Multiplex targeted high‐throughput sequencing for Mendelian cardiac disorders

Mendelian cardiomyopathies and arrhythmias are characterized by an important genetic heterogeneity, rendering Sanger sequencing very laborious and expensive. As a proof of concept, we explored multiplex targeted high‐throughput sequencing (HTS) as a fast and cost‐efficient diagnostic method for individuals suffering from Mendelian cardiac disorders. We designed a DNA capture assay including all exons from 130 genes involved in cardiovascular Mendelian disorders and analysed simultaneously four samples by multiplexing. Two patients had familial hypertrophic cardiomyopathy (HCM) and two patients suffered from long QT syndrome (LQTS). In patient 1 with HCM, we identified two known pathogenic missense variants in the two most frequently mutated sarcomeric genes MYH7 and MYBPC. In patient 2 with HCM, a known acceptor splice site variant in MYBPC3 was found. In patient 3 with LQTS, two missense variants in the genes SCN5A and KCNQ were identified. Finally, in patient 4 with LQTS a known missense variant was found in MYBPC3, which is usually mutated in patients with cardiomyopathy. Our results showed that multiplex targeted HTS works as an efficient and cost‐effective tool for molecular diagnosis of heterogeneous disorders in clinical practice and offers new insights in the pathogenesis of these complex diseases.     

Integrating high‐throughput screening and sequencing for monoclonal antibody discovery and engineering

Monoclonal antibody discovery and engineering is a field that has traditionally been dominated by high‐throughput screening platforms (e.g. hybridomas and surface display). In recent years the emergence of high‐throughput sequencing has made it possible to obtain large‐scale information on antibody repertoire diversity. Additionally, it has now become more routine to perform high‐throughput sequencing on antibody repertoires to also directly discover antibodies. In this review, we provide an overview of the progress in this field to date and show how high‐throughput screening and sequencing are converging to deliver powerful new workflows for monoclonal antibody discovery and engineering.     

A rapid,high‐throughput screening method for carriage of methicillin‐resistant Staphylococcus aureus

Rapid screening of methicillin‐resistant Staphylococcus aureus (MRSA) colonization prior to hospital admittance is important to reduce nosocomial infections and health care costs. Molecular detection of mecA and S. aureus specific target genes has become widely established for this purpose. However, there are still limitations in potential for high‐throughput screening in the methods described. We have compared the time aspects and workload of four different DNA preparation platforms, resulting in an automated and simple MRSA screening method which combines two liquid handling systems and a simple lysis buffer. We have further transferred our in‐house dual real‐time PCR to a fast‐PCR protocol, reducing the time and labour spent on these samples to a minimum.     

A high‐throughput shotgun mutagenesis approach to mapping B‐cell antibody epitopes

Characterizing the binding sites of monoclonal antibodies (mAbs) on protein targets, their ‘epitopes’, can aid in the discovery and development of new therapeutics, diagnostics and vaccines. However, the speed of epitope mapping techniques has not kept pace with the increasingly large numbers of mAbs being isolated. Obtaining detailed epitope maps for functionally relevant antibodies can be challenging, particularly for conformational epitopes on structurally complex proteins. To enable rapid epitope mapping, we developed a high‐throughput strategy, shotgun mutagenesis, that enables the identification of both linear and conformational epitopes in a fraction of the time required by conventional approaches. Shotgun mutagenesis epitope mapping is based on large‐scale mutagenesis and rapid cellular testing of natively folded proteins. Hundreds of mutant plasmids are individually cloned, arrayed in 384‐well microplates, expressed within human cells, and tested for mAb reactivity. Residues are identified as a component of a mAb epitope if their mutation (e.g. to alanine) does not support candidate mAb binding but does support that of other conformational mAbs or allows full protein function. Shotgun mutagenesis is particularly suited for studying structurally complex proteins because targets are expressed in their native form directly within human cells. Shotgun mutagenesis has been used to delineate hundreds of epitopes on a variety of proteins, including G protein‐coupled receptor and viral envelope proteins. The epitopes mapped on dengue virus prM/E represent one of the largest collections of epitope information for any viral protein, and results are being used to design better vaccines and drugs.     

