Global and local ancestry estimation in a captive baboon colony

The last couple of decades have highlighted the importance of studying hybridization, particularly among primate species, as it allows us to better understand our own evolutionary trajectory. Here, we report on genetic ancestry estimates using dense, full genome data from 881 olive (Papio anubus), yellow (Papio cynocephalus), or olive-yellow crossed captive baboons from the Southwest National Primate Research Center. We calculated global and local ancestry information, imputed low coverage genomes (n = 830) to improve marker quality, and updated the genetic resources of baboons available to assist future studies. We found evidence of historical admixture in some putatively purebred animals and identified errors within the Southwest National Primate Research Center pedigree. We also compared the outputs between two different phasing and imputation pipelines along with two different global ancestry estimation software. There was good agreement between the global ancestry estimation software, with R2 > 0.88, while evidence of phase switch errors increased depending on what phasing and imputation pipeline was used. We also generated updated genetic maps and created a concise set of ancestry informative markers (n = 1,747) to accurately obtain global ancestry estimates.

Screening women for distress during pregnancy: the impact of including 'Possibly' as a response option

OBJECTIVES

To investigate the impact of including the response option of 'Possibly' in the Distress question on the Matthey Generic Mood Questionnaire (MGMQ) during antenatal emotional health screening in English-speaking women.

BACKGROUND

Some distress screening questions only allow respondents to choose between 'Yes' or 'No' to the presence of distress. The MGMQ, however, allows respondents to chose between 'Yes', 'Possibly', or 'No', which may be preferable if a participant is reluctant to state she definitely feels distressed.

METHOD

In Study 1, women undergoing routine antenatal psychosocial screening were allocated to either completing the MGMQ Distress question with the usual three-option response format of 'Yes, Possibly, No' (N = 960), or just a 'Yes, No' response format (N = 771). The proportion of responses were compared in each group, as were the proportion then screening positive on the MGMQ's Bother question. In Study 2, women (N = 113) attending routine antenatal clinic appointments were asked about their preference between these response formats.

RESULTS

Including 'Possibly' resulted in only a slight increase in the proportion giving a positive response to the Distress question, and then also screening positive on the Bother question. In Study 2, a substantial majority of women (80%) preferred having 'Possibly' in the response options.

CONCLUSION

While the impact of including 'Possibly' is small, it allows for more women to communicate how they are feeling on the full MGMQ. Given the large majority of women preferring having 'Possibly' included, we believe that the Distress Question is enhanced by having this as a response option.

Evolution of the Mutation Spectrum Across a Mammalian Phylogeny

Although evolutionary biologists have long theorized that variation in DNA repair efficacy might explain some of the diversity of lifespan and cancer incidence across species, we have little data on the variability of normal germline mutagenesis outside of humans. Here, we shed light on the spectrum and etiology of mutagenesis across mammals by quantifying mutational sequence context biases using polymorphism data from thirteen species of mice, apes, bears, wolves, and cetaceans. After normalizing the mutation spectrum for reference genome accessibility and k-mer content, we use the Mantel test to deduce that mutation spectrum divergence is highly correlated with genetic divergence between species, whereas life history traits like reproductive age are weaker predictors of mutation spectrum divergence. Potential bioinformatic confounders are only weakly related to a small set of mutation spectrum features. We find that clock-like mutational signatures previously inferred from human cancers cannot explain the phylogenetic signal exhibited by the mammalian mutation spectrum, despite the ability of these signatures to fit each species' 3-mer spectrum with high cosine similarity. In contrast, parental aging signatures inferred from human de novo mutation data appear to explain much of the 1-mer spectrum's phylogenetic signal in combination with a novel mutational signature. We posit that future models purporting to explain the etiology of mammalian mutagenesis need to capture the fact that more closely related species have more similar mutation spectra; a model that fits each marginal spectrum with high cosine similarity is not guaranteed to capture this hierarchy of mutation spectrum variation among species.

South Asian medical cohorts reveal strong founder effects and high rates of homozygosity

The benefits of large-scale genetic studies for healthcare of the populations studied are well documented, but these genetic studies have traditionally ignored people from some parts of the world, such as South Asia. Here we describe whole genome sequence (WGS) data from 4806 individuals recruited from the healthcare delivery systems of Pakistan, India and Bangladesh, combined with WGS from 927 individuals from isolated South Asian populations. We characterize population structure in South Asia and describe a genotyping array (SARGAM) and imputation reference panel that are optimized for South Asian genomes. We find evidence for high rates of reproductive isolation, endogamy and consanguinity that vary across the subcontinent and that lead to levels of rare homozygotes that reach 100 times that seen in outbred populations. Founder effects increase the power to associate functional variants with disease processes and make South Asia a uniquely powerful place for population-scale genetic studies.

