Whole-genome sequencing of follicular thyroid carcinomas reveal recurrent mutations in microRNA processing subunit DGCR8 Whole-genome sequencing of follicular thyroid carcinomas reveal recurrent mutations in microRNA processing subunit DGCR8 2021-108-1-1 https://doi.org/10.5878/6fcv-1795 Swedish National Data Service Svensk nationell datatjänst Landing page Whole-genome sequencing of follicular thyroid carcinomas reveal recurrent mutations in microRNA processing subunit DGCR8 Whole-genome sequencing of follicular thyroid carcinomas reveal recurrent mutations in microRNA processing subunit DGCR8 2021-108-1-1 https://doi.org/10.5878/6fcv-1795 oai:DiVA.org:uu-459861 10.1210/clinem/dgab471 Juhlin, Christofer Juhlin, Christofer Paulsson, Johan Paulsson, Johan Swedish National Data Service Svensk nationell datatjänst Landing page HUMAN GENETICS HUMANGENETIK Endocrine Gland Neoplasms Tumörer i endokrina körtlar Thyroid Neoplasms Sköldkörteltumörer Thyroid Nodule Sköldkörtelknuta Data availability This dataset can only be shared within Sweden due to legal restrictions. Background The genomic and transcriptomic landscape of widely invasive follicular thyroid carcinomas (wiFTCs) is poorly characterized, and a large subset of these tumours lack information on credible genetic driver events. The aim of this study was to bridge this gap. Methods We performed whole-genome and RNA sequencing and subsequent bioinformatic analyses of 13 wiFTCs with a particularly poor prognosis, and matched normal tissue. Results Ten out of thirteen (77%) tumours exhibited one or several mutations in established genes ranked as the top 20 mutated in thyroid cancer, including TERT (n=4), NRAS (n=3), HRAS, KRAS, AKT, PTEN, PIK3CA, MUTYH and MEN1 (n=1 each). Recurrent somatic mutations in three genes were annotated as significant according to MutSig2CV: FAM72D (n=3), TP53 (n=3) and EIF1AX (n=3), with DGCR8 (n=2) as borderline significant. Of interest, both DGCR8 mutations were recurrent p.E518K missense alterations, a mutation known to cause familial multinodular goiter (MNG) via disruption of microRNA (miRNA) processing. Expression analyses pinpointed a trend towards reduced DGCR8 mRNA expression in FTCs in general. Copy number analyses revealed recurrent gains of loci on chromosomes 4, 6 and 10, and fusion gene analyses revealed 27 high-quality events. Based on the transcriptome data FTCs clustered in two principal clusters, displaying significant differences in expression of genes associated with metabolic pathways. Conclusion In summary, we describe the genomic and transcriptomic landscape in wiFTCs and identify novel recurrent mutations and copy number alterations with possible driver properties and lay the foundation for future studies. The dataset consists of tables and lists containing underlying data, and supplementary figures for a manuscript submitted to "Journal of Clinical Endocrinology & Metabolism". It includes 8 tables and 3 figures: File name: T1_Detailed-characteristics-of-the-study-cohort.csv Contains "Table 1: Detailed characteristics of the study cohort."  File name: T2_List-of-Somatic-SNVs.csv Contains "Table 2: List of Somatic SNV's (Small nucleotide variants)."  File name: T3_MutSig2CV-input-genes.csv Contains "Table 3: MutSig2CV input genes."  File name: T4_MutSig2CV-genes-ranked-by-p-value.csv Contains "Table 4: MutSig2CV genes ranked by p-value." File name: T5_Genes-in-copy-number-altered-minimal-region-of-amplification.csv Contains "Table 5: List of genes in copy number altered minimal region of amplification."  File name: T6_Aberrant-cell-fraction-and-ploidy-as-determined-by-ASCAT.csv Contains "Table 6: Aberrant cell fraction and ploidy as determined by ASCAT."  File name: T7_High-confidence-structural-variations-in-the-tumor-cohort.csv Contains "Table 7: List of high-confidence structural variations in the tumor cohort."  File name: T8_Significant-differentially-expressed-genes-in-tumor-vs-normal-thyroid.csv Contains "Table 8: List of significant differentially expressed genes in tumor versus normal thyroid." File name: List_of_variables.pdf Contains List of variables: Metadata and abbreviation explanations for Table 1-8. File name: Whole-genome-sequencing-follicular-thyroid-carcinomas_Figures.pdf Contains Supplementary Figure S1-S3: - Supplementary Figure S1: Somatic mutational overview in the WGS cohort.  - Supplementary Figure S2: Normalized DGCR8 mRNA expression in tumours with or without loss of heterozygosity (LOH) of the DGCR8 locus.  - Supplementary Figure S3: a Gene set enrichment analysis (GSEA). Tillgänglighet för data Datasetet kan endast delas inom Sverige på grund av juridiska restriktioner. Bakgrund Det fullständiga genomiska och transkriptomiska landskapet i widely invasive follikulära tyreoideacancrar är ännu ej helt kartlagt och en stor andel av dessa tumörer har ingen identifierad driver. Målet med denna studie var att identifiera fler drivers. Metod Studien innefattar helgenom- och transkriptomsekvensering samt bioinformatiska analyser av 13 stycken fall av widely invasive follikulära tyreoideacancrar med parad normal vävnad. Resultat Tio av tretton tumörer visade mutationer i tyreoideacancer-relaterade gener, TERT (n=4), NRAS (n=3), HRAS, KRAS, AKT, PTEN, PIK3CA, MUTYH and MEN1 (n=1 each). MutSig2CV-analysen visade signifikant återkommande mutationer i FAM72D (n=3), TP53 (n=3), EIF1AX (n=3), och DGCR8 (n=2). Båda DGCR8-mutationerna var p.E518K missense som är en mutation som visats orsaka ärftlig multinodös struma genom dysreglering av mikro-RNA-maskineriet. Inga fler DGCR8-mutationer hittades i en utökad kohort av follikulära tumörer men expressionsanalys visade signifikant nedreglerad DGCR8-uttryck i maligna jämfört med benigna follikulära tumörer. Vidare visade kopieantalsanalys återkommande amplifiering av cytoband på kromosom 4, 6 och 10. Konklusion Sammanfattningsvis presenterar vi det fullständiga genomiska och transkriptomiska landskapet i widely invasive follikulära tyreoideacancrar och vi identifierade återkommande mutationer och kopieantalsförändringar som kan utgöra viktiga faktorer i tumörutvecklingen av dessa tumörer. Datasetet består av tabeller och listor med underliggande data samt kompletterande bilder, för ett manuskript skickat till "Journal of Clinical Endocrinology & Metabolism". Det innehåller 8 tabeller och 3 bilder: Filnamn: T1_Detailed-characteristics-of-the-study-cohort.csv Innehåller "Table 1: Detailed characteristics of the study cohort."  File name: T2_List-of-Somatic-SNVs.csv Innehåller "Table 2: List of Somatic SNV's (Small nucleotide variants)."  Filnamn: T3_MutSig2CV-input-genes.csv Innehåller "Table 3: MutSig2CV input genes."  Filnamn: T4_MutSig2CV-genes-ranked-by-p-value.csv Innehåller "Table 4: MutSig2CV genes ranked by p-value." Filnamn: T5_Genes-in-copy-number-altered-minimal-region-of-amplification.csv Innehåller "Table 5: List of genes in copy number altered minimal region of amplification."  Filnamn: T6_Aberrant-cell-fraction-and-ploidy-as-determined-by-ASCAT.csv Innehåller "Table 6: Aberrant cell fraction and ploidy as determined by ASCAT."  Filnamn: T7_High-confidence-structural-variations-in-the-tumor-cohort.csv Innehåller "Table 7: List of high-confidence structural variations in the tumor cohort."  Filnamn: T8_Significant-differentially-expressed-genes-in-tumor-vs-normal-thyroid.csv Innehåller "Table 8: List of significant differentially expressed genes in tumor versus normal thyroid." Filnamn: List_of_variables.pdf Innehåller Variabellista med metadata och förkortningsuttydningar för Table 1-8. Filnamn: Whole-genome-sequencing-follicular-thyroid-carcinomas_Figures.pdf Innehåller Supplementary Figure S1-S3: - Supplementary Figure S1: Somatic mutational overview in the WGS cohort.  - Supplementary Figure S2: Normalized DGCR8 mRNA expression in tumours with or without loss of heterozygosity (LOH) of the DGCR8 locus.  - Supplementary Figure S3: a Gene set enrichment analysis (GSEA). Sweden Sverige The study included 13 patients with follicular thyroid carcinoma. All diagnosed at the Karolinska University Hospital, Stockholm. Studien inkluderade 13 fall av patienter med follikulär tyreoideacancer. Samtliga fall diagnosticerades på Karolinska Universitetssjukhuset. Text Still image Measurements and testsMeasurements and tests Mätningar och testerMätningar och tester Access to data through SND. Access to data is restricted. Åtkomst till data via SND. Tillgång till data är begränsad. restrictedAccess Paulsson, J. O., Rafati, N., DiLorenzo, S., Chen, Y., Haglund, F., Zedenius, J., & Juhlin, C. C. (n.d.). Whole-genome Sequencing of Follicular Thyroid Carcinomas Reveal Recurrent Mutations in MicroRNA Processing Subunit DGCR8. In Journal of Clinical Endocrinology and Metabolism (Vol. 106, Issue 11, pp. 3265–3282). https://doi.org/10.1210/clinem/dgab471 Paulsson, J. O., Rafati, N., DiLorenzo, S., Chen, Y., Haglund, F., Zedenius, J., & Juhlin, C. C. (n.d.). Whole-genome Sequencing of Follicular Thyroid Carcinomas Reveal Recurrent Mutations in MicroRNA Processing Subunit DGCR8. In Journal of Clinical Endocrinology and Metabolism (Vol. 106, Issue 11, pp. 3265–3282). https://doi.org/10.1210/clinem/dgab471 10.1210/clinem/dgab471 oai:DiVA.org:uu-459861 2021 oai:DiVA.org:uu-459861