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51. IMI 2021 Yearly Digest

Author

Jong, Monica, Jonas, J.B., Wolffsohn, J.S., Berntsen, D.A., Cho, P., Clarkson-Townsend, D., Flitcroft, D.I., Gifford, K.L., Haarman, A.E.G., Pardue, M.T., Richdale, K., Sankaridurg, P., Tedja, M.S., Wildsoet, C.F., Bailey-Wilson, J.E., Guggenheim, J.A., Hammond, C.J., Kaprio, J., MacGregor, S., Mackey, D.A., Musolf, A.M., Klaver, C.C.W., Verhoeven, V.J.M., Vitart, V., Smith, E.L., 3rd, Jong, Monica, Jonas, J.B., Wolffsohn, J.S., Berntsen, D.A., Cho, P., Clarkson-Townsend, D., Flitcroft, D.I., Gifford, K.L., Haarman, A.E.G., Pardue, M.T., Richdale, K., Sankaridurg, P., Tedja, M.S., Wildsoet, C.F., Bailey-Wilson, J.E., Guggenheim, J.A., Hammond, C.J., Kaprio, J., MacGregor, S., Mackey, D.A., Musolf, A.M., Klaver, C.C.W., Verhoeven, V.J.M., Vitart, V., and Smith, E.L., 3rd

Abstract

Item does not contain fulltext, PURPOSE: The International Myopia Institute (IMI) Yearly Digest highlights new research considered to be of importance since the publication of the first series of IMI white papers. METHODS: A literature search was conducted for articles on myopia between 2019 and mid-2020 to inform definitions and classifications, experimental models, genetics, interventions, clinical trials, and clinical management. Conference abstracts from key meetings in the same period were also considered. RESULTS: One thousand articles on myopia have been published between 2019 and mid-2020. Key advances include the use of the definition of premyopia in studies currently under way to test interventions in myopia, new definitions in the field of pathologic myopia, the role of new pharmacologic treatments in experimental models such as intraocular pressure-lowering latanoprost, a large meta-analysis of refractive error identifying 336 new genetic loci, new clinical interventions such as the defocus incorporated multisegment spectacles and combination therapy with low-dose atropine and orthokeratology (OK), normative standards in refractive error, the ethical dilemma of a placebo control group when myopia control treatments are established, reporting the physical metric of myopia reduction versus a percentage reduction, comparison of the risk of pediatric OK wear with risk of vision impairment in myopia, the justification of preventing myopic and axial length increase versus quality of life, and future vision loss. CONCLUSIONS: Large amounts of research in myopia have been published since the IMI 2019 white papers were released. The yearly digest serves to highlight the latest research and advances in myopia.

Published
2021

52. Genome-wide meta-analysis identifies 127 open-angle glaucoma loci with consistent effect across ancestries

Author

Gharahkhani, P., Jorgenson, E., Hysi, P., Khawaja, A.P., Pendergrass, S., Han, X., Ong, J.S., Hewitt, A.W., Segrè, A.V., Rouhana, J.M., Hamel, A.R., Igo, R.P., Jr., Choquet, H., Qassim, A., Josyula, N.S., Bailey, J.N., Bonnemaijer, P.W.M., Iglesias, A., Siggs, O.M., Young, T.L., Vitart, V., Thiadens, A., Karjalainen, J., Uebe, S., Melles, R.B., Nair, K.S., Luben, R., Simcoe, M., Amersinghe, N., Cree, A.J., Hohn, R., Poplawski, A., Chen, L.J., Rong, S.S., Aung, T., Vithana, E.N., Tamiya, G., Shiga, Y., Yamamoto, M., Nakazawa, T., Currant, H., Birney, E., Wang, X, Auton, A., Lupton, M.K., Martin, N.G., Ashaye, A., Olawoye, O., Williams, S.E., Akafo, S., Ramsay, M., Hashimoto, K., Kamatani, Y., Akiyama, M., Momozawa, Y., Foster, P.J., Khaw, P.T., Morgan, J.E., Strouthidis, N.G., Kraft, P., Kang, J.H., Pang, C.P., Pasutto, F., Mitchell, P., Lotery, A.J., Palotie, A., Duijn, C. van, Haines, J.L., Hammond, C., Pasquale, L.R., Klaver, C.C.W., Hauser, M., Khor, C.C., Mackey, D.A., Kubo, M., Cheng, C.Y., Craig, J.E., MacGregor, S., Wiggs, J.L., Gharahkhani, P., Jorgenson, E., Hysi, P., Khawaja, A.P., Pendergrass, S., Han, X., Ong, J.S., Hewitt, A.W., Segrè, A.V., Rouhana, J.M., Hamel, A.R., Igo, R.P., Jr., Choquet, H., Qassim, A., Josyula, N.S., Bailey, J.N., Bonnemaijer, P.W.M., Iglesias, A., Siggs, O.M., Young, T.L., Vitart, V., Thiadens, A., Karjalainen, J., Uebe, S., Melles, R.B., Nair, K.S., Luben, R., Simcoe, M., Amersinghe, N., Cree, A.J., Hohn, R., Poplawski, A., Chen, L.J., Rong, S.S., Aung, T., Vithana, E.N., Tamiya, G., Shiga, Y., Yamamoto, M., Nakazawa, T., Currant, H., Birney, E., Wang, X, Auton, A., Lupton, M.K., Martin, N.G., Ashaye, A., Olawoye, O., Williams, S.E., Akafo, S., Ramsay, M., Hashimoto, K., Kamatani, Y., Akiyama, M., Momozawa, Y., Foster, P.J., Khaw, P.T., Morgan, J.E., Strouthidis, N.G., Kraft, P., Kang, J.H., Pang, C.P., Pasutto, F., Mitchell, P., Lotery, A.J., Palotie, A., Duijn, C. van, Haines, J.L., Hammond, C., Pasquale, L.R., Klaver, C.C.W., Hauser, M., Khor, C.C., Mackey, D.A., Kubo, M., Cheng, C.Y., Craig, J.E., MacGregor, S., and Wiggs, J.L.

Abstract

Contains fulltext : 235429.pdf (Publisher’s version ) (Open Access), Primary open-angle glaucoma (POAG), is a heritable common cause of blindness world-wide. To identify risk loci, we conduct a large multi-ethnic meta-analysis of genome-wide association studies on a total of 34,179 cases and 349,321 controls, identifying 44 previously unreported risk loci and confirming 83 loci that were previously known. The majority of loci have broadly consistent effects across European, Asian and African ancestries. Cross-ancestry data improve fine-mapping of causal variants for several loci. Integration of multiple lines of genetic evidence support the functional relevance of the identified POAG risk loci and highlight potential contributions of several genes to POAG pathogenesis, including SVEP1, RERE, VCAM1, ZNF638, CLIC5, SLC2A12, YAP1, MXRA5, and SMAD6. Several drug compounds targeting POAG risk genes may be potential glaucoma therapeutic candidates.