Development of a high‐throughput genotoxicity assay using Umu test strains expressing human cytochrome P450s and NADPH‐P450 reductase and bacterial O‐acetyltransferase

Umu test is one of the in vitro genotoxicity test that has been used widely. It was developed as a high‐throughput test system using the 96‐well microplate. We have previously constructed new umu test strains for the evaluation of genotoxicity of procarcinogenic metabolic products formed by cytochrome P450 (CYP) enzymes. In this study, a highly sensitive high‐throughput genotoxicity test was developed using four umu test strains (OY1002/1A1, OY1002/1B1, OY1002/1A2, and OY1002/3A4) that express human CYPs and NADPH‐P450 reductase. We found that the modified umu‐microplate method was more sensitive than the conventional microplate method using strain OY1002/1A2. In addition, the new microplate method was better able to detect genotoxicity than the test tube method when the strain OY1002/1A2 was used and had similar sensitivity for the remaining three strains. When the microplate method was used, OY1002/1A2 showed stronger umuC gene expression in the presence of 2‐amino‐6‐methyldipyrido[1,2‐a:3',2'‐d]imidazole, 2‐amino‐3‐methylimidazo[4,5‐f]quinoline, 2‐amino‐3,4‐dimethylimidazo[4,5‐f]quinoline, 2‐amino‐3,8‐dimethylimidazo[4,5‐f]quinoxaline, 2‐aminofluorene, and 2‐aminoanthracene compared to other strains. We also confirmed CYP1A2 expression in OY1002/1A2 in this condition. These results indicate that the microplate version of this test system can detect the genotoxicity of heterocyclic and aromatic amines with high sensitivity and can be used for high‐throughput screening of potentially genotoxic compounds. Environ. Mol. Mutagen. 58:209–216, 2017. © 2017 Wiley Periodicals, Inc.     

Multiplex targeted high‐throughput sequencing in a series of 352 patients with congenital limb malformations

Congenital limb malformations (CLM) comprise many conditions affecting limbs and more than 150 associated genes have been reported. Due to this large heterogeneity, a high proportion of patients remains without a molecular diagnosis. In the last two decades, advances in high throughput sequencing have allowed new methodological strategies in clinical practice. Herein, we report the screening of 52 genes/regulatory sequences by multiplex high‐throughput targeted sequencing, in a series of 352 patients affected with various CLM, over a 3‐year period of time. Patients underwent a clinical triage by expert geneticists in CLM. A definitive diagnosis was achieved in 35.2% of patients, the yield varying considerably, depending on the phenotype. We identified 112 single nucleotide variants and 26 copy‐number variations, of which 52 are novel pathogenic or likely pathogenic variants. In 6% of patients, variants of uncertain significance have been found in good candidate genes. We showed that multiplex targeted high‐throughput sequencing works as an efficient and cost‐effective tool in clinical practice for molecular diagnosis of congenital limb malformations. Careful clinical evaluation of patients may maximize the yield of CLM panel testing.     

An evaluation of 25 selected ToxCast chemicals in medium‐throughput assays to detect genotoxicity

ToxCast is a multiyear effort to develop a cost‐effective approach for the US EPA to prioritize chemicals for toxicity testing. Initial evaluation of more than 500 high‐throughput (HT) microwell‐based assays without metabolic activation showed that most lacked high specificity and sensitivity for detecting genotoxicants. Thus, EPA initiated a pilot project to investigate the use of standard genotoxicity endpoints using medium‐throughput genotoxicity (MTG) assays in the context of a large testing program. Twenty‐five chemicals were selected from the ToxCast program based in part on their known genotoxicity. The two MTG assays used were the Ames II^? assay and 96‐well In Vitro MicroFlow^® Micronucleus (MN) assay. The Ames II assay showed a reasonable correlation with published Ames test data and industry submissions, though specificity was much better than sensitivity due to restraints on top concentrations as prescribed by ToxCast. Overall concordance was 73% both with and without metabolic activation. The flow MN assay had concordances of 71% and 58% with and without metabolic activation, respectively, when compared to published data and submissions. Importantly, a comparison of results without S9 from the MTG assays to an HT ToxCast p53 activation assay showed a fairly good degree of concordance (67%). The results reported here indicate that assays for genotoxicity endpoints can be conducted in a MT format and have the potential to add to the interpretation of results from large‐scale testing programs such as EPA's ToxCast program. Inherent limitations such as the top concentrations used in large scale testing programs are discussed. Environ. Mol. Mutagen. 56:468–476, 2015. © 2014 Wiley Periodicals, Inc.     

