Identifying Thyroid Carcinoma-Related Genes by Integrating GWAS and eQTL Data

Shen, Fei; Gan, Xiao‐Xiong; Zhong, Ruiying; Feng, Jianhua; Chen, Zhe; Guo, Mingming; Li, Yayi; Zhaofeng, Wu; Cai, Wei; Xu, Bo

doi:10.3389/fcell.2021.645275

Cited by 5 publications

(5 citation statements)

References 51 publications

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“…This analysis demonstrated the existence of shared genetic variants across the different cancer types grouped as hormone-sensitive cancers. For these genetic variants, we replicated 36 independent SNPs associated with the risk of a specific type of cancer, such as breast, prostate, uterine or ovarian cancer, which were identified in previous GWAS 30 – 36 . Significant signals for each independent hormone-sensitive cancer involves 8q24.1, 10q26.13, 11q13.3, 16q12.1, and 17q12 genomic regions, of which 12 were for breast, 18 for prostate, 2 for uterine cancer, and 1 for ovarian cancer corresponded to previously identified as causal variants involved in the components of hormone-sensitive cancer (Supplementary Table 7 ).…”

Section: Resultsmentioning

confidence: 84%

Considering hormone-sensitive cancers as a single disease in the UK biobank reveals shared aetiology

et al. 2022

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Hormone-related cancers, including cancers of the breast, prostate, ovaries, uterine, and thyroid, globally contribute to the majority of cancer incidence. We hypothesize that hormone-sensitive cancers share common genetic risk factors that have rarely been investigated by previous genomic studies of site-specific cancers. Here, we show that considering hormone-sensitive cancers as a single disease in the UK Biobank reveals shared genetic aetiology. We observe that a significant proportion of variance in disease liability is explained by the genome-wide single nucleotide polymorphisms (SNPs), i.e., SNP-based heritability on the liability scale is estimated as 10.06% (SE 0.70%). Moreover, we find 55 genome-wide significant SNPs for the disease, using a genome-wide association study. Pair-wise analysis also estimates positive genetic correlations between some pairs of hormone-sensitive cancers although they are not statistically significant. Our finding suggests that heritable genetic factors may be a key driver in the mechanism of carcinogenesis shared by hormone-sensitive cancers.

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Section: Resultsmentioning

confidence: 84%

Considering hormone-sensitive cancers as a single disease in the UK biobank reveals shared aetiology

et al. 2022

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“…This analysis demonstrated the existence of shared genetic variants across the different cancer types grouped as hormone-sensitive cancers. For these genetic variants, we replicated 36 independent SNPs associated with the risk of a speci c type of cancer, such as breast, prostate, endometrial or ovarian cancer, which were identi ed in previous GWAS 17,18,19,20,21,22,23 . Signi cant signals for each independent hormone-sensitive cancer involves 8q24.1, 10q26.13, 11q13.3, 16q12.1 & 17q12 genomic regions, of which 12 were for breast, 18 for prostate, 2 for endometrial cancer, and 1 for ovarian cancer corresponded to previously identi ed as causal variants involved in the components of hormone-sensitive cancer (Supplementary Table 6).…”

Section: Snp-based Heritability (Snp-h2) For Groups Of Cancersmentioning

confidence: 87%

Heritability And Genetic Correlations For Hormone-Sensitive Cancers In The UK Biobank: A Molecular Evidence of Shared Aetiology

Ahmed

Mäkinen

Mulugeta

et al. 2021

Preprint

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Hormone-related cancers, including cancers of the breast, prostate, ovaries, uterine, and thyroid, globally contribute to the majority of cancer incidence. We hypothesize that hormone-sensitive cancers share common genetic risk factors that have rarely been investigated by previous genomic studies of site-specific cancers. To test this hypothesis, we analysed five hormone-sensitive cancers in the UK Biobank as a single disease. We observed that a significant proportion of variance in disease liability was explained by the genome-wide single nucleotide polymorphisms (SNPs), i.e., SNP-based heritability on the liability scale was estimated as 10.06% (SE 0.70%) for the disease. Moreover, we found 55 genome-wide significant SNPs for the disease, using a genome-wide association study. Our finding suggests that heritable genetic factors may be a key driver in the mechanism of carcinogenesis shared by hormone-sensitive cancers.