Published
2021

53. Germline variation in the insulin-like growth factor pathway and risk of Barrett's esophagus and esophageal adenocarcinoma

Author

Dighe, S.G., Chen, J., Yan, L., He, Q., Gharahkhani, P., Onstad, L., Levine, D.M., Palles, C., Ye, W., Gammon, M.D., Iyer, P.G., Anderson, L.A., Liu, G., Wu, A.H., Dai, J.Y., Chow, W.H., Risch, H.A., Lagergren, J., Shaheen, N.J., Bernstein, L., Corley, D.A., Prenen, H., DeCaestecker, J., MacDonald, D., Moayyedi, P., Barr, H., Love, S.B., Chegwidden, L., Attwood, S., Watson, P., Harrison, R., Ott, K., Moebus, S., Venerito, M., Lang, H., Mayershofer, R., Knapp, M., Veits, L., Gerges, C., Weismüller, J., Gockel, I., Vashist, Y., Nöthen, M.M., Izbicki, J.R., Manner, H., Neuhaus, H., Rösch, T., Böhmer, A.C., Hölscher, A.H., Anders, M., Pech, O., Schumacher, B., Schmidt, C., Schmidt, T., Noder, T., Lorenz, D., Vieth, M., May, A., Hess, T., Kreuser, N., Becker, J., Ell, C., Ambrosone, C.B., Moysich, K.B., MacGregor, S., Tomlinson, I., Whiteman, D.C., Jankowski, J., Schumacher, J., Vaughan, T.L., Madeleine, M.M., Hardie, L.J., Buas, M.F., Dighe, S.G., Chen, J., Yan, L., He, Q., Gharahkhani, P., Onstad, L., Levine, D.M., Palles, C., Ye, W., Gammon, M.D., Iyer, P.G., Anderson, L.A., Liu, G., Wu, A.H., Dai, J.Y., Chow, W.H., Risch, H.A., Lagergren, J., Shaheen, N.J., Bernstein, L., Corley, D.A., Prenen, H., DeCaestecker, J., MacDonald, D., Moayyedi, P., Barr, H., Love, S.B., Chegwidden, L., Attwood, S., Watson, P., Harrison, R., Ott, K., Moebus, S., Venerito, M., Lang, H., Mayershofer, R., Knapp, M., Veits, L., Gerges, C., Weismüller, J., Gockel, I., Vashist, Y., Nöthen, M.M., Izbicki, J.R., Manner, H., Neuhaus, H., Rösch, T., Böhmer, A.C., Hölscher, A.H., Anders, M., Pech, O., Schumacher, B., Schmidt, C., Schmidt, T., Noder, T., Lorenz, D., Vieth, M., May, A., Hess, T., Kreuser, N., Becker, J., Ell, C., Ambrosone, C.B., Moysich, K.B., MacGregor, S., Tomlinson, I., Whiteman, D.C., Jankowski, J., Schumacher, J., Vaughan, T.L., Madeleine, M.M., Hardie, L.J., and Buas, M.F.

Abstract

Contains fulltext : 235640.pdf (Publisher’s version ) (Closed access), Genome-wide association studies (GWAS) of esophageal adenocarcinoma (EAC) and its precursor, Barrett's esophagus (BE), have uncovered significant genetic components of risk, but most heritability remains unexplained. Targeted assessment of genetic variation in biologically relevant pathways using novel analytical approaches may identify missed susceptibility signals. Central obesity, a key BE/EAC risk factor, is linked to systemic inflammation, altered hormonal signaling and insulin-like growth factor (IGF) axis dysfunction. Here, we assessed IGF-related genetic variation and risk of BE and EAC. Principal component analysis was employed to evaluate pathway-level and gene-level associations with BE/EAC, using genotypes for 270 single-nucleotide polymorphisms (SNPs) in or near 12 IGF-related genes, ascertained from 3295 BE cases, 2515 EAC cases and 3207 controls in the Barrett's and Esophageal Adenocarcinoma Consortium (BEACON) GWAS. Gene-level signals were assessed using Multi-marker Analysis of GenoMic Annotation (MAGMA) and SNP summary statistics from BEACON and an expanded GWAS meta-analysis (6167 BE cases, 4112 EAC cases, 17 159 controls). Global variation in the IGF pathway was associated with risk of BE (P = 0.0015). Gene-level associations with BE were observed for GHR (growth hormone receptor; P = 0.00046, false discovery rate q = 0.0056) and IGF1R (IGF1 receptor; P = 0.0090, q = 0.0542). These gene-level signals remained significant at q < 0.1 when assessed using data from the largest available BE/EAC GWAS meta-analysis. No significant associations were observed for EAC. This study represents the most comprehensive evaluation to date of inherited genetic variation in the IGF pathway and BE/EAC risk, providing novel evidence that variation in two genes encoding cell-surface receptors, GHR and IGF1R, may influence risk of BE.

Published
2021

54. A comprehensive re-assessment of the association between vitamin D and cancer susceptibility using Mendelian randomization

Author

Ong, JS, Dixon-Suen, Suzanne, Han, X, An, J, Fitzgerald, R, Buas, M, Gammon, MD, Corley, DA, Shaheen, NJ, Hardie, LJ, Bird, NC, Reid, BJ, Chow, WH, Risch, HA, Ye, W, Liu, G, Romero, Y, Bernstein, L, Wu, AH, Whiteman, DE, Vaughan, T, Agee, M, Alipanahi, B, Auton, A, Bell, RK, Bryc, K, Elson, SL, Fontanillas, P, Furlotte, NA, Hinds, DA, Huber, KE, Kleinman, A, Litterman, NK, McIntyre, MH, Mountain, JL, Noblin, ES, Northover, CAM, Pitts, SJ, Sathirapongsasuti, JF, Sazonova, OV, Shelton, JF, Shringarpure, S, Tian, C, Tung, JY, Vacic, V, Wilson, CH, Liyanage, U, Dusingize, JC, Schumacher, J, Gockel, I, Böhmer, A, Jankowski, J, Palles, C, O’Mara, T, Spurdle, A, Law, MH, Iles, MM, Pharoah, P, Berchuck, A, Zheng, W, Thrift, AP, Olsen, C, Neale, RE, Gharahkhani, P, Webb, PM, MacGregor, S, Ong, JS, Dixon-Suen, Suzanne, Han, X, An, J, Fitzgerald, R, Buas, M, Gammon, MD, Corley, DA, Shaheen, NJ, Hardie, LJ, Bird, NC, Reid, BJ, Chow, WH, Risch, HA, Ye, W, Liu, G, Romero, Y, Bernstein, L, Wu, AH, Whiteman, DE, Vaughan, T, Agee, M, Alipanahi, B, Auton, A, Bell, RK, Bryc, K, Elson, SL, Fontanillas, P, Furlotte, NA, Hinds, DA, Huber, KE, Kleinman, A, Litterman, NK, McIntyre, MH, Mountain, JL, Noblin, ES, Northover, CAM, Pitts, SJ, Sathirapongsasuti, JF, Sazonova, OV, Shelton, JF, Shringarpure, S, Tian, C, Tung, JY, Vacic, V, Wilson, CH, Liyanage, U, Dusingize, JC, Schumacher, J, Gockel, I, Böhmer, A, Jankowski, J, Palles, C, O’Mara, T, Spurdle, A, Law, MH, Iles, MM, Pharoah, P, Berchuck, A, Zheng, W, Thrift, AP, Olsen, C, Neale, RE, Gharahkhani, P, Webb, PM, and MacGregor, S

Abstract

Previous Mendelian randomization (MR) studies on 25-hydroxyvitamin D (25(OH)D) and cancer have typically adopted a handful of variants and found no relationship between 25(OH)D and cancer; however, issues of horizontal pleiotropy cannot be reliably addressed. Using a larger set of variants associated with 25(OH)D (74 SNPs, up from 6 previously), we perform a unified MR analysis to re-evaluate the relationship between 25(OH)D and ten cancers. Our findings are broadly consistent with previous MR studies indicating no relationship, apart from ovarian cancers (OR 0.89; 95% C.I: 0.82 to 0.96 per 1 SD change in 25(OH)D concentration) and basal cell carcinoma (OR 1.16; 95% C.I.: 1.04 to 1.28). However, after adjustment for pigmentation related variables in a multivariable MR framework, the BCC findings were attenuated. Here we report that lower 25(OH)D is unlikely to be a causal risk factor for most cancers, with our study providing more precise confidence intervals than previously possible

Published
2021

55. Genetic variation affects morphological retinal phenotypes extracted from UK Biobank optical coherence tomography images

Author

Currant, H., Hysi, P., Fitzgerald, T.W., Gharahkhani, P., Bonnemaijer, P.W.M., Senabouth, A., Hewitt, A.W., Atan, D., Aung, T., Charng, J., Choquet, H., Craig, J., Khaw, P.T., Klaver, C.C.W., Kubo, M., Ong, J.S., Pasquale, L.R., Reisman, C.A., Daniszewski, M., Powell, J.E., Pébay, A., Simcoe, M.J., Thiadens, A., Duijn, C.M. van, Yazar, S., Jorgenson, E., MacGregor, S., Hammond, C.J., Mackey, D.A., Wiggs, J.L., Foster, P.J., Patel, P.J., Birney, E., Khawaja, A.P., Currant, H., Hysi, P., Fitzgerald, T.W., Gharahkhani, P., Bonnemaijer, P.W.M., Senabouth, A., Hewitt, A.W., Atan, D., Aung, T., Charng, J., Choquet, H., Craig, J., Khaw, P.T., Klaver, C.C.W., Kubo, M., Ong, J.S., Pasquale, L.R., Reisman, C.A., Daniszewski, M., Powell, J.E., Pébay, A., Simcoe, M.J., Thiadens, A., Duijn, C.M. van, Yazar, S., Jorgenson, E., MacGregor, S., Hammond, C.J., Mackey, D.A., Wiggs, J.L., Foster, P.J., Patel, P.J., Birney, E., and Khawaja, A.P.