"Evolution of the mutation spectrum across a mammalian phylogeny"

Little is known about how the spectrum and etiology of germline mutagenesis might vary among mammalian species. To shed light on this mystery, we quantify variation in mutational sequence context biases using polymorphism data from thirteen species of mice, apes, bears, wolves, and cetaceans. After normalizing the mutation spectrum for reference genome accessibility and k -mer content, we use the Mantel test to deduce that mutation spectrum divergence is highly correlated with genetic divergence between species, whereas life history traits like reproductive age are weaker predictors of mutation spectrum divergence. Potential bioinformatic confounders are only weakly related to a small set of mutation spectrum features. We find that clocklike mutational signatures previously inferred from human cancers cannot explain the phylogenetic signal exhibited by the mammalian mutation spectrum, despite the ability of these clocklike signatures to fit each species' 3-mer spectrum with high cosine similarity. In contrast, parental aging signatures inferred from human de novo mutation data appear to explain much of the mutation spectrum's phylogenetic signal when fit to non-context-dependent mutation spectrum data in combination with a novel mutational signature. We posit that future models purporting to explain the etiology of mammalian mutagenesis need to capture the fact that more closely related species have more similar mutation spectra; a model that fits each marginal spectrum with high cosine similarity is not guaranteed to capture this hierarchy of mutation spectrum variation among species.

Pandemic preparedness of diagnostic radiographers during COVID-19: A scoping review

INTRODUCTION

As chest imaging is a tool for detecting coronavirus disease 2019 (COVID-19), diagnostic radiographers are a key component of the frontline workforce. Due to its unforeseen nature, COVID-19 has challenged radiographers' preparedness in combating its effects. Despite its importance, literature specifically investigating radiographers' readiness is limited. However, the documented experiences are prognostic of pandemic preparedness. Hence, this study aimed to map this literature by addressing the question: 'what does the existing literature reveal about the pandemic preparedness of diagnostic radiographers during COVID-19?'.

METHODS

Using Arksey and O'Malley's framework, this scoping review searched for empirical studies in MEDLINE, Embase, Scopus, and CINAHL. Consequently, 970 studies were yielded and underwent processes of deduplication, title and abstract screening, full-text screening, and backward citation searching. Forty-four articles were deemed eligible for data extraction and analysis.

RESULTS

Four themes that reflected pandemic preparedness were extrapolated: infection control and prevention, knowledge and education, clinical workflow, and mental health. Notably, the findings highlighted pronounced trends in adaptation of infection protocols, adequate infection knowledge, and pandemic-related fears. However, inconsistencies in the provision of personal protective equipment, training, and psychological support were revealed.

CONCLUSION

Literature suggests that radiographers are equipped with infection knowledge, but the changing work arrangements and varied availability of training and protective equipment weakens their preparedness. The disparate access to resources facilitated uncertainty, affecting radiographers' mental health.

IMPLICATIONS FOR PRACTICE

By reiterating the current strengths and weaknesses in pandemic preparedness, the findings can guide clinical practice and future research to correct inadequacies in infrastructure, education, and mental health support for radiographers in the current and future disease outbreaks.

Deleterious Variation in Natural Populations and Implications for Conservation Genetics

Deleterious mutations decrease reproductive fitness and are ubiquitous in genomes. Given that many organisms face ongoing threats of extinction, there is interest in elucidating the impact of deleterious variation on extinction risk and optimizing management strategies accounting for such mutations. Quantifying deleterious variation and understanding the effects of population history on deleterious variation are complex endeavors because we do not know the strength of selection acting on each mutation. Further, the effect of demographic history on deleterious mutations depends on the strength of selection against the mutation and the degree of dominance. Here we clarify how deleterious variation can be quantified and studied in natural populations. We then discuss how different demographic factors, such as small population size, nonequilibrium population size changes, inbreeding, and gene flow, affect deleterious variation. Lastly, we provide guidance on studying deleterious variation in nonmodel populations of conservation concern.

