Multiethnic genome‐wide association study of differentiated thyroid cancer in the <scp>EPITHYR</scp> consortium

Truong, Thérèse; Lesueur, Fabienne; Sugier, Pierre‐Emmanuel; Guibon, Julie; Xhaard, Constance; Karimi, Mojgan; Kulkarni, Om; Lucotte, Elise A.; Bacq‐Daian, Delphine; Boland‐Augé, Anne; Mulot, Claire; Laurent‐Puig, Pierre; Schvartz, Claire; Guizard, Anne‐Valérie; Ren, Yan; Adjadj, Élisabeth; Rachédi, Frédérique; Borson‐Chazot, Françoise; Ortiz, Rosa María Bravo; Lence-Anta, Juan J; Pereda, Celia M; Comiskey, Daniel F.; He, Hao; Liyanarachchi, Sandya; Chapelle, Albert de la; Elisei, Rossella; Gemignani, Federica; Thomsen, Hauke; Försti, Asta; Herzig, Anthony F.; Leutenegger, Anne‐Louise; Rubino, Carole; Ostroumova, Evgenia; Kesminiene, Ausrele; Boutron‐Ruault, Marie‐Christine; Deleuze, Jean‐François; Guénel, Pascal; Vathaire, Florent de

doi:10.1002/ijc.33488

Cited by 13 publications

(16 citation statements)

References 52 publications

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“…This association was replicated in subsequent studies conducted in diverse populations [75, 79, 80, 82-84, 87-89, 92-94]. However, the most recent GWAS, conducted in several European populations [72,73] and in one Asian population from Korea [74], analyzed a higher number of SNPs (using genotyped and imputed SNPs) and reported the strongest signal for respectively rs368187 and rs34081947 (r 2 = 0.98 in Europeans and r 2 = 0.90 in East Asians from the 1000 Genomes Project), which are in moderate LD with rs944289 (r 2 <0.70 in Europeans or East Asians from the 1000 Genomes Project). The recent European GWAS also reported an independent signal at rs116909374 and rs368187.…”

Section: Locus 14q133mentioning

confidence: 63%

“…GWAS are usually composed with one discovery phase that aims to analyze a large number of variants, followed by a replication phase consisting of validation of the most significant variants in an independent sample. Since 2009, seven GWAS were published on NMTC risk, of which six were conducted in individuals of European ancestry [68][69][70][71][72][73] and one was conducted in individuals of Asian ancestry from Korea [74] (Table 2). The latest GWAS conducted by Truong et al [73] also included a small discovery sample of individuals of Oceanian ancestry but with no replication set.…”

Section: Findings From Association Studiesmentioning

confidence: 99%

“…Since 2009, seven GWAS were published on NMTC risk, of which six were conducted in individuals of European ancestry [68][69][70][71][72][73] and one was conducted in individuals of Asian ancestry from Korea [74] (Table 2). The latest GWAS conducted by Truong et al [73] also included a small discovery sample of individuals of Oceanian ancestry but with no replication set. Among the GWAS conducted in the European ancestry population, one study focused on radiation-related PTC, with cases recruited in Belarus and aged 0−18 years old at the time of the Chernobyl accident [69].…”

Section: Findings From Association Studiesmentioning

confidence: 99%

See 2 more Smart Citations

Genetic Susceptibility to Differentiated Thyroid Cancer

Lesueur,

Truong

2023

Thyroid Cancer - The Road From Genes to Successful Treatment

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Differentiated thyroid carcinoma (DTC) represents more than 90% of all thyroid cancer histological types. Its incidence has increased at a faster rate than most other malignancies during the last three decades and varies considerably around the world. The familial form of the disease has also become more common than previously reported, accounting for 5−15% of DTC cases. The main established risk factor of thyroid cancer is exposure to ionizing radiation, particularly if occurred during childhood. Thyroid cancer (including DTC) is also characterized by having one of the highest familial risks of any cancer supporting heritable predisposition. In spite of such a high familial risk, linkage analysis in non-syndromic DTC families (i.e. families where DTC is the primary cancer) performed two decades ago mapped several susceptibility loci but did not lead to the identification of high-penetrance causal germline variants. More recently, genome-wide association studies based on population case–control studies identified a limited number of DTC-associated loci and suggested that multiple low penetrance genes are involved in predisposition to DTC. This chapter reviews known genetic factors predisposing to DTC as well as approaches used to map them in various populations, and opens up on alternative strategies that could help to understand DTC tumorigenesis.