Abstract

Contains fulltext : 235428.pdf (Publisher’s version ) (Open Access), Optical Coherence Tomography (OCT) enables non-invasive imaging of the retina and is used to diagnose and manage ophthalmic diseases including glaucoma. We present the first large-scale genome-wide association study of inner retinal morphology using phenotypes derived from OCT images of 31,434 UK Biobank participants. We identify 46 loci associated with thickness of the retinal nerve fibre layer or ganglion cell inner plexiform layer. Only one of these loci has been associated with glaucoma, and despite its clear role as a biomarker for the disease, Mendelian randomisation does not support inner retinal thickness being on the same genetic causal pathway as glaucoma. We extracted overall retinal thickness at the fovea, representative of foveal hypoplasia, with which three of the 46 SNPs were associated. We additionally associate these three loci with visual acuity. In contrast to the Mendelian causes of severe foveal hypoplasia, our results suggest a spectrum of foveal hypoplasia, in part genetically determined, with consequences on visual function.

Published
2021

56. IMI 2021 Yearly Digest

Author

Jong, M, Jonas, JB, Wolffsohn, JS, Berntsen, DA, Cho, P, Clarkson-Townsend, D, Flitcroft, DI, Gifford, KL, Haarman, AEG, Pardue, MT, Richdale, K, Sankaridurg, P, Tedja, MS, Wildsoet, CF, Bailey-Wilson, JE, Guggenheim, JA, Hammond, CJ, Kaprio, J, MacGregor, S, Mackey, DA, Musolf, AM, Klaver, CCW, Verhoeven, VJM, Vitart, V, Smith, EL, Jong, M, Jonas, JB, Wolffsohn, JS, Berntsen, DA, Cho, P, Clarkson-Townsend, D, Flitcroft, DI, Gifford, KL, Haarman, AEG, Pardue, MT, Richdale, K, Sankaridurg, P, Tedja, MS, Wildsoet, CF, Bailey-Wilson, JE, Guggenheim, JA, Hammond, CJ, Kaprio, J, MacGregor, S, Mackey, DA, Musolf, AM, Klaver, CCW, Verhoeven, VJM, Vitart, V, and Smith, EL

Abstract

PURPOSE: The International Myopia Institute (IMI) Yearly Digest highlights new research considered to be of importance since the publication of the first series of IMI white papers. METHODS: A literature search was conducted for articles on myopia between 2019 and mid-2020 to inform definitions and classifications, experimental models, genetics, interventions, clinical trials, and clinical management. Conference abstracts from key meetings in the same period were also considered. RESULTS: One thousand articles on myopia have been published between 2019 and mid-2020. Key advances include the use of the definition of premyopia in studies currently under way to test interventions in myopia, new definitions in the field of pathologic myopia, the role of new pharmacologic treatments in experimental models such as intraocular pressure-lowering latanoprost, a large meta-analysis of refractive error identifying 336 new genetic loci, new clinical interventions such as the defocus incorporated multisegment spectacles and combination therapy with low-dose atropine and orthokeratology (OK), normative standards in refractive error, the ethical dilemma of a placebo control group when myopia control treatments are established, reporting the physical metric of myopia reduction versus a percentage reduction, comparison of the risk of pediatric OK wear with risk of vision impairment in myopia, the justification of preventing myopic and axial length increase versus quality of life, and future vision loss. CONCLUSIONS: Large amounts of research in myopia have been published since the IMI 2019 white papers were released. The yearly digest serves to highlight the latest research and advances in myopia.

Published
2021

57. Cardiovascular Disease Predicts Structural and Functional Progression in Early Glaucoma

Author

Marshall, H, Mullany, S, Qassim, A, Siggs, O, Hassall, M, Ridge, B, Thi, N, Awadalla, M, Andrew, NH, Healey, PR, Agar, A, Galanopoulos, A, Hewitt, AW, MacGregor, S, Graham, SL, Mills, R, Shulz, A, Landers, J, Casson, RJ, Craig, JE, Marshall, H, Mullany, S, Qassim, A, Siggs, O, Hassall, M, Ridge, B, Thi, N, Awadalla, M, Andrew, NH, Healey, PR, Agar, A, Galanopoulos, A, Hewitt, AW, MacGregor, S, Graham, SL, Mills, R, Shulz, A, Landers, J, Casson, RJ, and Craig, JE

Abstract

PURPOSE: To investigate the association between cardiovascular disease and baseline structural defects and disease progression in glaucoma. DESIGN: Prospective, longitudinal study of preperimetric and perimetric glaucoma. PARTICIPANTS: Two thousand six hundred twenty-eight eyes from 1314 participants recruited to the Progression Risk of Glaucoma: Relevant SNPs with Significant Association (PROGRESSA) study were evaluated for baseline and longitudinal structural thinning using spectral-domain OCT and for visual field progression on Humphrey visual field (HVF) assessment. METHODS: Patients were classified as either predominantly macula ganglion cell-inner plexiform layer (mGCIPL), predominantly peripapillary retinal nerve fiber layer (pRNFL), or both mGCIPL and pRNFL structural change at enrollment, and then evaluated for longitudinal OCT or HVF progression. Cardiovascular disease and medication characteristics of the participants were compared with a reference group of stable patients. MAIN OUTCOME MEASURES: OCT and HVF baseline status and longitudinal progression. RESULTS: After accounting for age and cardiovascular characteristics, patients with predominantly mGCIPL thinning at baseline showed a higher prevalence of hypertension (odds ratio [OR], 2.70; 95% confidence interval [CI], 1.66-4.41; P < 0.001), antihypertensive use (OR, 2.03; 95% CI, 1.20-3.46; P = 0.008), and statin use (OR, 1.98; 95% CI, 1.07-3.66; P = 0.029) than reference patients. Patients with predominantly pRNFL thinning exhibited a comparable prevalence of cardiovascular disease or medication with reference patients. Review of longitudinal OCT and HVF data (mean follow-up, 5.34 ± 1.29 years) showed that hypertension was associated with an increased risk of both OCT (OR, 1.79; 95% CI, 1.17-2.75; P = 0.006) and HVF progression (OR, 1.92; 95% CI, 1.18-3.15; P = 0.013). A 1-standard deviation (approximately 21 mmHg) increase in systolic blood pressure at baseline was associated with a greater risk of

