Increasing early disease detection

In a three-year precision medicine study, researchers have used whole genome sequencing (WGS) and deep phenotyping via metabolomics, advanced imaging and clinical laboratory tests to identify people at risk for major health conditions. The prospective study of 1,190 adults had four objectives: Assess genotype and phenotype associations in specific disease areas, such as cancer, cardiomyopathy, arrhythmia and diabetes; show where lack of genotype and phenotype associations my lead uncertainty in patient care strategies; analyze cases of autosomal recessive carriers with a phenotype manifestation observed in imaging or blood metabolites; and pursue research using WGS with deep phenotyping data. The analysis, using a precision medicine platform, yielded actionable findings. Of the 1,190 participants, 17.3% had at least one genetic variant predisposing them to disease, most of which were previously unknown, and 11.5% had genotype and phenotype associations. A further breakdown of diseases and disease risk identified in the study includes: insulin resistance and/or impaired glucose tolerance, 34.2%; elevated liver fat, 29.2%; cardiac structure or function abnormalities, such as valvular disorders, 16.2%; significant calcified coronary artery plaque (calcium score > 100), 11.4%; elevated liver iron, 9.3%; cardiac arrhythmias, such as atrial fibrillation, 6.1%; cardiac conduction disorders, 4.8%; and early-stage tumors, most malignant, 1.7%. “Compared with large-scale gene panel approaches using EHRs such as DiscovEHR … and UK Biobank studies …, our genome-wide analysis combined with the prospective deep phenotype assessment had increased sensitivity (... approximately fivefold) to identify previously undiagnosed adults with genetic disorders,” the authors wrote. Their work appeared online Jan. 24, 2020, in the Proceedings of the National Academy of Sciences.

Adapting NGS for coronavirus surveillance

In work that is proving prescient, researchers at the Wuhan Institute of Virology and Duke-National University of Singapore have adapted next-generation sequencing (NGS) for coronavirus surveillance. The emergence of 2019-nCoV as a pandemic threat is the third serious public health threat by coronaviruses, pointing to a need for surveillance. However, coronaviruses are a large and genetically very diverse family, and it is likely that many of its members remain undiscovered. In such a situation, neither targeted PCR nor NGS are good options for surveillance because PCR will miss genomic diversity, and NGS will miss low-abundance species – and be very costly. In their work, which was conducted prior to the emergence of 2019-nCoV, the team combined NGS on coronavirus-enriched samples based on eight strains of coronavirus. They demonstrated that “within these datasets, the ratios of viral reads to total number of reads increased by almost 100% for captured samples, in contrast to the ratios of less than 1% for most of the unbiased NGS. The high ratio of viral to total reads in conjunction with decreased data size reduces the sequencing cost and data analysis burden.” The team acknowledged that the method needs additional improvements, including better capture of diverse spike regions, but concluded that “this methodology could thus greatly facilitate large-scale surveillance studies.” Their work appeared in the Jan. 29, 2020, online issue of mSphere.

AD and HHV: Still a mystery

Researchers at the National Institute of Neurological Disorders and Stroke have tested the hypothesis that viral infections of the central nervous system, in particular herpesvirus, may play a role in the development of Alzheimer’s disease, and they have come up with an inconclusive result. Some previous studies suggested that viral infections may raise the risk of neurodegenerative disorders down the line, prompting the authors to test the postmortem brains of AD patients for more than 100 different viral infections. Neither DNA- nor RNA-based detection methods, however, showed a higher frequency of viral infections in individuals with AD. The authors said their findings “do not support an association between HHV-6 and AD but also do not rule it out. … If viruses (and HHV-6 in particular) do play a role in AD pathogenesis, then the agents may no longer be present in a form that can be PCR amplified or sufficiently expressed. Rather, these virus(es) may be associated with an earlier ‘triggering’ event or be present at copy numbers below the limit of laboratory detection.” They reported their findings in the Jan. 23, 2020, issue of Neuron.

Increasing accuracy of malaria diagnoses

Rapid diagnostic tests (RDTs) are the primary tool, along with microscopy, in managing malaria outbreaks. They are easy and quick to perform and enable diagnoses in remote regions where microscopy is limited. While the majority of RDTs detect Plasmodium falciparum histidine-rich protein 2 (hrp2) and hrp3, they do not detect parasites carrying hrp2/hrp3, leading to false negative results and delay in treatment for patients at risk of severe malaria complications. To address this concern, researchers at in Germany and Gabon developed a hydrolysis probe-based, quantitative, real-time PCR (4plex qPCR) to detect and differentiate P. falciparum infection and hrp2/hrp3 gene status and validate the outcome. The test proved to be more accurate in detecting deletions that conventional PCR, “with no nested amplification rounds and reduced risk of misclassifying a sample as a deletion when the reason was a parasite density below the detection limit.” In a cross-sectional accuracy test to in Gabon, the 4plex qPCR was 1,000 times more sensitive than either thick blood smear or RDT. “WHO classifies hrp2/hrp3 deletions as a biological threat to malaria control and elimination and requests accurate and reliable monitoring and mapping of deletions to circumvent … [high-risk] scenarios by timely adoption of malaria policies….We provide here a robust and accurate methodology that can be directly applied to ongoing surveys of P. falciparum infections and mapping of hrp2 and hrp3 single and double deletions that enables well-founded and timely policy adaptation when necessary in malaria endemic regions,” the authors wrote. The study was published online Nov. 21, 2019, in EBioMedicine.