Validity Assessment of Low-risk SCORE Function and SCORE Function Calibrated to the Spanish Population in the FRESCO Cohorts

Abstract Background Genome-wide association studies have identified thousands of disease-associated single nucleotide polymorphisms (SNPs). A subset of these SNPs may be additively combined to generate genetic risk scores (GRSs) that confer risk for a specific disease. Although the clinical validity of GRSs to predict risk of specific diseases has been well established, there is still a great need to determine their clinical utility by applying GRSs in primary care for cancer risk assessment and targeted intervention. Methods This clinical study involved 281 primary care patients without a personal history of breast, prostate or colorectal cancer who were 40–70 years old. DNA was obtained from a pre-existing biobank at NorthShore University HealthSystem. GRSs for colorectal cancer and breast or prostate cancer were calculated and shared with participants through their primary care provider. Additional data was gathered using questionnaires as well as electronic medical record information. A t-test or Chi-square test was applied for comparison of demographic and key clinical variables among different groups. Results The median age of the 281 participants was 58 years and the majority were female (66.6%). One hundred one (36.9%) participants received 2 low risk scores, 99 (35.2%) received 1 low risk and 1 average risk score, 37 (13.2%) received 1 low risk and 1 high risk score, 23 (8.2%) received 2 average risk scores, 21 (7.5%) received 1 average risk and 1 high risk score, and no one received 2 high risk scores. Before receiving GRSs, younger patients and women reported significantly more worry about risk of developing cancer. After receiving GRSs, those who received at least one high GRS reported significantly more worry about developing cancer. There were no significant differences found between gender, age, or GRS with regards to participants’ reported optimism about their future health neither before nor after receiving GRS results. Conclusions Genetic risk scores that quantify an individual’s risk of developing breast, prostate and colorectal cancers as compared with a race-defined population average risk have potential clinical utility as a tool for risk stratification and to guide cancer screening in a primary care setting.

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Identification of a two-gene prognostic model associated with cytolytic activity for colon cancer

Cancer Cell International ◽

10.1186/s12935-021-01782-6 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Xiaoye Jiang ◽

Zhongxiang Jiang ◽

Lichun Xiang ◽

Xuenuo Chen ◽

Jiao Wu ◽

...

Keyword(s):

Colon Cancer ◽

Risk Score ◽

Immune Checkpoint ◽

Prognostic Model ◽

Quantitative Polymerase Chain Reaction ◽

Cytolytic Activity ◽

Low Risk ◽

Gene Set Enrichment Analysis ◽

Aberrant Expression ◽

Immune Activity

Abstract Background Increasing evidence has shown that cytolytic activity (CYT) is a new immunotherapy biomarker that characterises the antitumour immune activity of cytotoxic T cells and macrophages. In this study, we established a prognostic model associated with CYT. Methods A prognostic model based on CYT-related genes was developed. Furthermore, aberrant expression of genes of the model in colon cancer (CC) was identified by reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and immunohistochemistry (IHC) assays. Next, the correlation between the model and T-cell infiltration in the CC microenvironment was analysed. The Tumour Immune Dysfunction and Exclusion (TIDE) algorithm and subclass mapping were used to predict clinical responses to immune checkpoint inhibitors. Results In total, 280 of the 1418 genes were differentially expressed based on CYT. A prognostic model (including HOXC8 and MS4A2) was developed based on CYT-related genes. The model was validated using the testing set, the whole set and a Gene Expression Omnibus (GEO) cohort (GSE41258). Gene set enrichment analysis (GSEA) and other analyses showed that the levels of immune infiltration and antitumour immune activation in low-risk-score tumours were greater than those in high-risk-score tumours. CC patients with a low-risk-score showed more promise in the response to anti-immune checkpoint therapy. Conclusions Overall, our model may precisely predict the overall survival of CC and reflect the strength of antitumour immune activity in the CC microenvironment. Furthermore, the model may be a predictive factor for the response to immunotherapy.

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Short-term risk stratification using CADILLAC risk score in patients with ST elevation myocardial infarction

European Heart Journal ◽

10.1093/ehjci/ehaa946.1352 ◽

2020 ◽

Vol 41 (Supplement_2) ◽

Author(s):

T Satou ◽

H Kitahara ◽

K Ishikawa ◽

T Nakayama ◽

Y Fujimoto ◽

...