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“…In addition, genotype-phenotype causality can be useful for understanding other complex traits such as predisposition to depression and anxiety [14]. Through the analysis of genetic data and observations of phenotypes, it is possible to determine which genes are responsible for these traits and understand how they interact with each other [15,16].…”

Section: Discussionmentioning

confidence: 99%

Evaluation of the influence of single-nucleotide polymorphisms of vitamin D receptor (rs2228570), BDNF (rs6265), and NMDA (rs4880213) genes on gene expression in different tissues

Kamyshna

Pavlovych

Pankiv

et al. 2023

Mìžnarodnij endokrinologìčnij žurnal

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Background. Questions regarding the association of individual and combined gene variations and mutations with thyroid disease and nervous system disorders remain insufficiently researched and require further study to facilitate early diagnosis of nervous system damage on the background of thyroid pathology, disease prognosis, and timely treatment and prevention. An important issue is the identification of the influence of individual polymorphisms in these genes on the functional activity of cells, including gene expression. Currently, gene expression genetics largely depends on the identification of expression quantitative trait loci (eQTL), which are the links between gene expression and genotype at a locus. The purpose of the study was to search for eQTL in single nucleotide polymorphisms (SNPs) of the BDNF gene (rs6265), VDR gene (rs2228570), and NMDA gene (rs4880213). The results were presented as nominal p-values for each SNP of the BDNF, VDR, and NMDA genes. Materials and methods. We use publicly available databases (QTLbase: http://www.mulinlab.org/qtlbase/index.html, GTExPortal: https://gtexportal.org). Results. Using the QTLbase, we identified statistically significant (p ≤ 0.05) associations of rs6265 with the expression of 17 genes (BDNF-AS, BDNF, LDHC, AC104563.1, BBOX1, SPTY2D1OS, YWHABP2, LINC00678, LIN7C, GTF2H1, METTL15, IMMP1L, KIF18A, HPS5, NAV2, LGR4, CCDC34) in various tissues. For rs4880213, we found a significant association with the expression levels of 49 genes (ARRDC1-AS1, TPRN, SSNA1, SAPCD2, UAP1L1, NPDC1, MAN1B1, PTGDS, SNHG7, NDOR1, TRAF2, PHPT1, EGFL7, EHMT1, RNF208, PNPLA7, LCNL1, DPP7, LCN12, STPG3, CCDC183-AS1, ABCA2, RNF224, ENTPD2, PAXX, CLIC3, C9orf163, LCN15, MAN1B1-DT, FAM166A, FAM166A, LRRC26, STPG3-AS1, AGPAT2, ANAPC2, DPH7, ZMYND19, NSMF, MRPL41, EXD3, TUBB4B, NELFB, ARRDC1, EDF1, FBXW5, DIPK1B, MAMDC4, RABL6, TMEM141, TMEM203) in 16 different tissues. Additionally, we identified statistically significant (p ≤ 0.05) associations of rs2228570 with the expression of 29 genes (ASB8, TMEM106C, KANSL2, DDX23, CCNT1, HDAC7, RPAP3, PFKM, SENP1, RND1, PCED1B, AC004466.1, AMIGO2, ZNF641, ENDOU, RAPGEF3, VDR, AC004241.1, AC004801.2, AC121338.1, LINC02354, SNORA2A, LINC02416, AC074029.3, AC004241.5, AC008083.3, COL2A1, CCDC184, SLC48A1) in 17 different tissues. Conclusions. Single nucleotide polymorphisms of the BDNF (rs6265), VDR (rs2228570), and NMDA genes (rs4880213) affect gene expression in various cells and tissues. The use of this extensive eQTL catalog provides an important resource for understanding the molecular basis of common genetic diseases.

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Identifying Thyroid Carcinoma-Related Genes by Integrating GWAS and eQTL Data

Cited by 5 publications

References 51 publications

Considering hormone-sensitive cancers as a single disease in the UK biobank reveals shared aetiology

Considering hormone-sensitive cancers as a single disease in the UK biobank reveals shared aetiology

Heritability And Genetic Correlations For Hormone-Sensitive Cancers In The UK Biobank: A Molecular Evidence of Shared Aetiology

Evaluation of the influence of single-nucleotide polymorphisms of vitamin D receptor (rs2228570), BDNF (rs6265), and NMDA (rs4880213) genes on gene expression in different tissues

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