Published
2021

58. Identification of a Locus Near ULK1 Associated With Progression-Free Survival in Ovarian Cancer

Author

Quinn, MCJ, McCue, K, Shi, W, Johnatty, SE, Beesley, J, Civitarese, A, O'Mara, TA, Glubb, DM, Tyrer, JP, Armasu, SM, Ong, J-S, Gharahkhani, P, Lu, Y, Gao, B, Patch, A-M, Fasching, PA, Beckmann, MW, Lambrechts, D, Vergote, I, Edwards, DRV, Beeghly-Fadiel, A, Benitez, J, Garcia, MJ, Goodman, MT, Doerk, T, Duerst, M, Modugno, F, Moysich, K, du Bois, A, Pfisterer, J, Bauman, K, Karlan, BY, Lester, J, Cunningham, JM, Larson, MC, McCauley, BM, Kjaer, SK, Jensen, A, Hogdall, CK, Hogdall, E, Schildkraut, JM, Riggan, MJ, Berchuck, A, Cramer, DW, Terry, KL, Bjorge, L, Webb, PM, Friedlander, M, Pejovic, T, Moffitt, M, Glasspool, R, May, T, Ene, GE, Huntsman, DG, Woo, M, Carney, ME, Hinsley, S, Heitz, F, Fereday, S, Kennedy, CJ, Edwards, SL, Winham, SJ, deFazio, A, Pharoah, PDP, Goode, EL, MacGregor, S, Chenevix-Trench, G, Quinn, MCJ, McCue, K, Shi, W, Johnatty, SE, Beesley, J, Civitarese, A, O'Mara, TA, Glubb, DM, Tyrer, JP, Armasu, SM, Ong, J-S, Gharahkhani, P, Lu, Y, Gao, B, Patch, A-M, Fasching, PA, Beckmann, MW, Lambrechts, D, Vergote, I, Edwards, DRV, Beeghly-Fadiel, A, Benitez, J, Garcia, MJ, Goodman, MT, Doerk, T, Duerst, M, Modugno, F, Moysich, K, du Bois, A, Pfisterer, J, Bauman, K, Karlan, BY, Lester, J, Cunningham, JM, Larson, MC, McCauley, BM, Kjaer, SK, Jensen, A, Hogdall, CK, Hogdall, E, Schildkraut, JM, Riggan, MJ, Berchuck, A, Cramer, DW, Terry, KL, Bjorge, L, Webb, PM, Friedlander, M, Pejovic, T, Moffitt, M, Glasspool, R, May, T, Ene, GE, Huntsman, DG, Woo, M, Carney, ME, Hinsley, S, Heitz, F, Fereday, S, Kennedy, CJ, Edwards, SL, Winham, SJ, deFazio, A, Pharoah, PDP, Goode, EL, MacGregor, S, and Chenevix-Trench, G

Abstract

BACKGROUND: Many loci have been found to be associated with risk of epithelial ovarian cancer (EOC). However, although there is considerable variation in progression-free survival (PFS), no loci have been found to be associated with outcome at genome-wide levels of significance. METHODS: We carried out a genome-wide association study (GWAS) of PFS in 2,352 women with EOC who had undergone cytoreductive surgery and standard carboplatin/paclitaxel chemotherapy. RESULTS: We found seven SNPs at 12q24.33 associated with PFS (P < 5 × 10-8), the top SNP being rs10794418 (HR = 1.24; 95% CI, 1.15-1.34; P = 1.47 × 10-8). High expression of a nearby gene, ULK1, is associated with shorter PFS in EOC, and with poor prognosis in other cancers. SNP rs10794418 is also associated with expression of ULK1 in ovarian tumors, with the allele associated with shorter PFS being associated with higher expression, and chromatin interactions were detected between the ULK1 promoter and associated SNPs in serous and endometrioid EOC cell lines. ULK1 knockout ovarian cancer cell lines showed significantly increased sensitivity to carboplatin in vitro. CONCLUSIONS: The locus at 12q24.33 represents one of the first genome-wide significant loci for survival for any cancer. ULK1 is a plausible candidate for the target of this association. IMPACT: This finding provides insight into genetic markers associated with EOC outcome and potential treatment options.See related commentary by Peres and Monteiro, p. 1604.

Published
2021

59. Genetic variation affects morphological retinal phenotypes extracted from UK Biobank optical coherence tomography images

Author

Hauser, MA, Currant, H, Hysi, P, Fitzgerald, TW, Gharahkhani, P, Bonnemaijer, PWM, Senabouth, A, Hewitt, AW, Atan, D, Aung, T, Charng, J, Choquet, H, Craig, J, Khaw, PT, Klaver, CCW, Kubo, M, Ong, J-S, Pasquale, LR, Reisman, CA, Daniszewski, M, Powell, JE, Pebay, A, Simcoe, MJ, Thiadens, AAHJ, van Duijn, CM, Yazar, S, Jorgenson, E, MacGregor, S, Hammond, CJ, Mackey, DA, Wiggs, JL, Foster, PJ, Patel, PJ, Birney, E, Khawaja, AP, Hauser, MA, Currant, H, Hysi, P, Fitzgerald, TW, Gharahkhani, P, Bonnemaijer, PWM, Senabouth, A, Hewitt, AW, Atan, D, Aung, T, Charng, J, Choquet, H, Craig, J, Khaw, PT, Klaver, CCW, Kubo, M, Ong, J-S, Pasquale, LR, Reisman, CA, Daniszewski, M, Powell, JE, Pebay, A, Simcoe, MJ, Thiadens, AAHJ, van Duijn, CM, Yazar, S, Jorgenson, E, MacGregor, S, Hammond, CJ, Mackey, DA, Wiggs, JL, Foster, PJ, Patel, PJ, Birney, E, and Khawaja, AP

Abstract

Optical Coherence Tomography (OCT) enables non-invasive imaging of the retina and is used to diagnose and manage ophthalmic diseases including glaucoma. We present the first large-scale genome-wide association study of inner retinal morphology using phenotypes derived from OCT images of 31,434 UK Biobank participants. We identify 46 loci associated with thickness of the retinal nerve fibre layer or ganglion cell inner plexiform layer. Only one of these loci has been associated with glaucoma, and despite its clear role as a biomarker for the disease, Mendelian randomisation does not support inner retinal thickness being on the same genetic causal pathway as glaucoma. We extracted overall retinal thickness at the fovea, representative of foveal hypoplasia, with which three of the 46 SNPs were associated. We additionally associate these three loci with visual acuity. In contrast to the Mendelian causes of severe foveal hypoplasia, our results suggest a spectrum of foveal hypoplasia, in part genetically determined, with consequences on visual function.

Published
2021

60. A multi-ethnic genome-wide association study implicates collagen matrix integrity and cell differentiation pathways in keratoconus

Author

Hardcastle, AJ, Liskova, P, Bykhovskaya, Y, McComish, BJ, Davidson, AE, Inglehearn, CF, Li, X, Choquet, H, Habeeb, M, Lucas, SEM, Sahebjada, S, Pontikos, N, Lopez, KER, Khawaja, AP, Ali, M, Dudakova, L, Skalicka, P, Van Dooren, BTH, Geerards, AJM, Haudum, CW, Lo Faro, V, Tenen, A, Simcoe, MJ, Patasova, K, Yarrand, D, Yin, J, Siddiqui, S, Rice, A, Farraj, LA, Chen, Y-DI, Rahi, JS, Krauss, RM, Theusch, E, Charlesworth, JC, Szczotka-Flynn, L, Toomes, C, Meester-Smoor, MA, Richardson, AJ, Mitchell, PA, Taylor, KD, Melles, RB, Aldave, AJ, Mills, RA, Cao, K, Chan, E, Daniell, MD, Wang, JJ, Rotter, JI, Hewitt, AW, MacGregor, S, Klaver, CCW, Ramdas, WD, Craig, JE, Iyengar, SK, O'Brart, D, Jorgenson, E, Baird, PN, Rabinowitz, YS, Burdon, KP, Hammond, CJ, Tuft, SJ, Hysi, PG, Hardcastle, AJ, Liskova, P, Bykhovskaya, Y, McComish, BJ, Davidson, AE, Inglehearn, CF, Li, X, Choquet, H, Habeeb, M, Lucas, SEM, Sahebjada, S, Pontikos, N, Lopez, KER, Khawaja, AP, Ali, M, Dudakova, L, Skalicka, P, Van Dooren, BTH, Geerards, AJM, Haudum, CW, Lo Faro, V, Tenen, A, Simcoe, MJ, Patasova, K, Yarrand, D, Yin, J, Siddiqui, S, Rice, A, Farraj, LA, Chen, Y-DI, Rahi, JS, Krauss, RM, Theusch, E, Charlesworth, JC, Szczotka-Flynn, L, Toomes, C, Meester-Smoor, MA, Richardson, AJ, Mitchell, PA, Taylor, KD, Melles, RB, Aldave, AJ, Mills, RA, Cao, K, Chan, E, Daniell, MD, Wang, JJ, Rotter, JI, Hewitt, AW, MacGregor, S, Klaver, CCW, Ramdas, WD, Craig, JE, Iyengar, SK, O'Brart, D, Jorgenson, E, Baird, PN, Rabinowitz, YS, Burdon, KP, Hammond, CJ, Tuft, SJ, and Hysi, PG

