Simple Summary Genetic variants explaining approximately 40% of familial breast cancer risk have been identified, thus leaving a significant fraction of the heritability of this disease still... Show moreSimple Summary Genetic variants explaining approximately 40% of familial breast cancer risk have been identified, thus leaving a significant fraction of the heritability of this disease still unexplained. The exact nature of this missing fraction is unknown; more extensive sequencing efforts could potentially identify new moderate-penetrance breast cancer risk alleles. The aim of this study was to perform a large-scale whole-exome sequencing study, followed by a targeted validation, in breast cancer patients and healthy women of European descent. We identified 20 novel genes with modest evidence of association (p-value < 0.05) for either overall or subtype-specific breast cancer; however, much larger studies are needed to confirm the exact role of these genes in susceptibility to breast cancer. Rare variants in at least 10 genes, including BRCA1, BRCA2, PALB2, ATM, and CHEK2, are associated with increased risk of breast cancer; however, these variants, in combination with common variants identified through genome-wide association studies, explain only a fraction of the familial aggregation of the disease. To identify further susceptibility genes, we performed a two-stage whole-exome sequencing study. In the discovery stage, samples from 1528 breast cancer cases enriched for breast cancer susceptibility and 3733 geographically matched unaffected controls were sequenced. Using five different filtering and gene prioritization strategies, 198 genes were selected for further validation. These genes, and a panel of 32 known or suspected breast cancer susceptibility genes, were assessed in a validation set of 6211 cases and 6019 controls for their association with risk of breast cancer overall, and by estrogen receptor (ER) disease subtypes, using gene burden tests applied to loss-of-function and rare missense variants. Twenty genes showed nominal evidence of association (p-value < 0.05) with either overall or subtype-specific breast cancer. Our study had the statistical power to detect susceptibility genes with effect sizes similar to ATM, CHEK2, and PALB2, however, it was underpowered to identify genes in which susceptibility variants are rarer or confer smaller effect sizes. Larger sample sizes would be required in order to identify such genes. Show less
AimsTo examine the association between UCP1, UCP2, and UCP3 gene polymorphisms with adiposity markers in European adolescents and to test if there were gene interactions with objectively measured... Show moreAimsTo examine the association between UCP1, UCP2, and UCP3 gene polymorphisms with adiposity markers in European adolescents and to test if there were gene interactions with objectively measured physical activity and adiposity.MethodsA cross-sectional study that involves 1.057 European adolescents (12-18years old) from the Healthy Lifestyle in Europe by Nutrition in Adolescence Cross-Sectional Study. A total of 18 polymorphisms in UCP1, UCP2, and UCP3 genes were genotyped. We measured weight, height, waist, and hip circumferences and triceps and subscapular skinfold thickness. Physical activity was objectively measured by accelerometry during 7days.ResultsThe C allele of the UCP1 rs6536991 polymorphism was associated with a lower risk of overweight (odds ratio [OR]: T/C+C/C vs T/T)=0.72; 95% confidence interval [CI]: 0.53-0.98; P=0.034; false discovery rate [FDR]=0.048). There was a significant interaction between UCP1 rs2071415 polymorphism and physical activity with waist-to-hip ratio (P=0.006; FDR=0.026). Adolescents who did not meet the physical activity recommendations (less than 60min/day of moderate to vigorous physical activity) and carrying the C/C genotype had higher waist-to-hip ratio (+ 0.067; 95% CI, 0.028-0.106; P=0.003), while no differences across genotypes were observed in adolescents meeting the recommendations.ConclusionsTwo UCP1 polymorphisms were associated with adiposity in European adolescents. Meeting the daily physical activity recommendations may overcome the effect of the UCP1 rs2071415 polymorphism on obesity-related traits. Show less
Germline mutations in the major melanoma susceptibility gene CDKN2A explain genetic predisposition in only 10-40% of melanoma-prone families. In our study we comprehensively characterized 488... Show moreGermline mutations in the major melanoma susceptibility gene CDKN2A explain genetic predisposition in only 10-40% of melanoma-prone families. In our study we comprehensively characterized 488 melanoma cases from 451 non-CDKN2A/CDK4 families for mutations in 30 established and candidate melanoma susceptibility genes using a custom-designed targeted gene panel approach. We identified (likely) pathogenic variants in established melanoma susceptibility genes in 18 families (n = 3 BAP1, n = 15 MITF p.E318K; diagnostic yield 4.0%). Among the three identified BAP1-families, there were no reported diagnoses of uveal melanoma or malignant mesothelioma. We additionally identified two potentially deleterious missense variants in the telomere maintenance genes ACD and TERF2IP, but none in the POT1 gene. MC1R risk variants were strongly enriched in our familial melanoma cohort compared to healthy controls (R variants: OR 3.67, 95% CI 2.88-4.68, p <0.001). Several variants of interest were also identified in candidate melanoma susceptibility genes, in particular rare (pathogenic) variants in the albinism gene OCA2 were repeatedly found. We conclude that multigene panel testing for familial melanoma is appropriate considering the additional 4% diagnostic yield in non-CDKN2A/CDK4 families. Our study shows that BAP1 and MITF are important genes to be included in such a diagnostic test. Show less
