Population-scale genomics-Enabling precision public health

Construction of a trio-based structural variation panel utilizing activated T lymphocytes and long-read sequencing technology

Long-read sequencing technology enable better characterization of structural variants (SVs). To adapt the technology to population-scale analyses, one critical issue is to obtain sufficient amount of high-molecular-weight genomic DNA. Here, we propose utilizing activated T lymphocytes, which can be established efficiently in a biobank to stably supply high-grade genomic DNA sufficiently. We conducted nanopore sequencing of 333 individuals constituting 111 trios with high-coverage long-read sequencing data (depth 22.2x, N50 of 25.8 kb) and identified 74,201 SVs. Our trio-based analysis revealed that more than 95% of the SVs were concordant with Mendelian inheritance. We also identified SVs associated with clinical phenotypes, all of which appear to be stably transmitted from parents to offspring. Our data provide a catalog of SVs in the general Japanese population, and the applied approach using the activated T-lymphocyte resource will contribute to biobank-based human genetic studies focusing on SVs at the population scale.

Long-read sequencing on activated T-cells from a sample of 333 Japanese individuals (representing 111 parent-offspring trios) provides a useful reference dataset of structural variation in the Japanese population.

Exploring the Kinh Vietnamese genomic database for the polymorphisms of the P450 genes toward precision public health

BACKGROUND

Human cytochrome P450 (CYPs) genes are essential in metabolizing drugs. Due to their high polymorphism, population-specific studies are of great interest.

AIM

This research examined the six CYP genes, including CYP2B6, CYP2C9, CYP2C19, CYP2D6, CYP3A5, and CYP4F2 in the Kinh Vietnamese (KHV) for population-scale precision medicine.

SUBJECTS AND METHODS

We processed data from a genomics database of 206 healthy and unrelated KHV individuals to calculate CYP allele frequencies. First, we compared the CYP genes of the KHV to six other populations retrieved from the 1000 Genomes Project. Second, we searched the PharmGBK database for drug-CYP interaction data to compile a drug dosage recommendation for KHV.

RESULTS

We observed diverging trends in the genetic variations of CYP2B6, CYP2D6, and CYP3A5 in KHV. In terms of the phenotypic drug responses in KHV, CYP2C19 exhibited all of the metabolic phenotypes at a non-trivial frequency. CYP3A5 metabolized drugs at a lower rate than the other five CYPs.

CONCLUSION

This is the first large-scale study to investigate multiple CYP genes in the KHV for precision medicine from a public health perspective. Differences found in the distributions of metabolizers for the KHV suggest careful prescriptions for CYP2C19 and CYP3A5-metabolized drugs.

Genetic Variation of G6PD and CYP2D6: Clinical Implications on the Use of Primaquine for Elimination of Plasmodium vivax

Primaquine, an 8-aminoquinoline, is the only medication approved by the World Health Organization to treat the hypnozoite stage of Plasmodium vivax and P. ovale malaria. Relapse, triggered by activation of dormant hypnozoites in the liver, can occur weeks to years after primary infection, and provides the predominant source of transmission in endemic settings. Hence, primaquine is essential for individual treatment and P. vivax elimination efforts. However, primaquine use is limited by the risk of life-threatening acute hemolytic anemia in glucose-6-phosphate dehydrogenase (G6PD) deficient individuals. More recently, studies have demonstrated decreased efficacy of primaquine due to cytochrome P450 2D6 (CYP2D6) polymorphisms conferring an impaired metabolizer phenotype. Failure of standard primaquine therapy has occurred in individuals with decreased or absent CYP2D6 activity. Both G6PD and CYP2D6 are highly polymorphic genes, with considerable geographic and interethnic variability, adding complexity to primaquine use. Innovative strategies are required to overcome the dual challenge of G6PD deficiency and impaired primaquine metabolism. Further understanding of the pharmacogenetics of primaquine is key to utilizing its full potential. Accurate CYP2D6 genotype-phenotype translation may optimize primaquine dosing strategies for impaired metabolizers and expand its use in a safe, efficacious manner. At an individual level the current challenges with G6PD diagnostics and CYP2D6 testing limit clinical implementation of pharmacogenetics. However, further characterisation of the overlap and spectrum of G6PD and CYP2D6 activity may optimize primaquine use at a population level and facilitate region-specific dosing strategies for mass drug administration. This precision public health approach merits further investigation for P. vivax elimination.