Abstract

Keratoconus is characterised by reduced rigidity of the cornea with distortion and focal thinning that causes blurred vision, however, the pathogenetic mechanisms are unknown. It can lead to severe visual morbidity in children and young adults and is a common indication for corneal transplantation worldwide. Here we report the first large scale genome-wide association study of keratoconus including 4,669 cases and 116,547 controls. We have identified significant association with 36 genomic loci that, for the first time, implicate both dysregulation of corneal collagen matrix integrity and cell differentiation pathways as primary disease-causing mechanisms. The results also suggest pleiotropy, with some disease mechanisms shared with other corneal diseases, such as Fuchs endothelial corneal dystrophy. The common variants associated with keratoconus explain 12.5% of the genetic variance, which shows potential for the future development of a diagnostic test to detect susceptibility to disease.

Published
2021

61. Associations of sleep apnoea with glaucoma and age-related macular degeneration: an analysis in the United Kingdom Biobank and the Canadian Longitudinal Study on Aging

Author

Han, X, Lee, SS-Y, Ingold, N, McArdle, N, Khawaja, AP, MacGregor, S, Mackey, DA, Han, X, Lee, SS-Y, Ingold, N, McArdle, N, Khawaja, AP, MacGregor, S, and Mackey, DA

Abstract

BACKGROUND: Sleep apnoea, a common sleep-disordered breathing condition, is characterised by upper airway collapse during sleep resulting in transient hypoxia, hypoperfusion of the optic nerve, and spike in intracranial pressure. Previous studies have reported conflicting findings on the association of sleep apnoea with glaucoma, and there are limited reports on the link between sleep apnoea and age-related macular degeneration (AMD). METHODS: Middle-aged and older participants from the longitudinal United Kingdom (UK) Biobank (n = 502,505) and the Canadian Longitudinal Study on Aging (CLSA; n = 24,073) were included in this analysis. Participants in the UK Biobank and the CLSA were followed for 8 and 3 years, respectively. Participants with diagnosed glaucoma or AMD at baseline were excluded from the analysis. In the UK Biobank, sleep apnoea and incident cases of glaucoma and AMD were identified through hospital inpatient admission, primary care records, and self-reported data. Multivariable Cox proportional hazards models were used to explore associations of sleep apnoea with incidence of glaucoma or AMD. RESULTS: During the 8-year follow-up in the UK Biobank, glaucoma incidence rates per 1000 person-years were 2.46 and 1.59 for participants with and without sleep apnoea, and the AMD incidence rates per 1000 person-years were 2.27 and 1.42 for participants with and without sleep apnoea, respectively. Multivariable adjusted hazard ratios of glaucoma and AMD risk for sleep apnoea were 1.33 (95% confidence interval [CI] 1.10-1.60, P = 0.003) and 1.39 (95% CI 1.15-1.68, P < 0.001) relative to participants without sleep apnoea. In the CLSA cohort, disease information was collected through in-person interview questionnaires. During the 3-year follow-up, glaucoma incidence rates per 1000 person-years for those with and without sleep apnoea were 9.31 and 6.97, and the AMD incidence rates per 1000 person-years were 8.44 and 6.67, respectively. In the CLSA, similar associa

Published
2021

62. Time spent outdoors in childhood is associated with reduced risk of myopia as an adult

Author

Lingham, G, Yazar, S, Lucas, RM, Milne, E, Hewitt, AW, Hammond, CJ, MacGregor, S, Rose, KA, Chen, FK, He, M, Guggenheim, JA, Clarke, MW, Saw, S-M, Williams, C, Coroneo, MT, Straker, L, Mackey, DA, Lingham, G, Yazar, S, Lucas, RM, Milne, E, Hewitt, AW, Hammond, CJ, MacGregor, S, Rose, KA, Chen, FK, He, M, Guggenheim, JA, Clarke, MW, Saw, S-M, Williams, C, Coroneo, MT, Straker, L, and Mackey, DA

Abstract

Myopia (near-sightedness) is an important public health issue. Spending more time outdoors can prevent myopia but the long-term association between this exposure and myopia has not been well characterised. We investigated the relationship between time spent outdoors in childhood, adolescence and young adulthood and risk of myopia in young adulthood. The Kidskin Young Adult Myopia Study (KYAMS) was a follow-up of the Kidskin Study, a sun exposure-intervention study of 1776 children aged 6-12 years. Myopia status was assessed in 303 (17.6%) KYAMS participants (aged 25-30 years) and several subjective and objective measures of time spent outdoors were collected in childhood (8-12 years) and adulthood. Index measures of total, childhood and recent time spent outdoors were developed using confirmatory factor analysis. Logistic regression was used to assess the association between a 0.1-unit change in the time outdoor indices and risk of myopia after adjusting for sex, education, outdoor occupation, parental myopia, parental education, ancestry and Kidskin Study intervention group. Spending more time outdoors during childhood was associated with reduced risk of myopia in young adulthood (multivariable odds ratio [OR] 0.82, 95% confidence interval [CI] 0.69, 0.98). Spending more time outdoors in later adolescence and young adulthood was associated with reduced risk of late-onset myopia (≥ 15 years of age, multivariable OR 0.79, 95% CI 0.64, 0.98). Spending more time outdoors in both childhood and adolescence was associated with less myopia in young adulthood.

Published
2021

63. Genetic variation affects morphological retinal phenotypes extracted from UK Biobank optical coherence tomography images (vol 17, e1009497, 2021)

Author

Currant, H, Hysi, P, Fitzgerald, TW, Gharahkhani, P, Bonnemaijer, PWM, Senabouth, A, Hewitt, AW, Atan, D, Aung, T, Charng, J, Choquet, H, Craig, J, Khaw, PT, Klaver, CCW, Kubo, M, Ong, J-S, Pasquale, LR, Reisman, CA, Daniszewski, M, Powell, JE, Pebay, A, Simcoe, MJ, Thiadens, AAHJ, van Duijn, CM, Yazar, S, Jorgenson, E, MacGregor, S, Hammond, CJ, Mackey, DA, Wiggs, JL, Foster, PJ, Patel, PJ, Birney, E, Khawaja, AP, Currant, H, Hysi, P, Fitzgerald, TW, Gharahkhani, P, Bonnemaijer, PWM, Senabouth, A, Hewitt, AW, Atan, D, Aung, T, Charng, J, Choquet, H, Craig, J, Khaw, PT, Klaver, CCW, Kubo, M, Ong, J-S, Pasquale, LR, Reisman, CA, Daniszewski, M, Powell, JE, Pebay, A, Simcoe, MJ, Thiadens, AAHJ, van Duijn, CM, Yazar, S, Jorgenson, E, MacGregor, S, Hammond, CJ, Mackey, DA, Wiggs, JL, Foster, PJ, Patel, PJ, Birney, E, and Khawaja, AP

Abstract

[This corrects the article DOI: 10.1371/journal.pgen.1009497.].

