Whole-genome sequence-based analysis of thyroid function
Open accessAbstract
Normal thyroid function is essential for health, but its genetic architecture remains poorly understood. Here, for the heritable thyroid traits thyrotropin (TSH) and free thyroxine (FT4), we analyse whole-genome sequence data from the UK10K project (N=2,287). Using additional whole-genome sequence and deeply imputed data sets, we report meta-analysis results for common variants (MAF≥1%) associated with TSH and FT4 (N=16,335). For TSH, we identify a novel variant in SYN2 (MAF=23.5%, P=6.15 × 10−9) and a new independent variant in PDE8B (MAF=10.4%, P=5.94 × 10−14). For FT4, we report a low-frequency variant near B4GALT6/SLC25A52 (MAF=3.2%, P=1.27 × 10−9) tagging a rare TTR variant (MAF=0.4%, P=2.14 × 10−11). All common variants explain ≥20% of the variance in TSH and FT4. Analysis of rare variants (MAF<1%) using sequence kernel association testing reveals a novel association with FT4 in NRG1. Our results demonstrate that increased coverage in whole-genome sequence association studies identifies novel variants associated with thyroid function.
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The largest thyroid GWASs have identified over 100 genetic variants associated with TSH or FT4 concentrations, or both.
“The largest thyroid GWASs have focused on variations in thyroid hormone concentrations in the general population, identifying over 100 genetic variants associated with TSH or FT4 concentrations, or both.[45][46][47]”
From Hypothyroidism (2024) · cites this paper as [47]
The Results (Single-point association analysis; page not provided) report associations with TSH and FT4, supporting the claim that genetic variants have been identified for these traits. But the Results (GCTA and polygenic score analysis; page not provided) refer to 67 SNPs previously associated with thyroid function in GWAS; this paper does not substantiate the cited sentence’s count of over 100 variants. (LLM, conf=0.88)
Experimental — accuracy not yet measuredThyroid hormone levels are largely genetically determined, with similar genetic effects observed in children and adults.
“Furthermore, thyroid hormone levels are largely genetically determined [6–8] with similar genetic effects observed in children and adults [8].”
From Age-related variation in thyroid function – a narrative review highlighting important implications for research and clinical practice (2023) · cites this paper as [8]
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Self-citation
- Authors
- Taylor, P. N., Porcu, E., Chew, S., Campbell, P. J., Traglia, M., Brown, S. J., Mullin, B. H., Shihab, H. A., Min, J., Walter, K., Memari, Y., Huang, J., Barnes, M. R., Beilby, J. P., Charoen, P., Danecek, P., Dudbridge, F., Forgetta, V., Greenwood, C., Grundberg, E., Johnson, A. D., Hui, J., Lim, E. M., McCarthy, S., Muddyman, D., Panicker, V., Perry, J. R. B., Bell, J. T., Yuan, W., Relton, C., Gaunt, T., Schlessinger, D., Abecasis, G., Cucca, F., Surdulescu, G. L., Woltersdorf, W., Zeggini, E., Zheng, H.