Evaluation of modifiable factors and polygenic risk score in thyroid cancer

2021 ◽  
Author(s):  
Tung Hoang ◽  
Quy Nguyen Ngoc ◽  
Jeonghee Lee ◽  
Eun Kyung Lee ◽  
Yul Hwangbo ◽  
...  
Keyword(s):  
Thyroid Cancer ◽  
Alcohol Consumption ◽  
Risk Score ◽  
Tobacco Smoking ◽  
Cumulative Effect ◽  
European Ancestry ◽  
Polygenic Risk Score ◽  
Regular Exercise ◽  
Polygenic Risk ◽  
Modifiable Factors

The cumulative effect of single-nucleotide polymorphisms (SNPs) on thyroid cancer has been adequately defined in individuals of European ancestry; however, similar evidence in the Korean population is limited. This study aimed to investigate the influence of modifiable factors and the polygenic risk score (PRS) and their interactive and combined effects on thyroid cancer. Using data from the Cancer Screenee Cohort, this study included 759 thyroid cancer cases and 759 age- and sex-matched controls. We examined the effects of tobacco smoking, alcohol consumption, and regular exercise habits, body mass index (BMI), and the PRS of 6 SNPs on thyroid cancer. Odds ratios (ORs) and 95% confidence intervals (CIs) for the associations were obtained using a conditional logistic regression model. The results indicated that family history, obesity, and the unweighted and weighted PRS were independently associated with susceptibility to thyroid cancer, with ORs (95% CIs) of 2.96 (1.63-5.36), 1.72 (1.20-2.48), 1.46 (1.10-1.93), and 1.56 (1.19-2.03), respectively, whereas the effect of smoking, drinking, and regular exercise was not significant. The contribution of the PRS remained after stratifying participants with healthy behaviours, such as nonsmokers/nondrinkers, and regular exercise. Although the PRS did not significantly contribute to the risk for thyroid cancer when participants were stratified according to BMI, BMI and the PRS had a cumulative effect on thyroid cancer risk. The combined effect of genetic polymorphisms on predisposition to thyroid cancer may differ based on tobacco smoking, alcohol consumption, regular exercise behaviours and cumulative BMI. Larger population-based studies are needed to validate these findings.

scholarly journals Polygenic risk score and risk of monoclonal B-cell lymphocytosis in caucasians and risk of chronic lymphocytic leukemia (CLL) in African Americans

Leukemia ◽  
2021 ◽  
Author(s):  
Geffen Kleinstern ◽  
J. Brice Weinberg ◽  
Sameer A. Parikh ◽  
Esteban Braggio ◽  
Sara J. Achenbach ◽  
...  
Keyword(s):  
Environmental Factors ◽  
B Cell ◽  
Risk Score ◽  
Genetic Factors ◽  
Strong Predictor ◽  
Lymphocytic Leukemia ◽  
European Ancestry ◽  
Polygenic Risk Score ◽  
Polygenic Risk ◽  
C Statistic

AbstractMonoclonal B-cell lymphocytosis (MBL) is a precursor to CLL. Other than age, sex, and CLL family-history, little is known about factors associated with MBL risk. A polygenic-risk-score (PRS) of 41 CLL-susceptibility variants has been found to be associated with CLL risk among individuals of European-ancestry(EA). Here, we evaluate these variants, the PRS, and environmental factors for MBL risk. We also evaluate these variants and the CLL-PRS among African-American (AA) and EA-CLL cases and controls. Our study included 560 EA MBLs, 869 CLLs (696 EA/173 AA), and 2866 controls (2631 EA/235 AA). We used logistic regression, adjusting for age and sex, to estimate odds ratios (OR) and 95% confidence intervals within each race. We found significant associations with MBL risk among 21 of 41 variants and with the CLL-PRS (OR = 1.86, P = 1.9 × 10−29, c-statistic = 0.72). Little evidence of any association between MBL risk and environmental factors was observed. We observed significant associations of the CLL-PRS with EA-CLL risk (OR = 2.53, P = 4.0 × 10−63, c-statistic = 0.77) and AA-CLL risk (OR = 1.76, P = 5.1 × 10−5, c-statistic = 0.62). Inherited genetic factors and not environmental are associated with MBL risk. In particular, the CLL-PRS is a strong predictor for both risk of MBL and EA-CLL, but less so for AA-CLL supporting the need for further work in this population.

