Causally interpretable meta-analysis combining aggregate and individual participant data.

Recent work in causally-interpretable meta-analysis (CIMA) has bridged the gap between traditional meta-analysis and causal inference. While traditional meta-analysis results generally do not apply to any well-defined population, CIMA approaches specify a target population to which meta-analytic treatment effect estimates are transported. While theoretically attractive, these approaches currently have some practical limitations. Most assume that all studies in the meta-analysis have individual participant data (IPD), which is rare in practice because most trials share only aggregate data. We propose a method to perform CIMA using a combination of aggregate data and IPD. This method borrows information from studies with IPD to augment the aggregate data and create aggregate-matched synthetic IPD (AMSIPD), which can be used readily in the existing CIMA framework. By allowing use of both aggregate data and IPD, the method opens CIMA to more applications and can avoid biases arising from using only studies with IPD. We present a case study and simulations showing the AMSIPD approach is promising and merits further investigation as an advancement of CIMA.

Identification of nine novel HLA alleles by next-generation sequencing in individuals from India.

Nine novel HLA alleles were identified when HLA typing individuals from the Indian population.

Tidal Versus Intermittent Peritoneal Dialysis in Chronic Peritoneal Dialysis Patients: Randomized, Open-Label, Prospective Control Study.

BACKGROUND: Tidal peritoneal dialysis (TPD) provides better fluid flow mechanics and is more comfortable for the patient, owing to fewer alarms and less pain during inflow and outflow. The long-term characteristics of patients with TPD were not evident. In this randomized controlled follow-up study, we aimed to explore the characteristics of patients with TPD, compared to IPD. METHODS: A total of 85 patients were randomized to either IPD or 70% TPD between January 2019 and December 2020, and all patients were followed up on December 2021. The characteristics of patients between the two groups were analyzed using a t-test or chi-square as appropriate. The overall survival and technical survival were analyzed using Kaplan-Meier analysis. RESULTS: Forty-two patients were assigned to IPD, and 43 patients were assigned to TPD. The basal characteristics of patients were not different between the two groups. In an average of 16 months of follow-up, 19 patients died, and 25 patients dropped out of peritoneal dialysis. The two groups had no difference in overall survival and technical survival. TPD was associated with high urine volume (p = 0.001), lower blood urea nitrogen (p = 0.002), lower phosphorus (p = 0.004), and fewer cycler alarms (p < 0.001). The chance of patients reporting abdominal fullness was higher in patients with TPD (p = 0.001). CONCLUSION: In the randomized, controlled, follow-up study, TPD may preserve residual renal function and is associated with lower urea nitrogen and phosphorus in chronic peritoneal dialysis patients. TPD is associated with fewer cycler alarms but may increase the chance of patients reporting abdominal distension.

Individual participant data meta-analysis to examine linear or non-linear treatment-covariate interactions at multiple time-points for a continuous outcome.

Individual participant data (IPD) meta-analysis projects obtain, harmonise, and synthesise original data from multiple studies. Many IPD meta-analyses of randomised trials are initiated to identify treatment effect modifiers at the individual level, thus requiring statistical modelling of interactions between treatment effect and participant-level covariates. Using a two-stage approach, the interaction is estimated in each trial separately and combined in a meta-analysis. In practice, two complications often arise with continuous outcomes: examining non-linear relationships for continuous covariates and dealing with multiple time-points. We propose a two-stage multivariate IPD meta-analysis approach that summarises non-linear treatment-covariate interaction functions at multiple time-points for continuous outcomes. A set-up phase is required to identify a small set of time-points; relevant knot positions for a spline function, at identical locations in each trial; and a common reference group for each covariate. Crucially, the multivariate approach can include participants or trials with missing outcomes at some time-points. In the first stage, restricted cubic spline functions are fitted and their interaction with each discrete time-point is estimated in each trial separately. In the second stage, the parameter estimates defining these multiple interaction functions are jointly synthesised in a multivariate random-effects meta-analysis model accounting for within-trial and across-trial correlation. These meta-analysis estimates define the summary non-linear interactions at each time-point, which can be displayed graphically alongside confidence intervals. The approach is illustrated using an IPD meta-analysis examining effect modifiers for exercise interventions in osteoarthritis, which shows evidence of non-linear relationships and small gains in precision by analysing all time-points jointly.

