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08/09/2022

Hot Topics of the Day are picked by experts to capture the latest information and publications on public health genomics and precision health for various diseases and health topics. Sources include published scientific literature, reviews, blogs and popular press articles.

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Covid-19: What we know about the BA.4 and BA.5 omicron variants
E Mahase, BMJ, August 9, 2022

BA.4 and BA.5 were first detected in South Africa in January and February 2022, respectively.1 They are offshoots of the omicron variant BA.2, though their additional mutations seem to have given them a transmission advantage. The World Health Organization has said that BA.5 now accounts for more than half of the world’s cases, while BA.4 accounts for just over one in 10.3. Why BA.5 has overtaken BA.4 is a mystery, because they’re so similar. Speaking at a Royal Society of Medicine event, Thomas Peacock, a virologist at Imperial College London, said, “They have identical spikes, more or less. So that means it has to be something outside the spike. And really our understanding of that from a virological perspective is very poor.”

Olfactory Dysfunction in Patients With Mild COVID-19 During Gamma, Delta, and Omicron Waves in Rio de Janeiro, Brazil
CC Cardoso et al, JAMA, August 9, 2022

This study found that individuals with mild COVID-19 infected during the Gamma and Omicron waves had lower odds of reporting olfactory dysfunction than individuals infected during the period of the original lineages. These results suggest that the type of SARS-CoV-2 variant might be a risk factor for olfactory dysfunction, along with host genetic susceptibility.

Finding Ways to Improve Patients’ Cancer Immunotherapy Response
HD Larkin, JAMA, August 9, 2022

An investigational tool using whole-exome sequencing (WES) more accurately identified genes and pathways that predict whether patients with cancer will respond to immune checkpoint blockade (ICB) than current tumor mutation burden (TMB) tests alone, a new research study reported. TMB is often used to determine ICB eligibility and is generally calculated from a few hundred genes. The researchers sought to improve its performance by broadening analysis to the nearly 20?000 genes consistently captured by WES.

cfDNA methylome profiling for detection and subtyping of small cell lung cancers.
Chemi Francesca et al. Nature cancer 2022 8

We describe a robust workflow for genome-wide DNA methylation profiling applied to both patient-derived models and to patients' circulating cell-free DNA (cfDNA). Tumor-specific methylation patterns were readily detected in cfDNA samples from patients with SCLC and were correlated with survival outcomes. cfDNA methylation also discriminated between the transcription factor SCLC subtypes, a precedent for a liquid biopsy cfDNA-methylation approach to molecularly subtype SCLC. Our data reveal the potential clinical utility of cfDNA methylation profiling as a universally applicable liquid biopsy approach for the sensitive detection, monitoring and molecular subtyping of patients with SCLC.

Circulating tumour DNA - looking beyond the blood.
Tivey Ann et al. Nature reviews. Clinical oncology 2022 8

To date, the majority of research in the area of liquid biopsies has focused on blood-based biomarkers, predominantly using plasma-derived circulating tumour DNA (ctDNA). However, ctDNA can also be obtained from various non-blood sources and these might offer unique advantages over plasma ctDNA. In this Review, we discuss advances in the analysis of ctDNA from non-blood sources, focusing on urine, cerebrospinal fluid, and pleural or peritoneal fluid, but also consider other sources of ctDNA.

TPMT and NUDT15 Genotyping Recommendations: A Joint Consensus Recommendation of the Association for Molecular Pathology, Clinical Pharmacogenetics Implementation Consortium, College of American Pathologists, Dutch Pharmacogenetics Working Group of the Royal Dutch Pharmacists Association, European Society for Pharmacogenomics and Personalized Therapy, and Pharmacogenomics Knowledgebase.
Pratt Victoria M et al. The Journal of molecular diagnostics : JMD 2022 8

This document series provides recommendations for a minimum panel of variant alleles ("Tier 1") and an extended panel of variant alleles ("Tier 2") that will aid clinical laboratories when designing assays for PGx testing. The AMP PGx Working Group considered functional impact of the variant alleles, allele frequencies in multiethnic populations, the availability of reference materials, as well as other technical considerations for PGx testing when developing these recommendations.

Predicting chronic morbidity in childhood cancer survivors.
Vrooman Lynda M et al. Nature medicine 2022 8

Approximately 85% of children diagnosed with cancer will be cured of their primary cancer, but epidemiologic and clinical studies have characterized a significant burden of morbidity, as well as excess early mortality, in survivors. Two recent studies show that incorporating genetic factors into risk models improves the prediction of severe obesity for survivors of childhood cancer, which could promote early interventions and better long-term care.

Pepinemab antibody blockade of SEMA4D in early Huntington's disease: a randomized, placebo-controlled, phase 2 trial.
Feigin Andrew et al. Nature medicine 2022 8

SIGNAL is a multicenter, randomized, double-blind, placebo-controlled phase?2 study established to evaluate pepinemab, a semaphorin?4D (SEMA4D)-blocking antibody, for treatment of Huntington’s disease (HD). The trial enrolled a total of 265?HD gene expansion carriers with either early manifest (EM, n?=?179) or late prodromal (LP, n?=?86) HD, randomized (1:1) to receive 18?monthly infusions of pepinemab (n?=?91 EM, 41?LP) or placebo (n?=?88 EM, 45?LP). Pepinemab was generally well tolerated, with a relatively low frequency of serious treatment-emergent adverse events of 5% with pepinemab compared to 9% with placebo,

Unified classification and risk-stratification in Acute Myeloid Leukemia.
Tazi Yanis et al. Nature communications 2022 8 (1) 4622

Clinical recommendations for Acute Myeloid Leukemia (AML) classification and risk-stratification remain heavily reliant on cytogenetic findings at diagnosis, which are present in <50% of patients. Using comprehensive molecular profiling data from 3,653 patients we characterize and validate 16 molecular classes describing 100% of AML patients. Each class represents diverse biological AML subgroups, and is associated with distinct clinical presentation, likelihood of response to induction chemotherapy, risk of relapse and death over time


Disclaimer: Articles listed in Hot Topics of the Day are selected by the CDC Office of Public Health Genomics to provide current awareness of the scientific literature and news. Inclusion in the update does not necessarily represent the views of the Centers for Disease Control and Prevention nor does it imply endorsement of the article's methods or findings. CDC and DHHS assume no responsibility for the factual accuracy of the items presented. The selection, omission, or content of items does not imply any endorsement or other position taken by CDC or DHHS. Opinion, findings and conclusions expressed by the original authors of items included in the Clips, or persons quoted therein, are strictly their own and are in no way meant to represent the opinion or views of CDC or DHHS. References to publications, news sources, and non-CDC Websites are provided solely for informational purposes and do not imply endorsement by CDC or DHHS.
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