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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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147 hot topic(s) found with the query "Omics"

Challenges and best practices in omics benchmarking.
Thomas G Brooks et al. Nat Rev Genet 2024 1 (Posted: Jan 15, 2024 10AM)

From the abstract: "Benchmarking refers to the process of objectively comparing and evaluating the performance of different computational or analytical techniques when processing and analysing large-scale biological data sets, such as transcriptomics, proteomics and metabolomics. With thousands of omics benchmarking studies published over the past 25 years, the field has matured to the point where the foundations of benchmarking have been established and well described. "

What Will 2024 Mean for NGS and Genomics?
J Lemieux, GenNew, January 12, 2024 (Posted: Jan 14, 2024 10AM)

From the article: "Recent technological innovations in next-generation sequencing (NGS) have users spoiled for choice. At first, new options began trickling in. But then the floodgates opened in 2022. Folding into this market expansion is the growth in the demand for sequencing, not only from directed genomic sequencing, but also from the growth of other omics technologies such as single-cell genomics and spatial transcriptomics, and of clinical applications such as liquid biopsy—all of which rely on sequencing."

Computational immunogenomic approaches to predict response to cancer immunotherapies.
Venkateswar Addala et al. Nat Rev Clin Oncol 2023 11 (Posted: Nov 03, 2023 8AM)

From the abstract: " Cancer immunogenomics is an emerging field that bridges genomics and immunology. The establishment of large-scale genomic collaborative efforts along with the development of new single-cell transcriptomic techniques and multi-omics approaches have enabled characterization of the mutational and transcriptional profiles of many cancer types and helped to identify clinically actionable alterations as well as predictive and prognostic biomarkers. Researchers have developed computational approaches and machine learning algorithms to accurately obtain clinically useful information from genomic and transcriptomic sequencing data. "

Multi-Omics for Health and Disease (Multi-Omics)
NIH, September 2023 Brand (Posted: Sep 16, 2023 2PM)

From the website: "While single ‘omic analyses have produced valuable insights, recent studies have shown that integrative (or multi-omic) analysis approaches can improve the classification of disease into clinically relevant subgroups and potentially identify biomarkers of health or disease. Multi-omic analyses can also help define relationships among ‘omic data types to unravel biological networks regulating transitions from health to disease. This initiative is expected to produce consensus approaches, best practices, and standards that can be generalized across diseases and populations. "

From Mendel to multi-omics: shifting paradigms
TB Mersha, EJHG, July 20, 2023 (Posted: Jul 20, 2023 7AM)

Multi-omics analysis is an emerging approach that aims to better understand health and disease through the convergence of different omics studies (genomics, transcriptomics, proteomics, metabolomics, metagenomics, phenomics, exposomics). Although technical limitations related to the analysis of high-dimensional multi-omics datasets and use of fairly small samples have hindered our ability to conduct multi-omic research, emerging technology and computational tools have facilitated impactful multi-omic research.

Integrated multi-omics for rapid rare disease diagnosis on a national scale.
Sebastian Lunke et al. Nat Med 2023 6 (Posted: Jun 09, 2023 8AM)

Critically ill infants and children with rare diseases need equitable access to rapid and accurate diagnosis to direct clinical management. Over 2 years, the Acute Care Genomics program provided whole-genome sequencing to 290 families whose critically ill infants and children were admitted to hospitals throughout Australia with suspected genetic conditions. The average time to result was 2.9?d and diagnostic yield was 47%.

Precision Medicine in Oral Health and Diseases: A Systematic Review
G Malcangi et al, J Per Med, April 25, 2023 (Posted: Apr 25, 2023 7AM)

Precision medicine (PM) is personalized medicine that can develop targeted medical therapies for the individual patient, in which “omics” sciences lead to an integration of data that leads to highly predictive models of the functioning of the individual biological system. They enable rapid diagnosis, assessment of disease dynamics, identification of targeted treatment protocols, and reduction of costs and psychological stress. “Precision dentistry” (DP) is one promising application that need further investigation; the purpose of this paper is therefore to give physicians an overview of the knowledge they need to enhance treatment planning and patient response to therapy.

Predicting response to enzalutamide and abiraterone in metastatic prostate cancer using whole-omics machine learning.
Anouk C de Jong et al. Nature communications 2023 4 (1) 1968 (Posted: Apr 10, 2023 7AM)

Response to androgen receptor signaling inhibitors (ARSI) varies widely in metastatic castration resistant prostate cancer (mCRPC). To improve treatment guidance, biomarkers are needed. We use whole-genomics (WGS; n?=?155) with matching whole-transcriptomics (WTS; n?=?113) from biopsies of ARSI-treated mCRPC patients for unbiased discovery of biomarkers and development of machine learning-based prediction models. Tumor mutational burden (q?<?0.001), structural variants (q?<?0.05), tandem duplications (q?<?0.05) and deletions (q?<?0.05) are enriched in poor responders, coupled with distinct transcriptomic expression profiles.