Keyword(s):

Myocardial Infarction ◽

High Risk ◽

Adverse Events ◽

Risk Score ◽

Risk Group ◽

Risk Groups ◽

Low Risk ◽

Short Term ◽

Recurrent Myocardial Infarction ◽

St Elevation

Abstract Background The recent reperfusion therapy for ST-elevation myocardial infarction (STEMI) has made the length of hospital stay shorter without adverse events. CADILLAC risk score is reportedly one of the risk scores predicting the long-term prognosis in STEMI patients. Purpose To invenstigate the usefulness of CADILLAC risk score for predicting short-term outcomes in STEMI patients. Methods Consecutive patients admitted to our university hospital and our medical center with STEMI (excluding shock, arrest case) who underwent primary PCI between January 2012 and April 2018 (n=387) were enrolled in this study. The patients were classified into 3 groups according to the CADILLAC risk score: low risk (n=176), intermediate risk (n=87), and high risk (n=124). Data on adverse events within 30 days after hospitalization, including in-hospital death, sustained ventricular arrhythmia, recurrent myocardial infarction, heart failure requiring intravenous treatment, stroke, or clinical hemorrhage, were collected. Results In the low risk group, adverse events within 30 days were significantly less observed, compared to the intermediate and high risk groups (n=13, 7.4% vs. n=13, 14.9% vs. n=58, 46.8%, p<0.001). In particular, all adverse events occurred within 3 days in the low risk group, although adverse events, such as heart failure (n=4), recurrent myocardial infarction (n=1), stroke (n=1), and gastrointestinal bleeding (n=1), were substantially observed after day 4 of hospitalization in the intermediate and high risk groups. Conclusions In STEMI patients with low CADILLAC risk score, better short-term prognosis was observed compared to the intermediate and high risk groups, and all adverse events occurred within 3 days of hospitalization, suggesting that discharge at day 4 might be safe in this study population. CADILLAC risk score may help stratify patient risk for short-term prognosis and adjust management of STEMI patients. Initial event occurrence timing Funding Acknowledgement Type of funding source: None

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Validation of the Zwolle score for selection of very low-risk STEMI patients treated with primary angioplasty

European Heart Journal ◽

10.1093/ehjci/ehaa946.1840 ◽

2020 ◽

Vol 41 (Supplement_2) ◽

Author(s):

A Cordero ◽

B Cid ◽

P Monteiro ◽

J.M Garcia-Acuna ◽

M Rodriguez-Manero ◽

...

Keyword(s):

Hospital Mortality ◽

Risk Score ◽

Mortality Risk ◽

Area Under The Curve ◽

Coronary Intervention ◽

Low Risk ◽

Individual Risk ◽

Care Organization ◽

Grace Score ◽

Selection Of

Abstract Background The Zwolle risk score was designed to stratify the actual in-hospital mortality risk of ST-elevation myocardial infarction (STEMI) patients treated with primary percutaneous coronary intervention (p-PCI) but, also, for decision-making related to patients location in an intensive care unit or not. Since the GRACE score continues being the gold-standard for individual risk assessment in STEMI in most institutions we assessed the specificity of both scores for in-hospital mortality. Methods We assessed the accuracy of Zwolle risk score for in-hospital mortality estimation as compared to the GRACE score in all patients admitted for STEMI in 3 tertitary hospitals. Patients with Zwolle risk score <3 would qualify as “low risk”, 3–5 as “intermediate risk” and ≥6 as “high risk”. Patients with GRACE score <140 were classified as low-risk. Specificity, sensitivity and classification were assessed by ROC curves and the area under the curve (AUC). Results We included 4,446 patients, mean age 64.7 (13.6) years, 24% women and 39% with diabetes. Mean GRACE score was 157.3 (4.9) and Zwolle was 2.8 (3.3). In-hospital mortality was 10.6% (471 patients). Patients who died had higher GRACE score (218.4±4.9 vs. 149.6±37.5; p<0.001) and Zwolle score (7.6±4.3 vs. 2.3±2.18; p<0.001); a statistically significant increase of in-hospital mortality risk, adjusted adjusted by age, gender and revascularization, was observed with both scores (figure). A total of 1,629 patients (40.0%) were classified as low risk by the GRACE score and 2,962 (66.6%) by the Zwolle score; in-hospital mortality was 1.6% and 2.7%, respectively. Moreover, the was a significant increase of in-hospital mortality rate according to Zwolle categories (2.7%; 13.0%; 41.6%)The AUC of both score was the same (p=0.49) but the specificity of GRACE score <140 was 43.1% as compared to 72.6% obtained by Zwolle score <3; patients accurately classified was also lower with the GRACE score threshold (48.8% vs. 73.7%). Conclusions Selection of low-risk STEMI patients treated with p-PCI based on the Zwolle risk score has higher specificity than the GRACE score and might be useful for the care organization in clinical practice. Funding Acknowledgement Type of funding source: None

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A prognostic model based on seven immune-related genes predicts the overall survival of patients with hepatocellular carcinoma

BioData Mining ◽

10.1186/s13040-021-00261-y ◽

2021 ◽

Vol 14 (1) ◽

Author(s):

Qian Yan ◽

Wenjiang Zheng ◽

Boqing Wang ◽

Baoqian Ye ◽

Huiyan Luo ◽

...

