ntEdit+Sealer: Efficient Targeted Error Resolution and Automated Finishing of Long-Read Genome Assemblies

High‐quality genome assemblies are crucial to many biological studies, and utilizing long sequencing reads can help achieve higher assembly contiguity. While long reads can resolve complex and repetitive regions of a genome, their relatively high associated error rates are still a major limitation. Long reads generally produce draft genome assemblies with lower base quality, which must be corrected with a genome polishing step. Hybrid genome polishing solutions can greatly improve the quality of long‐read genome assemblies by utilizing more accurate short reads to validate bases and correct errors. Currently available hybrid polishing methods rely on read alignments, and are therefore memory‐intensive and do not scale well to large genomes. Here we describe ntEdit+Sealer, an alignment‐free, k‐mer‐based genome finishing protocol that employs memory‐efficient Bloom filters. The protocol includes ntEdit for correcting base errors and small indels, and for marking potentially problematic regions, then Sealer for filling both assembly gaps and problematic regions flagged by ntEdit. ntEdit+Sealer produces highly accurate, error‐corrected genome assemblies, and is available as a Makefile pipeline from https://github.com/bcgsc/ntedit_sealer_protocol. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC.

Basic Protocol: Automated long‐read genome finishing with short reads

Support Protocol: Selecting optimal values for k‐mer lengths (k) and Bloom filter size (b)

Long term non-invasive endothelial function assessment in patients with paediatric inflammatory multisystem syndrome temporarily associated with Covid 19 (PIMS TS)

Funding Acknowledgements

Type of funding sources: None.

Introduction

Patients with PIMS-TS present with features of vasculitis (bright coronary arteries and diffuse coronary ectasia on transthoracic echocardiography) and prothrombotic features (e.g. elevated D Dimers) indicating involvement of the endothelial layer in the inflammatory process. Impairment in endothelial function may contribute to the acute but also to possible long-term consequences in patients with PIMS-TS. The aim of this pilot study is to assess non-invasively the endothelial (dys)function using reactive hyperemic peripheral arterial tonometry (RH-PAT) 6 months after the acute inflammatory phase. 

Methods

Ten patients with previous diagnosis of PIMS-TS were compared to  age-matched controls. The endothelial function was assessed using the EndoPAT device which provides the reactive hyperemic index (RHI) of endothelial function in a 15-min test. Cardiac function indices by means of LV fractional shortening (FS) was also assessed.

Results

There were no significant differences regarding age (11.2 ± 3.0 vs 13.6 ± 2.4, p = 0.063), height, weight and body surface area, (BSA: 1.49 ± 0.36 vs 1.52 ± 0.25, p = 0.856) in patients with previous diagnosis of PIMS-TS and controls respectively. The two groups also had similar LV systolic function assessed by FS (36.3 ± 9.1% vs 36.7 ± 7.1%, p = 0.922). The RHI in the PIMS TS group was similar to the control group (1.65 ± 0.43 vs 1.81 ± 0.60, p = 0.533 respectively).

Conclusions.  Patients with PIMS-TS who may present with features of vasculitis during the acute phase, do not show evidence of endothelial dysfunction during the long term follow-up, suggesting resolution. Further studies are required to accurately determine the endothelial (dys)function during the acute phase of the inflammatory syndrome and course.

LongStitch: high-quality genome assembly correction and scaffolding using long reads

BACKGROUND

Generating high-quality de novo genome assemblies is foundational to the genomics study of model and non-model organisms. In recent years, long-read sequencing has greatly benefited genome assembly and scaffolding, a process by which assembled sequences are ordered and oriented through the use of long-range information. Long reads are better able to span repetitive genomic regions compared to short reads, and thus have tremendous utility for resolving problematic regions and helping generate more complete draft assemblies. Here, we present LongStitch, a scalable pipeline that corrects and scaffolds draft genome assemblies exclusively using long reads.

RESULTS

LongStitch incorporates multiple tools developed by our group and runs in up to three stages, which includes initial assembly correction (Tigmint-long), followed by two incremental scaffolding stages (ntLink and ARKS-long). Tigmint-long and ARKS-long are misassembly correction and scaffolding utilities, respectively, previously developed for linked reads, that we adapted for long reads. Here, we describe the LongStitch pipeline and introduce our new long-read scaffolder, ntLink, which utilizes lightweight minimizer mappings to join contigs. LongStitch was tested on short and long-read assemblies of Caenorhabditis elegans, Oryza sativa, and three different human individuals using corresponding nanopore long-read data, and improves the contiguity of each assembly from 1.2-fold up to 304.6-fold (as measured by NGA50 length). Furthermore, LongStitch generates more contiguous and correct assemblies compared to state-of-the-art long-read scaffolder LRScaf in most tests, and consistently improves upon human assemblies in under five hours using less than 23 GB of RAM.