Published
2021

64. Genome-wide meta-analysis identifies 127 open-angle glaucoma loci with consistent effect across ancestries

Author

Gharahkhani, P, Jorgenson, E, Hysi, P, Khawaja, AP, Pendergrass, S, Han, X, Ong, JS, Hewitt, AW, Segre, A, Rouhana, JM, Hamel, AR, Igo, RP, Choquet, H, Qassim, A, Josyula, NS, Bailey, JNC, Bonnemaijer, PWM, Iglesias, A, Siggs, OM, Young, TL, Vitart, V, Thiadens, AAHJ, Karjalainen, J, Uebe, S, Melles, RB, Nair, KS, Luben, R, Simcoe, M, Amersinghe, N, Cree, AJ, Hohn, R, Poplawski, A, Chen, LJ, Rong, S-S, Aung, T, Vithana, EN, Tamiya, G, Shiga, Y, Yamamoto, M, Nakazawa, T, Currant, H, Birney, E, Wang, X, Auton, A, Lupton, MK, Martin, NG, Ashaye, A, Olawoye, O, Williams, SE, Akafo, S, Ramsay, M, Hashimoto, K, Kamatani, Y, Akiyama, M, Momozawa, Y, Foster, PJ, Khaw, PT, Morgan, JE, Strouthidis, NG, Kraft, P, Kang, JH, Pang, CP, Pasutto, F, Mitchell, P, Lotery, AJ, Palotie, A, van Duijn, C, Haines, JL, Hammond, C, Pasquale, LR, Klaver, CCW, Hauser, M, Khor, CC, Mackey, DA, Kubo, M, Cheng, C-Y, Craig, JE, MacGregor, S, Wiggs, JL, Gharahkhani, P, Jorgenson, E, Hysi, P, Khawaja, AP, Pendergrass, S, Han, X, Ong, JS, Hewitt, AW, Segre, A, Rouhana, JM, Hamel, AR, Igo, RP, Choquet, H, Qassim, A, Josyula, NS, Bailey, JNC, Bonnemaijer, PWM, Iglesias, A, Siggs, OM, Young, TL, Vitart, V, Thiadens, AAHJ, Karjalainen, J, Uebe, S, Melles, RB, Nair, KS, Luben, R, Simcoe, M, Amersinghe, N, Cree, AJ, Hohn, R, Poplawski, A, Chen, LJ, Rong, S-S, Aung, T, Vithana, EN, Tamiya, G, Shiga, Y, Yamamoto, M, Nakazawa, T, Currant, H, Birney, E, Wang, X, Auton, A, Lupton, MK, Martin, NG, Ashaye, A, Olawoye, O, Williams, SE, Akafo, S, Ramsay, M, Hashimoto, K, Kamatani, Y, Akiyama, M, Momozawa, Y, Foster, PJ, Khaw, PT, Morgan, JE, Strouthidis, NG, Kraft, P, Kang, JH, Pang, CP, Pasutto, F, Mitchell, P, Lotery, AJ, Palotie, A, van Duijn, C, Haines, JL, Hammond, C, Pasquale, LR, Klaver, CCW, Hauser, M, Khor, CC, Mackey, DA, Kubo, M, Cheng, C-Y, Craig, JE, MacGregor, S, and Wiggs, JL

Abstract

Primary open-angle glaucoma (POAG), is a heritable common cause of blindness world-wide. To identify risk loci, we conduct a large multi-ethnic meta-analysis of genome-wide association studies on a total of 34,179 cases and 349,321 controls, identifying 44 previously unreported risk loci and confirming 83 loci that were previously known. The majority of loci have broadly consistent effects across European, Asian and African ancestries. Cross-ancestry data improve fine-mapping of causal variants for several loci. Integration of multiple lines of genetic evidence support the functional relevance of the identified POAG risk loci and highlight potential contributions of several genes to POAG pathogenesis, including SVEP1, RERE, VCAM1, ZNF638, CLIC5, SLC2A12, YAP1, MXRA5, and SMAD6. Several drug compounds targeting POAG risk genes may be potential glaucoma therapeutic candidates.

Published
2021

67. Germline variants are associated with increased primary melanoma tumor thickness at diagnosis

Author

Mangantig, E, MacGregor, S, Iles, MM, Scolyer, RA, Cust, AE, Hayward, NK, Montgomery, GW, Duffy, DL, Thompson, JF, Henders, A, Bowdler, L, Rowe, C, Cadby, G, Mann, GJ, Whiteman, DC, Long, GV, Ward, SV, Khosrotehrani, K, Barrett, JH, and Law, MH

Abstract

Germline genetic variants have been identified, which predispose individuals and families to develop melanoma. Tumor thickness is the strongest predictor of outcome for clinically localized primary melanoma patients. We sought to determine whether there is a heritable genetic contribution to variation in tumor thickness. If confirmed, this will justify the search for specific genetic variants influencing tumor thickness. To address this, we estimated the proportion of variation in tumor thickness attributable to genome-wide genetic variation (variant-based heritability) using unrelated patients with measured primary cutaneous melanoma thickness. As a secondary analysis, we conducted a genome-wide association study (GWAS) of tumor thickness. The analyses utilized 10 604 individuals with primary cutaneous melanoma drawn from nine GWAS datasets from eight cohorts recruited from the general population, primary care and melanoma treatment centers. Following quality control and filtering to unrelated individuals with study phenotypes, 8125 patients were used in the primary analysis to test whether tumor thickness is heritable. An expanded set of 8505 individuals (47.6% female) were analyzed for the secondary GWAS meta-analysis. Analyses were adjusted for participant age, sex, cohort and ancestry. We found that 26.6% (SE 11.9%, P = 0.0128) of variation in tumor thickness is attributable to genome-wide genetic variation. While requiring replication, a chromosome 11 locus was associated (P

Published
2020

68. Effect of surface deviation of solid insulation on impulsive flashover voltages under varying environmental conditions

Author

Macpherson, R. W., Wilson, M. P., Timoshkin, I. V., MacGregor, S. J., and Given, M. J.

Subjects
TK
Abstract

In pulsed power engineering, the modification of dielectric surfaces is a potential method in order to increase the flashover strength of solid insulation. In this work, dielectric materials are subjected to a knurled finish, where small indentations are machined on to the surface resulting in quick consistent modification. These flashover voltages from the knurled dielectric spacers have been compared to spacers with a ‘smooth’ machined finish. The three materials which have been tested are HDPE (High Density Polyethylene), Delrin (Polyoxymethylene) and Ultem (Polyetherimide). The materials were tested under a 100/700 ns impulse voltage. Cylindrical spacers made of these materials were located in the center of a parallel-plane electrode setup in air, which provided a quasi-uniform field distribution. Breakdown tests published in this work were performed in a sealed container at air pressures of −0.5, 0 and 0.5 bar gauge, with relative humidity levels of 90% RH.

Published
2020

69. Does polygenic risk influence associations between sun exposure and melanoma?: a prospective cohort analysis

Author

Olsen, CM, Pandeya, N, Law, MH, MacGregor, S, Iles, MM, Thompson, BS, Green, AC, Neale, RE, Whiteman, DC, and The QSkin Study

Abstract

Melanoma develops as the result of complex interactions between sun exposure and genetic factors. Data on these interactions from prospective studies are scant however. We aimed to quantify the association between ambient and personal ultraviolet (UV) exposure and incident melanoma in a large population‐based prospective study of men and women residing in a high ambient UV setting, and to examine potential gene‐environment interactions. Among participants with genetic data (n=15,373), 420 (2.7%) developed cutaneous melanoma (173 invasive, 247 in situ) during a median follow‐up time of 4.4 years. Country of birth, age at migration, having greater than 50 sunburns in childhood/adolescence and a history of keratinocyte cancer/actinic lesions were significantly associated with melanoma risk. An interaction with polygenic risk was suggested; among people at low polygenic risk, markers of cumulative sun exposure (as measured by actinic damage) were associated with melanoma. In contrast, among people at high polygenic risk, markers of high‐level early life ambient exposure (as measured by place of birth) were associated with melanoma (HR for born in Australia vs. overseas 3.16, 95% CI 1.39‐7.22). These findings suggest interactions between genotype and environment that are consistent with divergent pathways for melanoma development.