Sequencing‐based microsatellite instability testing using as few as six markers for high‐throughput clinical diagnostics

Microsatellite instability (MSI) testing of colorectal cancers (CRCs) is used to screen for Lynch syndrome (LS), a hereditary cancer‐predisposition, and can be used to predict response to immunotherapy. Here, we present a single‐molecule molecular inversion probe and sequencing‐based MSI assay and demonstrate its clinical validity according to existing guidelines. We amplified 24 microsatellites in multiplex and trained a classifier using 98 CRCs, which accommodates marker specific sensitivities to MSI. Sample classification achieved 100% concordance with the MSI Analysis System v1.2 (Promega) in three independent cohorts, totaling 220 CRCs. Backward–forward stepwise selection was used to identify a 6‐marker subset of equal accuracy to the 24‐marker panel. Assessment of assay detection limits showed that the 24‐marker panel is marginally more robust to sample variables than the 6‐marker subset, detecting as little as 3% high levels of MSI DNA in sample mixtures, and requiring a minimum of 10 template molecules to be sequenced per marker for >95% accuracy. BRAF c.1799 mutation analysis was also included to streamline LS testing, with all c.1799T>A variants being correctly identified. The assay, therefore, provides a cheap, robust, automatable, and scalable MSI test with internal quality controls, suitable for clinical cancer diagnostics.     

Identification of leucocyte surface protein interactions by high‐throughput screening with multivalent reagents

We describe a high-throughput screening system to detect interactions between leucocyte surface proteins, taking into account that these interactions are usually of very low affinity. The method involves producing the extracellular regions of leucocyte proteins with tags so that they can be bound to nanoparticles to provide an avid reagent to screen over an array of 36 similar proteins immobilized using the Proteon™ XPR36 with detection by surface plasmon resonance. The system was tested using established interactions that could be detected without spurious binding. The ability to detect new interactions was shown by identifying a new interaction between carcinoembryonic antigen-related cell adhesion molecule 1 and carcinoembryonic antigen-related cell adhesion molecule 8.     

A cell‐based high‐throughput protocol to screen entry inhibitors of highly pathogenic viruses with Traditional Chinese Medicines

Emerging viruses such as Ebola virus (EBOV), Lassa virus (LASV), and avian influenza virus H5N1 (AIV) are global health concerns. Since there is very limited options (either vaccine or specific therapy) approved for humans against these viruses, there is an urgent need to develop prophylactic and therapeutic treatments. Previously we reported a high‐throughput screening (HTS) protocol to identify entry inhibitors for three highly pathogenic viruses (EBOV, LASV, and AIV) using a human immunodeficiency virus–based pseudotyping platform which allows us to perform the screening in a BSL‐2 facility. In this report, we have adopted this screening protocol to evaluate traditional Chinese Medicines (TCMs) in an effort to discover entry inhibitors against these viruses. Here we show that extracts of the following Chinese medicinal herbs exhibit potent anti‐Ebola viral activities: Gardenia jasminoides Ellis, Citrus aurantium L., Viola yedoensis Makino, Prunella vulgaris L., Coix lacryma‐jobi L. var. mayuen (Roman.) Stapf, Pinellia ternata (Thunb.) Breit., and Morus alba L. This study represents a proof‐of‐principle investigation supporting the suitability of this assay for rapid screening TCMs and identifying putative entry inhibitors for these viruses. J. Med. Virol. 89:908–916, 2017 . © 2016 Wiley Periodicals, Inc.