An optimized scheme for detecting magneto-optic effects in ultrathin films with Sagnac interferometry

Sagnac interferometry is advantageous in measuring time-reversal-symmetry breaking effects in ferromagnetic and antiferromagnetic materials as it suppresses time-reversal symmetric birefringent effects that are ubiquitous and often overwhelming in optical detection systems. When its sensitivity is limited only by the amplifier noise in the photo-detector, one needs to optimize the optical power that returns to the detector. We demonstrate an experimental scheme that maximizes the returning optical power in a Sagnac interferometry when detecting the magneto-optic effect in ultrathin films. In this scheme, the optical beam bearing the Faraday effect on a thin film is reflected at a second surface coated with a highly reflective gold film. The gold film increases the returned optical power by a factor of 4-5. For a normal-incidence Sagnac interferometer, this scheme yields an increase in the signal-to-noise ratio by the same factor. For an oblique-incidence Sagnac interferometer, this scheme should yield an increase in the signal-to-noise ratio by a factor of 20-25. For illustration, this scheme is used to measure magnetization curves and Kerr rotation images of 4.5-unit-cell thick SrRuO₃(001) grown on SrTiO₃(001).

Effect of the Cyberattack Targeting the Irish Health System in May 2021 on Radiation Treatment at St. Luke's Radiation Oncology Network

On May 14, 2021, the Health Service Executive (HSE) of Ireland experienced a major ransomware cyberattack. The HSE initially took down all of its information technology systems to protect its core systems. All Internet connections within the HSE were unavailable from 7 am for approximetely three weeks which had a major effect on the radiation oncology service nationally within the public service. St. Luke's Radiation Oncology Network (SLRON) is a complex, 3-center radiation oncology service, and it is the largest in the country; with 14 linear accelerators, it is one of the largest radiation centers in Europe. This article details the response of SLRON to the outage resultant from the cyberattack. Although the outage affected all patient services, including laboratory, diagnostic imaging, and inpatient care, the article primarily focuses on our response to get the radiation oncology service restarted as quickly as possible and details the steps we took to reinstate our systems safely, how we prioritized patient treatments, and how we communicated with patients, staff, and the public without having access to standard communication pathways. All decisions were risk assessed and were made with the best resources available to us at the time to maximize the outcome for our patients and mitigate significant delays. The risk remains ongoing, and the onerous task of uploading backlogs and reconciling patient records is a continuing risk.

OP0190 COMPREHENSIVE GENETIC AND FUNCTIONAL ANALYSES OF Fc GAMMA RECEPTORS EXPLAIN RESPONSE TO RITUXIMAB THERAPY FOR AUTOIMMUNE RHEUMATIC DISEASES

Background

Rituximab is widely used to treat rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE) but clinical response varies. Efficacy is determined by the efficiency of depletion, which may depend on a variety of Fc gamma receptor (FcγR)-dependent mechanisms. Previous research was limited by complexity of the FCGR locus, not integrating copy number variation with functional SNP, and small sample size.

Objectives

The study objectives were to assess the effect of the full range of FcγRs variants on depletion, clinical response and functional effect on NK-cell-mediated killing in two rheumatic diseases with a view to personalised B-cell depleting therapies.

Methods

A prospective longitudinal cohort study was conducted in 873 patients [RA=611; SLE=262] from four cohorts (BSRBR-RA and BILAG-BR registries, Leeds RA and Leeds SLE Biologics). For RA, the outcome measures were 3C-DAS28CRP and 2C-DAS28CRP at 6 (+/-3) months post-rituximab (adjusted for baseline DAS28). For SLE, major clinical response (MCR) was defined as improvement of active BILAG-2004 domains to grade C/better at 6 months. B-cell depletion was evaluated by highly-sensitive flow cytometry. Qualitative and quantitative polymorphisms for five major FcγRs were measured using a commercial multiplex ligation-dependent probe amplification. Median NK cell FcγRIIIa expression (CD3-CD56+CD16+) and NK-cell degranulation (CD107a) in the presence of rituximab-coated Daudi/Raji B-cell lines were assessed using flow cytometry.