Enhanced Anti-Tumor Response Elicited by a Novel Oncolytic Pseudorabies Virus Engineered with a PD-L1 Inhibitor.

Oncolytic viruses combined with immunotherapy offer significant potential in tumor therapy. In this study, we engineered a further attenuated pseudorabies virus (PRV) vaccine strain that incorporates a PD-L1 inhibitor and demonstrated its promise as an oncolytic virus in tumor therapy. We first showed that the naturally attenuated PRV vaccine strain Bartha can efficiently infect tumor cells from multiple species, including humans, mice, and dogs in vitro. We then evaluated the safety and anti-tumor efficacy of this vaccine strain and its different single-gene deletion mutants using the B16-F10 melanoma mouse model. The TK deletion strain emerged as the optimal vector, and we inserted a PD-L1 inhibitor (iPD-L1) into it using CRISPR/Cas9 technology. Compared with the control, the recombinant PRV (rPRV-iPD-L1) exhibited more dramatic anti-tumor effects in the B16-F10 melanoma mouse model. Our study suggests that PRV can be developed not only as an oncolytic virus but also a powerful vector for expressing foreign genes to modulate the tumor microenvironment.

Checking the inventory: Illustrating different methods for individual participant data meta-analytic structural equation modeling.

Researchers may have at their disposal the raw data of the studies they wish to meta-analyze. The goal of this study is to identify, illustrate, and compare a range of possible analysis options for researchers to whom raw data are available, wanting to fit a structural equation model (SEM) to these data. This study illustrates techniques that directly analyze the raw data, such as multilevel and multigroup SEM, and techniques based on summary statistics, such as correlation-based meta-analytical structural equation modeling (MASEM), discussing differences in procedures, capabilities, and outcomes. This is done by analyzing a previously published collection of datasets using open source software. A path model reflecting the theory of planned behavior is fitted to these datasets using different techniques involving SEM. Apart from differences in handling of missing data, the ability to include study-level moderators, and conceptualization of heterogeneity, results show differences in parameter estimates and standard errors across methods. Further research is needed to properly formulate guidelines for applied researchers looking to conduct individual participant data MASEM.

Extending HLA allele sequences using next-generation sequencing technology.

Extended sequences for 13 HLA alleles were found which had limited coverage previously.

Effect of Childhood Pneumococcal Conjugate Vaccination on Invasive Disease Serotypes in Serbia.

In Serbia, PCV10 was introduced into the routine immunization for children under 2 in 2018 and replaced by PCV13 in 2022. We evaluated their impact on the distribution of invasive pneumococcal disease (IPD) serotypes across all age groups. Overall, 756 isolates were obtained from patients with IPD between 2010 and 2023 through laboratory surveillance. In the post-vaccination period, serotypes 14, 19F, 23F, and 6A significantly declined, while 3 and 19A considerably increased. This was especially evident in the ≤2 years group, making these serotypes the most prevalent among them. Serotype 3 dominated, representing 19.1% of all invasive isolates prior to 2018 and 33.1% thereafter. While serotype coverage of PCV10 has significantly decreased in the ≤2 years group (from 74.2% before 2018 to 29.5% after 2018), PCV13 coverage was 63.9% after 2018. In the post-PCV period, non-PCV13 serotypes, such as 9N, 10A, 15A, 15B, 15C, 22F, 6C, 6D, and 7C, increased across all isolates. Antibiotic non-susceptibility considerably decreased after 2018. MLST analysis showed shifts in sequence type prevalence, with pre-PCV lineages replaced and ongoing serotype 3 persistence, alongside potential capsule-switching events. These findings emphasize a noticeable shift in the distribution of serotypes and adaptability of pneumococcal populations, highlighting the importance of ongoing surveillance and the requirement for the urgent introduction of higher valent vaccines into the National Immunization Program.

