Welfare Genome Project: A Participatory Korean Personal Genome Project With Free Health Check-Up and Genetic Report Followed by Counseling

Precision medicine in Asia enhanced by next-generation sequencing: Implications for Thailand through a scoping review and interview study

Next-generation sequencing (NGS) significantly enhances precision medicine (PM) by offering personalized approaches to diagnosis, treatment, and prevention of unmet medical needs. Little is known about the current situation of PM in Asia. Thus, we aimed to conduct an overview of the progress and gaps in PM in Asia and enrich it with in-depth insight into the possibilities of future PM in Thailand. This scoping review focused on Asian countries starting with non-cancer studies, including rare and undiagnosed diseases (RUDs), non-communicable diseases (NCDs), infectious diseases (IDs), and pharmacogenomics, with a focus on NGS. Subsequent in-depth interviews with experts in Thailand were performed, and a thematic analysis served as the main qualitative methodology. Out of 2898 searched articles, 387 studies were included after the review. Although most of the studies focused on cancer, 89 (23.0%) studies were related to RUDs (17.1%), NCDs (2.8%), IDs (1.8%), and pharmacogenomics (1.3%). Apart from medicine and related sciences, the studies were mostly composed of PM (61.8%), followed by genetics medicine and bioinformatics. Interestingly, 28% of articles were conducted exclusively within the fields of medicine and related sciences, emphasizing interdisciplinary integration. The experts emphasized the need for sustainability-driven political will, nurturing collaboration, reinforcing computational infrastructure, and expanding the bioinformatic workforce. In Asia, developments of NGS have made remarkable progress in PM. Thailand has extended PM beyond cancer and focused on clinical implementation. We summarized the PM challenges, including equity and efficiency targeting, guided research funding, sufficient sample size, integrated collaboration, computational infrastructure, and sufficient trained human resources.

Comparison of genetic variation between primary colorectal cancer and metastatic peritoneal cancer

BACKGROUND

Among cancer metastases by primary colorectal cancer (CRC), peritoneal metastasis is the second most common metastatic lesion after liver metastasis. In treating metastatic CRC, it is very important to differentiate targeted-therapy and chemotherapy according to the characteristics of each lesion because the genetic variation of the primary and metastatic lesions are different. However, there are few studies of genetic characteristics on peritoneal metastasis caused by primary CRC, so molecular-level studies are continuously required.

OBJECTIVE

We propose an appropriate peritoneal metastasis treatment policy by identifying the genetic characteristics between primary CRC and synchronous peritoneal metastatic lesions.

METHODS

Primary CRC and synchronous peritoneal metastasis samples were analyzed in pairs from six patients using Comprehensive Cancer Panel (409 cancer-related genes, Thermo Fisher Scientific, USA) and next-generation sequencing (NGS).

RESULTS

The mutations were commonly found on the KMT2C and THBS1 genes in both primary CRC and peritoneal metastasis. The PDE4DIP gene was mutated in all cases except for on a sample of peritoneal metastasis. As a result of analysis using the mutation database, we confirmed that the gene mutations of primary CRC and the peritoneal metastasis derived from it showed the same tendency, although we did not accompany the gene expression level or epigenetic study.

CONCLUSION

It is thought that the treatment policy through molecular genetic testing of primary CRC can also be applied to peritoneal metastasis treatment. Our study is expected to be the basis for further peritoneal metastasis research.

Identification and validation of six acute myocardial infarction-associated variants, including a novel prognostic marker for cardiac mortality

Background

Acute myocardial infarction (AMI) is one of the leading causes of death worldwide, and approximately half of AMI-related deaths occur before the affected individual reaches the hospital. The present study aimed to identify and validate genetic variants associated with AMI and their role as prognostic markers.

Materials and methods

We conducted a replication study of 29 previously identified novel loci containing 85 genetic variants associated with early-onset AMI using a new independent set of 2,920 Koreans [88 patients with early- and 1,085 patients with late-onset AMI, who underwent percutaneous coronary intervention (PCI), and 1,747 healthy controls].