-F., Toniolo, D., Dayan, C. M., Naitza, S., Walsh, J. P., Spector, T., Davey Smith, G., Durbin, R., Brent Richards, J., Sanna, S., Soranzo, N., Timpson, N. J., Wilson, S. G., The UK10K Consortium, Turki, S. A., Anderson, C., Anney, R., Antony, D., Artigas, M. S., Ayub, M., Balasubramaniam, S., Barrett, J. C., Barroso, I., Beales, P., Bentham, J., Bhattacharya, S., Birney, E., Blackwood, D., Bobrow, M., Bochukova, E., Bolton, P., Bounds, R., Boustred, C., Breen, G., Calissano, M., Carss, K., Chatterjee, K., Chen, L., Ciampi, A., Cirak, S., Clapham, P., Clement, G., Coates, G., Collier, D., Cosgrove, C., Cox, T., Craddock, N., Crooks, L., Curran, S., Curtis, D., Daly, A., Day-Williams, A., Day, I. N. M., Down, T., Du, Y., Dunham, I., Edkins, S., Ellis, P., Evans, D., Faroogi, S., Fatemifar, G., Fitzpatrick, D. R., Flicek, P., Flyod, J., Foley, A. R., Franklin, C. S., Futema, M., Gallagher, L., Geihs, M., Geschwind, D., Griffin, H., Grozeva, D., Guo, X., Guo, X., Gurling, H., Hart, D., Hendricks, A., Holmans, P., Howie, B., Huang, L., Hubbard, T., Humphries, S. E., Hurles, M. E., Hysi, P., Jackson, D. K., Jamshidi, Y., Jing, T., Joyce, C., Kaye, J., Keane, T., Keogh, J., Kemp, J., Kennedy, K., Kolb-Kokocinski, A., Lachance, G., Langford, C., Lawson, D., Lee, I., Lek, M., Liang, J., Lin, H., Li, R., Li, Y., Liu, R., Lönnqvist, J., Lopes, M., Iotchkova, V., MacArthur, D., Marchini, J., Maslen, J., Massimo, M., Mathieson, I., Marenne, G., McGuffin, P., McIntosh, A., McKechanie, A. G., McQuillin, A., Metrustry, S., Mitchison, H., Moayyeri, A., Morris, J., Muntoni, F., Northstone, K., O'Donnovan, M., Onoufriadis, A., O'Rahilly, S., Oualkacha, K., Owen, M. J., Palotie, A., Panoutsopoulou, K., Parker, V., Parr, J. R., Paternoster, L., Paunio, T., Payne, F., Pietilainen, O., Plagnol, V., Quaye, L., Quail, M. A., Raymond, L., Rehnström, K., Ring, S., Ritchie, G. R. S., Roberts, N., Savage, D. B., Scambler, P., Schiffels, S., Schmidts, M., Schoenmakers, N., Semple, R. K., Serra, E., Sharp, S. I., Shin, S.-Y., Skuse, D., Small, K., Southam, L., Spasic-Boskovic, O., Clair, D. S., Stalker, J., Stevens, E., Pourcian, B. S., Sun, J., Suvisaari, J., Tachmazidou, I., Tobin, M. D., Valdes, A., Kogelenberg, M. V., Vijayarangakannan, P., Visscher, P. M., Wain, L. V., Walters, J. T. R., Wang, G., Wang, J., Wang, Y., Ward, K., Wheeler, E., Whyte, T., Williams, H., Williamson, K. A., Wilson, C., Wong, K., Xu, C., Yang, J., Zhang, F., & Zhang, P.
- Affiliations
- Cardiff University (GB)
- University of Sassari (IT)
- Sir Charles Gairdner Hospital (AU)
- IRCCS Ospedale San Raffaele (IT)
- The University of Western Australia (AU)
- University of Bristol (GB)
- Wellcome Sanger Institute (GB)
- Queen Mary University of London (GB)
- Mahidol University (TH)
- London School of Hygiene & Tropical Medicine (GB)
- Jewish General Hospital (CA)
- National Heart, Lung, and Blood Institute (US)
- University of Cambridge (GB)
- King's College London (GB)
- National Institutes of Health (US)
- Istituto di Genetica Molecolare (IT)
- Institute of Genetic and Biomedical Research (IT)
- Queen's University (CA)
- University College London (GB)
- Centre for Human Genetics (GB)
- European Bioinformatics Institute (GB)
- Royal Edinburgh Hospital (GB)
- Great Ormond Street Hospital (GB)
- McGill University (CA)
- University of Sussex (GB)
- Biogen (United States) (US)
- Guy's Hospital (GB)
- BGI Group (China) (CN)
- Translational Research Institute (AU)
- Western General Hospital (GB)
- University of California, Los Angeles (US)
- University of Oxford (GB)
- Adaptive Biotechnologies (United States) (US)
- St George's, University of London (GB)
- Massachusetts General Hospital (US)
- Finnish Institute for Health and Welfare (FI)
- Broad Institute (US)
- Harvard University (US)
- Université du Québec à Montréal (CA)
- Newcastle University (GB)
- University of Helsinki (FI)
- University of Aberdeen (GB)
- University of Leicester (GB)
- Corresponding author
- Taylor, Peter N.
