HostSeq: a Canadian whole genome sequencing and clinical data resource.

HostSeq was launched in April 2020 as a national initiative to integrate whole genome sequencing data from 10,000 Canadians infected with SARS-CoV-2 with clinical information related to their disease experience. The mandate of HostSeq is to support the Canadian and international research communities in their efforts to understand the risk factors for disease and associated health outcomes and support the development of interventions such as vaccines and therapeutics. HostSeq is a collaboration among 13 independent epidemiological studies of SARS-CoV-2 across five provinces in Canada. Aggregated data collected by HostSeq are made available to the public through two data portals: a phenotype portal showing summaries of major variables and their distributions, and a variant search portal enabling queries in a genomic region. Individual-level data is available to the global research community for health research through a Data Access Agreement and Data Access Compliance Office approval. Here we provide an overview of the collective project design along with summary level information for HostSeq. We highlight several statistical considerations for researchers using the HostSeq platform regarding data aggregation, sampling mechanism, covariate adjustment, and X chromosome analysis. In addition to serving as a rich data source, the diversity of study designs, sample sizes, and research objectives among the participating studies provides unique opportunities for the research community.

To skim or splice? Comparing the quantification of M-proteins using two peak-integration protocols across multiple electrophoresis platforms.

OBJECTIVES: M-protein quantification by peak integration in serum protein electrophoresis (SPE) plays a central role in diagnosing, prognosing and monitoring monoclonal gammopathies. The conventional perpendicular drop (PD) integration approach integrates M-spikes from the baseline, which performs acceptably when the M-protein concentration is relatively high compared to the amount of background proteins present. The alternative peak-integration protocol by tangential skim (TS), however, allows for more accurate M-protein estimations by excluding background proteins. Despite some guideline recommendations, TS has been poorly adopted, making an understanding of the differences between the two protocols and their potential impacts paramount when considering a change from PD to TS. DESIGN & METHODS: We conducted retrospective investigations of the differences in M-protein quantification over large concentration ranges between PD and TS on 3 of the most popular electrophoresis platforms. RESULTS: Compared to PD, TS gave consistently lower results; the differences between the two methods increased tremendously and became more sporadic as M-protein concentrations dropped below 15 g/L in all 3 platforms. At < 15 g/L, the average % difference ranged from -81 % to -95 %, while above 15 g/L, the average % difference was only -13 to -31 %. Medical decision point analyses using linear regression predicted statistically significant and platform-dependent differences, which could impact clinical interpretation. CONCLUSIONS: Careful consideration of the magnitude of concentration changes and the potential impacts on patient classification and management should be made when switching to TS for M-protein quantification.

Sample stability of autoantibodies: A tool for laboratory quality initiatives.

OBJECTIVES: Serum autoantibody measurement aids in diagnosing and monitoring various autoimmune conditions. Defining autoantibody stability limits can improve laboratory process quality. Here, we define short-term stability in a refrigerator, long-term stability in a freezer, and the effect of freeze-thaw cycles to improve autoantibody testing procedures. DESIGN AND METHODS: Seventy-nine residual serum samples were used to assess the stability of 11 autoantibodies (anti-dsDNA, anti-Ro52, anti-Ro60, anti-SSB, anti-RNP, anti-Sm, anti-aCL-IgG, anti-tTG-IgA, anti-tTG-IgG, anti-DGP-IgA, anti-DGP-IgG) and two screening assays (CTD screen, ENA7 screen) on the BIO-FLASH (Inova Diagnostics). Three storage conditions were assessed: 8 weeks at 2-8 °C, 12 months at -30 °C, and 6 freeze (-30 °C)-thaw cycles. The maximum permissible instability (MPI) for each autoantibody was set as 2x %CV, calculated as the weighted average CV from cumulative QC data over the study period. RESULTS: By considering both mean percent difference (MPD) and mean absolute relative difference (MARD), all autoantibodies were stable for up to 8 weeks stored at 2-8 °C, except for CTD screen and anti-dsDNA. All autoantibodies were stable for up to 12 months stored at -30 °C, except ENA screen, anti-dsDNA, anti-DGP-IgA, anti-cardiolipin, and CTD screen. Lastly, all autoantibodies were stable for up to 6 freeze(-30 °C)-thaw cycles, except anti-RNP, anti-Ro60, anti-cardiolipin and anti-dsDNA. CONCLUSIONS: It is important to develop laboratory procedures derived from evidence-based stability limits. This study will aid laboratories in undertaking quality assurance and improvement initiatives to enhance autoantibody testing by ensuring appropriate storage conditions that consider defined sample stability limits.

Assessment of carbon footprint emissions and environmental concerns of solid waste treatment and disposal techniques; case study of Malaysia.

Malaysian authorities has planned to minimize and stop when applicable unsanitary dumping of waste as it puts human health and the environment at elevated risk. Cost, energy and revenue are mostly adopted to draw the blueprint of upgrading municipal solid waste management system, while the carbon footprint emissions criterion rarely acts asa crucial factor. This study aims to alert Malaysian stakeholders on the uneven danger of carbon footprint emissions of waste technologies. Hence, three scenarios have been proposed and assessed mainly on the carbon footprint emissions using the 2006 IPCC methodology. The first scenario is waste dumping in sanitary landfills equipped with gas recovery system, while the second scenario includes anaerobic digestion of organics and recycling of recyclable wastes such as plastic, glass and textile wastes. The third scenario is waste incineration. Besides the carbon footprint emissions criterion, other environmental concerns were also examined. The results showed that the second scenario recorded the lowest carbon footprint emissions of 0.251t CO2 eq./t MSW while the third scenario had the highest emissions of 0.646t CO2 eq./t MSW. Additionally, the integration between anaerobic digestion and recycling techniques caused the highest avoided CO2 eq. emissions of 0.74t CO2 eq./t MSW. The net CO2 eq. emissions of the second scenario equaled -0.489t CO2 eq./t MSW due to energy recovery from the biogas and because of recycled plastic, glass and textile wastes that could replace usage of raw material. The outcomes also showed that the first scenario generates huge amount of leachate and hazardous air constituents. The study estimated that a ton of dumped waste inside the landfills generates approximately 0.88m3 of trace risky compounds and 0.188m3 of leachate. As for energy production, the results showed that the third scenario is capable of generating 639kWh/t MSW followed by the second scenario with 387.59kWh/t MSW. The first scenario produced 296.79kWh/t MSW. In conclusion, the outcomes of this study recommend an integrated scenario of anaerobic digestion and recycling techniques to be employed in Malaysia.

Lymphocyte phenotyping, using cluster-of-differentiation (CD) markers, in young Iraqi children with visceral leishmaniasis.

The lymphocytic phenotypes involved in the pathogenesis of visceral leishmaniasis (VL) in Iraqi children have recently been investigated, in a study based on cluster-of-differentiation (CD) markers. Each case of VL investigated was confirmed parasitologically by the observation of amastigotes in a bone-marrow smear. Compared with the values for the healthy children used as controls, a lymphocyte from an untreated VL case was significantly less likely to be CD3+ or CD4+, significantly more likely to be CD8+, and more (but not significantly more) likely to be CD22+. The untreated cases also had significantly lower CD4+/CD8+ ratios than the controls. Among the untreated cases, gender and age had no apparent effect on any of these variables. After 28 days of treatment with sodium stibogluconate, there was a trend towards normalization in the lymphocytic phenotypes of the VL cases, with significant increases in the CD4+/CD8+ ratios and the percentages of lymphocytes that were CD3+ or CD4+, and a significant decrease in the percentages of lymphocytes that were CD22+.