Results

In RA, for FCGR3A, carriage of V allele (coefficient -0.25 (SE 0.11); p=0.02) and increased copies of V allele (-0.20 (0.09); p=0.02) were associated with greater 2C-DAS28 response. Irrespective of FCGR3A genotype, increased gene copies were associated with a better response. In SLE, 177/262 (67.6%) achieved BILAG response [MCR=34.4%; Partial=33.2%]. MCR was associated with increased copies of FCGR3A-158V allele, OR 1.64 (95% CI 1.12-2.41) and FCGR2C-ORF allele 1.93 (1.09-3.40). Of patients with B-cells data in the combined cohort, 236/413 (57%) achieved complete depletion post-rituximab. Only homozygosity for FCGR3A-158V and increased FCGR3A-158V copy number were associated with increased odds of complete depletion. Patients with complete depletion had higher NK cell FcγRIIIa expression at rituximab initiation than those with incomplete depletion (p=0.04) and this higher expression was associated with improved EULAR response in RA. Moreover, for FCGR3A, degranulation activity was increased in V allele carriers vs FF genotype in the combined cohort; p=0.02.

Conclusion

FcγRIIIa is the major low affinity FcγR and increased copies of the FCGR3A-158V allele, encoding the allotype with a higher affinity for IgG1, was associated with clinical and biological responses to rituximab in two autoimmune diseases. This was supported by functional data on NK cell-mediated cytotoxicity. In SLE, increased copies of the FCGR2C-ORF allele was also associated with improved response. Our findings indicate that enhancing FcγR-effector functions could improve the next generation of CD20-depleting therapies and genotyping could stratify patients for optimal treatment protocols.

References

None

Acknowledgements

This research was funded/supported by the joint funding from the Medical Research Council (MRC) and Versus Arthritis of MATURA (grant codes 36661 and MR/K015346/1). MASTERPLANS was funded by the MRC (grant code MR/M01665X/1). The Leeds Biologics Cohort was part funded by programme grants from Versus Arthritis (grant codes 18475 and 18387), the National Institute for Health Research (NIHR) Leeds Biomedical Research Centre (BRC) and Diagnostic Evaluation Co-operative and the Ann Wilks Charitable Foundation. The BILAG-BR has received funding support from Lupus UK, and unrestricted grants from Roche and GSK.

The functional studies were in part supported through a NIHR/HEFCE Clinical Senior Lectureship and a Versus Arthritis Foundation Fellowship (grant code 19764) to AWM, the Wellcome Trust Institutional Strategic Support Fund to JIR and MYMY (204825/Z/16/Z), NIHR Doctoral Research Fellowship to MYMY (DRF-2014-07-155) and NIHR Clinician Scientist to EMV (CS-2013-13-032). . AWM, INB, JDI and PE were supported by NIHR Senior Investigator awards. Work in JDI’s laboratory is supported by the NIHR Newcastle BRC, the Research Into Inflammatory Arthritis Centre Versus Arthritis, and Rheuma Tolerance for Cure (European Union Innovative Medicines Initiative 2, grant number 777357). INB is funded by the NIHR Manchester BRC.

This article/paper/report presents independent research funded/supported by the NIHR Leeds BRC and the NIHR Guy’s and St Thomas’ BRC. The views expressed are those of the author(s) and not necessarily those of the NIHR or the Department of Health and Social Care.

Disclosure of Interests

Md Yuzaiful Md Yusof: None declared, James Robinson: None declared, Vinny Davies: None declared, Dawn Wild: None declared, Michael Morgan: None declared, John Taylor: None declared, Yasser El-Sherbiny: None declared, David Morris: None declared, Lu Liu: None declared, Andrew Rawstron: None declared, Maya H Buch: None declared, Darren Plant: None declared, Heather Cordell: None declared, John Isaacs: None declared, Ian N. Bruce: None declared, Paul Emery Speakers bureau: Roche, Consultant of: Roche, Grant/research support from: Roche, Anne Barton: None declared, Timothy Vyse: None declared, Jennifer Barrett: None declared, Edward Vital Consultant of: Roche, Grant/research support from: Roche, Ann Morgan Speakers bureau: Roche/Chugai, Consultant of: GSK, Roche, Chugai, AstraZeneka, Regeneron, Sanofi, Vifor, Grant/research support from: Roche, Kiniksa Pharmaceuticals

Virtual cardiac rehabilitation during the COVID-19 pandemic: a tertiary site experience

Funding Acknowledgements

Type of funding sources: Public Institution(s). Main funding source(s): University of British Columbia Clinician Investigator Program

Background

The COVID-19 pandemic resulted in the abrupt suspension of centre-based cardiac rehabilitation (CR). Multidisciplinary virtual CR (VCR) with the use of digital, telephone, and video communication was implemented for continued care access. Exercise therapy was delivered through synchronous video-supervised sessions, pre-recorded sessions, and self-directed physical activity.