CONCLUSIONS

Due to its effectiveness and efficiency in improving draft assemblies using long reads, we expect LongStitch to benefit a wide variety of de novo genome assembly projects. The LongStitch pipeline is freely available at https://github.com/bcgsc/longstitch .

Does an empowerment-based self-care supportive intervention save cost for improving self-care and health service utilization among heart failure patients

Background

Heart failure (HF) evolves as a global pandemic and strains the over-stretched hospital service. Ineffective self-care remains the key factor to explain the avoidable hospital admission. Patient empowerment is as a theory-based strategy to optimize the patients' self-care changes for disease management [1]. Its cost-effectiveness to enhance self-care and health service utilization has yet to be determined.

Purpose

This was a double-blind randomized controlled trial to compare the effects and cost-effectiveness of a 12-week empowerment self-care program with a didactic education program on self-care maintenance and management as well as health service utilization among the community-dwelling HF patients.

Methods

A total of 236 HF patients were recruited from the specialist clinics of the Department of Cardiology in two regional hospitals. They were randomized to receive either the 12-week empowerment self-care program (Figure 1) or the 12-week didactic education. Outcome evaluation using the Self-care Heart Failure Index (SCHFI) at baseline, post-intervention (T1) and three months thereafter (T2), with record on the number of emergency room (ER) attendance and hospital admission. Cost effectiveness analyses were performed on total cost (medical, intervention and societal costs) incurred in both interventions as well as incremental cost-effectiveness ratios (ICER) expressed as incremental cost per 1) a reflected clinically meaningful improvement in self-care (i.e. a half standard deviation increase in SCHFI), 2) an ER attendance reduced, 3) a day of hospital stay reduced.

Results

As compared with the education group, the empowerment group reported significantly greater improvement in self-care management at T1 [B=13.77 (95% CI=6.07, 21.46), p<0.001] and T2 [B=10.98 (95% CI=3.21, 18.75), p=0.006]. For cost-effective analysis, The ICER (empowerment-education) was −USD220/0.5 SD increase in SCHFI, indicating the mean cost saved per patient for making a clinically significant improvement in self-care was USD 220. The cost-effectiveness acceptability curve showed patients were willing to pay at USD 207- 441 for a 80–90% chance of improved self-care, indicating that the empowerment approach was a cost saving strategy. Although the empowerment approach was associated with a lower risk of ER attendance [IRR=0.55, 95% CI=0.31–0.95)] and hospital admission [IRR=0.38 (95% CI=0.31–0.95)], it is not cost saving for reducing hospital service utilization.

Conclusions

The empowerment-based self-care program is a cost-saving strategy to produce a clinical significant change in HF-related self-care. Although it is associated with lower risk for hospital service utilization, its effect is not significant enough to be cost-saving. Future care model may explore the need to integrate dyadic science [2] and e-health [3] to strengthen the care continuity and effects of self-care intervention.

Funding Acknowledgement

Type of funding sources: Public grant(s) – National budget only. Main funding source(s): Health and Medical Research Fund, Food and Health Bureau, Hong Kong Special Administrative Region Figure 1

565 Predictors of Single Versus Multi-Level Lumbar Spinal Fusion: A Retrospective Cohort Study

Aim

Degenerative spine disease (DSD) of the lumbar spine is a common disorder among the aging population in the world, with a substantial humanistic and economic burden. Although lumbar spinal fusion is currently the mainstay surgical management of DSD, surgery is also associated with adjacent segment disease due to the modification of spinal biomechanics. Therefore, it is important to identify potential risk factors of DSD in order to prevent progressive deterioration and provide early intervention before the surgical option is absolutely necessary.

Method

Adult patients who underwent posterior lumbar spinal fusion from 2006-2016 were identified via OPCS-4codes. Smoking status, weight, age of operation, gender, diagnosis of ischaemic heart disease (IHD) were obtained via TrakCare®. The degree of deprivation was extrapolated using the Scottish Index of Multiple Deprivation (SIMD) 2020 quintile score. Data were analysed using logistic regression.