Multiomic signatures of body mass index identify heterogeneous health phenotypes and responses to a lifestyle intervention.
Kengo Watanabe et al. Nature medicine 2023 3 (Posted: Mar 22, 2023 7AM)

We report an atlas of cross-sectional and longitudinal changes in 1,111 blood analytes associated with variation in body mass index (BMI), as well as multiomic associations with host polygenic risk scores and gut microbiome composition, from a cohort of 1,277 individuals enrolled in a wellness program (Arivale). Machine learning model predictions of BMI from blood multiomics captured heterogeneous phenotypic states of host metabolism and gut microbiome composition better than BMI, which was also validated in an external cohort (TwinsUK). Moreover, longitudinal analyses identified variable BMI trajectories for different omics measures in response to a healthy lifestyle intervention.

Cardiometabolic health, diet and the gut microbiome: a meta-omics perspective.
Mireia Valles-Colomer et al. Nature medicine 2023 3 (Posted: Mar 18, 2023 7PM)

High-throughput omics techniques applied on microbiome samples (meta-omics) hold the unprecedented potential to shed light on the intricate links between diet, the microbiome, the metabolome and cardiometabolic health, with a top-down approach. However, effective integration of complementary meta-omic techniques is an open challenge and their application on large cohorts is still limited. Here we review meta-omics techniques and discuss their potential in this context, highlighting recent large-scale efforts and the novel insights they provided. Finally, we look to the next decade of meta-omics research and discuss various translational and clinical pathways to improving cardiometabolic health.

Secrets of microbiota drug metabolism.
Andrew J Macpherson et al. Nature medicine 2023 2 (Posted: Feb 24, 2023 7AM)

High-resolution meta-omics have enabled the discovery of the microbial enzymes that inactivate an ulcerative colitis drug and predict subsequent treatment failure, an approach that could enable more personalized treatment of inflammatory bowel disease.

Gut microbial metabolism of 5-ASA diminishes its clinical efficacy in inflammatory bowel disease.
Raaj S Mehta et al. Nature medicine 2023 2 (Posted: Feb 24, 2023 7AM)

We developed a multi-omics workflow combining gut microbiome metagenomics, metatranscriptomics and metabolomics from the longitudinal IBDMDB cohort of 132 controls and patients with IBD. This associated 12 previously uncharacterized microbial acetyltransferases with 5-ASA inactivation, belonging to two protein superfamilies: thiolases and acyl-CoA N-acyltransferases. A cross-sectional analysis within the discovery cohort and subsequent prospective validation within the independent SPARC IBD cohort (n?=?208) found three of these microbial thiolases and one acyl-CoA N-acyltransferase to be epidemiologically associated with an increased risk of treatment failure among 5-ASA users.

Advancing CAR T cell therapy through the use of multidimensional omics data.
Jingwen Yang et al. Nature reviews. Clinical oncology 2023 1 (Posted: Feb 02, 2023 6AM)

In this Review, we summarize the multidimensional cellular and molecular profiling technologies that have been used to advance our mechanistic understanding of CAR T cell therapies. In addition, we discuss current applications and potential strategies leveraging multi-omics data to identify optimal target antigens and other molecular features that could be exploited to enhance the antitumour activity and minimize the toxicity of CAR T cell therapy.

Development and Trends in Artificial Intelligence in Critical Care Medicine: A Bibliometric Analysis of Related Research over the Period of 2010–2021
X Cui et al, J Per Med, December 27, 2022 (Posted: Dec 28, 2022 11AM)

Research related to artificial intelligence in CCM has been increasing over the years. The USA published the most articles and had the top 10 active affiliations. The top ten active journals are bioinformatics journals and are in JCR Q1. Prediction, diagnosis, and treatment strategy exploration of sepsis, pneumonia, and acute kidney injury were the most focused topics. Electronic health records (EHRs) were the most widely used data and the “-omics” data should be integrated further.

Multi-objective optimization identifies a specific and interpretable COVID-19 host response signature.
Cappuccio Antonio et al. Cell systems 2022 12 (12) 989-1001.e8 (Posted: Dec 26, 2022 0PM)

The identification of a COVID-19 host response signature in blood can increase the understanding of SARS-CoV-2 pathogenesis and improve diagnostic tools. Applying a multi-objective optimization framework to both massive public and new multi-omics data, we identified a COVID-19 signature regulated at both transcriptional and epigenetic levels. We validated the signature’s robustness in multiple independent COVID-19 cohorts. Using public data from 8,630 subjects and 53 conditions, we demonstrated no cross-reactivity with other viral and bacterial infections, COVID-19 comorbidities, or confounders.

The Use of Cell-free DNA in Clinical Practice: Work in Progress
M Clyne et al, CDC Blog Post, December 14, 2022 Brand (Posted: Dec 14, 2022 5PM)

Since its discovery in 1948, the utility of cfDNA has been studied extensively in screening, diagnosis, prognosis, therapy and monitoring disease progression. Although effort has focused on cancer, and mostly in NSCLC, other areas of research are ongoing, including autoimmune disease, metabolic disorders, Alzheimer’s disease, and other neurologic conditions, COVID-19, myocarditis and dilated cardiomyopathy, and refractory epilepsy. In addition to circulating cfDNA, potential clinical applications exist for other omics, including epigenetics and exosomal miRNAs, as well as use of cfDNA in other body fluids (e.g. urine).