Results

Of the 85 previously reported early-onset variants, six were confirmed in our genome-wide association study with a false discovery rate of less than 0.05. Notably, rs12639023, a cis-eQTL located in the intergenic region between LINC02005 and CNTN3, significantly increased longitudinal cardiac mortality and recurrent AMI. CNTN3 is known to play a role in altering vascular permeability. Another variant, rs78631167, located upstream of PLAUR and known to function in fibrinolysis, was moderately replicated in this study. By surveying the nearby genomic region around rs78631167, we identified a significant novel locus (rs8109584) located 13 bp downstream of rs78631167. The present study showed that six of the early-onset variants of AMI are applicable to both early- and late-onset cases.

Conclusion

Our results confirm markers that can potentially be utilized to predict, screen, prevent, and treat candidate patients with AMI and highlight the potential of rs12639023 as a prognostic marker for cardiac mortality in AMI.

Genome-wide analyses of early-onset acute myocardial infarction identify 29 novel loci by whole genome sequencing

Early-onset acute myocardial infarction (AMI) may have a higher genetic predisposition than late-onset AMI. The present study aimed to identify and characterize germline variants that affect early-onset AMI using whole-genome sequencing (WGS). We performed a genome-wide association study based on the WGS of 1239 Koreans, including 596 early-onset AMI patients and 643 healthy individuals. Patients with AMI who underwent percutaneous coronary intervention (PCI) caused by atherothrombotic occlusive lesions were included in the study. A total of 29 novel loci were found to be associated with early-onset AMI. These loci are involved in thrombosis, fibrinolysis, inflammation, and lipid metabolism. One of the associated single nucleotide variants (SNVs), rs1614576, located upstream of PRKCB, is known to be associated with thrombus formation. Additionally, the results revealed a novel locus, rs78631167, located upstream of PLAUR which plays a critical role in regulating plasminogen activation and is related to fibrinolysis. The association between early-onset AMI and rs9357455, which is located upstream of PHACTR1 and regulates inflammation in AMI, was found. Moreover, we identified a lipid metabolism related genetic risk locus, rs5072, in the APOA1-AS gene. This study provides new evidence supporting the genetic association between early-onset AMI and thrombosis and fibrinolysis, as well as inflammation and lipid metabolism, by analyzing the whole-genome of 596 patients with early-onset AMI who have been treated with PCI. Our findings highlight potential genetic markers for the prediction and management of AMI, as well as for understanding the etiology of AMI.

A Genomic Information Management System for Maintaining Healthy Genomic States and Application of Genomic Big Data in Clinical Research

Improvements in next-generation sequencing (NGS) technology and computer systems have enabled personalized therapies based on genomic information. Recently, health management strategies using genomics and big data have been developed for application in medicine and public health science. In this review, I first discuss the development of a genomic information management system (GIMS) to maintain a highly detailed health record and detect diseases by collecting the genomic information of one individual over time. Maintaining a health record and detecting abnormal genomic states are important; thus, the development of a GIMS is necessary. Based on the current research status, open public data, and databases, I discuss the possibility of a GIMS for clinical use. I also discuss how the analysis of genomic information as big data can be applied for clinical and research purposes. Tremendous volumes of genomic information are being generated, and the development of methods for the collection, cleansing, storing, indexing, and serving must progress under legal regulation. Genetic information is a type of personal information and is covered under privacy protection; here, I examine the regulations on the use of genetic information in different countries. This review provides useful insights for scientists and clinicians who wish to use genomic information for healthy aging and personalized medicine.

Identifying molecular targets for reverse aging using integrated network analysis of transcriptomic and epigenomic changes during aging

Aging is associated with widespread physiological changes, including skeletal muscle weakening, neuron system degeneration, hair loss, and skin wrinkling. Previous studies have identified numerous molecular biomarkers involved in these changes, but their regulatory mechanisms and functional repercussions remain elusive. In this study, we conducted next-generation sequencing of DNA methylation and RNA sequencing of blood samples from 51 healthy adults between 20 and 74 years of age and identified aging-related epigenetic and transcriptomic biomarkers. We also identified candidate molecular targets that can reversely regulate the transcriptomic biomarkers of aging by reconstructing a gene regulatory network model and performing signal flow analysis. For validation, we screened public experimental data including gene expression profiles in response to thousands of chemical perturbagens. Despite insufficient data on the binding targets of perturbagens and their modes of action, curcumin, which reversely regulated the biomarkers in the experimental dataset, was found to bind and inhibit JUN, which was identified as a candidate target via signal flow analysis. Collectively, our results demonstrate the utility of a network model for integrative analysis of omics data, which can help elucidate inter-omics regulatory mechanisms and develop therapeutic strategies against aging.