Classifiers of Data Sharing Statements in Clinical Trial Records.

Digital individual participant data (IPD) from clinical trials are increasingly distributed for potential scientific reuse. The identification of available IPD, however, requires interpretations of textual data-sharing statements (DSS) in large databases. Recent advancements in computational linguistics include pre-trained language models that promise to simplify the implementation of effective classifiers based on textual inputs. In a subset of 5,000 textual DSS from ClinicalTrials.gov, we evaluate how well classifiers based on domain-specific pre-trained language models reproduce original availability categories as well as manually annotated labels. Typical metrics indicate that classifiers that predicted manual annotations outperformed those that learned to output the original availability categories. This suggests that the textual DSS descriptions contain applicable information that the availability categories do not, and that such classifiers could thus aid the automatic identification of available IPD in large trial databases.

Calculating the power of a planned individual participant data meta-analysis to examine prognostic factor effects for a binary outcome.

Collecting data for an individual participant data meta-analysis (IPDMA) project can be time consuming and resource intensive and could still have insufficient power to answer the question of interest. Therefore, researchers should consider the power of their planned IPDMA before collecting IPD. Here we propose a method to estimate the power of a planned IPDMA project aiming to synthesise multiple cohort studies to investigate the (unadjusted or adjusted) effects of potential prognostic factors for a binary outcome. We consider both binary and continuous factors and provide a three-step approach to estimating the power in advance of collecting IPD, under an assumption of the true prognostic effect of each factor of interest. The first step uses routinely available (published) aggregate data for each study to approximate Fisher's information matrix and thereby estimate the anticipated variance of the unadjusted prognostic factor effect in each study. These variances are then used in step 2 to estimate the anticipated variance of the summary prognostic effect from the IPDMA. Finally, step 3 uses this variance to estimate the corresponding IPDMA power, based on a two-sided Wald test and the assumed true effect. Extensions are provided to adjust the power calculation for the presence of additional covariates correlated with the prognostic factor of interest (by using a variance inflation factor) and to allow for between-study heterogeneity in prognostic effects. An example is provided for illustration, and Stata code is supplied to enable researchers to implement the method.

Reducing self-harm in adolescents: the RISA-IPD individual patient data meta-analysis and systematic review.

Background: Self-harm is common in adolescents and a major public health concern. Evidence for effective interventions is lacking. An individual patient data meta-analysis has the potential to provide more reliable estimates of the effects of therapeutic interventions for self-harm than conventional meta-analyses, to explore which treatments are best suited to certain groups. Method: A systematic review and individual patient data meta-analysis of randomised controlled trials of therapeutic interventions to reduce repeat self-harm in adolescents who had a history of self-harm and presented to clinical services. Primary outcome was repetition of self-harm. The methods employed for searches, study screening and selection, and risk of bias assessment are described, with an overview of the outputs of the searching, selection and quality assessment processes. Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidance is followed. Results: We identified a total 39 eligible studies, from 10 countries, where we sought Individual Patient Data (IPD), of which the full sample of participants were eligible in 18 studies and a partial sample of participants were eligible in 21 studies. We obtained IPD from 26 studies of 3448 eligible participants. For our primary outcome, repetition of self-harm, only 6 studies were rated as low risk of bias with 10 rated as high risk (although 2 of these were for secondary outcomes only). Conclusions: Obtaining individual patient data for meta-analyses is possible but very time-consuming, despite clear guidance from funding bodies that researchers should share their data appropriately. More attention needs to be paid to seeking appropriate consent from study participants for (pseudo) anonymised data-sharing and institutions need to collaborate on agreeing template data-sharing agreements. Researchers and funders need to consider issues of research design more carefully. Our next step is to analyse all the data we have collected to see if it will tell us more about how we might prevent repetition of self-harm in young people. Funding: This article presents independent research funded by the National Institute for Health and Care Research (NIHR) Health Technology Assessment programme as award number 17/117/11. A plain language summary of this research article is available on the NIHR Journals Library Website https://doi.org/10.3310/GTNT6331.