Multi-omics signatures of the human early life exposome
L Maitre et al, Nature Comm, November 21, 2022 (Posted: Nov 21, 2022 8AM)

In the Human Early Life Exposome (HELIX) project, a multi-centre cohort of 1301 mother-child pairs, we associate individual exposomes consisting of >100 chemical, outdoor, social and lifestyle exposures assessed in pregnancy and childhood, with multi-omics profiles (methylome, transcriptome, proteins and metabolites) in childhood. We identify 1170 associations, 249 in pregnancy and 921 in childhood, which reveal potential biological responses and sources of exposure. Pregnancy exposures, including maternal smoking, cadmium and molybdenum, are predominantly associated with child DNA methylation changes.

Medicine and health of 21st Century: Not just a high biotech-driven solution.
Assidi Mourad et al. NPJ genomic medicine 2022 11 (1) 67 (Posted: Nov 16, 2022 8AM)

Although the potential of biotechnology is motivating, we should not lose sight of approaches that may not seem as glamorous but can have large impacts on the healthcare of many and across disparate population groups. A balanced approach of “omics and big data” solution in contemporary health systems along with a large scale, simpler, and suitable strategies should be defined with expectations properly managed.

Discovering a trans-omics biomarker signature that predisposes high risk diabetic patients to diabetic kidney disease
I W Wu et al, NPJ Digital Medicine, November 2, 2022 (Posted: Nov 03, 2022 8AM)

Diabetic kidney disease is the leading cause of end-stage kidney disease worldwide; however, the integration of high-dimensional trans-omics data to predict this diabetic complication is rare. We develop artificial intelligence (AI)-assisted models using machine learning algorithms to identify a biomarker signature that predisposes high risk patients with diabetes mellitus (DM) to diabetic kidney disease based on clinical information, untargeted metabolomics, targeted lipidomics and genome-wide single nucleotide polymorphism (SNP) datasets. This involves 618 individuals who are split into training and testing cohorts of 557 and 61 subjects, respectively.

Nanopore-based technologies beyond DNA sequencing
YL Ying et al, Nature Biotechnology, September 26, 2022 (Posted: Sep 27, 2022 7AM)

we present an overview of the broad applications of nanopores in molecular sensing and sequencing, chemical catalysis and biophysical characterization. We highlight the prospects of applying nanopores for single-protein analysis and sequencing, single-molecule covalent chemistry, clinical sensing applications for single-molecule liquid biopsy.

Longitudinal multi-omics analysis identifies early blood-based predictors of anti-TNF therapy response in inflammatory bowel disease
N Mishra et al, Genome Medicine, September 24, 2022 (Posted: Sep 26, 2022 6AM)

We performed a longitudinal, blood-based multi-omics study in two prospective IBD patient cohorts receiving first-time infliximab therapy (discovery: 14 patients, replication: 23 patients). Samples were collected at up to 7 time points (from baseline to 14 weeks after therapy induction). RNA-sequencing and genome-wide DNA methylation data were analyzed and correlated with clinical remission at week 14 as a primary endpoint.

Genetic discrimination still casts a large shadow in 2022
Y Joly et al, EJHG, September 26, 2022 (Posted: Sep 26, 2022 6AM)

Many countries have adopted laws to prevent genetic discrimination. One may wonder why in 2022, GD remains a problem in biomedical research and precision medicine. In fact, this issue remains so pervasive that one of the first questions asked by individuals that are considering undergoing a research, or clinical genetic (or other OMICS), test is very often ‘will this impact my insurability or that of my children?’

Integrating transcriptomics, metabolomics, and GWAS helps reveal molecular mechanisms for metabolite levels and disease risk.
Yin Xianyong et al. American journal of human genetics 2022 9 (Posted: Sep 08, 2022 10AM)

Transcriptomics data have been integrated with genome-wide association studies (GWASs) to help understand disease/trait molecular mechanisms. The utility of metabolomics, integrated with transcriptomics and disease GWASs, to understand molecular mechanisms for metabolite levels or diseases has not been thoroughly evaluated.

Big data in basic and translational cancer research.
Jiang Peng et al. Nature reviews. Cancer 2022 9 (Posted: Sep 07, 2022 8AM)

Fast data growth has given rise to an evolving concept of ‘big data’ in cancer, whose analysis demands large computational resources and can potentially bring novel insights into essential questions. Indeed, the combination of big data, bioinformatics and artificial intelligence has led to notable advances in our basic understanding of cancer biology and to translational advancements.

Social and scientific motivations to move beyond groups in allele frequencies: The TOPMed experience.
Nelson Sarah C et al. American journal of human genetics 2022 9 (9) 1582-1590 (Posted: Sep 04, 2022 8AM)

The NHLBI Trans-Omics for Precision Medicine (TOPMed) program considered the scientific and social implications of different approaches for adding stratified frequencies to the TOPMed BRAVO (Browse All Variants Online) variant server. We recommend a novel approach of presenting ancestry-specific allele frequencies using a statistical method based upon local genetic ancestry inference.

