Filling the gaps – The generation of full genomic sequences for 15 common and well-documented HLA class I alleles using next-generation sequencing technology

Many common and well-documented (CWD) HLA alleles have only been partially characterized. The DNA sequence of these incomplete alleles, as published in the IMGT/HLA database, is most often limited to exons that code for the extracellular domains of the mature protein. Here we describe the application of next-generation sequencing technology to obtain full length genomic sequence from a single long-range PCR amplicon for 15 common and well-documented HLA Class I alleles. This technology is well suited to fill in the gaps of the current HLA allele sequence database which is largely incomplete. A more comprehensive catalog of HLA allele sequences would be beneficial in the evaluation of mismatches in transplantation, studies of population genetics, the evolution of HLAs, regulatory mechanisms and HLA expression, and issues related to the genomic organization of the MHC.     

Retrospective analysis of a clinical exome sequencing cohort reveals the mutational spectrum and identifies candidate disease–associated loci for BAFopathies

PurposeBRG1/BRM-associated factor (BAF) complex is a chromatin remodeling complex that plays a critical role in gene regulation. Defects in the genes encoding BAF subunits lead to BAFopathies, a group of neurodevelopmental disorders with extensive locus and phenotypic heterogeneity.MethodsWe retrospectively analyzed data from 16,243 patients referred for clinical exome sequencing (ES) with a focus on the BAF complex. We applied a genotype-first approach, combining predicted genic constraints to propose candidate BAFopathy genes.ResultsWe identified 127 patients carrying pathogenic variants, likely pathogenic variants, or de novo variants of unknown clinical significance in 11 known BAFopathy genes. Those include 34 patients molecularly diagnosed using ES reanalysis with new gene–disease evidence (n = 21) or variant reclassifications in known BAFopathy genes (n = 13). We also identified de novo or predicted loss-of-function variants in 4 candidate BAFopathy genes, including ACTL6A, BICRA (implicated in Coffin-Siris syndrome during this study), PBRM1, and SMARCC1.ConclusionWe report the mutational spectrum of BAFopathies in an ES cohort. A genotype-driven and pathway-based reanalysis of ES data identified new evidence for candidate genes involved in BAFopathies. Further mechanistic and phenotypic characterization of additional patients are warranted to confirm their roles in human disease and to delineate their associated phenotypic spectrums.     

Analysis of degradation data of poly(l-lactide–co-l,d-lactide) and poly(l-lactide) obtained at elevated and physiological temperatures using mathematical models

The degradation of resorbable polymeric devices often takes months to years. Accelerated testing at elevated temperatures is an attractive but controversial technique. The purposes of this paper include: (a) to provide a summary of the mathematical models required to analyse accelerated degradation data and to indicate the pitfalls of using these models; (b) to improve the model previously developed by Han and Pan; (c) to provide a simple version of the model of Han and Pan with an analytical solution that is convenient to use; (d) to demonstrate the application of the improved model in two different poly(lactic acid) systems. It is shown that the simple analytical relations between molecular weight and degradation time widely used in the literature can lead to inadequate conclusions. In more general situations the rate equations are only part of a complete degradation model. Together with previous works in the literature, our study calls for care in using the accelerated testing technique.     

Prospective study of a panfungal PCR assay followed by sequencing,for the detection of fungal DNA in normally sterile specimens in a clinical setting: a complementary tool in the diagnosis of invasive fungal disease?

We prospectively analyzed 34 clinical biopsy samples from 23 patients with a suspected invasive fungal infection by fungal culture, histology and a panfungal PCR followed by sequencing. Results were compared to the composite diagnosis according the European Organization for Research and Treatment of Cancer (EORTC) criteria. In 34 samples, culture, histology and panfungal PCR were positive in 35%, 38% and 62%, respectively. On the sample level the panfungal PCR revealed a sensitivity of 69% and a specificity of 62.5% compared to proven IFI according postoperative EORTC criteria. On patient level, the sensitivity of the PCR approach was 100%, specificity 62.5%.     