Self-harm is very common in young people and leads to an increased risk of death by suicide. Research so far has not provided clear evidence about which interventions can help to prevent self-harm repetition when young people present to services having harmed themselves. One way to understand what might help is to pool the results from lots of different clinical trials ­ this is known as a meta-analysis. This has already been done using the data published in research articles but has not led to clearer conclusions. In part this is because the information available in published articles is patchy and inconsistent which makes pooling the information and analysing it, difficult. A more useful approach is to ask researchers who led the clinical trials for their original 'raw' data and then pool and analyse all that data ­ this is known as an individual patient data meta-analysis. This has the added benefit that it is possible to include studies where only some of the participants are young people. We did this, and were able to identify many more study participants along with their data, compared to earlier meta-analyses. In this article, we describe how we searched for relevant research studies and the methods we used to obtain individual patient data from other researchers. We also describe our rating of the research quality of the studies we identified. We identified more studies, with many more participants in total, than in previous pooled study research. Gathering the data from other researchers was very time-consuming and not everyone was willing or able to share their data. When we rated the quality of the studies that we found, many were not of high quality. Our next step is to analyse all the data we have collected to see if it will tell us more about how we might prevent repetition of self-harm in young people.

Pooled Cohort Profile: ReCoDID Consortium's Harmonized Acute Febrile Illness Arbovirus Meta-Cohort.

Infectious disease (ID) cohorts are key to advancing public health surveillance, public policies, and pandemic responses. Unfortunately, ID cohorts often lack funding to store and share clinical-epidemiological (CE) data and high-dimensional laboratory (HDL) data long term, which is evident when the link between these data elements is not kept up to date. This becomes particularly apparent when smaller cohorts fail to successfully address the initial scientific objectives due to limited case numbers, which also limits the potential to pool these studies to monitor long-term cross-disease interactions within and across populations. CE data from 9 arbovirus (arthropod-borne viruses) cohorts in Latin America were retrospectively harmonized using the Maelstrom Research methodology and standardized to Clinical Data Interchange Standards Consortium (CDISC). We created a harmonized and standardized meta-cohort that contains CE and HDL data from 9 arbovirus studies from Latin America. To facilitate advancements in cross-population inference and reuse of cohort data, the Reconciliation of Cohort Data for Infectious Diseases (ReCoDID) Consortium harmonized and standardized CE and HDL from 9 arbovirus cohorts into 1 meta-cohort. Interested parties will be able to access data dictionaries that include information on variables across the data sets via Bio Studies. After consultation with each cohort, linked harmonized and curated human cohort data (CE and HDL) will be made accessible through the European Genome-phenome Archive platform to data users after their requests are evaluated by the ReCoDID Data Access Committee. This meta-cohort can facilitate various joint research projects (eg, on immunological interactions between sequential flavivirus infections and for the evaluation of potential biomarkers for severe arboviral disease).

60 HLA class I and 115 HLA class II sequence confirmations submitted to the IPD-IMGT/HLA Database.

Sequence confirmations of 175 HLA class I and II alleles in the IPD-IMGT/HLA Database.

Serotype distribution of invasive pneumococcal disease from countries of the WHO Africa, Americas, Eastern Mediterranean, South-East Asia, and Western Pacific regions: a systematic literature review from 2010 to 2021.