Multi-omics data integration and modeling unravels new mechanisms for pancreatic cancer and improves prognostic prediction
NA Fraunhoffer et al, NPJ Precision Oncology, August 17, 2022 (Posted: Aug 18, 2022 1PM)

Pancreatic ductal adenocarcinoma (PDAC), has recently been found to be a heterogeneous disease, although the extension of its diversity remains to be fully understood. Here, we harmonize transcriptomic profiles derived from both PDAC epithelial and microenvironment cells to develop a Master Regulators (MR)-Gradient model that allows important inferences on transcriptional networks, epigenomic states, and metabolomics pathways that underlies this disease heterogeneity.

Precision Medicine in Diabetes, Current Research and Future Perspectives
R Franceschi, J Per Medicine, July 28, 2022 (Posted: Jul 28, 2022 6AM)

Recently the American Diabetes Association (ADA) and the European Association for the Study of Diabetes (EASD) have jointly released an expert opinion-based consensus report on precision medicine. The report defines precision diabetes medicine as “an approach to optimize the diagnosis, prediction, prevention, or treatment of diabetes by integrating multidimensional data, accounting for individual differences”, and it is characterized by six categories; precision diagnosis, precision therapeutics, precision prevention, precision treatment, precision prognosis and precision monitoring. Precision medicine in diabetes utilizes the individual’s unique genetic makeup, environment or context data (that can be collected from clinical records, wearable technology, genomics and other ‘omics data) and allows one to appreciate individual characteristics, differences, circumstances and preferences

Multi-omics provide evidence for an anti-inflammatory immune signature and metabolic alterations in patients with Long COVID Syndrome; an exploratory study
JJ Kovarik et al, MEDRXIV, July 12, 2022 (Posted: Jul 13, 2022 7AM)

Measuring biological age using omics data.
Rutledge Jarod et al. Nature reviews. Genetics 2022 6 (Posted: Jun 20, 2022 10AM)

Spurred by recent advances in high-throughput omics technologies, a new generation of tools to measure biological ageing now enables the quantitative characterization of ageing at molecular resolution. Epigenomic, transcriptomic, proteomic and metabolomic data can be harnessed with machine learning to build ‘ageing clocks’ with demonstrated capacity to identify new biomarkers of biological ageing.

An integrated multiomic approach as an excellent tool for the diagnosis of metabolic diseases: our first 3720 patients
LS Almeida et al, EJHG, May 25, 2022 (Posted: May 25, 2022 7AM)

To present our experience using a multiomic approach, which integrates genetic and biochemical testing as a first-line diagnostic tool for patients with inherited metabolic disorders (IMDs). A cohort of 3720 patients from 62 countries was tested using a panel including 206 genes with single nucleotide and copy number variant (SNV/CNV) detection, followed by semi-automatic variant filtering and reflex biochemical testing (25 assays). In 1389 patients (37%), a genetic diagnosis was achieved.

An ethical plan for including forcibly displaced persons in omics and digital technology research
F Taki et al, Nature Medicine,May 5, 2022 (Posted: May 09, 2022 7AM)

The use of novel technologies in this population, in addition to routine clinical care, provides an opportunity to reduce health disparities for forcibly displaced individuals. New technologies in healthcare are rapidly expanding, from three-dimensional bioprinting of tissues and organs to onsite portable sequencing to detect disease. Two novel technologies that are especially relevant to displaced persons, which have revolutionized healthcare for the general population in high-income countries, are omics and digital healthcare technology. Each of these can benefit forcibly displaced populations if applied appropriately and responsibly.

Multi-omics identify LRRC15 as a COVID-19 severity predictor and persistent pro-thrombotic signals in convalescence
JS Gisby et al, MEDRXIV, May 1, 2022 (Posted: May 02, 2022 9AM)

Cross-talk between red blood cells and plasma influences blood flow and omics phenotypes in severe COVID-19
SM Recktenwald et al, MEDRXIV, April 4, 2022 (Posted: Apr 05, 2022 7AM)

Cross-talk between red blood cells and plasma influences blood flow and omics phenotypes in severe COVID-19
SM. Recktenwald et al, MEDRXIV, March 31, 2022 (Posted: Apr 01, 2022 7AM)

Genetic modifiers of Huntington disease differentially influence motor and cognitive domains
JM Lee et al, AJHG, March 23, 2022 (Posted: Mar 24, 2022 9AM)

e have performed algorithmic prediction by using common motor and cognitive measures to predict age at other disease landmarks as additional phenotypes for GWASs. Combined with imputation with the Trans-Omics for Precision Medicine reference panel, predictions using integrated measures provided objective landmark phenotypes with greater power to detect most modifier loci. Importantly, substantial differences in the relative modifier signal across loci, highlighted by comparing common modifiers at MSH3 and FAN1, revealed that individual modifier effects can act preferentially in the motor or cognitive domains.

Multi-omics in COVID-19: Seeing the unseen but overlooked in the clinic
T Lu et al, Cell Reports Medicine, March 15, 2022 (Posted: Mar 18, 2022 0PM)

COVID-19 is an ongoing pandemic of global concern and is unlikely to disappear. This commentary discusses how multi-omics technologies have helped uncover the molecular processes and dynamics underlying COVID-19 initiation, progression, and transmission, and how lack of standardization has limited their application in clinical settings.

