In Retrospect: A decade of shared genomic associations

African genetic diversity and adaptation inform a precision medicine agenda

The deep evolutionary history of African populations, since the emergence of modern humans more than 300,000 years ago, has resulted in high genetic diversity and considerable population structure. Selected genetic variants have increased in frequency due to environmental adaptation, but recent exposures to novel pathogens and changes in lifestyle render some of them with properties leading to present health liabilities. The unique discoverability potential from African genomic studies promises invaluable contributions to understanding the genomic and molecular basis of health and disease. Globally, African populations are understudied, and precision medicine approaches are largely based on data from European and Asian-ancestry populations, which limits the transferability of findings to the continent of Africa. Africa needs innovative precision medicine solutions based on African data that use knowledge and implementation strategies aligned to its climatic, cultural, economic and genomic diversity.

Attitudes among South African university staff and students towards disclosing secondary genetic findings

The present study represents an initial step in understanding diverse academic perspectives on the disclosure of secondary findings (SFs) from genetic research conducted in Africa. Using an online survey completed by 674 university students and academic staff in South Africa, we elicited attitudes towards the return of SFs. Latent class analysis (LCA) was performed to classify sub-groups of participants according to their overall attitudes to returning SFs. We did not find substantial differences in attitudes towards the return of findings between staff and students. Overall, respondents were in favour of the return of SFs in genetics research, depending on the type. The majority of survey respondents (80%) indicated that research participants should be given the option of deciding whether to have genetic SFs returned. LCA revealed that the largest group (53%) comprised individuals with more favourable attitudes to the return of SFs in genetics research. Those with less favourable attitudes comprised only 4% of the sample. This study provides important insights that may, together with further empirical evidence, inform the development of research guidelines and policy to assist healthcare professionals and researchers.

Genetic association of molecular traits: A help to identify causative variants in complex diseases

In the past 15 years, major progresses have been made in the understanding of the genetic basis of regulation of gene expression. These new insights have revolutionized our approach to resolve the genetic variation underlying complex diseases. Gene transcript levels were the first expression phenotypes that were studied. They are heritable and therefore amenable to genome-wide association studies. The genetic variants that modulate them are called expression quantitative trait loci. Their study has been extended to other molecular quantitative trait loci (molQTLs) that regulate gene expression at the various levels, from chromatin state to cellular responses. Altogether, these studies have generated a wealth of basic information on the genome-wide patterns of gene expression and their inter-individual variation. Most importantly, molQTLs have become an invaluable asset in the genetic study of complex diseases. Although the identification of the disease-causing variants on the basis of their overlap with molQTLs requires caution, molQTLs can help to prioritize the relevant candidate gene(s) in the disease-associated regions and bring a functional interpretation of the associated variants, therefore, bridging the gap between genotypes and clinical phenotypes.

Common genetic variants shared among five major psychiatric disorders: a large-scale genome-wide combined analysis

Background. Genetic correlation and pleiotropic effects among psychiatric disorders have been reported. This study aimed to identify specific common genetic variants shared between five adult psychiatric disorders: schizophrenia, bipolar, major depressive disorder, attention deficit-hyperactivity disorder, and autism spectrum disorder. Methods. A combined p-value of about 8 million single nucleotide polymorphisms (SNPs) was calculated in an equivalent sample of 151,672 cases and 284,444 controls of European ancestry from published data based on the latest genome-wide association studies of five major psychiatric disorder. SNPs that achieved genome-wide significance (P<5x10-08) were mapped to loci and genomic regions for further investigation; gene annotation and clustering were performed to understand the biological process and molecular function of the loci identified. We also examined CNVs and performed expression quantitative trait loci analysis for SNPs by genomic region. Results. We find that 6,293 SNPs mapped to 336 loci shared by the three adult psychiatric disorders, 1,108 variants at 73 loci shared by the childhood disorders, and 713 variants at 47 genes shared by all five disorders at genome-wide significance (P<5x10-08). Of the 2,583 SNPs at the extended major histocompatibility complex identified for three adult disorders, none of them were associated with childhood disorders; and SNPs shared by all five disorders were located in regions that have been identified as containing copy number variation associated with autism and had largely neurodevelopmental functions. Conclusion. We show a number of specific SNPs associated with psychiatric disorders of childhood or adult-onset, illustrating not only genetic heterogeneity across these disorders but also developmental genes shared by them all.  These results provide a manageable list of anchors from which to investigate epigenetic mechanism or gene-gene interaction on the development of neuropsychiatric disorders and for developing a measurement matrix for disease risk to potentially develop a novel taxonomy for precision medicine.