Background: Most publications on invasive pneumococcal disease (IPD) serotype distribution are from about 20 countries (Australia, Canada, China, European Union members, Japan, New Zealand, South Korea, and USA). Here, we reviewed the literature among underrepresented countries in the Americas (AMRO), Africa (AFRO), Eastern Mediterranean (EMRO), South-East Asia (SEARO), and Western Pacific (WPRO) WHO regions. Methods: We performed a systematic review of the most recent IPD serotype surveillance publications (from 01/01/2010 to 31/12/2021, Medline/Embase) in those WHO regions. Selection criteria were delineated by contemporality, within-country geographical scope, and number of samples. Reported serotype distributions for each country were stratified by age group, pneumococcal conjugate vaccine (PCV) serotype category (considering undifferentiated serotypes), and PCV program period (pre-PCV, intermediate, or PCVhv [higher valency PCV formulation]). Pre-PCV period pooled data estimated PCV serotype category distribution by age group across WHO regions, while for the PCVhv period, country-level dataset tables were prepared. Results: Of 2,793 publications screened, 107 were included (58 pediatric, 11 adult, 37 all ages, and one comprising every age group). One-third of eligible countries (51/135) published serotype distribution, ranging from 30 to 43% by WHO region. Considering number of samples per WHO region, a few countries prevailed: AMRO (Brazil), AFRO (South Africa, Malawi, and Burkina Faso), and WPRO (Taiwan). In the pre-PCV period, PCV13 formulation serotypes predominated: ranging from 74 to 85% in children and 58-86% in adults in the different WHO regions. The PCVhv period represented half of the most recent IPD surveillance by countries (26/51). Undifferentiated serotypes represented >20% of IPD from most countries (34/51). Conclusion: Ubiquity of undifferentiated serotypes among the publications could constrain estimates of PCV program impact and of serotype coverage for newer PCVhv formulations; consequently, we recommend that countries favor techniques that identify serotypes specifically and, rather than reporting PCV formulation serotype distributions, provide serotype results individually. Systematic review registration: The protocol has been prospectively registered at PROSPERO, identifier: CRD42021278501. https://www.crd.york.ac.uk/prospero/display_record.php?RecordID=278501.

Clinical characteristics and risk factors for poor outcomes of invasive pneumococcal disease in pediatric patients in China.

BACKGROUND: Invasive pneumococcal disease (IPD) is a significant health concern in children worldwide. In this study, we aimed to analyze the clinical features, antibiotic resistance, and risk variables for poor outcomes in patients with IPD in Hangzhou. METHODS: A retrospective single-centre study was performed using the pediatric intensive care (PIC) database from 2010 to 2018. The clinical characteristics, laboratory data, antimicrobial resistance, and risk factors for in-hospital mortality and sepsis in patients with IPD in intensive care units (ICUs) were analyzed systematically. RESULTS: A total of 178 IPD patients were included in the study. The majority of the IPD children were 2-10 years old. Antimicrobial resistance tests of S. pneumoniae isolates revealed high resistance to erythromycin, tetracycline and compound sulfamethoxazole (SMZ-Co). All the isolates were sensitive to vancomycin, linezolid, moxifloxacin, telithromycin, ofloxacin, and levofloxacin. IPD patients may experience poor outcomes, including death and sepsis. The in-hospital mortality was 3.93%, and 34.27% of patients suffered from sepsis. Temperature (OR 3.80, 95% CI 1.62-8.87; P = 0.0021), Partial Pressure of Oxygen in Arterial Blood (PaO2) (OR 0.99, 95% CI 0.98-1.00; P = 0.0266), and albumin (OR 0.89, 95% CI 0.80-0.99; P = 0.0329) were found to be independent risk factors for sepsis in children with IPD. CONCLUSION: Pediatric IPD deserves attention in China. Appropriate surveillance and antibiotic selection are crucial in managing resistant strains. Early identification of high-risk individuals with risk factors contributes to the development of appropriate treatment strategies.

Invasive pneumococcal disease surveillance in Canada, 2021-2022.