Before the heart attack
EE Blaak et al, Nature Medicine, February 17, 2022 (Posted: Feb 19, 2022 7AM)

Integrated analysis of microbiome and metabolome profiles in unique cohorts reveals early and late markers of the transition towards ischemic heart disease. Ischemic heart disease (IHD), also known as coronary artery disease, can culminate in heart attack and is a major cause of morbidity and mortality worldwide. To improve clinical outcomes, more insight is required into the complex etiology of IHD. Two large-scale studies integrate extensive gut microbiome and serum metabolome profiles in the progression toward IHD, taking into account key confounders such as metabolic status and medication — and thereby providing insight into the etiology of IHD.

Immunopathological signatures in multisystem inflammatory syndrome in children and pediatric COVID-19
K Sacco et al, Nature Medicine, February 17, 2022 (Posted: Feb 17, 2022 8AM)

In this longitudinal multi-institutional study, we applied multi-omics (analysis of soluble biomarkers, proteomics, single-cell gene expression and immune repertoire analysis) to profile children with COVID-19 (n?=?110) and MIS-C (n?=?76), along with pediatric healthy controls (pHCs; n?=?76). pCOVID-19 was characterized by robust type I interferon (IFN) responses, whereas prominent type II IFN-dependent and NF-?B-dependent signatures, matrisome activation and increased levels of circulating spike protein were detected in MIS-C, with no correlation with SARS-CoV-2 PCR status around the time of admission.

Multi-omic machine learning predictor of breast cancer therapy response
SJ Sammut et al, Nature, December 7, 2021 (Posted: Dec 08, 2021 8AM)

We collected clinical, digital pathology, genomic and transcriptomic profiles of pre-treatment biopsies of breast tumors from 168 patients treated with chemotherapy +/- HER2-targeted therapy prior to surgery. Pathology endpoints (complete response or residual disease) at surgery3 were then correlated with multi-omic features in these diagnostic biopsies. Here we show that response to treatment is modulated by the pre-treated tumor ecosystem, and its multi-omics landscape can be integrated in predictive models using machine learning.

Pancreatic cancer evolution and heterogeneity: integrating omics and clinical data
AA Connor et al, Nat Rev Cancer, November 17, 2021 (Posted: Nov 17, 2021 10AM)

Decades of research have improved our understanding of pancreatic cancer, including characterizing germline predisposition, the cell of origin, precursor lesions, the sequence of genetic alterations, including simple and structural alterations, transcriptional changes and subtypes, tumor heterogeneity, metastatic progression and the tumor microenvironment. These fundamental advances inform contemporary translational efforts in primary prevention, screening and early detection, multidisciplinary management and survivorship, as prospective clinical trials begin to adopt molecular-based selection criteria to guide targeted therapies.

Deep learning in cancer diagnosis, prognosis and treatment selection.
Tran Khoa A et al. Genome medicine 2021 9 (1) 152 (Posted: Sep 29, 2021 6AM)

In this review, we provide an overview of emerging deep learning techniques and how they are being applied to oncology. We focus on the deep learning applications for omics data types, including genomic, methylation and transcriptomic data, as well as histopathology-based genomic inference, and provide perspectives on how the different data types can be integrated to develop decision support tools.

Multi-omics approach identifies novel age-, time- and treatment-related immunopathological signatures in MIS-C and pediatric COVID-19
K Sacco et al, MEDRXIV, September 27, 2021 (Posted: Sep 28, 2021 6AM)

The genetics of obesity: from discovery to biology
RJF Loos et al, Nat Rev Genetics, September 23, 2021 (Posted: Sep 24, 2021 6AM)

Genome-wide association studies (GWAS) with increasing sample sizes and advances in sequencing technology are the main drivers behind a recent flurry of new discoveries. However, it is the post-GWAS, cross-disciplinary collaborations, which combine new omics technologies and analytical approaches, that have started to facilitate translation of genetic loci into meaningful biology and new avenues for treatment.

Solve-RD: systematic pan-European data sharing and collaborative analysis to solve rare diseases
B Zurek et al, EJHG, June 1, 2021 (Posted: Jun 01, 2021 10AM)

Two major approaches are being pursued (i) massive data re-analysis of >19,000 unsolved rare disease patients and (ii) novel combined -omics approaches. The minimum requirement to be eligible for the analysis activities is an inconclusive exome that can be shared with controlled access. The first preliminary data re-analysis has already diagnosed 255 cases form 8393 exomes/genome datasets.

Solving unsolved rare neurological diseases—a Solve-RD viewpoint
R Schule et al, EJHG, May 10, 2021 (Posted: May 11, 2021 8AM)

To increase the diagnostic yield in rare neurological diseases - one of the four focus disease groups in Solve-RD - we follow two major approaches, that we will here present and exemplify: (i) systematic state-of the art re-analysis of large cohorts of unsolved whole-exome/genome sequencing (WES/WGS) RND datasets; and (ii) novel-omics approaches.

