients treated with adalimumab and switched to UPA as rescue therapy were included. ≥20/50/70% improvement in ACR criteria, DAS28(CRP), CDAI, and SDAI, as well as change from baseline in HAQ-DI and other patient-reported outcomes (PROs) were reported through 24 weeks. Non-responder imputation was used for all missing categorical outcomes; as observed (COMPARE) or multiple imputation (CHOICE, BEYOND) were used for missing continuous outcomes. Pooled safety results were presented as exposure-adjusted event rates (EAERs) with a cut-off of June 30, 2021.

Results

568 TNFi-IR patients were included: 146 from BEYOND, 263 from CHOICE, and 159 from COMPARE. Mean duration since RA diagnosis was longer for BEYOND and CHOICE versus COMPARE; cardiovascular (CV) risk factors were common among this refractory population (Table 1). ACR20/50/70 and disease activity outcomes observed in the TNFi-IR population were generally consistent with the overall BEYOND2 and CHOICE3 bDMARD-IR populations, and consistent across the three studies in the TNFi-IR subgroups (Figure 1). Improvements in PROs including HAQ-DI, fatigue, pain, and morning stiffness over 24 weeks were observed (data not shown). Pooled safety results reporting 1574.8 patient-years (PY) of exposure in the TNFi-IR subgroup showed similar results to the overall BEYOND2 and CHOICE3 bDMARD-IR study populations, with EAERs of 3.1 events/100 PY for herpes zoster and 0.8 events/100 PY for adjudicated major adverse CV events, adjudicated venous thromboembolism (VTE), and malignancy excluding non-melanoma skin cancer. The EAER of any AE leading to death was 1.4 events/100 PY.

Table 1.

Baseline characteristics of TNFi-IR patients treated with UPA 15 mg

n (%), unless specifiedSELECT-BEYOND (n=146)SELECT-CHOICE (n=263)SELECT-COMPARE (ADA → UPA) (n=159)Female122 (83.6)219 (83.3)133 (83.6)Mean (SD) age, years56.6 (11.0)55.5 (11.1)53.9 (10.6)Mean (SD) duration of RA diagnosis, years13.2 (9.5)12.5 (9.4)8.2 (8.5)Concomitant csDMARDs MTX alone100 (70.4)195 (74.1)159 (100.0) MTX and other csDMARDs20 (14.1)25 (9.5)0 csDMARDs other than MTX22 (15.5)38 (14.4)0Concomitant oral steroids73 (50.0)140 (53.2)98 (61.6)1 prior bDMARD68 (46.6)172 (65.4)142 (89.3)2 prior bDMARDs40 (27.4)62 (23.6)17 (10.7)a≥3 prior bDMARDs38 (26.0)29 (11.0)0Failed ≥1 prior TNFi due to lack of efficacyb131 (89.7)223 (84.8)159 (100.0)History of VTE / CV event3 (2.1) / 28 (19.2)6 (2.3) / 20 (7.6)4 (2.5) / 14 (8.8)CV risk factors Hypertension72 (49.3)109 (41.4)68 (42.8) Diabetes mellitus22 (15.1)34 (12.9)17 (10.7) Smoking (current former past)68 (46.6)109 (41.5)55 (34.6) Elevated LDL-C (≥3.36 mmol/L)38 (26.0)52 (20.0)48 (30.2) Low HDL-C (≤1.55 mmol/L)80 (54.8)171 (65.0)88 (55.3)

aThese patients received one bDMARD before entry into SELECT-COMPARE.

bRemaining patients were intolerant to ≥1 prior TNFi.

Conclusion

In this post hoc subgroup analysis, TNFi-IR patients treated with UPA 15 mg achieved clinically meaningful efficacy responses over 24 weeks, with safety consistent with the overall bDMARD-IR patient population in the Phase 3 program.

References

[1]Rendas-Baum R, et al. Arthritis Res Ther 2011;13:R25;

[2]Genovese C, et al. Lancet 2018;391:2513–24;

[3]Rubbert-Roth A, et al. NEJM 2020;383:1511–21;

[4]Fleischmann R, et al. Ann Rheum Dis 2019;78:1454–62.