     

Difficulties and challenges in the development of precision medicine

The rapid development of precision medicine is introducing a new era of significance in medicine. However, attaining precision medicine is an ambitious goal that is bound to encounter some challenges. Here, we have put forward some difficulties or questions that should be addressed by the progress in this field. The proposed issues include the long road to precision medicine for all types of diseases as the unknown domains of the human genome hinder the development of precision medicine. The challenges in the acquisition and analysis of large amounts of omics data, including difficulties in the establishment of a library of biological samples and large-scale data analysis, as well as the challenges of informed consent and medical ethics in precision medicine, must be overcome to attain the goals of precision medicine. To date, precision medicine programs have accomplished many preliminary achievements and will help to drive a dramatic revolution in clinical practices for the medical community. Through these advances, the diagnosis and treatment of many diseases will achieve many breakthroughs. This project is just beginning and requires a great deal of time and money. Precision medicine also requires extensive collaboration. Ultimately, these difficulties can be overcome. We should realize that precision medicine is good for patients, but there is still a long way to go.     

Aberrant BRAF splicing as an alternative mechanism for oncogenic B‐Raf activation in thyroid carcinoma

Activating BRAF mutations have recently been reported in 28–83% of papillary thyroid carcinomas (PTCs). However, it is not known whether aberrant BRAF splicing occurs in thyroid carcinoma. To investigate aberrant BRAF splicing and its association with BRAF mutation in thyroid tumours, we studied aberrant BRAF splicing and BRAF mutation from 68 thyroid tumours. BRAF^V600E mutation was detected in 20 of 43 PTCs and all three anaplastic thyroid carcinomas (ATCs). There is a higher frequency of BRAF mutation in PTC patients with stage III and IV tumours compared with stage I and II. Novel BRAF splicing variants were detected in 12 PTCs, three follicular variants of PTC (FVPTCs), and one ATC, as well as in two thyroid carcinoma cell lines, ARO and NPA. These variants did not have the N‐terminal auto‐inhibitory domain of wild‐type B‐Raf, resulting in an in‐frame truncated protein that contained only the C‐terminal kinase domain and caused constitutive activation of B‐Raf. These variants were significantly associated with advanced disease stage and BRAF^V600E mutation (p < 0.001, Fisher exact test). Furthermore, expression of these variants in NIH3T3 and CHO cells could activate the MAP kinase signalling pathway, transform them in vitro, and induce tumours in nude mice. These data suggest that BRAF splicing variants may function as an alternative mechanism for oncogenic B‐Raf activation. Combination of the BRAF^V600E mutation and its splicing variants may contribute towards disease progression to poorly differentiated thyroid carcinoma. Copyright © 2008 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.     

Determination of the appropriate b value and number of gradient directions for high‐angular‐resolution diffusion‐weighted imaging

High‐angular‐resolution diffusion‐weighted imaging (HARDI) is one of the most common MRI acquisition schemes for use with higher order models of diffusion. However, the optimal b value and number of diffusion‐weighted (DW) directions for HARDI are still undetermined, primarily as a result of the large number of available reconstruction methods and corresponding parameters, making it impossible to identify a single criterion by which to assess performance. In this study, we estimate the minimum number of DW directions and optimal b values required for HARDI by focusing on the angular frequency content of the DW signal itself. The spherical harmonic (SH) series provides the spherical analogue of the Fourier series, and can hence be used to examine the angular frequency content of the DW signal. Using high‐quality data acquired along 500 directions over a range of b values, we estimate that SH terms above l = 8 are negligible in practice for b values up to 5000 s/mm², implying that a minimum of 45 DW directions is sufficient to fully characterise the DW signal. l > 0 SH terms were found to increase as a function of b value, levelling off at b = 3000 s/mm², suggesting that this value already provides the highest achievable angular resolution. In practice, it is recommended to acquire more than the minimum of 45 DW directions to avoid issues with imperfections in the uniformity of the DW gradient directions and to meet signal‐to‐noise requirements of the intended reconstruction method. Copyright © 2013 John Wiley & Sons, Ltd.     

