Search bioRxiv⌕ Search

bioRxiv · 10.1101/619718

A genetic hazard score to personalize prostate cancer screening, applied to population data

Abstract

BackgroundGenetic risk stratification may inform decisions of whether--and when--a man should undergo prostate cancer (PCa) screening. We previously validated a polygenic hazard score (PHS), a weighted sum of 54 single-nucleotide polymorphism genotypes, for accurate prediction of age of onset of aggressive PCa and improved screening performance. We now assess the potential impact of PHS-informed screening.\n\nMethodsUnited Kingdom population data were fit to a continuous model of age-specific PCa incidence. Using hazard ratios estimated from ProtecT trial data, age-specific incidence rates were calculated for percentiles of genetic risk. Incidence of higher-grade PCa (Gleason[≥]7) was estimated from age-specific data from the linked CAP trial. PHS and incidence data were combined to give a risk-equivalent age, when a man with a given PHS percentile will have risk of higher-grade PCa equivalent to that of a typical man at age 50 (50-years standard). Positive predictive value (PPV) of PSA testing was calculated using PHS-adjusted (PCa-risk-equivalent age) groups identified from ProtecT.\n\nResultsExpected age of onset of higher-grade PCa is modulated by 19 years between the 1st and 99th PHS percentiles. A man with PHS in the 99th percentile reaches 50-years-standard risk at age 41; conversely, a man in the 1st percentile reaches this risk at age 60. PPV of PSA was higher for men with higher PHS-adjusted age.\n\nConclusionsPHS informs PCa screening strategies with individualized estimates of risk-equivalent age for higher-grade PCa. Screening initiation could be adjusted according to a mans genetic hazard score, improving PPV of PSA screening.

Explore related subjects

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Huynh-Le, M.-P., Fan, C. C., Karunamuni, R., Walsh, E. I., Turner, E. L., Lane, J. A., Martin, R. M., Neal, D. E., Donovan, J. L., Hamdy, F. C., Parsons, J. K., Eeles, R. A., Easton, D. F., Kote-Jarai, Z., Amin Al Olama, A., Benlloch Garcia, S., Muir, K., Gronberg, H., Wiklund, F., Aly, M., Schleutker, J., Sipeky, C., Tammela, T. L., Nordestgaard, B. G., Key, T. J., Travis, R. C., Pharoah, P., Pashayan, N., Khaw, K.-T., Thibodeau, S. N., McDonnell, S. K., Schaid, D. J., Maier, C., Vogel, W., Luedeke, M., Herkommer, K., Kibel, A. S., Cybulski, C., Wokolorczyk, D., Kluzniak, W., Cannon-Albright,. 2019-04-26. A genetic hazard score to personalize prostate cancer screening, applied to population data. https://doi.org/10.1101/619718

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

Deep transcriptomic analysis of molecular mediators of complex traits in heterogeneous stock (HS) rats

Rats are a powerful model organism for genome-wide association studies (GWAS) of physiological and behavioral traits. Heterogeneous Stock (HS) rats, which were created by intercrossing 8 inbred rat strains, are heavily used for this purpose because of their genetic diversity and accumulated recombinations due to over 100 generations of outbreeding, which improves mapping precision. However, functional genomics resources for post-GWAS interpretation of genomic findings have been limited. We processed 3,160 RNA-seq samples, 1,932 of which were previously unpublished, from 13 tissues as part of RatGTEx. We used Pantry to quantify six modalities of transcriptome regulation (expression, isoform ratio, intron excision ratio, alternative transcription start site (TSS), alternative poly(A), and RNA stability) in each sample, which allowed us to identify 144,876 independent quantitative trait loci (QTL) for 22,599 genes. We performed a transcriptome-wide association study (TWAS) with 19,796 unique genes across tissues and transcriptional modalities and 308 traits collected from 14 studies using FUSION, which identified 7,473 significant gene-trait associations. This work presents a significant expansion of the RatGTEx resource in terms of samples, modes of transcriptome regulation, and genetic analyses. Our findings provide molecular evidence for the involvement of specific genes in mediating GWAS signals through a range of transcriptome regulatory mechanisms. These gene-to-phenotype relationships can be easily applied to genetic analyses in humans and other species. Further experiments can use this evidence to confirm these molecular mediators and target them for the treatment of behavioral and physiological traits and disorders. To facilitate use of these results, we have updated results on RatGTEx.org and provided a new interactive TWAS web portal (twas.ratgtex.org).