Acknowledgements

AbbVie funded this study; contributed to its design; participated in data collection, analysis, and interpretation of the data; and participated in the writing, review, and approval of the abstract. AbbVie and the authors thank all study investigators for their contributions and the patients who participated in this study. No honoraria or payments were made for authorship. Medical writing support was provided by Amy Wilson, MSc, of 2 the Nth (Cheshire, UK), and was funded by AbbVie.

Disclosure of Interests

Roy M. Fleischmann Consultant of: AbbVie, Amgen, Bristol-Myers Squibb, Eli Lilly, Galvani, Gilead, GSK, Janssen, Novartis, Pfizer, and UCB, Grant/research support from: AbbVie, Amgen, Biosplice, Bristol-Myers Squibb, Flexion, Gilead, Horizon, Eli Lilly, Galvani, Janssen, Novartis, Pfizer, Sanofi-Aventis, Selecta, Teva, UCB, Viela, and Vorso, Louis Bessette Speakers bureau: AbbVie, Amgen, Bristol-Meyers Squibb, Celgene, Eli Lilly, Fresenius Kabi, Gilead, Janssen, Merck, Novartis, Pfizer, Roche, Sanofi-Aventis, Teva, and UCB, Consultant of: AbbVie, Amgen, Bristol-Meyers Squibb, Celgene, Eli Lilly, Fresenius Kabi, Gilead, Janssen, Merck, Novartis, Pfizer, Roche, Sanofi-Aventis, Teva, and UCB, Grant/research support from: AbbVie, Amgen, Bristol-Meyers Squibb, Celgene, Eli Lilly, Fresenius Kabi, Gilead, Janssen, Merck, Novartis, Pfizer, Roche, Sanofi-Aventis, Teva, and UCB, Jeffrey Sparks Consultant of: AbbVie, Amgen, Boehringer Ingelheim, Bristol-Myers Squibb, Gilead, Inova Diagnostics, Janssen, Optum, and Pfizer, Stephen Hall Consultant of: AbbVie, Amgen, Bristol-Meyers Sqibb, Eli Lilly, Gilead, Janssen, Merck, Novartis, and UCB, Grant/research support from: AbbVie, Amgen, Bristol-Meyers Sqibb, Eli Lilly, Gilead, Janssen, Merck, Novartis, and UCB, Manish Jain Consultant of: AbbVie, Amgen, Eli Lilly, Novartis, and Pfizer, Grant/research support from: AbbVie, Amgen, Eli Lilly, Novartis, and Pfizer, Adriana Kakehasi Speakers bureau: AbbVie, Amgen, Eli Lilly, Fresenius Kabi, Janssen, Novartis, Pfizer, Sandoz, and UCB, Consultant of: AbbVie, Amgen, Eli Lilly, Fresenius Kabi, Janssen, Novartis, Pfizer, Sandoz, and UCB, Grant/research support from: AbbVie, Amgen, Eli Lilly, Fresenius Kabi, Janssen, Novartis, Pfizer, Sandoz, and UCB, Yanna Song Shareholder of: AbbVie (may own stock or options), Employee of: AbbVie, Sebastian Meerwein Shareholder of: AbbVie (may own stock or options), Employee of: AbbVie, Ryan DeMasi Shareholder of: AbbVie (may own stock or options), Employee of: AbbVie, Jessica Suboticki Shareholder of: AbbVie (may own stock or options), Employee of: AbbVie, Andrea Rubbert-Roth Consultant of: AbbVie, AbbVie Deutschland, Amgen, Bristol-Myers Squibb, Chugai Pharmaceuticals, Eli Lilly, F. Hoffman-La Roche, Gilead Sciences, Janssen Global Services, Novartis, and Sanofi Pasteur

POS0506 DIFFERENT BIOACTIVE LIPID PROFILES PREDICT RESPONSE TO TNF OR IL6 INHIBITORS IN RHEUMATOID ARTHRITIS: RESULT OF THE CorEvitas CERTAIN COMPARATIVE EFFECTIVENESS STUDY

Background

Circulating bioactive lipids can provide information about the pathogenesis of specific diseases and potentially help predict therapeutic response. Choosing the right biological therapy earlier in the course of rheumatoid arthritis (RA) could help reach the goal of remission.