Background: Invasive pneumococcal disease (IPD, Streptococcus pneumoniae) has been a nationally notifiable disease in Canada since 2000. The use of conjugate vaccines has caused a shift in the distribution of serotypes over time. This report is a summary of the demographics, serotypes and antimicrobial resistance of IPD isolates collected in Canada in 2021 and 2022. Methods: The National Microbiology Laboratory (NML) of the Public Health Agency of Canada in Winnipeg, Manitoba collaborates with provincial and territorial public health laboratories to conduct national surveillance of IPD. There were 1,999 isolates reported in 2021 and 3,775 isolates in 2022. Serotype was determined by the Quellung reaction or whole-genome sequencing (WGS). Antimicrobial susceptibilities were determined by WGS methods, broth microdilution, or data shared by collaborators in the Canadian Antimicrobial Resistance Alliance program at the University of Manitoba. Population-based IPD incidence rates were obtained through the Canadian Notifiable Disease Surveillance System. Results: The incidence of IPD in Canada was 5.62 cases per 100,000 population in 2021, decreasing from the peak of 10.86 cases per 100,000 population in 2018. Serotypes with increasing trends (p<0.05) between 2018 and 2022 included: 4 (6.1%-12.4%), 9V (1.0%-5.1%) and 12F (4.8%-5.4%). The overall prevalence of PCV13 serotypes increased over the same period (31.2%-41.5%, p<0.05) while the prevalence of non-vaccine types decreased significantly (27.3%-21.5%, p<0.0001). The highest rates of antimicrobial resistance in 2021 and 2022 were seen with clarithromycin (21%, 2021; 24%, 2022) and erythromycin (22%, 2021; 24%, 2022). Multidrug-resistant IPD continued to increase from 2018 to 2022 (6.7%-12.6%, p<0.05). Conclusion: The number of cases of IPD continued to decrease in 2021 in comparison to previous years, however, 2022 saw a return to pre-COVID-19 levels. Disease due to PCV13 serotypes 3, 4, 9V and 19F, as well as non-PCV13 serotypes 12F and 20, is increasing in prevalence. Surveillance of IPD to monitor changing serotype distribution and antimicrobial resistance is essential.

Surveillance of invasive pneumococcal disease in Spain exploring the impact of the COVID-19 pandemic (2019-2023).

OBJECTIVES: Dynamic trends of invasive pneumococcal disease (IPD) including the evolution of prevalent serotypes are very useful to evaluate the impact of current and future pneumococcal conjugate vaccines (PCVs) and the rise of non-vaccine serotypes. In this study, we include epidemiological patterns of S. pneumoniae before and after COVID-19 pandemic. METHODS: We characterized all national IPD isolates from children and adults received at the Spanish Pneumococcal Reference Laboratory during 2019-2023. RESULTS: In the first pandemic year 2020, we found a general reduction in IPD cases across all age groups, followed by a partial resurgence in children in 2021 but not in adults. By 2022, IPD cases in children had returned to pre-pandemic levels, and partially in adults. In 2023, IPD rates surpassed those of the last pre-pandemic year. Notably, the emergence of serotype 3 is of significant concern, becoming the leading cause of IPD in both pediatric and adult populations over the last two years (2022-2023). Increase of serotype 4 in young adults occurred in the last epidemiological years. CONCLUSIONS: The COVID-19 pandemic led to a temporary decline in all IPD cases during 2020 attributable to non-pharmaceutical interventions followed by a subsequent rise. Employing PCVs with broader coverage and/or enhanced immunogenicity may be critical to mitigate the marked increase of IPD.

Objective measure of binaural processing: Acoustic change complex in response to interaural phase differences.

Combining cochlear implants with binaural acoustic hearing via preserved hearing in the implanted ear(s) is commonly referred to as combined electric and acoustic stimulation (EAS). EAS fittings can provide patients with significant benefit for speech recognition in complex noise, perceived listening difficulty, and horizontal-plane localization as compared to traditional bimodal hearing conditions with contralateral and monaural acoustic hearing. However, EAS benefit varies across patients and the degree of benefit is not reliably related to the underlying audiogram. Previous research has indicated that EAS benefit for speech recognition in complex listening scenarios and localization is significantly correlated with the patients' binaural cue sensitivity, namely interaural time differences (ITD). In the context of pure tones, interaural phase differences (IPD) and ITD can be understood as two perspectives on the same phenomenon. Through simple mathematical conversion, one can be transformed into the other, illustrating their inherent interrelation for spatial hearing abilities. However, assessing binaural cue sensitivity is not part of a clinical assessment battery as psychophysical tasks are time consuming, require training to achieve performance asymptote, and specialized programming and software all of which render this clinically unfeasible. In this study, we investigated the possibility of using an objective measure of binaural cue sensitivity by the acoustic change complex (ACC) via imposition of an IPD of varying degrees at stimulus midpoint. Ten adult listeners with normal hearing were assessed on tasks of behavioral and objective binaural cue sensitivity for carrier frequencies of 250 and 1000 Hz. Results suggest that 1) ACC amplitude increases with IPD; 2) ACC-based IPD sensitivity for 250 Hz is significantly correlated with behavioral ITD sensitivity; 3) Participants were more sensitive to IPDs at 250 Hz as compared to 1000 Hz. Thus, this objective measure of IPD sensitivity may hold clinical application for pre- and post-operative assessment for individuals meeting candidacy indications for cochlear implantation with low-frequency acoustic hearing preservation as this relatively quick and objective measure may provide clinicians with information identifying patients most likely to derive benefit from EAS technology.