Single-cell multi-omics analysis of the immune response in COVID-19
E Stephenson et al, Nature Medicine, April 20, 2021 (Posted: Apr 21, 2021 7AM)

We identified expansion of nonclassical monocytes expressing complement transcripts (CD16+C1QA/B/C+) that sequester platelets and were predicted to replenish the alveolar macrophage pool in COVID-19. Early, uncommitted CD34+ hematopoietic stem/progenitor cells were primed toward megakaryopoiesis, accompanied by expanded megakaryocyte-committed progenitors and increased platelet activation. Clonally expanded CD8+ T cells and an increased ratio of CD8+ effector T cells to effector memory T cells characterized severe disease, while circulating follicular helper T cells accompanied mild disease.

Multi-omics analyses reveal relationships among dairy consumption, gut microbiota and cardiometabolic health
M Shuai et al, Ebiomedicine, March 2021, (Posted: Mar 21, 2021 7AM)

Dairy consumption is associated with the gut microbial composition and a higher a-diversity, which provides new insights into the understanding of dairy-gut microbiota interactions and their relationship with cardiometabolic health.

The cellular immune response to COVID-19 deciphered by single cell multi-omics across three UK centres
E Stephenson et al, MEDRXIV, January 15, 2021 (Posted: Jan 16, 2021 3PM)

A novel multi-omics-based identification of symptoms, comorbid conditions, and possible long-term complications in COVID-19
D Barh et al, MEDRXIV, December 9, 2020 (Posted: Dec 09, 2020 10AM)

Functional genomics
PHG Foundation, November 2020 (Posted: Nov 27, 2020 9AM)

Functional genomics is a field of molecular biology where researchers attempt to understand the complex relationship between genotype and phenotype. While genetics and genomics cover the study of genes and all of an organism’s genetic material, respectively, functional genomics aims to answer biological questions about how genes are activated and operate in a dynamic, context dependent, and synergistic fashion, using a range of genomics and associated ‘omics datasets.

One in Eight Cancer Patients Harbors Inherited Mutation that Increases Risk of Disease Development
Clinical Omics, November 3, 2020 (Posted: Nov 04, 2020 8AM)

In a finding that bolsters the field of personalized medicine, a new large-scale study from the Mayo Clinic reports that one in eight cancer patients they followed had an inherited mutation that increases their risk of developing a malignancy. Further, the study showed that more than half of all patients with such mutations were being missed.

Translating the microbiome in health and disease
Genome Medicine special issue, October 2020 (Posted: Oct 23, 2020 7AM)

This issue captures insights into the human microbiome in health and disease including standards for microbiome analyses in basic and clinical research, microbiome analysis technologies, metagenomics and integrative multi-omics, antibiotics and the microbiome, microbial biochemistry and diet, translational interventions, and host-microbiome interactions.

Genetic markers and phosphoprotein forms of beta-catenin pβ-Cat552 and pβ-Cat675 are prognostic biomarkers of cervical cancer
SM Scholl et al, EBiomedicine, October 21, 2020 (Posted: Oct 22, 2020 9AM)

Survival analysis on 89 patients with all omics data available, suggested loss-of-function (LOF) or activating molecular alterations in nine genes to be candidate biomarkers for worse prognosis in patients treated by chemo-radiation while LOF of ATRX, MED13 as well as CASP8 were associated with better prognosis.

Exploring the coronavirus pandemic with the WashU Virus Genome Browser
Nature Genetics, September 9, 2020 (Posted: Sep 11, 2020 8AM)

This is a web-based portal for efficient visualization of viral ‘omics’ data in the context of a variety of annotation tracks and host infection responses. The browser features both a phylogenetic-tree-based view and a genomic-coordinate, track-based view in which users can analyze the sequence features of viral genomes, sequence diversity among viral strains, genomic sites of diagnostic tests, predicted immunogenic epitopes and a continuously updated repository of publicly available genomic datasets.

Integrating genetic and non-genetic determinants of cancer evolution by single-cell multi-omics
AS Nam et al, Nat Rev Genetics, August 17, 2020 (Posted: Aug 17, 2020 8AM)

n this Review, we discuss emerging analytic and experimental technologies for single-cell multi-omics that enable the capture and integration of multiple data modalities to inform the study of cancer evolution. These data show that cancer results from a complex interplay between genetic and non-genetic determinants of somatic evolution.

The Trans-omics Landscape of COVID-19
P Wu et al, MEDRXIV, July 22, 2020 (Posted: Jul 23, 2020 9AM)

The use of machine learning in rare diseases: a scoping review
J Schaefer et al, Orphanet J Rare Dis, June 9, 2020 (Posted: Jun 11, 2020 8AM)

Only a small proportion of studies evaluated their algorithms. As input data, images (32.2%), demographic data (27.0%) and “omics” data (26.5%) were used most frequently. Most studies used machine learning for diagnosis (40.8%) or prognosis (38.4%) whereas studies aiming to improve treatment were relatively scarce (4.7%). Patient numbers in the studies were small.