Objectives

We hypothesized that circulating bioactive lipids at baseline would identify specific metabolic profiles that predict patient response to therapy and define elements of metabolic pathobiology in arthritis.

Methods

Bioactive lipids were measured in plasma from two cohorts of RA patients from the CorEvitas (formerly known as Corrona) CERTAIN registry (1) at baseline prior to treatment with TNF inhibitors (all biologic naïve, N=102) or anti-IL6 (all previously exposed to biologics, N=114). Response to treatment was categorized by minimal clinically important difference (MCID) in Clinical Disease Activity Index (CDAI) (2) at 6 months after treatment initiation. Patients had to have a 6 month follow up visit and plasma available at both the baseline and the f/u time points. Liquid chromatography (LC) system coupled with high resolution QExactive orbitrap mass spectrometer (LC/MS) was used for bioactive lipids profiling. Around 300 spectral features were identified as potential oxylipins by searching against an in-house MS/MS library. Logistic regression analyses adjusted for gender, age and BMI was perfomed using R software.

Results

102 patients (average age 54, standard deviation [SD] 12.6, 82% female [83], average BMI 29.7, SD 6.7, average CDAI 27.1, SD 13.7) starting anti-TNF therapy and 114 patients (average age 57, SD 13, 90% female [102], average BMI 30.5, SD 7.4, average CDAI 28.7, SD 13.8) starting tocilizumab were analyzed. Twenty-five bioactive metabolites discriminated between RA patients classified as anti-TNF responders (R, n = 74) and non-responders (NR, n = 28). Among these, the anti-inflammatory oxylipin maresin 2 was higher in R while the pro-inflammatory oxylipins 15d PGJ2 and 5,6-diHETE were higher in NR. Twenty different metabolites discriminated anti-IL6 R (n=73) and NR (n=41) as shown in Figure 1. The anti-inflammatory oxylipin 14-15EET was higher in R while the pro-inflammatory oxylipins 16-HETE and 5S-HpETE were higher in NR.

Figure 1.

Volcano plots visualizing baseline metabolites associated with responders vs. non responders in a) anti-TNF and b) anti IL-6 therapy groups. Results are derived from multivariate logistic regression analysis of baseline metabolites and response to treatment categorized by MCID. Data plotted as the metabolite against its statistical significance, respectively reported as odds ratio (OR) and -log10(pvalue).

Conclusion

Circulating bioactive lipid analysis using LC/MS provided a rapid analysis of a wide range of metabolites and can be used to describe metabolic signatures that predict response to therapies. These results lay the groundwork for more deliberate investigations novel metabolic-based interventions to predict response to therapy and reduce arthritis morbidity.

References

[1]Pappas DA, Kremer JM, Reed G, Greenberg JD, Curtis JR. Design characteristics of the CORRONA CERTAIN study: a comparative effectiveness study of biologic agents for rheumatoid arthritis patients. BMC Musculoskeletal Disord 2014; 15: 113

[2]Curtis JR, Yang S, Chen L, Pope JE, Keystone EC, Haraoui B, Boire G, Thorne JC, Tin D, Hitchon CA, Bingham CO 3rd, Bykerk VP. Determining the Minimally Important Difference in the Clinical Disease Activity Index for Improvement and Worsening in Early Rheumatoid Arthritis Patients. Arthritis Care Res (Hoboken). 2015 Oct;67(10):1345-53. doi: 10.1002/acr.22606. PMID: 25988705; PMCID: PMC4580563.