A scientometric review of genome-wide association studies

This scientometric review of genome-wide association studies (GWAS) from 2005 to 2018 (3639 studies; 3508 traits) reveals extraordinary increases in sample sizes, rates of discovery and traits studied. A longitudinal examination shows fluctuating ancestral diversity, still predominantly European Ancestry (88% in 2017) with 72% of discoveries from participants recruited from three countries (US, UK, Iceland). US agencies, primarily NIH, fund 85% and women are less often senior authors. We generate a unique GWAS H-Index and reveal a tight social network of prominent authors and frequently used data sets. We conclude with 10 evidence-based policy recommendations for scientists, research bodies, funders, and editors.

Assortative mating on complex traits revisited: Double first cousins and the X-chromosome

Mate choice through direct assortment on heritable traits, assortative mating (AM), is predicted in theory to inflate the genetic variance in a population and the correlation between relatives. Here, we revisit the theory of AM, first established in the landmark 1918 paper from RA Fisher, and provide new theory and analytical results. In particular, we shed light on inconsistencies in the literature regarding the correlation between double first cousins under AM and provide a solution. We derive new theory for AM due to X-chromosome loci. We show in the latter case that the inflation of genetic variance induced under AM is twice as large in females compared to males. These two theoretical contributions are verified and illustrated through simulations. We also provide a more general unified framework for the correlation between relatives in a non-inbred population.

Genetic disease risks can be misestimated across global populations

BACKGROUND

Accurate assessment of health disparities requires unbiased knowledge of genetic risks in different populations. Unfortunately, most genome-wide association studies use genotyping arrays and European samples. Here, we integrate whole genome sequence data from global populations, results from thousands of genome-wide association studies (GWAS), and extensive computer simulations to identify how genetic disease risks can be misestimated.

RESULTS

In contrast to null expectations, we find that risk allele frequencies at known disease loci are significantly different for African populations compared to other continents. Strikingly, ancestral risk alleles are found at 9.51% higher frequency in Africa, and derived risk alleles are found at 5.40% lower frequency in Africa. By simulating GWAS with different study populations, we find that non-African cohorts yield disease associations that have biased allele frequencies and that African cohorts yield disease associations that are relatively free of bias. We also find empirical evidence that genotyping arrays and SNP ascertainment bias contribute to continental differences in risk allele frequencies. Because of these causes, polygenic risk scores can be grossly misestimated for individuals of African descent. Importantly, continental differences in risk allele frequencies are only moderately reduced if GWAS use whole genome sequences and hundreds of thousands of cases and controls. Finally, comparisons between uncorrected and corrected genetic risk scores reveal the benefits of considering whether risk alleles are ancestral or derived.

CONCLUSIONS

Our results imply that caution must be taken when extrapolating GWAS results from one population to predict disease risks in another population.

A collaborative translational research framework for evaluating and implementing the appropriate use of human genome sequencing to improve health

In a Policy Forum, Muin Khoury and colleagues discuss research on the clinical application of genome sequencing data.