Test–retest stability,convergent validity,and sensitivity to change for the Goal-Based Outcome tool for adolescents: Analysis of data from a randomized controlled trial

Objective(s)

To examine the psychometric properties of the idiographic Goal-Based Outcome (GBO) tool for young people: test–retest stability, convergent validity, and sensitivity to an intervention.

Methods

This measure validation study used data from a randomized controlled trial of school-based humanistic counseling. We used multilevel analyses to assess test–retest stability, convergent validity of the GBO tool against nomothetic measures of mental wellbeing, and sensitivity to an intervention.

Results

The GBO tool showed acceptable stability over a 6–24 week period; moderate convergent validity with nomothetic measures of mental well-being, self-esteem, and depression; and greater sensitivity to an intervention than a measure of psychological distress.

Conclusions

The GBO tool shows evidence of having acceptable psychometric properties and is suitable for monitoring change on individual goals. It may also have the capacity to function as a population-level indicator of outcomes in conjunction with the use of other measures of mental health and wellbeing.     

Isolation of Ani s 5, an excretory–secretory and highly heat-resistant allergen useful for the diagnosis of <Emphasis Type="Italic">Anisakis</Emphasis> larvae sensitization

Allergens Ani s 1 and Ani s 4 have demonstrated their utility for the diagnosis of the sensitization to larvae of the genus Anisakis. The aim was to determine the number of patients with compatible clinical history, who did not recognize Ani s 1 and Ani s 4, and characterize the allergens responsible for their sensitization. Eighty-four patients were studied by CAP and immunoglobulin E (IgE) immunoblotting. The 12% of the patients recognized allergens different from Ani s 1 and Ani s 4, being half sensitized to a heat-resistant 15-kDa allergen, which was isolated by ethanol fractionation, followed by a hydroxyapatite chromatography and a reversed-phase high-performance liquid chromatography and identified by its amino terminal sequence as Ani s 5. A total of 41 of the 84 patients studied (49%) showed specific IgE to Ani s 5 that was detected among the excretory-secretory products and immunohistochemically located at the excretory gland, ventriculus, and the luminal surface of the intestinal epithelium of the larvae.     

A pragmatic method for transforming clinical research data from the research electronic data capture “REDCap” to Clinical Data Interchange Standards Consortium (CDISC) Study Data Tabulation Model (SDTM): Development and evaluation of REDCap2SDTM

The Clinical Data Interchange Standards Consortium (CDISC) Study Data Tabulation Model (SDTM) can be used for new drug application studies as well as secondarily for creating a clinical research data warehouse to leverage clinical research study data across studies conducted within the same disease area. However, currently not all clinical research uses Clinical Data Acquisition Standards Harmonization (CDASH) beginning in the set-up phase of the study. Once already initiated, clinical studies that have not utilized CDASH are difficult to map in the SDTM format. In addition, most electronic data capture (EDC) systems are not equipped to export data in SDTM format; therefore, in many cases, statistical software is used to generate SDTM datasets from accumulated clinical data. In order to facilitate efficient secondary use of accumulated clinical research data using SDTM, it is necessary to develop a new tool to enable mapping of information for SDTM, even during or after the clinical research. REDCap is an EDC system developed by Vanderbilt University and is used globally by over 2100 institutions across 108 countries. In this study, we developed a simulated clinical trial to evaluate a tool called REDCap2SDTM that maps information in the Field Annotation of REDCap to SDTM and executes data conversion, including when data must be pivoted to accommodate the SDTM format, dynamically, by parsing the mapping information using R. We confirmed that generating SDTM data and the define.xml file from REDCap using REDCap2SDTM was possible. Conventionally, generation of SDTM data and the define.xml file from EDC systems requires the creation of individual programs for each clinical study. However, our proposed method can be used to generate this data and file dynamically without programming because it only involves entering the mapping information into the Field Annotation, and additional data into specific files. Our proposed method is adaptable not only to new drug application studies but also to all types of research, including observational and public health studies. Our method is also adaptable to clinical data collected with CDASH at the beginning of a study in non-standard format. We believe that this tool will reduce the workload of new drug application studies and will support data sharing and reuse of clinical research data in academia.     