Published
2020

71. Body mass index and height and risk of cutaneous melanoma: Mendelian randomization analyses

Author

Dusingize, JC, Olsen, CM, An, J, Pandeya, N, Law, MH, Thompson, BS, Goldstein, AM, Iles, MM, Webb, PM, Neale, RE, Ong, J-S, MacGregor, S, and Whiteman, DC

Abstract

Background Height and body mass index (BMI) have both been positively associated with melanoma risk, although findings for BMI have been less consistent than height. It remains unclear, however, whether these associations reflect causality or are due to residual confounding by environmental and lifestyle risk factors. We re-evaluated these associations using a two-sample Mendelian randomization (MR) approach. Methods We identified single nucleotide polymorphisms (SNPs) for BMI and height from separate genome-wide association study (GWAS) meta-analyses. We obtained melanoma SNPs from the most recent melanoma GWAS meta-analysis comprising 12 874 cases and 23 203 controls. We used the inverse variance-weighted estimator to derive separate causal risk estimates across all SNP instruments for BMI and height. Results Based on the combined estimate derived from 730 SNPs for BMI, we found no evidence of an association between genetically predicted BMI and melanoma [odds ratio (OR) per one standard deviation (1 SD) (4.6 kg/m2) increase in BMI 1.00, 95% confidence interval (CI): 0.91–1.11]. In contrast, we observed a positive association between genetically-predicted height (derived from a pooled estimate of 3290 SNPs) and melanoma risk [OR 1.08, 95% CI: 1.02–1.13, per 1 SD (9.27 cm) increase in height]. Sensitivity analyses using two alternative MR methods yielded similar results. Conclusions These findings provide no evidence for a causal association between higher BMI and melanoma, but support the notion that height is causally associated with melanoma risk. Mechanisms through which height influences melanoma risk remain unclear, and it remains possible that the effect could be mediated through diverse pathways including growth factors and even socioeconomic status.

Published
2020

72. Multiplex melanoma families are enriched for polygenic risk

Author

Law, MH, Aoude, LG, Duffy, DL, Long, GV, Johansson, PA, Pritchard, AL, Khosrotehrani, K, Mann, GJ, Montgomery, GW, Iles, MM, Cust, AE, Palmer, JM, Melanoma GWAS Consortium, Shannon, KF, Spillane, AJ, Stretch, JR, Thompson, JF, Saw, RPM, Scolyer, RA, Martin, NG, Hayward, NK, and MacGregor, S

Subjects
neoplasms
Abstract

Cancers, including cutaneous melanoma, can cluster in families. In addition to environmental aetiological factors such as ultraviolet radiation, cutaneous melanoma has a strong genetic component. Genetic risks for cutaneous melanoma range from rare, high-penetrance mutations to common, low-penetrance variants. Known high-penetrance mutations account for only about half of all densely affected cutaneous melanoma families and the causes of familial clustering in the remainder is unknown. We hypothesise that some clustering is due to the cumulative effect of a large number of variants of individually small effect. Common, low-penetrance genetic risk variants can be combined into polygenic risk scores. We used a polygenic risk score for cutaneous melanoma to compare families without known high-penetrance mutations with unrelated melanoma cases and melanoma-free controls. Family members had significantly higher mean polygenic load for cutaneous melanoma than unrelated cases or melanoma-free healthy controls (Bonferroni corrected t-test P = 1.5 × 10−5 and 6.3 × 10−45, respectively). Whole genome sequencing of germline DNA from 51 members of 21 families with low polygenic risk for melanoma identified a CDKN2A p.G101W mutation in a single family but no other candidate new high-penetrance melanoma susceptibility genes. This work provides further evidence that melanoma, like many other common complex disorders, can arise from the joint action of multiple predisposing factors, including rare high-penetrance mutations, as well as via a combination of large numbers of alleles of small effect.

Published
2020

74. Overlapping genetic architecture between Parkinson disease and melanoma

Author

Dube, Umber Ibanez, Laura Budde, John P. Benitez, Bruno A. and Davis, Albert A. Harari, Oscar Iles, Mark M. Law, Matthew H. Brown, Kevin M. Agee, Michelle Alipanahi, Babak and Auton, Adam Bell, Robert K. Bryc, Katarzyna Elson, Sarah L. Fontanillas, Pierre Furlotte, Nicholas A. Hinds, David A. and Huber, Karen E. Kleinman, Aaron Litterman, Nadia K. and McCreight, Jennifer C. McIntyre, Matthew H. Mountain, Joanna L. and Noblin, Elizabeth S. Northover, Carrie A. M. Pitts, Steven J. Sathirapongsasuti, J. Fah Sazonova, Olga V. Shelton, Janie F. Shringarpure, Suyash Tian, Chao Tung, Joyce Y. and Vacic, Vladimir Wilson, Catherine H. Law, M. H. Law, M. H. and Bishop, D. T. Lee, J. E. Brossard, M. Martin, N. G. and Moses, E. K. Song, F. Barrett, J. H. Kumar, R. Easton, D. F. Pharoah, P. D. Swerdlow, A. J. Kypreou, K. P. and Taylor, J. C. Harland, M. Randerson-Moor, J. Akslen, L. A. and Andresen, P. A. Avril, M. F. Azizi, E. Scarra, G. B. and Brown, K. M. Debniak, T. Duffy, D. L. Elder, D. E. Fang, S. Friedman, E. Galan, P. Ghiorzo, P. Gillanders, E. M. and Goldstein, A. M. Gruis, N. A. Hansson, J. Helsing, P. and Hocevar, M. Hoiom, V. Ingvar, C. Kanetsky, P. A. and Chen, W. V. Landi, M. T. Lang, J. Lathrop, G. M. and Lubinski, J. Mackie, R. M. Mann, G. J. Molven, A. and Montgomery, G. W. Novakovic, S. Olsson, H. Puig, S. and Puig-Butille, J. A. Wu, W. Qureshi, A. A. Radford-Smith, G. L. Van der Stoep, N. Van Doorn, R. Whiteman, D. C. and Craig, J. E. Schadendorf, E. Simms, L. A. Burdon, K. P. and Nyholt, D. R. Pooley, K. A. Orr, N. Stratigos, A. J. and Cust, A. E. Ward, S. V. Hayward, N. K. Han, J. Schulze, H. J. Dunning, A. M. Bishop, J. A. Demenais, F. Amos, C. I. MacGregor, S. Iles, M. M. Cruchaga, Carlos 23andMe Research Team Melanoma Meta Analysis Consortium

Abstract

Epidemiologic studies have reported inconsistent results regarding an association between Parkinson disease (PD) and cutaneous melanoma (melanoma). Identifying shared genetic architecture between these diseases can support epidemiologic findings and identify common risk genes and biological pathways. Here, we apply polygenic, linkage disequilibrium-informed methods to the largest available case-control, genome-wide association study summary statistic data for melanoma and PD. We identify positive and significant genetic correlation (correlation: 0.17, 95% CI 0.10-0.24; P = 4.09 x 10(-06)) between melanoma and PD. We further demonstrate melanoma and PD-inferred gene expression to overlap across tissues (correlation: 0.14, 95% CI 0.06 to 0.22; P = 7.87 x 10(-04)) and highlight seven genes including PIEZO1, TRAPPC2L, and SOX6 as potential mediators of the genetic correlation between melanoma and PD. These findings demonstrate specific, shared genetic architecture between PD and melanoma that manifests at the level of gene expression.

Published
2020

75. Statistical analysis of impulsive flashover voltages across solid-air interfaces

Author

Macpherson, R. W., Wilson, M. P., Given, M. J., Timoshkin, I. V., and MacGregor, S. J.