Keyword(s):

Hepatocellular Carcinoma ◽

Overall Survival ◽

High Risk ◽

Risk Score ◽

Immune Cells ◽

Prognostic Model ◽

Risk Groups ◽

Low Risk ◽

Prognostic Performance ◽

Immune Related Genes

Abstract Background Hepatocellular carcinoma (HCC) is a disease with a high incidence and a poor prognosis. Growing amounts of evidence have shown that the immune system plays a critical role in the biological processes of HCC such as progression, recurrence, and metastasis, and some have discussed using it as a weapon against a variety of cancers. However, the impact of immune-related genes (IRGs) on the prognosis of HCC remains unclear. Methods Based on The Cancer Gene Atlas (TCGA) and Immunology Database and Analysis Portal (ImmPort) datasets, we integrated the ribonucleic acid (RNA) sequencing profiles of 424 HCC patients with IRGs to calculate immune-related differentially expressed genes (DEGs). Survival analysis was used to establish a prognostic model of survival- and immune-related DEGs. Based on genomic and clinicopathological data, we constructed a nomogram to predict the prognosis of HCC patients. Gene set enrichment analysis further clarified the signalling pathways of the high-risk and low-risk groups constructed based on the IRGs in HCC. Next, we evaluated the correlation between the risk score and the infiltration of immune cells, and finally, we validated the prognostic performance of this model in the GSE14520 dataset. Results A total of 100 immune-related DEGs were significantly associated with the clinical outcomes of patients with HCC. We performed univariate and multivariate least absolute shrinkage and selection operator (Lasso) regression analyses on these genes to construct a prognostic model of seven IRGs (Fatty Acid Binding Protein 6 (FABP6), Microtubule-Associated Protein Tau (MAPT), Baculoviral IAP Repeat Containing 5 (BIRC5), Plexin-A1 (PLXNA1), Secreted Phosphoprotein 1 (SPP1), Stanniocalcin 2 (STC2) and Chondroitin Sulfate Proteoglycan 5 (CSPG5)), which showed better prognostic performance than the tumour/node/metastasis (TNM) staging system. Moreover, we constructed a regulatory network related to transcription factors (TFs) that further unravelled the regulatory mechanisms of these genes. According to the median value of the risk score, the entire TCGA cohort was divided into high-risk and low-risk groups, and the low-risk group had a better overall survival (OS) rate. To predict the OS rate of HCC, we established a gene- and clinical factor-related nomogram. The receiver operating characteristic (ROC) curve, concordance index (C-index) and calibration curve showed that this model had moderate accuracy. The correlation analysis between the risk score and the infiltration of six common types of immune cells showed that the model could reflect the state of the immune microenvironment in HCC tumours. Conclusion Our IRG prognostic model was shown to have value in the monitoring, treatment, and prognostic assessment of HCC patients and could be used as a survival prediction tool in the near future.

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Non-Lynch Familial and Early-Onset Colorectal Cancer Explained by Accumulation of Low-Risk Genetic Variants

Cancers ◽

10.3390/cancers13153857 ◽

2021 ◽

Vol 13 (15) ◽

pp. 3857

Author(s):

Pilar Mur ◽

Nuria Bonifaci ◽

Anna Díez-Villanueva ◽

Elisabet Munté ◽

Maria Henar Alonso ◽

...