Disclosure of Interests

Mona Alotaibi: None declared, Roxana Coras: None declared, Dimitrios A Pappas Speakers bureau: Sanofi, Novartis, Paid instructor for: Novartis, Consultant of: Roche, Sanofi, Joel M Kremer Speakers bureau: Pfizer, Consultant of: BMS, Geoffrey Thiele: None declared, Ted Mikuls Consultant of: Pfizer, Gilead, BMS, Sanofi, Mohit Jain Employee of: Sapient Bio, Monica Guma Grant/research support from: Pfizer, Novartis.

PrecisionFDA Truth Challenge V2: Calling variants from short and long reads in difficult-to-map regions

The precisionFDA Truth Challenge V2 aimed to assess the state of the art of variant calling in challenging genomic regions. Starting with FASTQs, 20 challenge participants applied their variant-calling pipelines and submitted 64 variant call sets for one or more sequencing technologies (Illumina, PacBio HiFi, and Oxford Nanopore Technologies). Submissions were evaluated following best practices for benchmarking small variants with updated Genome in a Bottle benchmark sets and genome stratifications. Challenge submissions included numerous innovative methods, with graph-based and machine learning methods scoring best for short-read and long-read datasets, respectively. With machine learning approaches, combining multiple sequencing technologies performed particularly well. Recent developments in sequencing and variant calling have enabled benchmarking variants in challenging genomic regions, paving the way for the identification of previously unknown clinically relevant variants.

Nanopore ReCappable sequencing maps SARS-CoV-2 5' capping sites and provides new insights into the structure of sgRNAs

The SARS-CoV-2 virus has a complex transcriptome characterised by multiple, nested subgenomic RNAsused to express structural and accessory proteins. Long-read sequencing technologies such as nanopore direct RNA sequencing can recover full-length transcripts, greatly simplifying the assembly of structurally complex RNAs. However, these techniques do not detect the 5' cap, thus preventing reliable identification and quantification of full-length, coding transcript models. Here we used Nanopore ReCappable Sequencing (NRCeq), a new technique that can identify capped full-length RNAs, to assemble a complete annotation of SARS-CoV-2 sgRNAs and annotate the location of capping sites across the viral genome. We obtained robust estimates of sgRNA expression across cell lines and viral isolates and identified novel canonical and non-canonical sgRNAs, including one that uses a previously un-annotated leader-to-body junction site. The data generated in this work constitute a useful resource for the scientific community and provide important insights into the mechanisms that regulate the transcription of SARS-CoV-2 sgRNAs.

Epigenetic patterns in a complete human genome

The completion of a telomere-to-telomere human reference genome, T2T-CHM13, has resolved complex regions of the genome, including repetitive and homologous regions. Here, we present a high-resolution epigenetic study of previously unresolved sequences, representing entire acrocentric chromosome short arms, gene family expansions, and a diverse collection of repeat classes. This resource precisely maps CpG methylation (32.28 million CpGs), DNA accessibility, and short-read datasets (166,058 previously unresolved chromatin immunoprecipitation sequencing peaks) to provide evidence of activity across previously unidentified or corrected genes and reveals clinically relevant paralog-specific regulation. Probing CpG methylation across human centromeres from six diverse individuals generated an estimate of variability in kinetochore localization. This analysis provides a framework with which to investigate the most elusive regions of the human genome, granting insights into epigenetic regulation.

The complete sequence of a human genome

Since its initial release in 2000, the human reference genome has covered only the euchromatic fraction of the genome, leaving important heterochromatic regions unfinished. Addressing the remaining 8% of the genome, the Telomere-to-Telomere (T2T) Consortium presents a complete 3.055 billion-base pair sequence of a human genome, T2T-CHM13, that includes gapless assemblies for all chromosomes except Y, corrects errors in the prior references, and introduces nearly 200 million base pairs of sequence containing 1956 gene predictions, 99 of which are predicted to be protein coding. The completed regions include all centromeric satellite arrays, recent segmental duplications, and the short arms of all five acrocentric chromosomes, unlocking these complex regions of the genome to variational and functional studies.