Comparison of the performance in detection of HPV infections between the high‐risk HPV genotyping real time PCR and the PCR‐reverse dot blot assays

A new multiplex real‐time PCR assay, the high‐risk HPV genotyping real time PCR assay (HR HPV RT‐PCR), has been developed to detect 15 high‐risk HPV types with respective viral loads. In this report, a total of 684 cervical specimens from women diagnosed with vaginitis were assessed by the HR HPV RT‐PCR and the PCR reaction and reverse dot blot (PCR‐RDB) assays, using a PCR‐sequencing method as a reference standard. A total coincidence of 97.7% between the HR HPV RT PCR and the PCR‐RDB assays was determined with a Kappa value of 0.953. The HR HPV RT PCR assay had sensitivity, specificity, and concordance rates (accuracy) of 99.7%, 99.7%, and 99.7%, respectively, as confirmed by PCR‐sequencing, while the PCR‐RDB assay had respective rates of 98.8%, 97.1%, and 98.0%. The overall rate of HPV infection, determined by PCR‐sequencing, in women diagnosed with vaginitis was 49.85%, including 36.26% of single infection and 13.6% of multiple infections. The most common infections among the 15 high‐risk HPV types in women diagnosed with vaginitis were HPV‐52, HPV‐16, and HPV‐58, with a total detection rate of 10.23%, 7.75%, and 5.85%, respectively. We conclude that the HR HPV RT PCR assay exhibits better clinical performance than the PCR‐RDB assay, and is an ideal alternative method for HPV genotyping. In addition, the HR HPV RT PCR assay provides HPV DNA viral loads, and could serve as a quantitative marker in the diagnosis and treatment of single and multiple HPV infections.     

Positioning the principles of precision medicine in care pathways for allergic rhinitis and chronic rhinosinusitis – A EUFOREA‐ARIA‐EPOS‐AIRWAYS ICP statement

Precision medicine (PM) is increasingly recognized as the way forward for optimizing patient care. Introduced in the field of oncology, it is now considered of major interest in other medical domains like allergy and chronic airway diseases, which face an urgent need to improve the level of disease control, enhance patient satisfaction and increase effectiveness of preventive interventions. The combination of personalized care, prediction of treatment success, prevention of disease and patient participation in the elaboration of the treatment plan is expected to substantially improve the therapeutic approach for individuals suffering from chronic disabling conditions. Given the emerging data on the impact of patient stratification on treatment outcomes, European and American regulatory bodies support the principles of PM and its potential advantage over current treatment strategies. The aim of the current document was to propose a consensus on the position and gradual implementation of the principles of PM within existing adult treatment algorithms for allergic rhinitis (AR) and chronic rhinosinusitis (CRS). At the time of diagnosis, prediction of success of the initiated treatment and patient participation in the decision of the treatment plan can be implemented. The second‐level approach ideally involves strategies to prevent progression of disease, in addition to prediction of success of therapy, and patient participation in the long‐term therapeutic strategy. Endotype‐driven treatment is part of a personalized approach and should be positioned at the tertiary level of care, given the efforts needed for its implementation and the high cost of molecular diagnosis and biological treatment.     

High‐throughput sequencing of T‐cell receptors reveals a homogeneous repertoire of tumour‐infiltrating lymphocytes in ovarian cancer

The cellular adaptive immune system mounts a response to many solid tumours mediated by tumour‐infiltrating T lymphocytes (TILs). Basic measurements of these TILs, including total count, show promise as prognostic markers for a variety of cancers, including ovarian and colorectal. In addition, recent therapeutic advances are thought to exploit this immune response to effectively fight melanoma, with promising studies showing efficacy in additional cancers. However, many of the basic properties of TILs are poorly understood, including specificity, clonality, and spatial heterogeneity of the T‐cell response. We utilize deep sequencing of rearranged T‐cell receptor beta (TCRB) genes to characterize the basic properties of TILs in ovarian carcinoma. Due to somatic rearrangement during T‐cell development, the TCR beta chain sequence serves as a molecular tag for each T‐cell clone. Using these sequence tags, we assess similarities and differences between infiltrating T cells in discretely sampled sections of large tumours and compare to T cells from peripheral blood. Within the limits of sensitivity of our assay, the TIL repertoires show strong similarity throughout each tumour and are distinct from the circulating T‐cell repertoire. We conclude that the cellular adaptive immune response within ovarian carcinomas is spatially homogeneous and distinct from the T‐cell compartment of peripheral blood. Copyright © 2013 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.     