Keyword(s):

Colorectal Cancer ◽

Risk Score ◽

Early Onset ◽

Low Risk ◽

Polygenic Risk Score ◽

Polygenic Risk ◽

Pathogenic Variants ◽

Predisposing Genes ◽

The Mean ◽

Early Onset Colorectal Cancer

A large proportion of familial and/or early-onset cancer patients do not carry pathogenic variants in known cancer predisposing genes. We aimed to assess the contribution of previously validated low-risk colorectal cancer (CRC) alleles to familial/early-onset CRC (fCRC) and to serrated polyposis. We estimated the association of CRC with a 92-variant-based weighted polygenic risk score (wPRS) using 417 fCRC patients, 80 serrated polyposis patients, 1077 hospital-based incident CRC patients, and 1642 controls. The mean wPRS was significantly higher in fCRC than in controls or sporadic CRC patients. fCRC patients in the highest (20th) wPRS quantile were at four-fold greater CRC risk than those in the middle quantile (10th). Compared to low-wPRS fCRC, a higher number of high-wPRS fCRC patients had developed multiple primary CRCs, had CRC family history, and were diagnosed at age ≥50. No association with wPRS was observed for serrated polyposis. In conclusion, a relevant proportion of mismatch repair (MMR)-proficient fCRC cases might be explained by the accumulation of low-risk CRC alleles. Validation in independent cohorts and development of predictive models that include polygenic risk score (PRS) data and other CRC predisposing factors will determine the implementation of PRS into genetic testing and counselling in familial and early-onset CRC.

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Identifying individuals with high risk of Alzheimer’s disease using polygenic risk scores

Nature Communications ◽

10.1038/s41467-021-24082-z ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Ganna Leonenko ◽

Emily Baker ◽

Joshua Stevenson-Hoare ◽

Annerieke Sierksma ◽

Mark Fiers ◽

...

Keyword(s):

High Risk ◽

Risk Score ◽

Genetic Risk ◽

Prediction Accuracy ◽

Genetic Risk Score ◽

Low Risk ◽

Risk Scores ◽

Sample Mean ◽

Polygenic Risk ◽

Reliable Identification

AbstractPolygenic Risk Scores (PRS) for AD offer unique possibilities for reliable identification of individuals at high and low risk of AD. However, there is little agreement in the field as to what approach should be used for genetic risk score calculations, how to model the effect of APOE, what the optimal p-value threshold (pT) for SNP selection is and how to compare scores between studies and methods. We show that the best prediction accuracy is achieved with a model with two predictors (APOE and PRS excluding APOE region) with pT<0.1 for SNP selection. Prediction accuracy in a sample across different PRS approaches is similar, but individuals’ scores and their associated ranking differ. We show that standardising PRS against the population mean, as opposed to the sample mean, makes the individuals’ scores comparable between studies. Our work highlights the best strategies for polygenic profiling when assessing individuals for AD risk.

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Development and Verification of the Hypoxia- and Immune-Associated Prognostic Signature for Pancreatic Ductal Adenocarcinoma

Frontiers in Immunology ◽

10.3389/fimmu.2021.728062 ◽

2021 ◽

Vol 12 ◽

Author(s):

Dongjie Chen ◽

Hui Huang ◽

Longjun Zang ◽

Wenzhe Gao ◽

Hongwei Zhu ◽

...

Keyword(s):

High Risk ◽

Pancreatic Ductal Adenocarcinoma ◽

Risk Score ◽

Cox Regression ◽

Pearson Correlation ◽

Risk Groups ◽

Low Risk ◽

Ductal Adenocarcinoma ◽

Prognostic Signature ◽

Score Model

We aim to construct a hypoxia- and immune-associated risk score model to predict the prognosis of patients with pancreatic ductal adenocarcinoma (PDAC). By unsupervised consensus clustering algorithms, we generate two different hypoxia clusters. Then, we screened out 682 hypoxia-associated and 528 immune-associated PDAC differentially expressed genes (DEGs) of PDAC using Pearson correlation analysis based on the Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression project (GTEx) dataset. Seven hypoxia and immune-associated signature genes (S100A16, PPP3CA, SEMA3C, PLAU, IL18, GDF11, and NR0B1) were identified to construct a risk score model using the Univariate Cox regression and the Least Absolute Shrinkage and Selection Operator (LASSO) Cox regression, which stratified patients into high- and low-risk groups and were further validated in the GEO and ICGC cohort. Patients in the low-risk group showed superior overall survival (OS) to their high-risk counterparts (p < 0.05). Moreover, it was suggested by multivariate Cox regression that our constructed hypoxia-associated and immune-associated prognosis signature might be used as the independent factor for prognosis prediction (p < 0.001). By CIBERSORT and ESTIMATE algorithms, we discovered that patients in high-risk groups had lower immune score, stromal score, and immune checkpoint expression such as PD-L1, and different immunocyte infiltration states compared with those low-risk patients. The mutation spectrum also differs between high- and low-risk groups. To sum up, our hypoxia- and immune-associated prognostic signature can be used as an approach to stratify the risk of PDAC.

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