Multi-omic strategies for transcriptome-wide prediction and association studies
BIORXIV, April 18, 2020 (Posted: Apr 18, 2020 8AM)

Machine Learning, COVID-19 (2019-nCoV), and multi-OMICS.
Tárnok Attila et al. Cytometry. Part A : the journal of the International Society for Analytical Cytology 2020 97(3) 215-216 (Posted: Mar 25, 2020 9AM)

Advances in omics-based methods to identify novel targets for malaria and other parasitic protozoan infections
AN Cowell et al, Genome Medicine, October 22, 2019 (Posted: Oct 23, 2019 8AM)

Here, we review recent studies that have used omics-based methods to identify novel targets for interventions against protozoan parasites, focusing on malaria, and we highlight the advantages and limitations of the approaches used. These approaches have also been extended to other protozoan pathogens.

NIH’s All of Us Partners with HudsonAlpha on Long-Read Sequencing Project
Clinical Omics, October 18, 2019 (Posted: Oct 21, 2019 10AM)

The NIH’s All of Us Research Program will assess the use of DNA sequencing technologies for diagnosis and treatment of common and rare diseases. The project will use long-read whole genome sequencing technologies to generate genetic data on about 6,000 samples from participants of different backgrounds.

Heart Failure in the Era of Precision Medicine: A Scientific Statement From the American Heart Association.
Cresci Sharon et al. Circulation. Genomic and precision medicine 2019 Sep HCG0000000000000058 (Posted: Sep 13, 2019 10AM)

The goals of this scientific statement are to provide a comprehensive overview of the current state of these omics as they relate to the development and progression of heart failure and to consider the current and potential future applications of these data for precision medicine with respect to prevention, diagnosis, and therapy.

The Evolving Field Of Genetic Epidemiology: From Familial Aggregation To Genomic Sequencing.
Duggal Priya et al. American journal of epidemiology 2019 Sep (Posted: Sep 12, 2019 7AM)

In the last two decades, the available tools for genetic epidemiology have expanded from a genetic focus (one gene at a time) to a genomic focus (the entire genome), and now further expanding to integrate information from other “-omics” (e.g. epigenomics, transcriptomics as measured by RNA expression) both at the individual level and at the population level.

Machine Learning Classifiers for Endometriosis Using Transcriptomics and Methylomics Data
S Akter et al, Front Genetics, September 2019 (Posted: Sep 06, 2019 7AM)

Leveraging Omics Profiling to Advance the Treatment of Pediatric Obesity.
Koch Sarah et al. JAMA pediatrics 2019 Aug (Posted: Aug 27, 2019 7AM)

UnitedHealthcare To Cover Genetic Testing for Precision Medicine in Depression, Anxiety
Clinical Omics, August 2, 2019 (Posted: Aug 05, 2019 8AM)

Leveraging -omics for asthma endotyping
SR Tyler et al, JACI, July 2019 (Posted: Jul 02, 2019 0PM)

Asthma is a highly heterogeneous disease, The eliciting factors, natural history, underlying molecular biology, and clinical management of asthma vary highly among affected subjects. Because of this variation, many efforts have gone into subtyping asthma. Endotypes are subtypes of disease based on distinct pathophysiologic mechanisms. We discuss the application of -omics approaches, including transcriptomics, epigenomics, microbiomics, metabolomics, and proteomics, to asthma endotyping. -Omics approaches have provided supporting evidence for many existing endotyping paradigms and also suggested novel ways to conceptualize asthma endotypes.

Meta-omics analysis of elite athletes identifies a performance-enhancing microbe that functions via lactate metabolism
J Scheiman et al, Nature Medicine, June 24, 2019 (Posted: Jun 24, 2019 1PM)

The metabolic repertoire of the gut microbiome is vast, but the health implications of these bacterial pathways are poorly understood. A closer look at the gut microbiome of elite marathon runners unveils a microbe-encoded enzymatic process that contributes to enhanced athletic performance

"Omics" Education in Dietetic Curricula: A Comparison between Two Institutions in the USA and Mexico.
VanBuren Christine et al. Lifestyle genomics 2019 May 1-11 (Posted: May 15, 2019 8AM)

What did we learn from multiple omics studies in asthma?
Ivanova Olga et al. Allergy 2019 Apr (Posted: May 06, 2019 2PM)

Gene Therapy Leaders Push for Germline Editing Moratorium
Clinical Omics, April 24, 2019 (Posted: Apr 29, 2019 11AM)

Systematic benchmarking of omics computational tools.
Mangul Serghei et al. Nature communications 2019 Mar (1) 1393 (Posted: Apr 01, 2019 9AM)

Challenges in the Integration of Omics and Non-Omics Data.
López de Maturana Evangelina et al. Genes 2019 Mar 10(3) (Posted: Mar 27, 2019 8AM)

Dynamic molecular changes during the first week of human life follow a robust developmental trajectory
AH Lee et al, Nature Communications, March 2019 (Posted: Mar 20, 2019 8AM)

Rise of Deep Learning for Genomic, Proteomic, and Metabolomic Data Integration in Precision Medicine.
Grapov Dmitry et al. Omics : a journal of integrative biology 2018 Aug (Posted: Aug 22, 2018 11AM)

Exposure to tobacco smoke and low birth weight: from epidemiology to metabolomics.
Dessì Angelica et al. Expert review of proteomics 2018 Jul (Posted: Jul 30, 2018 8AM)