- Wilson, Scott G.
- ORCID
- Taylor, Peter N.
- Porcu, Eleonora
- Campbell, Purdey J.
- Traglia, Michela
- Brown, Suzanne J.
- Mullin, Benjamin H.
- Min, Josine
- Walter, Klaudia
- Memari, Yasin
- Huang, Jie
- Barnes, Michael R.
- Beilby, John P.
- Charoen, Pimphen
- Danecek, Petr
- Dudbridge, Frank
- Forgetta, Vincenzo
- Greenwood, Celia
- Grundberg, Elin
- Johnson, Andrew D.
- Hui, Jennie
- Lim, Ee M.
- McCarthy, Shane
- Panicker, Vijay
- Perry, John R.B.
- Bell, Jordana T.
- Relton, Caroline
- Gaunt, Tom
- Cucca, Francesco
- Zeggini, Eleftheria
- Zheng, Hou-Feng
- Toniolo, Daniela
- Dayan, Colin M.
- Naitza, Silvia
- Walsh, John P.
- Spector, Tim
- Durbin, Richard
- Sanna, Serena
- Soranzo, Nicole
- Timpson, Nicholas J.
- Wilson, Scott G.
- Anderson, Carl
- Anney, Richard
- Ayub, Muhammad
- Barrett, Jeffrey C.
- Barroso, Inês
- Bhattacharya, Shoumo
- Birney, Ewan
- Blackwood, Douglas
- Bochukova, Elena
- Bounds, Rebecca
- Breen, Gerome
- Carss, Keren
- Chatterjee, Krishna
- Chen, Lu
- Ciampi, Antonio
- Coates, Guy
- Collier, David
- Craddock, Nick
- Crooks, Lucy
- Curran, Sarah
- Down, Thomas
- Dunham, Ian
- Edkins, Sarah
- Evans, David
- Fatemifar, Ghazaleh
- Fitzpatrick, David R.
- Flicek, Paul
- Foley, A. Reghan
- Futema, Marta
- Gallagher, Louise
- Geihs, Matthias
- Geschwind, Daniel
- Grozeva, Detelina
- Guo, Xueqin
- Hart, Deborah
- Hendricks, Audrey
- Holmans, Peter
- Hubbard, Tim
- Humphries, Steve E.
- Hurles, Matthew E.
- Hysi, Pirro
- Jackson, David K.
- Jamshidi, Yalda
- Kaye, Jane
- Keane, Thomas
- Keogh, Julia
- Kemp, John
- Langford, Cordelia
- Lee, Irene
- Lek, Monkol
- Lönnqvist, Jouko
- Iotchkova, Valentina
- MacArthur, Daniel
- Marchini, Jonathan
- Mathieson, Iain
- Marenne, Gaëlle
- McIntosh, Andrew
- McKechanie, Andrew G.
- McQuillin, Andrew
- Metrustry, Sarah
- Mitchison, Hannah
- Moayyeri, Alireza
- Morris, James
- Northstone, Kate
- Onoufriadis, Alexandros
- Oualkacha, Karim
- Owen, Michael J.
- Palotie, Aarno
- Panoutsopoulou, Kalliope
- Parker, Victoria
- Parr, Jeremy R.
- Paternoster, Lavinia
- Paunio, Tiina
- Payne, Felicity
- Plagnol, Vincent
- Quail, Michael A.
- Ring, Susan
- Ritchie, Graham R.S.
- Roberts, Nicola
- Savage, David B.
- Scambler, Peter
- Schmidts, Miriam
- Schoenmakers, Nadia
- Semple, Robert K.
