Benchmarking small-variant genotyping in polyploids

Genotyping from sequencing is the basis of emerging strategies in the molecular breeding of polyploid plants. However, compared with the situation for diploids, where genotyping accuracies are confidently determined with comprehensive benchmarks, polyploids have been neglected; there are no benchmarks measuring genotyping error rates for small variants using real sequencing reads. We previously introduced a variant calling method - Octopus - that accurately calls germline variants in diploids and somatic mutations in tumors. Here, we evaluate Octopus and other popular tools on whole-genome tetraploid and hexaploid datasets created using in silico mixtures of diploid Genome In a Bottle (GIAB) samples. We find that genotyping errors are abundant for typical sequencing depths, but that Octopus makes 25% fewer errors than other methods on average. We supplement our benchmarks with concordance analysis in real autotriploid banana datasets.

Validation and Concordance Analysis of a New Lateral Flow Assay for Detection of Histoplasma Antigen in Urine

Histoplasmosis is a major cause of mortality in people living with HIV (PLHIV). Rapid methods to diagnose Histoplasma capsulatum disease could dramatically decrease the time to initiate treatment, resulting in reduced mortality. The aim of this study was to validate a MiraVista® Diagnostics (MVD) Histoplasma urine antigen lateral flow assay (MVD LFA) for the detection of H. capsulatum antigen (Ag) in urine and compare this LFA against the MVista® Histoplasma Ag quantitative enzyme immunoassays (MVD EIA). We assessed the MVD LFA using a standardized reference panel of urine specimens from Colombia. We tested 100 urine specimens, 26 from PLHIV diagnosed with histoplasmosis, 42 from PLHIV with other infectious diseases, and 32 from non-HIV infected persons without histoplasmosis. Sensitivity and specificity of the MVD LFA was 96%, compared with 96% sensitivity and 77% specificity of the MVD EIA. Concordance analysis between MVD LFA and the MVD EIA displayed an 84% agreement, and a Kappa of 0.656. The MVD LFA evaluated in this study has several advantages, including a turnaround time for results of approximately 40 min, no need for complex laboratory infrastructure or highly trained laboratory personnel, use of urine specimens, and ease of performing.

An algorithm combining VVSYmQ® and VCSS scores may help to predict disease severity in C2 patients

Objectives The purpose was to assess whether combining patient reported scores (VVSymQ®) and physician reported scores (VCSS) stratifies disease severity in C2 patients. Methods Consecutive patients were pooled from the VANISH-1 and VANISH-2 cohorts. VCSS and VVSymQ® were calculated for each patient. The relationship between scoring systems was evaluated using Pearson’s correlation and frequency distribution analysis. Results Two-hundred and ten C2 limbs were included. Scoring systems demonstrated: VVSymQ®: mean = 8.72; VCSS: mean = 6.32; correlation (r = 0.22, p = 0.05). Frequency distribution analysis demonstrated 61.4% of patients had low VVSymQ® and low VCSS; 31.3% had elevated VVSymQ® and increased VCSS; 7.3% were inconsistent with C2 disease. Strict concordance analysis revealed 40.5% had VVSymQ® (< 9)/VCSS (0-6), 18.6% had VVSymQ® (≥ 9)/VCSS (7-9), and 2.9% had VVSymQ® (≥9)/VCSS (≥10). Conclusions For combined elevated VVSymQ® and VCSS, moderate/severe disease is corroborated, and intervention may be indicated. For combined lower scores, the disease severity is mild and conservative therapy is more appropriate.

Risk of vaccine preventable diseases in UK migrants: a serosurvey and concordance analysis, 2020

We conducted a serosurvey in 2020, amongst 149 adult migrants living in the United Kingdom, to determine seroprotection rates for measles, varicella zoster, and rubella. Findings suggest a gap in seroprotection against measles (89.3%). Younger migrants and those from Europe and Central Asia may be more susceptible; self-reported vaccine/disease status is a poor predictor of seroprotection. Understanding factors associated with seroprotection among migrants is critical for informing the delivery of SARS-CoV-2 vaccine.