Integrating -Omics Approaches into Human Population-Based Studies of Prenatal and Early-Life Exposures.
Everson Todd M et al. Current environmental health reports 2018 Jul (Posted: Jul 30, 2018 8AM)

Next-generation sequencing and prenatal 'omics: advanced diagnostics and new insights into human development.
Vora Neeta L et al. Genetics in medicine : official journal of the American College of Medical Genetics 2018 Jul (Posted: Jul 23, 2018 11AM)

Multi-omics monitoring of drug response in rheumatoid arthritis in pursuit of molecular remission.
Tasaki Shinya et al. Nature communications 2018 Jul (1) 2755 (Posted: Jul 19, 2018 9AM)

Precision Medicine in Targeted Therapies for Severe Asthma: Is There Any Place for "Omics" Technology?
Galeone Carla et al. BioMed research international 2018 20184617565 (Posted: Jul 18, 2018 9AM)

Precision Medicine Goes Global: How to Get It Right? Four Ways to Mobilize Scientific Knowledge.
Özdemir Vural et al. Omics : a journal of integrative biology 2018 Jul (Posted: Jul 18, 2018 9AM)

Translational -omics: Future potential and current challenges in precision medicine.
Wafi Arsalan et al. Methods (San Diego, Calif.) 2018 May (Posted: May 29, 2018 2PM)

Genomics and Epigenomics of Congenital Heart Defects: Expert Review and Lessons Learned in Africa.
Thomford Nicholas Ekow et al. Omics : a journal of integrative biology 2018 May 22(5) 301-321 (Posted: May 17, 2018 1PM)

Omics of Blood Pressure and Hypertension
DK Arnett et al, Circulation Res, May 2018 (Posted: May 12, 2018 10AM)

Building Global Genomics Initiatives and Enabling Data Sharing: Insights from Multiple Case Studies.
Fusi Federica et al. Omics : a journal of integrative biology 2018 Mar (Posted: Apr 04, 2018 11AM)

Beyond fitness tracking: The use of consumer-grade wearable data from normal volunteers in cardiovascular and lipidomics research.
Lim Weng Khong et al. PLoS biology 2018 Feb (2) e2004285 (Posted: Mar 03, 2018 9AM)

Food allergy and omics.
Dhondalay Gopal Krishna et al. The Journal of allergy and clinical immunology 2018 Jan (1) 20-29 (Posted: Feb 27, 2018 9AM)

The use of omics profiling to improve outcomes of bone regeneration and osseointegration. How far are we from personalized medicine in dentistry?
Calciolari E et al. Journal of proteomics 2018 Feb (Posted: Feb 27, 2018 9AM)

Academic medical centers as innovation ecosystems to address population -omics challenges in precision medicine.
Silva Patrick J et al. Journal of translational medicine 2018 Feb (1) 28 (Posted: Feb 27, 2018 9AM)

Integrative omics for health and disease.
Karczewski Konrad J et al. Nature reviews. Genetics 2018 Feb (Posted: Feb 27, 2018 9AM)

Personal Genome Project Canada Makes Case for WGS in Healthcare
Clinical Omics, Feb 5, 2018 (Posted: Feb 06, 2018 10AM)

From pharmacogenomics to pharmaco-omics – individualized care for every patient
S Rosen, Mayo Clinic, Individualized Medicine Blog, 2017 (Posted: Feb 02, 2018 11AM)

Precision Health: Use of Omics to Optimize Self-Management of Chronic Pain in Aging.
Dorsey Susan G et al. Research in gerontological nursing 2018 Jan (1) 7-13 (Posted: Feb 02, 2018 10AM)

Integrative Personal Omics Profiles during Periods of Weight Gain and Loss.
Piening Brian D et al. Cell systems 2018 Jan (Posted: Jan 26, 2018 9AM)

Application of "Omics" and Systems Biology to Sarcoidosis Research.
Crouser Elliott D et al. Annals of the American Thoracic Society 2017 Dec (Supplement_6) S445-S451 (Posted: Jan 03, 2018 11AM)

LinkedOmics: analyzing multi-omics data within and across 32 cancer types.
Vasaikar Suhas V et al. Nucleic acids research 2017 Nov (Posted: Nov 25, 2017 11AM)

Improving -Omics-Based Research and Precision Health in Minority Populations: Recommendations for Nurse Scientists.
Taylor Jacquelyn Y et al. Journal of nursing scholarship : an official publication of Sigma Theta Tau International Honor Society of Nursing 2017 Nov (Posted: Nov 21, 2017 9AM)

Advancing stroke genomic research in the age of Trans-Omics big data science: Emerging priorities and opportunities.
Owolabi Mayowa et al. Journal of the neurological sciences 2017 Nov 18-28 (Posted: Nov 15, 2017 9AM)

Using omics approaches to understand pulmonary diseases.
Kan Mengyuan et al. Respiratory research 2017 Aug (1) 149 (Posted: Oct 25, 2017 3PM)

New Data on Microbiome Triples Number of Identified Bacterial Genes
Clinical Omics, Oct 3, 2017 (Posted: Oct 04, 2017 8AM)


Disclaimer: Articles listed in Hot Topics of the Day are selected by Public Health Genomics Branch 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.