Abstract PO-163: Genome-wide polygenic risk score of prostate cancer in African and European ancestry men

2022 ◽  
Author(s):  
Burcu F. Darst ◽  
Ravi K Madduri ◽  
Alexis A. Rodriguez ◽  
Xin Sheng ◽  
Rosalind A. Eeles ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Risk Score ◽  
European Ancestry ◽  
Polygenic Risk Score ◽  
Polygenic Risk ◽  
Genome Wide

scholarly journals The undiagnosed disease burden associated with alpha-1 antitrypsin deficiency genotypes

2020 ◽  
Vol 56 (6) ◽  
pp. 2001441 ◽  
Author(s):  
Tomoko Nakanishi ◽  
Vincenzo Forgetta ◽  
Tomohiro Handa ◽  
Toyohiro Hirai ◽  
Vincent Mooser ◽  
...  
Keyword(s):  
Risk Score ◽  
Disease Burden ◽  
Forced Expiratory Volume ◽  
European Ancestry ◽  
Polygenic Risk Score ◽  
Uk Biobank ◽  
Polygenic Risk ◽  
Antitrypsin Deficiency ◽  
Alpha 1 Antitrypsin Deficiency ◽  
Alpha 1 Antitrypsin

Alpha-1 antitrypsin deficiency (AATD), mainly due to the PI*ZZ genotype in SERPINA1, is one of the most common inherited diseases. Since it is associated with a high disease burden and partially prevented by smoking cessation, identification of PI*ZZ individuals through genotyping could improve health outcomes.We examined the frequency of the PI*ZZ genotype in individuals with and without diagnosed AATD from UK Biobank, and assessed the associations of the genotypes with clinical outcomes and mortality. A phenome-wide association study (PheWAS) was conducted to reveal disease associations with genotypes. A polygenic risk score (PRS) for forced expiratory volume in 1 s (FEV1)/forced vital capacity (FVC) ratio was used to evaluate variable penetrance of PI*ZZ.Among 458 164 European-ancestry participants in UK Biobank, 140 had the PI*ZZ genotype and only nine (6.4%, 95% CI 3.4–11.7%) of them were diagnosed with AATD. Those with PI*ZZ had a substantially higher odds of COPD (OR 8.8, 95% CI 5.8–13.3), asthma (OR 2.0, 95% CI 1.4–3.0), bronchiectasis (OR 7.3, 95%CI 3.2–16.8), pneumonia (OR 2.7, 95% CI 1.5–4.9) and cirrhosis (OR 7.8, 95% CI 2.5–24.6) diagnoses and a higher hazard of mortality (2.4, 95% CI 1.2–4.6), compared to PI*MM (wildtype) (n=398 424). These associations were stronger among smokers. PheWAS demonstrated associations with increased odds of empyema, pneumothorax, cachexia, polycythaemia, aneurysm and pancreatitis. Polygenic risk score and PI*ZZ were independently associated with FEV1/FVC <0.7 (OR 1.4 per 1-sd change, 95% CI 1.4–1.5 and OR 4.5, 95% CI 3.0–6.9, respectively).The important underdiagnosis of AATD, whose outcomes are partially preventable through smoking cession, could be improved through genotype-guided diagnosis.

scholarly journals Partial Support for an Interaction Between a Polygenic Risk Score for Major Depressive Disorder and Prenatal Maternal Depressive Symptoms on Infant Right Amygdalar Volumes

2020 ◽  
Vol 30 (12) ◽  
pp. 6121-6134 ◽  
Author(s):  
H Acosta ◽  
K Kantojärvi ◽  
N Hashempour ◽  
J Pelto ◽  
N M Scheinin ◽  
...  
Keyword(s):  
Major Depressive Disorder ◽  
Depressive Symptoms ◽  
Depressive Disorder ◽  
Risk Score ◽  
European Ancestry ◽  
Polygenic Risk Score ◽  
Maternal Depressive Symptoms ◽  
Major Depressive ◽  
Polygenic Risk ◽  
Asian Cohort

Abstract Psychiatric disease susceptibility partly originates prenatally and is shaped by an interplay of genetic and environmental risk factors. A recent study has provided preliminary evidence that an offspring polygenic risk score for major depressive disorder (PRS-MDD), based on European ancestry, interacts with prenatal maternal depressive symptoms (GxE) on neonatal right amygdalar (US and Asian cohort) and hippocampal volumes (Asian cohort). However, to date, this GxE interplay has only been addressed by one study and is yet unknown for a European ancestry sample. We investigated in 105 Finnish mother–infant dyads (44 female, 11–54 days old) how offspring PRS-MDD interacts with prenatal maternal depressive symptoms (Edinburgh Postnatal Depression Scale, gestational weeks 14, 24, 34) on infant amygdalar and hippocampal volumes. We found a GxE effect on right amygdalar volumes, significant in the main analysis, but nonsignificant after multiple comparison correction and some of the control analyses, whose direction paralleled the US cohort findings. Additional exploratory analyses suggested a sex-specific GxE effect on right hippocampal volumes. Our study is the first to provide support, though statistically weak, for an interplay of offspring PRS-MDD and prenatal maternal depressive symptoms on infant limbic brain volumes in a cohort matched to the PRS-MDD discovery sample.

