Personalized testing based on polygenic risk score is promising for more efficient population-based screening programs for common oncological diseases

A Genomic Test for Colorectal Cancer Risk: Is This Acceptable and Feasible in Primary Care?

INTRODUCTION

Genomic tests can predict risk and tailor screening recommendations for colorectal cancer (CRC). Primary care could be suitable for their widespread implementation.

OBJECTIVE

We aimed to assess the feasibility and acceptability of administering a CRC genomic test in primary care.

METHODS

Participants aged 45-74 years recruited from 4 Australian general practices were offered a genomic CRC risk test. Participants received brief verbal information about the test comprising 45 CRC-associated single-nucleotide polymorphisms, before choosing whether to undertake the test. Personalized risks were given to testers. Uptake and knowledge of the genomic test, cancer-specific anxiety (Cancer Worry Scale), psychosocial impact (Multidimensional Impact of Cancer Risk Assessment [MICRA] score), and impact on CRC screening behaviour within 6 months were measured.

RESULTS

In 150 participants, test uptake was high (126, 84%), with 125 (83%) having good knowledge of the genomic test. Moderate risk participants were impacted more by the test (MICRA mean: 15.9) than average risk participants (mean: 9.5, difference in means: 6.4, 95% confidence interval (CI): 1.5, 11.2, p = 0.01), but all scores were low. Average risk participants' cancer-specific anxiety decreased (mean differences from baseline: 1 month -0.5, 95% CI: -1.0, -0.1, p = 0.03; 6 months -0.6, 95% CI: -1.0, -0.2, p = 0.01). We found limited evidence for genomic testers being more likely to complete the risk-appropriate CRC screening than non-testers (41 vs. 17%, odds ratio = 3.4, 95% CI: 0.6, 34.8, p = 0.19), but some mediators of screening behaviour were altered in genomic testers.

CONCLUSIONS

Genomic testing for CRC risk in primary care is acceptable and likely feasible. Further development of the risk assessment intervention could strengthen the impact on screening behaviour.

Assessing thyroid cancer risk using polygenic risk scores

Genome-wide association studies (GWASs) have identified at least 10 single-nucleotide polymorphisms (SNPs) associated with papillary thyroid cancer (PTC) risk. Most of these SNPs are common variants with small to moderate effect sizes. Here we assessed the combined genetic effects of these variants on PTC risk by using summarized GWAS results to build polygenic risk score (PRS) models in three PTC study groups from Ohio (1,544 patients and 1,593 controls), Iceland (723 patients and 129,556 controls), and the United Kingdom (534 patients and 407,945 controls). A PRS based on the 10 established PTC SNPs showed a stronger predictive power compared with the clinical factors model, with a minimum increase of area under the receiver-operating curve of 5.4 percentage points (P ≤ 1.0 × 10^-9). Adding an extended PRS based on 592,475 common variants did not significantly improve the prediction power compared with the 10-SNP model, suggesting that most of the remaining undiscovered genetic risk in thyroid cancer is due to rare, moderate- to high-penetrance variants rather than to common low-penetrance variants. Based on the 10-SNP PRS, individuals in the top decile group of PRSs have a close to sevenfold greater risk (95% CI, 5.4-8.8) compared with the bottom decile group. In conclusion, PRSs based on a small number of common germline variants emphasize the importance of heritable low-penetrance markers in PTC.

A systems biology approach uncovers cell-specific gene regulatory effects of genetic associations in multiple sclerosis

Genome-wide association studies (GWAS) have identified more than 50,000 unique associations with common human traits. While this represents a substantial step forward, establishing the biology underlying these associations has proven extremely difficult. Even determining which cell types and which particular gene(s) are relevant continues to be a challenge. Here, we conduct a cell-specific pathway analysis of the latest GWAS in multiple sclerosis (MS), which had analyzed a total of 47,351 cases and 68,284 healthy controls and found more than 200 non-MHC genome-wide associations. Our analysis identifies pan immune cell as well as cell-specific susceptibility genes in T cells, B cells and monocytes. Finally, genotype-level data from 2,370 patients and 412 controls is used to compute intra-individual and cell-specific susceptibility pathways that offer a biological interpretation of the individual genetic risk to MS. This approach could be adopted in any other complex trait for which genome-wide data is available.

Comparison of the efficiency of colorectal cancer screening programs based on age and genetic risk for reduction of colorectal cancer mortality

Given that colorectal cancer risk depends partly on inherited factors, screening program efficiency may be increased by incorporating genetic factors. We compared the efficiency of screening based on age and genetic risk in a simulated population. We simulated a population matching the size, age distribution and colorectal cancer incidence and mortality of Australia. We also simulated the distribution of genetic risk for colorectal cancer based on the expected number of inherited risk alleles of 45 single-nucleotide polymorphisms (SNPs) previously reported as associated with colorectal cancer. We compared the expected colorectal cancer deaths under three screening programs; age-based, genetic-based and combined age-based and genetic-based. The age-based program would prevent 25.4 deaths per 100 000 invited to screen, none of which would be under age 50; the genetic program would prevent 26.2 deaths per 100 000 invited to screen, 16 of which would be under age 50; and the combined program would prevent 24.4 deaths per 100 000 invited to screen, 16 of which would be under age 50. Genetic testing of 1.5 million 45-49 year olds would identify 91% of the people aged under 50 at sufficient risk to warrant screening, potentially saving 16 colorectal cancer deaths each year. Screening eligibility based on genetic risk profile for age is as efficient as eligibility based on age alone for preventing colorectal cancer mortality, but identifies an additional 7% of the population at sufficient risk to benefit from screening who would not normally be screened given they are aged under 50 years.