Evaluation of high‐fat high‐fructose diet treatment in factor VIII (coagulation factor)‐deficient mouse model

Non‐alcoholic fatty liver disease (NAFLD)‐like conditions enhance the production and action of clotting factors in humans. However, studies examining the effect of NAFLD due to high‐fat high‐fructose (HFHF) diet in factor VIII‐deficient (haemophilia A) animals or patients have not been reported previously. In this study, we investigated the individual role of factor VIII in the progression of diet‐induced NAFLD in the factor 8^?/? (F8^?/?) mouse model system and its consequences on the haemophilic status of the mice. The F8^?/? mice were fed with HFHF diet for 14 weeks. Physiological, biochemical, haematological, molecular, pathological, and immune histochemical analyses were performed to evaluate the effect of this diet. The F8^?/? mice developed hepatic steatosis after 14 weeks HFHF diet and displayed lower energy metabolism, higher myeloid cell infiltration in the liver, decreased platelet count, upregulated de novo fatty acid synthesis, lipid accumulation, and collagen deposition. This study helps to understand the role of factor VIII in NAFLD pathogenesis and to analyse the severity and consequences of steatosis in haemophilic patients as compared to normal population. This study suggests that haemophilic animals (F8^?/? mice) are highly prone to hepatic steatosis and thrombocytopenia.     

Melanoma differentiation‐associated gene 5 in zebrafish provoking higher interferon‐promoter activity through signalling enhancing of its shorter splicing variant

Melanoma differentiation‐associated gene 5 (MDA5) is one of the three members in the retinoic acid‐inducible gene I‐like receptor (RLR) family, which are cytoplasmic pathogen recognition receptors recognizing intracellular viruses. In the present study, MDA5 and its spliced shorter forms, named as MDA5a and MDA5b, were identified in zebrafish. MDA5a and MDA5b can be up‐regulated in cell lines following the infection of a negative ssRNA virus, the spring viraemia of carp virus (SVCV), and an intracellular Gram‐negative bacterial pathogen Edwardsiella tarda, implying that the RLR may also be able to sense elements released from bacteria. The over‐expression of MDA5a and MDA5b in fish cells resulted in significant induction of type I interferon promoter activity and enabled the protection of transfected cells against SVCV infection. Furthermore, the shorter spliced form, MDA5b when co‐transfected with MDA5a or mitochondrial antiviral signalling protein (MAVS), induced a significantly higher level of interferon promoter activity, indicating that MDA5b may function as an enhancer in the interaction between MDA5 and MAVS.     

Cardiovascular pharmacogenetics: a promise for genomically‐guided therapy and personalized medicine

Cardiovascular disease (CVD) is the leading cause of death worldwide. The basic causes of CVD are not fully understood yet. Substantial evidence suggests that genetic predisposition plays a vital role in the physiopathology of this complex disease. Hence, identification of genetic contributors to CVD will likely add diagnostic accuracy and better prediction of an individual's risk. With high‐throughput genetics and genomics technology and newer genome‐wide study approaches, a number of genetic variations across the human genome were uncovered. Evidence suggests that genetic defects could influence CVD development and inter‐individual responses to widely used cardiovascular drugs like clopidogrel, aspirin, warfarin, and statins, and therefore, they may be integrated into clinical practice. If clinically validated, better understanding of these genetic variations may provide new opportunities for personalized diagnostic, pharmacogenetic‐based drug selection and best treatment in personalized medicine. However, numerous gaps remain unsolved due to the lack of underlying pathological mechanisms for how genetic predisposition could contribute to CVD. This review provides an overview of the extraordinary scientific progress in our understanding of genetic and genomic basis of CVD as well as the development of relevant genetic biomarkers for this disease. Some of the actual limitations to the promise of these markers and their translation for the benefit of patients will be discussed.