scholarly journals Development and Implementation of Polygenic Risk Score in Vietnamese Population

2019 ◽  
Vol 2019 (2) ◽  
pp. 75-83
Author(s):  
Nguyễn Trần Thế Hùng ◽  
Lê Đức Hậu
Keyword(s):  
Risk Score ◽  
Prediction Models ◽  
European Ancestry ◽  
Polygenic Risk Score ◽  
Clinical Settings ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Polygenic Risk ◽  
Vietnamese Population ◽  
Artery Disease

Recent technological advancements and availability of genetic databases have facilitated the integration of genetic factors into risk prediction models. A Polygenic Risk Score (PRS) combines the effect of many Single Nucleotide Polymorphisms (SNP) into a single score. This score has lately been shown to have a clinically predictive value in various common diseases. Some clinical interpretations of PRS are summarized in this review for coronary artery disease, breast cancer, prostate cancer, diabetes mellitus, and Alzheimer’s disease. While these findings gave support to the implementation of PRS in clinical settings, the populations of interest were derived mainly from European ancestry. Therefore, applying these findings to non-European ancestry (Vietnamese in this context) requires many efforts and cautions. This review aims to articulate the evidence supporting the clinical use of PRS, the concepts behind the validity of PRS, approach to implement PRS in Vietnamese population, and cautions in selecting methods and thresholds to develop an appropriate PRS.

scholarly journals Capturing additional genetic risk from family history for improved polygenic risk prediction

2022 ◽  
Author(s):  
Tianyuan Lu ◽  
Vincenzo Forgetta ◽  
J Brent Richards ◽  
Celia MT Greenwood
Keyword(s):  
Family History ◽  
Risk Prediction ◽  
Risk Score ◽  
Genetic Risk ◽  
Adult Height ◽  
Prediction Models ◽  
European Ancestry ◽  
Polygenic Risk Score ◽  
Parental History ◽  
Polygenic Risk

Family history of complex traits may reflect transmitted rare pathogenic variants, intrafamilial shared exposures to environmental and lifestyle factors, as well as a common genetic predisposition. We developed a latent factor model to quantify trait heritability in excess of that captured by a common variant-based polygenic risk score, but inferable from family history. We applied our model to predict adult height for 941 children in the Avon Longitudinal Study of Parents and Children cohort as well as 11 complex diseases for ~400,000 European ancestry participants in the UK Biobank. Parental history brought consistent significant improvements in the predictive power of polygenic risk prediction. For instance, a joint predictor was able to explain ~55% of the total variance in sex-adjusted adult height z-scores, close to the estimated heritability. Our work showcases an innovative paradigm for risk calculation, and supports incorporation of family history into polygenic risk score-based genetic risk prediction models.

scholarly journals Novel Common Genetic Susceptibility Loci for Colorectal Cancer

2018 ◽  
Vol 111 (2) ◽  
pp. 146-157 ◽  
Author(s):  
Stephanie L Schmit ◽  
Christopher K Edlund ◽  
Fredrick R Schumacher ◽  
Jian Gong ◽  
Tabitha A Harrison ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Relative Risk ◽  
Risk Score ◽  
European Ancestry ◽  
Polygenic Risk Score ◽  
Susceptibility Loci ◽  
Polygenic Risk ◽  
Control Subjects ◽  
Genome Wide ◽  
Familial Relative Risk