Results

In total, 313 met inclusion criteria and had data available, of which 205 and 108 patients underwent single and multi-level lumbar fusion respectively. Within the study population, 66.8% (206) and 33.2% (104) were female and male. Adjusted for all outcome measures, age of operation achieved statistical significance (p = 0.040). There was a 1.021-fold increase in risk of multi-level spinal fusion with each additional year of age. Weight was approaching statistical significance (p = 0.068).

Conclusions

Lumbar spinal health declines over time, but some patients experience more progressive deterioration. While some components of the spine are irreparable, early prescription of regimented exercise programs may strengthen spinal musculature to maintain a healthy sagittal balance, particularly in older, overweight, female patients.

ONTbarcoder and MinION barcodes aid biodiversity discovery and identification by everyone, for everyone

BACKGROUND

DNA barcodes are a useful tool for discovering, understanding, and monitoring biodiversity which are critical tasks at a time of rapid biodiversity loss. However, widespread adoption of barcodes requires cost-effective and simple barcoding methods. We here present a workflow that satisfies these conditions. It was developed via "innovation through subtraction" and thus requires minimal lab equipment, can be learned within days, reduces the barcode sequencing cost to < 10 cents, and allows fast turnaround from specimen to sequence by using the portable MinION sequencer.

RESULTS

We describe how tagged amplicons can be obtained and sequenced with the real-time MinION sequencer in many settings (field stations, biodiversity labs, citizen science labs, schools). We also provide amplicon coverage recommendations that are based on several runs of the latest generation of MinION flow cells ("R10.3") which suggest that each run can generate barcodes for > 10,000 specimens. Next, we present a novel software, ONTbarcoder, which overcomes the bioinformatics challenges posed by MinION reads. The software is compatible with Windows 10, Macintosh, and Linux, has a graphical user interface (GUI), and can generate thousands of barcodes on a standard laptop within hours based on only two input files (FASTQ, demultiplexing file). We document that MinION barcodes are virtually identical to Sanger and Illumina barcodes for the same specimens (> 99.99%) and provide evidence that MinION flow cells and reads have improved rapidly since 2018.

CONCLUSIONS

We propose that barcoding with MinION is the way forward for government agencies, universities, museums, and schools because it combines low consumable and capital cost with scalability. Small projects can use the flow cell dongle ("Flongle") while large projects can rely on MinION flow cells that can be stopped and re-used after collecting sufficient data for a given project.

Acute kidney injury following hepatectomy and its impact on long-term survival for patients with hepatocellular carcinoma

Background

Acute kidney injury (AKI) is increasingly being recognized after hepatectomy. This study aimed to identify factors predicting its occurrence and its impact on long-term outcome among patients with hepatocellular carcinoma (HCC).

Methods

This was a retrospective analysis of the incidence of AKI, factors predicting its occurrence, and its impact on patients undergoing hepatectomy between September 2007 and December 2018. A subgroup analysis included patients with histologically proven HCC.

Results

The incidence of AKI was 9.2 per cent in 930 patients. AKI was associated with increased mortality, morbidity, posthepatectomy liver failure (PHLF), and a longer hospital stay. On multivariable analysis, study period December 2013 to December 2018, diabetes mellitus, mean intraoperative BP below 72.1 mmHg, operative blood loss exceeding 377ml, high Model for End-Stage Liver Disease (MELD) score, and PHLF were predictive factors for AKI. Among 560 patients with HCC, hypertension, BP below 76.9 mmHg, blood loss greater than 378ml, MELD score, and PHLF were predictive factors. The 1-, 3-, and 5-year overall survival rates were 74.1, 59.2, and 51.6 per cent respectively for patients with AKI, and 91.8, 77.9, and 67.3 per cent for those without AKI. Corresponding 1-, 3-, and 5-year disease-free survival rates were 56.9, 42.3, and 35.4 per cent respectively in the AKI group, and 71.7, 54.5, and 46.2 per cent in the no-AKI group. AKI was an independent predictor of survival in multivariable analysis.

Conclusion

AKI is associated with longer hospital stay, and higher morbidity and mortality rates. It is also associated with shorter long-term survival among patients with HCC. To avoid AKI, control of blood loss and maintaining a reasonable BP (72–77 mmHg) during hepatectomy is important.