genetics↗

Genomic and Epigenomic Relationships Capture Different Patterns of Genotype-by-Environment Interaction in Grapevine Clones

Genotype-by-environment interaction (GEI) challenges selection in clonally propagated perennial crops by reducing the consistency of clone performance across years. In perennial crops, both genetic and epigenetic variation are likely to contribute to complex trait variation among clones. However, the extent to which each molecular source contribute to GEI remains poorly understood. Here, we used UMR-seq, an assay that recovers SNPs and unmethylated-region (UMR; DNA methylation) profiles from a single library, to generate paired genomic and epigenomic profiles for 206 Riesling (Vitis vinifera L.) clones phenotyped for yield and juice quality traits across nine growing seasons. We then partitioned the contribution of each omic layer to clonal variation and GEI, and examined the genomic distribution of their effects. In models without explicit GEI, environmental and residual effects were the largest source of phenotypic variance and the clonal main effect was modest. Genomic relationships accounted for most of the clonal variance in four of five traits, and adding an epigenomic relationship matrix (ERM) to the genomic relationship matrix (GRM) had little effect. In contrast, when GEI effects were modelled using factor-analytic covariance structures, the epigenomic layer captured a substantial proportion of GEI variance and exceeded the genomic contribution in four of five traits. The two omic layers differed not only in the amount of GEI captured, but also in the pattern of clone re-ranking across years. When back-solved effects were aggregated into genomic windows, the largest genomic and epigenomic effects tended to fall in different regions, with overlap no greater than expected by chance. Together, these results show that genomic and epigenomic relationships capture complementary components of year-to-year variation in clone performance, with the epigenomic contribution expressed primarily through GEI. These findings provide a basis for investigating the molecular drivers of GEI and for testing whether genomic and epigenomic information can inform selection for stable clonal performance across variable environments.

genetics↗

Transportability of mouse gene knockout models to human complex phenotypes

Mouse gene knockout studies are a valuable resource for understanding human gene function and the mechanisms underlying disease. However, translating insights to humans requires causal similarities between mouse and human phenotypes. A mouse model is transportable if gene perturbations that impact the mouse phenotype also affect (in orthologous genes) the corresponding human phenotype of interest, with consistent directionality. To assess the transportability of mouse models to human complex traits we combined laboratory mouse gene perturbation data from the high-throughput International Mouse Phenotyping Consortium with predicted loss-of-function data from the UK Biobank within the Gene Perturbation Analysis for Transportability (GPAT) framework. Applying GPAT to 30 matched mouse-human phenotype pairs, we found evidence of transportability for 12 mouse phenotypes including biochemical (e.g. total cholesterol), cellular (e.g. lymphocyte counts) and anthropometric (e.g. length/height) phenotypes. In contrast, there was limited evidence for others such as fat mass and body mass index in the context of the murine experimental conditions. We also found some evidence of transportability of mouse glucose measurements to diabetes mellitus in humans. Genome-wide perturbation effects on matched phenotypes were on average positively correlated between mice and humans (meta-analysis GPAT P = 2.3x10-27). However, the degree of correlation was generally modest and heterogeneous across phenotypes with some gene perturbations strongly associated in both species in opposite directions. Our framework illustrates how perturbation data can be used to quantitatively validate experimental models for understanding human disease aetiology and highlights the need for a range of orthogonal model systems, which may include challenges and perturbations to the mouse knockouts, to interrogate the mechanistic basis of human genetic associations.

genetics↗