Purpose

To describe patient characteristics, completion rates, and safety outcomes in a real-world VCR population.

Methods

Prospective observational study of a tertiary academic CR program. VCR was implemented at pandemic onset (March 2020). Patients who were enrolled in, and either completed or dropped out, during the study period were included. Completers were defined as completing 6 months of virtual enrolment and an exit assessment. Risk was defined by the AACPVR 2020 risk categorization. Adverse cardiovascular events were defined as a patient-initiated event requiring medical assessment and stratified as exercise or non-exercise related. Continuous variables are presented as means and SD or medians and IQR. Student’s t-test was used for between group comparisons. Categorical variables are presented as n (%) and compared using the χ2 test or Fischer’s exact test. A p-value <0.05 was considered significant.

Results

Between March 13th, 2020, and August 31st, 2021, 222 [mean age 61.8 years (SD, 12.6) 77% male], were enrolled and discharged from the VCR program (Table 1). There were 160 completers and 62 non-completers (completion rate 72%). Among the non-completers 26 attended the MD intake assessment only. The remaining 36 completed a median of 85 days (IQR 25-197). This cohort included 21 (9%) high-risk and 35 (16%) moderate risk patients. Those at moderate risk were more likely to be non-completers and those at low risk were more likely to be completers (Table 1). Two exercise and 17 non-exercise adverse events were observed (median clinical surveillance 217 days [IQR 205-240]) (Table 2). Exercise related adverse events included neurally mediated syncope during a synchronous video exercise session in a low risk patient. This was responded to as per centre developed virtual safety protocols. A second syncope related to heart block occurred in a moderate risk patient during independent physical activity and required permanent pacemaker insertion. Both patients completed the program. Three non-exercise adverse cardiac events resulted in cessation of participation included one death and two heart failure hospitalizations (Table 2). One stroke and 13 emergency department visits for cardiac symptoms occurred in completers.

Conclusion

Real world VCR is feasible, including in those at moderate to high risk. Modest completion rates and a low exercise related adverse event rate were observed. Synchronous video exercise sessions with video monitoring and safety protocols may improve response to adverse exercise related events.

Radionuclide ventriculography phase analysis for risk stratification of patients undergoing cardiotoxic cancer therapy

BACKGROUND

Accurate diagnostic tools to identify patients at risk of cancer therapy-related cardiac dysfunction (CTRCD) are critical. For patients undergoing cardiotoxic cancer therapy, ejection fraction assessment using radionuclide ventriculography (RNVG) is commonly used for serial assessment of left ventricular (LV) function.

METHODS

In this retrospective study, approximate entropy (ApEn), synchrony, entropy, and standard deviation from the phase histogram (phase SD) were investigated as potential early markers of LV dysfunction to predict CTRCD. These phase parameters were calculated from the baseline RNVG phase image for 177 breast cancer patients before commencing cardiotoxic therapy.

RESULTS

Of the 177 patients, 11 had a decline in left ventricular ejection fraction (LVEF) of over 10% to an LVEF below 50% after treatment had commenced. This patient group had a significantly higher ApEn at baseline to those who maintained a normal LVEF throughout treatment. Of the parameters investigated, ApEn was superior for predicting the risk of CTRCD. Combining ApEn with the baseline LVEF further improved the discrimination between the groups.

CONCLUSIONS

The results suggest that RNVG phase analysis using approximate entropy may aid in the detection of sub-clinical LV contraction abnormalities, not detectable by baseline LVEF measurement, predicting a subsequent decline in LVEF.