Genetic diversity of 'Very Important Pharmacogenes' in two South-Asian populations

Objectives

Reliable identification of population-specific variants is important for building the single nucleotide polymorphism (SNP) profile. In this study, genomic variation using allele frequency differences of pharmacologically important genes for Gujarati Indians in Houston (GIH) and Indian Telugu in the U.K. (ITU) from the 1000 Genomes Project vis-à-vis global population data was studied to understand its role in drug response.

Methods

Joint genotyping approach was used to derive variants of GIH and ITU independently. SNPs of both these populations with significant allele frequency variation (minor allele frequency ≥ 0.05) with super-populations from the 1000 Genomes Project and gnomAD based on Chi-square distribution with p-value of ≤ 0.05 and Bonferroni’s multiple adjustment tests were identified. Population stratification and fixation index analysis was carried out to understand genetic differentiation. Functional annotation of variants was carried out using SnpEff, VEP and CADD score.

Results

Population stratification of VIP genes revealed four clusters viz., single cluster of GIH and ITU, one cluster each of East Asian, European, African populations and Admixed American was found to be admixed. A total of 13 SNPs belonging to ten pharmacogenes were identified to have significant allele frequency variation in both GIH and ITU populations as compared to one or more super-populations. These SNPs belong to VKORC1 (rs17708472, rs2359612, rs8050894) involved in Vitamin K cycle, cytochrome P450 isoforms CYP2C9 (rs1057910), CYP2B6 (rs3211371), CYP2A2 (rs4646425) and CYP2A4 (rs4646440); ATP-binding cassette (ABC) transporter ABCB1 (rs12720067), DPYD1 (rs12119882, rs56160474) involved in pyrimidine metabolism, methyltransferase COMT (rs9332377) and transcriptional factor NR1I2 (rs6785049). SNPs rs1544410 (VDR), rs2725264 (ABCG2), rs5215 and rs5219 (KCNJ11) share high fixation index (≥ 0.5) with either EAS/AFR populations. Missense variants rs1057910 (CYP2C9), rs1801028 (DRD2) and rs1138272 (GSTP1), rs116855232 (NUDT15); intronic variants rs1131341 (NQO1) and rs115349832 (DPYD) are identified to be ‘deleterious’.

Conclusions

Analysis of SNPs pertaining to pharmacogenes in GIH and ITU populations using population structure, fixation index and allele frequency variation provides a premise for understanding the role of genetic diversity in drug response in Asian Indians.

Pharmacogenomic landscape of COVID-19 therapies from Indian population genomes

Aim: Numerous drugs are being widely prescribed for COVID-19 treatment without any direct evidence for the drug safety/efficacy in patients across diverse ethnic populations. Materials & methods: We analyzed whole genomes of 1029 Indian individuals (IndiGen) to understand the extent of drug–gene (pharmacogenetic), drug–drug and drug–drug–gene interactions associated with COVID-19 therapy in the Indian population. Results: We identified 30 clinically significant pharmacogenetic variants and 73 predicted deleterious pharmacogenetic variants. COVID-19-associated pharmacogenes were substantially overlapped with those of metabolic disorder therapeutics. CYP3A4, ABCB1 and ALB are the most shared pharmacogenes. Fifteen COVID-19 therapeutics were predicted as likely drug–drug interaction candidates when used with four CYP inhibitor drugs. Conclusion: Our findings provide actionable insights for future validation studies and improved clinical decisions for COVID-19 therapy in Indians.

Precision, Equity, and Public Health and Epidemiology Informatics - A Scoping Review

OBJECTIVES

This scoping review synthesizes the recent literature on precision public health and the influence of predictive models on health equity with the intent to highlight central concepts for each topic and identify research opportunities for the biomedical informatics community.