- Serra, Eva
- Sharp, Sally I.
- Skuse, David
- Small, Kerrin
- Southam, Lorraine
- Clair, David St
- Sun, Jianping
- Suvisaari, Jaana
- Tobin, Martin D.
- Valdes, Ana
- Visscher, Peter M.
- Wain, Louise V.
- Walters, James T.R.
- Wang, Guangbiao
- Wang, Jun
- Wang, Yu
- Ward, Kirsten
- Williams, Hywel
- Williamson, Kathleen A.
- Wong, Kim
- Yang, Jian
- Zhang, Pingbo
- Venue
- Nature Communications
- Published
- 2015-03-06
- Volume
- 6
- Issue
- 1
- Pages
- 5681-5681
- ISSN
- 2041-1723 (ISSN-L)
- PMC
- PMC4366514
- OpenAlex
- W2109761709
- Cited by
- 104
- References
- 43
- Citations by year
- 2026: 1 · 2025: 4 · 2024: 8 · 2023: 10 · 2022: 6 · 2021: 15 · 2020: 10 · 2019: 5 · 2018: 11 · 2017: 14 · 2016: 8 · 2015: 12
- FWCI
- 10.48
- Type
- journal article
- Language
- en
- Update notices
- erratum (2015-05-20)
- Open access
- gold
- doi.org
- Locations
- Nature Communications (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- UWA Profiles and Research Repository (UWA) (publishedVersion, other-oa)
- PubMed (publishedVersion)
- Research Portal (King's College London) (publishedVersion, cc-by)
- Research at the University of Copenhagen (University of Copenhagen) (publishedVersion, other-oa)
- ORCA Online Research @Cardiff (Cardiff University) (acceptedVersion, cc-by)
- St George's Online Research Archive (St George's University of London) (acceptedVersion)
- Archipel (Université du Québec à Montréal) (acceptedVersion)
- LSHTM Research Online (London School of Hygiene and Tropical Medicine) (acceptedVersion)
- Minerva Access (University of Melbourne) (submittedVersion, cc-by)
- Sussex Research Online (University of Sussex) (submittedVersion, cc-by)
- Digital Access to Scholarship at Harvard (DASH) (Harvard University) (submittedVersion, cc-by)
- RePEc: Research Papers in Economics (submittedVersion)
- UCL Discovery (University College London) (submittedVersion)
- Figshare (submittedVersion, cc-by)
- Työväentutkimus Vuosikirja (submittedVersion)
- University of Birmingham Research Portal (University of Birmingham) (submittedVersion, other-oa)
- Edinburgh Research Explorer (University of Edinburgh) (submittedVersion, cc-by)
- Queen Mary Research Online (Queen Mary University of London) (submittedVersion, cc-by)
- Bristol Research (University of Bristol) (submittedVersion)
- Explore Bristol Research (submittedVersion)
- Newcastle University ePrints (Newcastle Univesity) (cc-by)
- Funders
- Wellcome Trust (095515, 091551, 098498, 100574, UK10K, 102215, 100140, WT091310, 096599)
- British Heart Foundation (RG/10/17/28553)
- Medical Research Council (MC_UU_12015/2, MR/K006215/1, MR/L010305/1, MC_PC_15018)
- Biotechnology and Biological Sciences Research Council (BB/I025263/1, BB/I025751/1)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Health Sciences › Medicine › Endocrinology, Diabetes and Metabolism › Thyroid Disorders and Treatments
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
- Keywords
- thyroid function, thyroid-stimulating hormone, free thyroxine, genetic architecture, common genetic variants, rare variants, PDE8B, TTR variants, neuregulin-1
- MeSH terms
- United Kingdom, Humans, Thyroid Gland, Thyrotropin, Thyroxine, 3',5'-Cyclic-AMP Phosphodiesterases, Cohort Studies, Synapsins, DNA Methylation, Genomics, Genetic Association Studies
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
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