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Section: Locus 14q133mentioning

confidence: 63%

Section: Findings From Association Studiesmentioning

confidence: 99%

Section: Findings From Association Studiesmentioning

confidence: 99%

See 1 more Smart Citation

Genetic Susceptibility to Differentiated Thyroid Cancer

Lesueur,

Truong

2023

Thyroid Cancer - The Road From Genes to Successful Treatment

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“…We used individual-level data from CECILE study [ 32 ], a French population-based case-control study on breast cancer (1,125 cases and 1,172 controls) and from the french case-control studies included in the EPITHYR consortium on thyroid cancer (CATHY, Young-thyr, and E3N studies totalling 1,129 women cases and 1,174 women controls) [ 33 ]. Only women of European ancestry were kept for the analyses.…”

Section: Methodsmentioning

confidence: 99%

“…Additional SNPs included dense coverage across known loci associated with common cancers, including breast cancer but not thyroid cancer. We added 13,759 custom markers of possible interest for thyroid cancer to the design of the chip [ 33 ]. Imputation of data from EPITHYR were then performed using the 1000 Genomes Project dataset as the reference panel (release of October 2014, version 3).…”

Section: Methodsmentioning

confidence: 99%

Leveraging pleiotropic association using sparse group variable selection in genomics data

Sutton

Sugier

Truong

et al. 2022

BMC Med Res Methodol

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Background Genome-wide association studies (GWAS) have identified genetic variants associated with multiple complex diseases. We can leverage this phenomenon, known as pleiotropy, to integrate multiple data sources in a joint analysis. Often integrating additional information such as gene pathway knowledge can improve statistical efficiency and biological interpretation. In this article, we propose statistical methods which incorporate both gene pathway and pleiotropy knowledge to increase statistical power and identify important risk variants affecting multiple traits. Methods We propose novel feature selection methods for the group variable selection in multi-task regression problem. We develop penalised likelihood methods exploiting different penalties to induce structured sparsity at a gene (or pathway) and SNP level across all studies. We implement an alternating direction method of multipliers (ADMM) algorithm for our penalised regression methods. The performance of our approaches are compared to a subset based meta analysis approach on simulated data sets. A bootstrap sampling strategy is provided to explore the stability of the penalised methods. Results Our methods are applied to identify potential pleiotropy in an application considering the joint analysis of thyroid and breast cancers. The methods were able to detect eleven potential pleiotropic SNPs and six pathways. A simulation study found that our method was able to detect more true signals than a popular competing method while retaining a similar false discovery rate. Conclusion We developed feature selection methods for jointly analysing multiple logistic regression tasks where prior grouping knowledge is available. Our method performed well on both simulation studies and when applied to a real data analysis of multiple cancers.

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Common and novel haplotype structures between different types of cancer

Gholami

2024

Cancer Reports

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BackgroundBackground: Genome‐wide association studies (GWAS) have identified hundreds of genetic variants associated with cancer risk. GWAS data are important for cancer prevention and understanding the underlying mechanisms of cancer.AimsThis study aimed to investigate the genetic association between different types of cancer using GWAS data and a bioinformatics approach.Methods and resultsThe significant GWAS variants associated with more than one cancer type were identified. Common linkage disequilibrium (LD) variants between different types of cancer were identified by 1000 genomes phase 3 LD data. Haplotype blocks were identified by analyzing 1000 Genomes phase 3 genotyping data in the GWAS populations. Subsequent analyses included functional SNP analyses and TCGA gene expression. The results associated with significant GWAS variants (P<5E‐8) showed the following haplotype associations in European population: GT rs4808075‐rs8170 haplotype on BABAM1 with breast and ovarian cancers, GC rs16857609‐rs11693806 haplotype on DIRC3 with breast and thyroid cancers, GCG rs380286‐rs401681‐rs31487 haplotype on CLPTM1L with skin and lung cancers, GGG rs4430796‐rs11651052‐rs11263763 haplotype on HNF1B with prostate and endometrial cancers, and GT rs10505477‐rs6983267 haplotype on CASC8 associated with colorectal and prostate cancers. All these genes had significantly different expressions in tumor tissues (P<1E‐3). In addition, the rs11693806 variant is located in the hsa‐miR‐873‐5p binding site and has an enhancing effect on the hsa‐miR‐873‐5p:DIRC3 interaction.ConclusionThese novel haplotype structures and miRNA:lncRNA interactions are important for understanding the common genetic link between cancers. These results can potentially be used in genetic panels.

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Multiethnic genome‐wide association study of differentiated thyroid cancer in the EPITHYR consortium

Cited by 13 publications

References 52 publications

Genetic Susceptibility to Differentiated Thyroid Cancer

Genetic Susceptibility to Differentiated Thyroid Cancer

Leveraging pleiotropic association using sparse group variable selection in genomics data

Common and novel haplotype structures between different types of cancer

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