Abstract Background Previous genome-wide association studies (GWAS) have identified 42 loci (P < 5 × 10−8) associated with risk of colorectal cancer (CRC). Expanded consortium efforts facilitating the discovery of additional susceptibility loci may capture unexplained familial risk. Methods We conducted a GWAS in European descent CRC cases and control subjects using a discovery–replication design, followed by examination of novel findings in a multiethnic sample (cumulative n = 163 315). In the discovery stage (36 948 case subjects/30 864 control subjects), we identified genetic variants with a minor allele frequency of 1% or greater associated with risk of CRC using logistic regression followed by a fixed-effects inverse variance weighted meta-analysis. All novel independent variants reaching genome-wide statistical significance (two-sided P < 5 × 10−8) were tested for replication in separate European ancestry samples (12 952 case subjects/48 383 control subjects). Next, we examined the generalizability of discovered variants in East Asians, African Americans, and Hispanics (12 085 case subjects/22 083 control subjects). Finally, we examined the contributions of novel risk variants to familial relative risk and examined the prediction capabilities of a polygenic risk score. All statistical tests were two-sided. Results The discovery GWAS identified 11 variants associated with CRC at P < 5 × 10−8, of which nine (at 4q22.2/5p15.33/5p13.1/6p21.31/6p12.1/10q11.23/12q24.21/16q24.1/20q13.13) independently replicated at a P value of less than .05. Multiethnic follow-up supported the generalizability of discovery findings. These results demonstrated a 14.7% increase in familial relative risk explained by common risk alleles from 10.3% (95% confidence interval [CI] = 7.9% to 13.7%; known variants) to 11.9% (95% CI = 9.2% to 15.5%; known and novel variants). A polygenic risk score identified 4.3% of the population at an odds ratio for developing CRC of at least 2.0. Conclusions This study provides insight into the architecture of common genetic variation contributing to CRC etiology and improves risk prediction for individualized screening.

scholarly journals Exploration of a Polygenic Risk Score for Alcohol Consumption: A Longitudinal Analysis from the ALSPAC Cohort

PLoS ONE ◽  
2016 ◽  
Vol 11 (11) ◽  
pp. e0167360 ◽  
Author(s):  
Michelle Taylor ◽  
Andrew J. Simpkin ◽  
Philip C. Haycock ◽  
Frank Dudbridge ◽  
Luisa Zuccolo
Keyword(s):  
Alcohol Consumption ◽  
Risk Score ◽  
Longitudinal Analysis ◽  
Polygenic Risk Score ◽  
Polygenic Risk

scholarly journals Comprehensive Breast Cancer Risk Assessment for CHEK2 and ATM Pathogenic Variant Carriers Incorporating a Polygenic Risk Score and the Tyrer-Cuzick Model

2021 ◽  
pp. 1073-1081
Author(s):  
Shannon Gallagher ◽  
Elisha Hughes ◽  
Allison W. Kurian ◽  
Susan M. Domchek ◽  
Judy Garber ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Risk Assessment ◽  
Breast Cancer Risk ◽  
Cancer Risk ◽  
Risk Score ◽  
Pathogenic Variant ◽  
European Ancestry ◽  
Polygenic Risk Score ◽  
Polygenic Risk ◽  
Clinical Records

PURPOSE Breast cancer risks for CHEK2 and ATM pathogenic variant (PV) carriers are modified by an 86-single nucleotide polymorphism polygenic risk score (PRS) and individual clinical factors. Here, we describe comprehensive risk prediction models for women of European ancestry combining PV status, PRS, and individual clinical variables. MATERIALS AND METHODS This study included deidentified clinical records from 358,095 women of European ancestry who received testing with a multigene panel (September 2013 to November 2019). Model development included CHEK2 PV carriers (n = 4,286), ATM PV carriers (n = 2,666), and women negative for other breast cancer risk gene PVs (n = 351,143). Odds ratios (ORs) were calculated using multivariable logistic regression with adjustment for familial cancer history. Risk estimates incorporating PV status, PRS, and Tyrer-Cuzick v7.02 were calculated using a Fixed-Stratified method that accounts for correlations between risk factors. Stratification of PV carriers into risk categories on the basis of remaining lifetime risk (RLR) was assessed in independent cohorts of PV carriers. RESULTS ORs for association of PV status with breast cancer were 2.01 (95% CI, 1.88 to 2.16) and 1.83 (95% CI, 1.68 to 2.00) for CHEK2 and ATM PV carriers, respectively. ORs for PRS per one standard deviation were 1.51 (95% CI, 1.37 to 1.66) and 1.45 (95% CI, 1.30 to 1.64) in CHEK2 and ATM PV carriers, respectively. Using the combined model (PRS plus Tyrer-Cuzick plus PV status), RLR was low (≤ 20%) for 24.2% of CHEK2 PV carriers, medium (20%-50%) for 63.8%, and high (> 50%) for 12.0%. Among ATM PV carriers, RLR was low for 31.5% of patients, medium for 58.5%, and high for 9.7%. CONCLUSION In CHEK2 and ATM PV carriers, risk assessment including PRS, Tyrer-Cuzick, and PV status has the potential for more precise direction of screening and prevention strategies.

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