Accelerated identification of disease-causing variants with ultra-rapid nanopore genome sequencing

Whole-genome sequencing (WGS) can identify variants that cause genetic disease, but the time required for sequencing and analysis has been a barrier to its use in acutely ill patients. In the present study, we develop an approach for ultra-rapid nanopore WGS that combines an optimized sample preparation protocol, distributing sequencing over 48 flow cells, near real-time base calling and alignment, accelerated variant calling and fast variant filtration for efficient manual review. Application to two example clinical cases identified a candidate variant in <8 h from sample preparation to variant identification. We show that this framework provides accurate variant calls and efficient prioritization, and accelerates diagnostic clinical genome sequencing twofold compared with previous approaches.

A streamlined sequencing process enables identification of disease-causing variants in the clinic within 8 hours.

Identification of high-confidence human poly(A) RNA isoform scaffolds using nanopore sequencing

Nanopore sequencing devices read individual RNA strands directly. This facilitates identification of exon linkages and nucleotide modifications; however, using conventional direct RNA nanopore sequencing, the 5' and 3' ends of poly(A) RNA cannot be identified unambiguously. This is due in part to RNA degradation in vivo and in vitro that can obscure transcription start and end sites. In this study, we aimed to identify individual full-length human RNA isoforms among ∼4 million nanopore poly(A)-selected RNA reads. First, to identify RNA strands bearing 5' m⁷G caps, we exchanged the biological cap for a modified cap attached to a 45-nt oligomer. This oligomer adaptation method improved 5' end sequencing and ensured correct identification of the 5' m⁷G capped ends. Second, among these 5'-capped nanopore reads, we screened for features consistent with a 3' polyadenylation site. Combining these two steps, we identified 294,107 individual high-confidence full-length RNA scaffolds from human GM12878 cells, most of which (257,721) aligned to protein-coding genes. Of these, 4876 scaffolds indicated unannotated isoforms that were often internal to longer, previously identified RNA isoforms. Orthogonal data for m⁷G caps and open chromatin, such as CAGE and DNase-HS seq, confirmed the validity of these high-confidence RNA scaffolds.

Synthesis of modified nucleotide polymers by the poly(U) polymerase Cid1: application to direct RNA sequencing on nanopores

Understanding transcriptomes requires documenting the structures, modifications, and abundances of RNAs as well as their proximity to other molecules. The methods that make this possible depend critically on enzymes (including mutant derivatives) that act on nucleic acids for capturing and sequencing RNA. We tested two 3' nucleotidyl transferases, Saccharomyces cerevisiae poly(A) polymerase and Schizosaccharomyces pombe Cid1, for the ability to add base and sugar modified rNTPs to free RNA 3' ends, eventually focusing on Cid1. Although unable to polymerize ΨTP or 1meΨTP, Cid1 can use 5meUTP and 4thioUTP. Surprisingly, Cid1 can use inosine triphosphate to add poly(I) to the 3' ends of a wide variety of RNA molecules. Most poly(A) mRNAs efficiently acquire a uniform tract of about 50 inosine residues from Cid1, whereas non-poly(A) RNAs acquire longer, more heterogeneous tails. Here we test these activities for use in direct RNA sequencing on nanopores, and find that Cid1-mediated poly(I)-tailing permits detection and quantification of both mRNAs and non-poly(A) RNAs simultaneously, as well as enabling the analysis of nascent RNAs associated with RNA polymerase II. Poly(I) produces a different current trace than poly(A), enabling recognition of native RNA 3' end sequence lost by in vitro poly(A) addition. Addition of poly(I) by Cid1 offers a broadly useful alternative to poly(A) capture for direct RNA sequencing on nanopores.