Efficacies of different proton pump inhibitor-based 14-day bismuth–furazolidone quadruple regimens for the initial eradication of <Emphasis Type="Italic">Helicobacter pylori</Emphasis> in the southeast coastal region of China: an open-label,randomized clinical trial

To evaluate potency and safety of 14-day bismuth–furazolidone quadruple regimens and to compare efficacies of five proton pump inhibitors (PPIs) for the initial eradication of Helicobacter pylori (H. pylori), 175 eligible patients were enrolled and randomly assigned to 14-day quadruple regimens consisting of bismuth (400 mg), amoxicillin (1 g), furazolidone (100 mg), and a PPI, twice a day. PPIs used were Group A (pantoprazole capsules, 40 mg), Group B (pantoprazole tablets, 40 mg), Group C (lansoprazole, 30 mg), Group D (esomeprazole, 20 mg), and Group E (rabeprazole, 10 mg). H. pylori status was reassessed by ¹³C urea breath test on day 56 as the primary outcome. Gastrointestinal symptoms, parenteral side effects, compliance, and stool type were recorded simultaneously. The total eradication rates were 86.9% (152/175 [95% CI 80.9–91.5%]) and 95.6% (152/159 [91.1–98.2%]) by intention-to-treat (ITT) and per-protocol (PP) analysis. The efficacies of Group A, B, C, D, and E by ITT analysis were 91.4% (32/35 [76.9–98.2%]), 85.7% (30/35 [69.7–95.2%]), 88.6% (31/35 [73.3–96.8%]), 85.7% (30/35 [69.7–95.2%]), and 82.9% (29/35 [66.4–93.4%]) (p?>?0.05). In the PP analysis, the efficacies were 97.0% (32/33), 93.8% (30/32), 93.9% (31/33), 100% (30/30), and 93.5% (29/31) (p?>?0.05). Gastrointestinal symptoms and stool type were improved significantly (p?<?0.05). Total side effects rate and poor compliance rate were 15.7% (25/159) and 5.0% (8/159). Fourteen-day bismuth–furazolidone quadruple regimens are of high potency and safety for the initial eradication of H. pylori. Efficacies of different PPIs and different dosages (9–32 mg omeprazole equivalents) showed no significant difference. The appropriate PPI can thus be chosen by clinicians.     

Which are the best nations and institutions for revolutionary science 1987–2006? Analysis using a combined metric of Nobel prizes,Fields medals,Lasker awards and Turing awards (NFLT metric)

I have previously suggested that Nobel prizes can be used as a scientometric measurement of 'revolutionary science'; and that for this purpose it would be better if more Nobel prizes were awarded, especially in three new subjects of mathematics, medicine and computing science which have become major sciences over recent decades. In the following analysis of the last 20 years from 1987 to 2006, I use three prestigious prizes in mathematics (Fields medal), medicine (Lasker award for Clinical Medical Research) and computing science (A.M. Turing award) which are plausible surrogates for Nobel prizes. The combined Nobel-Fields-Lasker-Turing (NFLT) metric is strongly dominated by the USA. However the distribution implies that revolutionary science may be somewhat more broadly distributed than the pure Nobel metric suggests. The UK and France seem to be significant nations in some types of revolutionary science (although the UK has declined substantially as a centre of revolutionary science); and Germany, Switzerland, Japan, Russia, Denmark and Norway also feature. The top world institutions for revolutionary science according to NFLT are MIT, Stanford and Princeton - all in the USA - and the USA has 19 institutions with at least three prize-winners. Second is France, with three institutions having three or more winners; the UK and Norway have one each. The NFLT metric confirms previous observations that many public universities in the Western USA have now become a major focus of revolutionary science; and that Harvard has declined from its previous status as the top world centre of revolutionary science to about seventh-place. This analysis confirms the potential value of increasing the number of Nobel prizes as a means of identifying and monitoring centres of excellence in revolutionary science.