Replicability and Prediction: Lessons and Challenges from GWAS

Since the publication of the Wellcome Trust Case Control Consortium (WTCCC) landmark study a decade ago, genome-wide association studies (GWAS) have led to the discovery of thousands of risk variants involved in disease etiology. This success story has two angles that are often overlooked. First, GWAS findings are highly replicable. This is an unprecedented phenomenon in complex trait genetics, and indeed in many areas of science, which in past decades have been plagued by false positives. At a time of increasing concerns about the lack of reproducibility, we examine the biological and methodological reasons that account for the replicability of GWAS and identify the challenges ahead. In contrast to the exemplary success of disease gene discovery, at present GWAS findings are not useful for predicting phenotypes. We close with an overview of the prospects for individualized prediction of disease risk and its foreseeable impact in clinical practice.

Functional genomics and assays of regulatory activity detect mechanisms at loci for lipid traits and coronary artery disease

Many genome-wide association studies (GWAS) have identified signals located in non-coding regions, and an increasing number of functional genomics annotations of regulatory elements and assays of regulatory activity have been used to investigate mechanisms. Genome-wide datasets that characterize chromatin structure help detect potential regulatory elements. Assays to experimentally assess candidate variants include transcriptional reporter assays, and recently, massively parallel reporter assays (MPRAs). Additionally, the effect of candidate regulatory elements and variants on gene expression and function can be evaluated using genomic editing with the CRISPR-Cas9 technology. We highlight some recent studies that employed these strategies to identify variant effects and elucidate molecular and/or biological mechanisms at GWAS loci for lipid traits and coronary artery disease.

Long- and short-term outcomes in renal allografts with deceased donors: A large recipient and donor genome-wide association study

Improvements in immunosuppression have modified short-term survival of deceased-donor allografts, but not their rate of long-term failure. Mismatches between donor and recipient HLA play an important role in the acute and chronic allogeneic immune response against the graft. Perfect matching at clinically relevant HLA loci does not obviate the need for immunosuppression, suggesting that additional genetic variation plays a critical role in both short- and long-term graft outcomes. By combining patient data and samples from supranational cohorts across the United Kingdom and European Union, we performed the first large-scale genome-wide association study analyzing both donor and recipient DNA in 2094 complete renal transplant-pairs with replication in 5866 complete pairs. We studied deceased-donor grafts allocated on the basis of preferential HLA matching, which provided some control for HLA genetic effects. No strong donor or recipient genetic effects contributing to long- or short-term allograft survival were found outside the HLA region. We discuss the implications for future research and clinical application.

Nonhuman Primates and Translational Research: Progress, Opportunities, and Challenges

Nonhuman primates (NHPs) are the closest animal models to humans regarding genetics, physiology and behavior. Therefore, NHPs are usually a critical component in translational research projects aimed at developing therapeutics, vaccines, devices or other interventions aimed at preventing, curing or ameliorating human disease. NHPs are often used in conjunction with other animal models, such as rodents, and results obtained using NHPs must often be used as the final criterion for establishing the potential efficacy of a pharmaceutical or vaccine before transition to human clinical trails. In some cases, NHPs may be the only relevant animal models for a particlular translational study. This issue of the ILAR journal brings together, in one place, articles that discuss the use of NHP models for studying human diseases that are highly prevalent and that cause extraordinary human suffering and financial and social burdens. Topics covered in detail include: tuberculosis; viral hepatitis; HIV/AIDS; neurodegenerative disorders; Substance abuse disorders; vision and prevention of blindness; disorder associated with psychosocial processes, such as anxiety, depression and loneliness; cardiovascular disease; metabolic disease, such as obesity and metabolic syndrome; respiratory disease; and female reproduction, prenatal development and women's health. Proper husbandry of NHPs that reduces stress and maintains animal health is critical for the development of NHP models. This issue of the journal includes a review of procedures for environmental enrichment, which helps assure animal health and wellbeing. Taken together, these articles provide detailed reviews of the use of NHP models for translational investigations and discuss successes, limitations, challenges and opportunities associated with this research.