Haplotype-aware variant calling with PEPPER-Margin-DeepVariant enables high accuracy in nanopore long-reads

Long-read sequencing has the potential to transform variant detection by reaching currently difficult-to-map regions and routinely linking together adjacent variations to enable read-based phasing. Third-generation nanopore sequence data have demonstrated a long read length, but current interpretation methods for their novel pore-based signal have unique error profiles, making accurate analysis challenging. Here, we introduce a haplotype-aware variant calling pipeline, PEPPER-Margin-DeepVariant, that produces state-of-the-art variant calling results with nanopore data. We show that our nanopore-based method outperforms the short-read-based single-nucleotide-variant identification method at the whole-genome scale and produces high-quality single-nucleotide variants in segmental duplications and low-mappability regions where short-read-based genotyping fails. We show that our pipeline can provide highly contiguous phase blocks across the genome with nanopore reads, contiguously spanning between 85% and 92% of annotated genes across six samples. We also extend PEPPER-Margin-DeepVariant to PacBio HiFi data, providing an efficient solution with superior performance over the current WhatsHap-DeepVariant standard. Finally, we demonstrate de novo assembly polishing methods that use nanopore and PacBio HiFi reads to produce diploid assemblies with high accuracy (Q35+ nanopore-polished and Q40+ PacBio HiFi-polished).

Direct Nanopore Sequencing of Individual Full Length tRNA Strands

We describe a method for direct tRNA sequencing using the Oxford Nanopore MinION. The principal technical advance is custom adapters that facilitate end-to-end sequencing of individual transfer RNA (tRNA) molecules at subnanometer precision. A second advance is a nanopore sequencing pipeline optimized for tRNA. We tested this method using purified E. coli tRNA^fMet, tRNA^Lys, and tRNA^Phe samples. 76-92% of individual aligned tRNA sequence reads were full length. As a proof of concept, we showed that nanopore sequencing detected all 43 expected isoacceptors in total E. coli MRE600 tRNA as well as isodecoders that further define that tRNA population. Alignment-based comparisons between the three purified tRNAs and their synthetic controls revealed systematic nucleotide miscalls that were diagnostic of known modifications. Systematic miscalls were also observed proximal to known modifications in total E. coli tRNA alignments, including a highly conserved pseudouridine in the T loop. This work highlights the potential of nanopore direct tRNA sequencing as well as improvements needed to implement tRNA sequencing for human healthcare applications.

Direct Nanopore Sequencing of Individual Full Length tRNA Strands

We describe a method for direct tRNA sequencing using the Oxford Nanopore MinION. The principal technical advance is custom adapters that facilitate end-to-end sequencing of individual transfer RNA (tRNA) molecules at subnanometer precision. A second advance is a nanopore sequencing pipeline optimized for tRNA. We tested this method using purified E. coli tRNA^fMet, tRNA^Lys, and tRNA^Phe samples. 76-92% of individual aligned tRNA sequence reads were full length. As a proof of concept, we showed that nanopore sequencing detected all 43 expected isoacceptors in total E. coli MRE600 tRNA as well as isodecoders that further define that tRNA population. Alignment-based comparisons between the three purified tRNAs and their synthetic controls revealed systematic nucleotide miscalls that were diagnostic of known modifications. Systematic miscalls were also observed proximal to known modifications in total E. coli tRNA alignments, including a highly conserved pseudouridine in the T loop. This work highlights the potential of nanopore direct tRNA sequencing as well as improvements needed to implement tRNA sequencing for human healthcare applications.

A community challenge to evaluate RNA-seq, fusion detection, and isoform quantification methods for cancer discovery

The accurate identification and quantitation of RNA isoforms present in the cancer transcriptome is key for analyses ranging from the inference of the impacts of somatic variants to pathway analysis to biomarker development and subtype discovery. The ICGC-TCGA DREAM Somatic Mutation Calling in RNA (SMC-RNA) challenge was a crowd-sourced effort to benchmark methods for RNA isoform quantification and fusion detection from bulk cancer RNA sequencing (RNA-seq) data. It concluded in 2018 with a comparison of 77 fusion detection entries and 65 isoform quantification entries on 51 synthetic tumors and 32 cell lines with spiked-in fusion constructs. We report the entries used to build this benchmark, the leaderboard results, and the experimental features associated with the accurate prediction of RNA species. This challenge required submissions to be in the form of containerized workflows, meaning each of the entries described is easily reusable through CWL and Docker containers at https://github.com/SMC-RNA-challenge. A record of this paper's transparent peer review process is included in the supplemental information.