Moderators of treatment effect of non-steroidal anti-inflammatory drugs for patients with (sub) acute low back pain: Protocol for a systematic review with individual participant data meta-analysis.

A Cochrane review found that non-steroidal anti-inflammatory drugs (NSAIDs) are slightly more effective than placebo on acute and subacute low back pain (LBP) outcomes (pain intensity, disability, and global improvement). Our objectives are: (1) to assess the overall treatment effect of NSAIDs in adults with acute and subacute LBP; (2) to identify the moderation of baseline patients' characteristics on treatment effect. We will conduct a systematic search of RCTs on effectiveness of NSAIDs compared with placebo in adults with non-chronic LBP in Medline ALL, Embase, Cochrane Central Register of Controlled Trials*. We will screen the records after January 2020, and include eligible RCTs before January 2020 screened by the Cochrane review mentioned above. Our primary outcomes are pain intensity, disability, and health-related quality of life, secondary outcomes are adverse events. Our IPD dataset will consist of the information on each eligible trial characteristics and included variables according to a predefined coding scheme. We will assess risk-of-bias of included RCTs with the Cochrane Risk Of Bias (RoB)-2 assessment tool. We will perform power calculations with closed-form solutions and prioritize a one-stage approach for IPD-MA. For reporting the results, we will adhere to the PRISMA-IPD statement.

A novel framework for human leukocyte antigen (HLA) genotyping using probe capture-based targeted next-generation sequencing and computational analysis.

Human leukocyte antigen (HLA) genes play pivotal roles in numerous immunological applications. Given the immense number of polymorphisms, achieving accurate high-throughput HLA typing remains challenging. This study aimed to harness the human pan-genome reference consortium (HPRC) resources as a potential benchmark for HLA reference materials. We meticulously annotated specific four field-resolution alleles for 11 HLA genes (HLA-A, -B, -C, -DPA1, -DPB1, -DQA1, -DQB1, -DRB1, -DRB3, -DRB4 and -DRB5) from 44 high-quality HPRC personal genome assemblies. For sequencing, we crafted HLA-specific probes and conducted capture-based targeted sequencing of the genomic DNA of the HPRC cohort, ensuring focused and comprehensive coverage of the HLA region of interest. We used publicly available short-read whole-genome sequencing (WGS) data from identical samples to offer a comparative perspective. To decipher the vast amount of sequencing data, we employed seven distinct software tools: OptiType, HLA-VBseq, HISAT genotype, SpecHLA, T1K, QzType, and DRAGEN. Each tool offers unique capabilities and algorithms for HLA genotyping, allowing comprehensive analysis and validation of the results. We then compared these results with benchmarks derived from personal genome assemblies. Our findings present a comprehensive four-field-resolution HLA allele annotation for 44 HPRC samples. Significantly, our innovative targeted next-generation sequencing (NGS) approach for HLA genes showed superior accuracy compared with conventional short-read WGS. An integrated analysis involving QzType, T1K, and DRAGEN was developed, achieving 100% accuracy for all 11 HLA genes. In conclusion, our study highlighted the combination of targeted short-read sequencing and astute computational analysis as a robust approach for HLA genotyping. Furthermore, the HPRC cohort has emerged as a valuable assembly-based reference in this realm.