METHODS

Searches were conducted using PubMed for publications between 2017-01-01 and 2019-12-31.

RESULTS

Precision public health is defined as the use of data and evidence to tailor interventions to the characteristics of a single population. It differs from precision medicine in terms of its focus on populations and the limited role of human genomics. High-resolution spatial analysis in a global health context and application of genomics to infectious organisms are areas of progress. Opportunities for informatics research include (i) the development of frameworks for measuring non-clinical concepts, such as social position, (ii) the development of methods for learning from similar populations, and (iii) the evaluation of precision public health implementations. Just as the effects of interventions can differ across populations, predictive models can perform systematically differently across subpopulations due to information bias, sampling bias, random error, and the choice of the output. Algorithm developers, professional societies, and governments can take steps to prevent and mitigate these biases. However, even if the steps to avoid bias are clear in theory, they can be very challenging to accomplish in practice.

CONCLUSIONS

Both precision public health and predictive modelling require careful consideration in how subpopulations are defined and access to data on subpopulations can be challenging. While the theory for both topics has advanced considerably, there is much work to be done in understanding how to implement and evaluate these approaches in practice.

A pediatric perspective on genomics and prevention in the twenty-first century

We present evidence from diverse disciplines and populations to identify the current and emerging role of genomics in prevention from both medical and public health perspectives as well as key challenges and potential untoward consequences of increasing the role of genomics in these endeavors. We begin by comparing screening in healthy populations (newborn screening), with testing in symptomatic populations, which may incidentally identify secondary findings and at-risk relatives. Emerging evidence suggests that variants in genes subject to the reporting of secondary findings are more common than expected in patients who otherwise would not meet the criteria for testing and population testing for variants in these genes may more precisely identify discrete populations to target for various prevention strategies starting in childhood. Conversely, despite its theoretical promise, recent studies attempting to demonstrate benefits of next-generation sequencing for newborn screening have instead demonstrated numerous barriers and pitfalls to this approach. We also examine the special cases of pharmacogenomics and polygenic risk scores as examples of ways genomics can contribute to prevention amongst a broader population than that affected by rare Mendelian disease. We conclude with unresolved questions which will benefit from future investigations of the role of genomics in disease prevention.

Searching Deep and Wide: Advances in the Molecular Understanding of Dental Caries and Periodontal Disease

During the past decades, remarkable progress has been made in the understanding of the molecular basis of the 2 most common oral diseases, dental caries and periodontal disease. Improvements in our knowledge of the diseases' underlying biology have illuminated previously unrecognized aspects of their pathogenesis. Importantly, the key role of the oral (supragingival and subgingival) microbiome is now well recognized, and both diseases are now best understood as dysbiotic. From a host susceptibility standpoint, some progress has been made in dissecting the "hyperinflammatory" trait and other pathways of susceptibility underlying periodontitis, and novel susceptibility loci have been reported for dental caries. Nevertheless, there is a long road to the translation of these findings and the realization of precision oral health. There is promise and hope that the rapidly increasing capacity of generating multiomics data layers and the aggregation of study samples and cohorts comprising thousands of participants will accelerate the discovery and translation processes. A first key element in this process has been the identification and interrogation of biologically informed disease traits-these "deep" or "precise" traits have the potential of revealing biologically homogeneous disease signatures and genetic susceptibility loci that might present with overlapping or heterogeneous clinical signs. A second key element has been the formation of international consortia with the goals of combining and harmonizing oral health data of thousands of individuals from diverse settings-these "wide" collaborative approaches leverage the power of large sample sizes and are aimed toward the discovery or validation of genetic influences that would otherwise be impossible to detect. Importantly, advancements via these directions require an unprecedented engagement of systems biology and team science models. The article highlights novel insights into the molecular basis of dental caries and chronic periodontitis that have been gained from recent and ongoing studies involving "deep" and "wide" analytical approaches.