Validation of the novel susceptibility loci for prostate cancer in a Chinese population

Wu, Yishuo; Chen, Haitao; Ji, Ying; Na, Rong; Mo, Zengnan; Ye, Dingwei; Wang, Meilin; Qi, Jun; Lin, Xiaoling; Ding, Qiang; Xu, Jianfeng; Zheng, S. Lilly; Sun, Yinghao; Wang, Meng

doi:10.3892/ol.2017.7602

Cited by 4 publications

(4 citation statements)

References 22 publications

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“…Up to now, conclusions on etiology of prostate carcinogenesis is still inconsistent. In recent decades, researchers pay more attention to the relationship between single‐nucleotide polymorphism and cancer susceptibility, including PCa . Previous clinical studies and in vitro experiments showed evidence that CDKN1B is a significant tumor suppressor gene in the development of PCa .…”

Section: Discussionmentioning

confidence: 99%

“…In recent decades, researchers pay more attention to the relationship between singlenucleotide polymorphism and cancer susceptibility, including PCa. [31][32][33] Previous clinical studies and in vitro experiments showed evidence that CDKN1B is a significant tumor suppressor gene in the development of PCa. 25,34 Several polymorphisms of CDKN1B gene have been reported to be correlated with PCa risk, however, only the Val 109 Gly variant located in exon area could lead to one amino acid change.…”

Section: Discussionmentioning

confidence: 99%

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CDKN1B Val 109 Gly variant is not related to risk of prostate cancer

Zhu

Jun

Yue

et al. 2019

J of Cellular Biochemistry

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Association between CDKN1B gene Val 109 Gly polymorphism and prostate cancer (PCa) susceptibility has been investigated in several studies but with inconsistent conclusions. We adopted odds ratios (ORs) and 95% confidence intervals (CIs) to assess the correlation between CDKN1B Val 109 Gly variant and PCa susceptibility. Moreover, we used in‐silico tools to evaluate the relationship of CDKN1B expression and overall survival (OS) or disease free survival (DFS) time in PCa patients. The overall results demonstrated no association of the CDKN1B variant on PCa risk [allelic contrast (OR = 0.78, 95% CI = 0.45 − 1.35, Pheterogeneity = 0.038); GV vs VV (OR = 0.83, 95% CI = 0.56 − 1.25, Pheterogeneity = 0.253); GG vs VV (OR = 0.48, 95% CI = 0.23 − 1.01, Pheterogeneity = 0.161); GG+GV vs VV (OR = 0.75, 95% CI = 0.52 −1.08, Pheterogeneity = 0.132) and GG vs GV+VV (OR = 0.63, 95% CI = 0.25 − 1.11, Pheterogeneity = 0.152)]. In subgroup analysis by ethnicity and source of control, we also identified similar results. In‐silico results showed that expression of CDKN1B was decreased in PCa tissue, especially in less advanced PCa (Gleason score = 6 or 7). No significant difference of OS or DFS time was indicated between the low and high expression of CDKN1B. Our present study showed evidence that CDKN1B Val 109 Gly variant is not related to PCa risk. Future studies with large sample size are needed to confirm this correlation in more details.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

CDKN1B Val 109 Gly variant is not related to risk of prostate cancer

Zhu

Jun

Yue

et al. 2019

J of Cellular Biochemistry

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“…Since these SNPs exhibited a cumulative effect on PCa risk, several polygenic risk score (PRS) methods have been used for measuring the cumulative association of SNPs 4 . The PRS derived from PCa risk‐associated SNPs based on different populations were well‐established and able to evaluate an individual's risk of PCa in previous studies 5–8 . It could be used either for inherited risk assessment among general population or help differentiate the individuals at higher risk of positive biopsies in biopsy cohorts as an add‐on to PSA and other examinations.…”

Section: Introductionmentioning

confidence: 99%

“…4 The PRS derived from PCa riskassociated SNPs based on different populations were well-established and able to evaluate an individual's risk of PCa in previous studies. [5][6][7][8] It could be used either for inherited risk assessment among general population or help differentiate the individuals at higher risk of positive biopsies in biopsy cohorts as an add-on to PSA and other examinations. A population-standardized PRS is calculated by multiplying by all SNPs and each SNP is standardized against the general population, so its expected mean value shall always be 1.0 in a general population, regardless of the number of SNPs included in the calculation.…”

Section: Introductionmentioning

confidence: 99%

Systematic evaluation of narrow‐sense validity of polygenic risk score for prostate cancer in a Chinese prostate biopsy cohort

Ruan

Gao

et al. 2023

Clinical Genetics

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The aim of this study was to assess the narrow‐sense validity of polygenic risk score (PRS) for prostate cancer (PCa) in a Chinese prostate biopsy cohort. We performed an observational prospective study with 2640 men who underwent prostate biopsy. Germline DNA samples were genotyped and PRS was calculated for each subject using 17 PCa risk‐associated genetic variants. Additional GWAS data of the ChinaPCa dataset was also used to compliment the evaluation process. The mean PRS was 1.02 in patients with negative biopsy results, which met the baseline benchmark. The mean PRS was significantly higher in the PCa cases (1.32 vs. 1.02, p = 5.56 × 10−17). Significant dose–response associations between PRS values and odds ratios for PCa were observed. However, the raw calibration slope was 0.524 and the average bias score between the observed risk and uncorrected PRS value was 0.307 in the entire biopsy cohort. After applying a correction factor derived from a training set, the corrected calibration slope improved to 1.002 in a testing set. Similar and satisfied results were also seen in the ChinaPCa dataset and two datasets combined, while the calibration results were inaccurate when the calibration process were performed mutually between two different study populations. In conclusion, assessing the narrow‐sense validity of PRS is necessary prior to its clinical implementation for accurate individual risk assessment.

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Cross-population analysis for functional characterization of type II diabetes variants

Elmansy

Koyutürk

2019

BMC Bioinformatics

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Background As Genome-Wide Association Studies (GWAS) have been increasingly used with data from various populations, it has been observed that data from different populations reveal different sets of Single Nucleotide Polymorphisms (SNPs) that are associated with the same disease. Using Type II Diabetes (T2D) as a test case, we develop measures and methods to characterize the functional overlap of SNPs associated with the same disease across populations. Results We introduce the notion of an Overlap Matrix as a general means of characterizing the functional overlap between different SNP sets at different genomic and functional granularities. Using SNP-to-gene mapping, functional annotation databases, and functional association networks, we assess the degree of functional overlap across nine populations from Asian and European ethnic origins. We further assess the generalizability of the method by applying it to a dataset for another complex disease – Prostate Cancer. Our results show that more overlap is captured as more functional data is incorporated as we go through the pipeline, starting from SNPs and ending at network overlap analyses. We hypothesize that these observed differences in the functional mechanisms of T2D across populations can also explain the common use of different prescription drugs in different populations. We show that this hypothesis is concordant with the literature on the functional mechanisms of prescription drugs. Conclusion Our results show that although the etiology of a complex disease can be associated with distinct processes that are affected in different populations, network-based annotations can capture more functional overlap across populations. These results support the notion that it can be useful to take ethnicity into account in making personalized treatment decisions for complex diseases.

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Validation of the novel susceptibility loci for prostate cancer in a Chinese population

Cited by 4 publications

References 22 publications

CDKN1B Val 109 Gly variant is not related to risk of prostate cancer

CDKN1B Val 109 Gly variant is not related to risk of prostate cancer

Systematic evaluation of narrow‐sense validity of polygenic risk score for prostate cancer in a Chinese prostate biopsy cohort

Cross-population analysis for functional characterization of type II diabetes variants

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