Deep sr-DDL: Deep structurally regularized dynamic dictionary learning to integrate multimodal and dynamic functional connectomics data for multidimensional clinical characterizations

We propose a novel integrated framework that jointly models complementary information from resting-state functional MRI (rs-fMRI) connectivity and diffusion tensor imaging (DTI) tractography to extract biomarkers of brain connectivity predictive of behavior. Our framework couples a generative model of the connectomics data with a deep network that predicts behavioral scores. The generative component is a structurally-regularized Dynamic Dictionary Learning (sr-DDL) model that decomposes the dynamic rs-fMRI correlation matrices into a collection of shared basis networks and time varying subject-specific loadings. We use the DTI tractography to regularize this matrix factorization and learn anatomically informed functional connectivity profiles. The deep component of our framework is an LSTM-ANN block, which uses the temporal evolution of the subject-specific sr-DDL loadings to predict multidimensional clinical characterizations. Our joint optimization strategy collectively estimates the basis networks, the subject-specific time-varying loadings, and the neural network weights. We validate our framework on a dataset of neurotypical individuals from the Human Connectome Project (HCP) database to map to cognition and on a separate multi-score prediction task on individuals diagnosed with Autism Spectrum Disorder (ASD) in a five-fold cross validation setting. Our hybrid model outperforms several state-of-the-art approaches at clinical outcome prediction and learns interpretable multimodal neural signatures of brain organization.

Effect of body mass index on cardiac injury/cardiovascular outcomes in coronavirus disease 2019: a systematic review and meta-analysis

 

Coronavirus disease 2019 has affected millions of people worldwide. Its clinical spectrum ranges from completely asymptomatic to significant respiratory and non-respiratory symptoms leading to critical illness, including death. We aimed to study the effects of body mass index (BMI) on cardiovascular and other critical illness outcomes in these patients in the USA. We conducted a systematic search of three databases for the period of November 2019 to August 2020 and selected 37 studies for analysis. One study showed a non-significant difference in cardiac injury among BMI groups, but there is a paucity of data on cardiovascular outcomes among different BMI groups; hence, meta-analysis was not done for cardiovascular outcomes. Both high BMI and cardiac injury are independent predictors of poor outcomes in these patients. Pooled analysis showed obesity as a significant risk factor for intensive care unit admission (OR=1.547, CI=1.208–1.981, P=0.001) and intubation /mechanical ventilation (OR=1.744, CI=1.363–2.231 P=0.000). Therefore, BMI should be considered an important part of risk stratification, and vaccination should be prioritized for obese patients when it becomes widely available.

Funding Acknowledgement

Type of funding sources: None. Risk of intubation

An online Sexual Health and Rehabilitation eClinic (TrueNTH SHAReClinic) for prostate cancer patients: a feasibility study

Purpose

The primary objective was to determine the feasibility of implementing the TrueNTH SHAReClinic as a pan-Canadian sexual health and rehabilitation intervention for patients treated for localized prostate cancer.

Methods

The feasibility study was designed to evaluate the accessibility and acceptability of the intervention. Participants from five institutions across Canada were enrolled to attend one pre-treatment and five follow-up online clinic visits over 1 year following their prostate cancer (PC) treatment.

Results

Sixty-five patients were enrolled in the intervention. Website analytics revealed that 71% completed the intervention in its entirety, including the educational modules, with an additional 10% completing more than half of the intervention. Five thousand eighty-three views of the educational modules were made along with 654 views of the health library items. Over 1500 messages were exchanged between participants and their sexual health coaches. At 12 months, the intervention received an overall average participant rating of 4.1 out of 5 on a single item satisfaction measure.

Conclusion

Results support the TrueNTH SHAReClinic as highly acceptable to participants as defined by intervention adherence and engagement. The TrueNTH SHAReClinic demonstrated promise for being a feasible and potentially resource-efficient approach to effectively improving the sexual well-being of patients after PC treatment.

Accurate assembly of the olive baboon (Papio anubis) genome using long-read and Hi-C data

BACKGROUND

Baboons are a widely used nonhuman primate model for biomedical, evolutionary, and basic genetics research. Despite this importance, the genomic resources for baboons are limited. In particular, the current baboon reference genome Panu_3.0 is a highly fragmented, reference-guided (i.e., not fully de novo) assembly, and its poor quality inhibits our ability to conduct downstream genomic analyses.

FINDINGS

Here we present a de novo genome assembly of the olive baboon (Papio anubis) that uses data from several recently developed single-molecule technologies. Our assembly, Panubis1.0, has an N50 contig size of ∼1.46 Mb (as opposed to 139 kb for Panu_3.0) and has single scaffolds that span each of the 20 autosomes and the X chromosome.

CONCLUSIONS

We highlight multiple lines of evidence (including Bionano Genomics data, pedigree linkage information, and linkage disequilibrium data) suggesting that there are several large assembly errors in Panu_3.0, which have been corrected in Panubis1.0.