Subjects
TK
Abstract

Within the pulsed power industry, a key factor determining the achievable output voltage of a HV system is the flashover voltage of the insulating parts. Statistical analysis of the breakdown voltages associated with solid-gas interfaces can reveal useful information to aid system designers in the selection of solid materials. However, it is important to test the applicability of the distribution being applied, to ensure that the fitting parameters obtained are truly representative of the distribution of the data. Normal, lognormal, 2-parameter Weibull and 3-parameter Weibull cumulative distribution functions (CDF) were plotted, to enable extraction of the specific fitting parameters associated with each distribution. The CDF for each statistical method has been plotted alongside the empirical cumulative distribution function (ECDF), found from the flashover voltages recorded during experimental testing. The distribution of best fit was then analysed by using the Kolmogorov-Smirnov (K-S) test, in order to determine the CDF that best represented the ECDF. Maximum values have been compared to the α = 0.05, K-S critical value, in order to reject or accept the null hypothesis based on how the data fits the specified distributions. This will facilitate a comparison between different statistical distributions, applied to experimental data on breakdown/flashover voltages of gas-solid interfaces, generated at a fixed pressure, and different levels of RH

Published
2020
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76. Genome-wide association meta-analyses combining multiple risk phenotypes provide insights into the genetic architecture of cutaneous melanoma susceptibility

Author

Landi MT, Bishop DT, MacGregor S, Machiela MJ, Stratigos AJ, Ghiorzo P, Brossard M, Calista D, Choi J, Fargnoli MC, Zhang T, Rodolfo M, Trower AJ, Menin C, Martinez J, Hadjisavvas A, Song L, Stefanaki I, Scolyer R, Yang R, Goldstein AM, Potrony M, Kypreou KP, Pastorino L, Queirolo P, Pellegrini C, Cattaneo L, Zawistowski M, Gimenez-Xavier P, Rodriguez A, Elefanti L, Manoukian S, Rivoltini L, Smith BH, Loizidou MA, Del Regno L, Massi D, Mandala M, Khosrotehrani K, Akslen LA, Amos CI, Andresen PA, Avril MF, Azizi E, Soyer HP, Bataille V, Dalmasso B, Bowdler LM, Burdon KP, Chen WV, Codd V, Craig JE, Debniak T, Falchi M, Fang S, Friedman E, Simi S, Galan P, Garcia-Casado Z, Gillanders EM, Gordon S, Green A, Gruis NA, Hansson J, Harland M, Harris J, Helsing P, Henders A, Hocevar M, Höiom V, Hunter D, Ingvar C, Kumar R, Lang J, Lathrop GM, Lee JE, Li X, Lubinski J, Mackie RM, Malt M, Malvehy J, McAloney K, Mohamdi H, Molven A, Moses EK, Neale RE, Novakovic S, Nyholt DR, Olsson H, Orr N, Fritsche LG, Puig-Butille JA, Qureshi AA, Radford-Smith GL, Randerson-Moor J, Requena C, Rowe C, Samani NJ, Sanna M, Schadendorf D, Schulze HJ, Simms LA, Smithers M, Song F, Swerdlow AJ, van der Stoep N, Kukutsch NA, Visconti A, Wallace L, Ward SV, Wheeler L, Sturm RA, Hutchinson A, Jones K, Malasky M, Vogt A, Zhou W, Pooley KA, Elder DE, Han J, Hicks B, Hayward NK, Kanetsky PA, Brummett C, Montgomery GW, Olsen CM, Hayward C, Dunning AM, Martin NG, Evangelou E, Mann GJ, Long G, Pharoah PDP, Easton DF, Barrett JH, Cust AE, Abecasis G, Duffy DL, Whiteman DC, Gogas H, De Nicolo A, Tucker MA, Newton-Bishop JA, GenoMEL Consortium, Q-MEGA and QTWIN Investigators, ATHENS Melanoma Study Group, 23andMe, SDH Study Group, IBD Investigators, Essen-Heidelberg Investigators, AMFS Investigators, MelaNostrum Consortium, Peris K, Chanock SJ, Demenais F, Brown KM, Puig S, Nagore E, Shi J, Iles MM, and Law MH

Abstract

Meta-analysis of 36,760 cases and 375,188 controls identifies 54 loci associated with susceptibility to cutaneous melanoma. Further analysis combining nevus count and hair color GWAS results provide insights into the genetic architecture of melanoma. Most genetic susceptibility to cutaneous melanoma remains to be discovered. Meta-analysis genome-wide association study (GWAS) of 36,760 cases of melanoma (67% newly genotyped) and 375,188 controls identified 54 significant (P < 5 x 10(-8)) loci with 68 independent single nucleotide polymorphisms. Analysis of risk estimates across geographical regions and host factors suggests the acral melanoma subtype is uniquely unrelated to pigmentation. Combining this meta-analysis with GWAS of nevus count and hair color, and transcriptome association approaches, uncovered 31 potential secondary loci for a total of 85 cutaneous melanoma susceptibility loci. These findings provide insights into cutaneous melanoma genetic architecture, reinforcing the importance of nevogenesis, pigmentation and telomere maintenance, together with identifying potential new pathways for cutaneous melanoma pathogenesis.

Published
2020

77. Genome-wide association meta-analyses combining multiple risk phenotypes provide insights into the genetic architecture of cutaneous melanoma susceptibility

Author

Landi, M.T. Bishop, D.T. MacGregor, S. Machiela, M.J. Stratigos, A.J. Ghiorzo, P. Brossard, M. Calista, D. Choi, J. Fargnoli, M.C. Zhang, T. Rodolfo, M. Trower, A.J. Menin, C. Martinez, J. Hadjisavvas, A. Song, L. Stefanaki, I. Scolyer, R. Yang, R. Goldstein, A.M. Potrony, M. Kypreou, K.P. Pastorino, L. Queirolo, P. Pellegrini, C. Cattaneo, L. Zawistowski, M. Gimenez-Xavier, P. Rodriguez, A. Elefanti, L. Manoukian, S. Rivoltini, L. Smith, B.H. Loizidou, M.A. Del Regno, L. Massi, D. Mandala, M. Khosrotehrani, K. Akslen, L.A. Amos, C.I. Andresen, P.A. Avril, M.-F. Azizi, E. Soyer, H.P. Bataille, V. Dalmasso, B. Bowdler, L.M. Burdon, K.P. Chen, W.V. Codd, V. Craig, J.E. Dębniak, T. Falchi, M. Fang, S. Friedman, E. Simi, S. Galan, P. Garcia-Casado, Z. Gillanders, E.M. Gordon, S. Green, A. Gruis, N.A. Hansson, J. Harland, M. Harris, J. Helsing, P. Henders, A. Hočevar, M. Höiom, V. Hunter, D. Ingvar, C. Kumar, R. Lang, J. Lathrop, G.M. Lee, J.E. Li, X. Lubiński, J. Mackie, R.M. Malt, M. Malvehy, J. McAloney, K. Mohamdi, H. Molven, A. Moses, E.K. Neale, R.E. Novaković, S. Nyholt, D.R. Olsson, H. Orr, N. Fritsche, L.G. Puig-Butille, J.A. Qureshi, A.A. Radford-Smith, G.L. Randerson-Moor, J. Requena, C. Rowe, C. Samani, N.J. Sanna, M. Schadendorf, D. Schulze, H.-J. Simms, L.A. Smithers, M. Song, F. Swerdlow, A.J. van der Stoep, N. Kukutsch, N.A. Visconti, A. Wallace, L. Ward, S.V. Wheeler, L. Sturm, R.A. Hutchinson, A. Jones, K. Malasky, M. Vogt, A. Zhou, W. Pooley, K.A. Elder, D.E. Han, J. Hicks, B. Hayward, N.K. Kanetsky, P.A. Brummett, C. Montgomery, G.W. Olsen, C.M. Hayward, C. Dunning, A.M. Martin, N.G. Evangelou, E. Mann, G.J. Long, G. Pharoah, P.D.P. Easton, D.F. Barrett, J.H. Cust, A.E. Abecasis, G. Duffy, D.L. Whiteman, D.C. Gogas, H. De Nicolo, A. Tucker, M.A. Newton-Bishop, J.A. Peris, K. Chanock, S.J. Demenais, F. Brown, K.M. Puig, S. Nagore, E. Shi, J. Iles, M.M. Law, M.H. GenoMEL Consortium Q-MEGA QTWIN Investigators ATHENS Melanoma Study Group 23andMe The SDH Study Group IBD Investigators Essen-Heidelberg Investigators AMFS Investigators MelaNostrum Consortium

Abstract

Most genetic susceptibility to cutaneous melanoma remains to be discovered. Meta-analysis genome-wide association study (GWAS) of 36,760 cases of melanoma (67% newly genotyped) and 375,188 controls identified 54 significant (P < 5 × 10−8) loci with 68 independent single nucleotide polymorphisms. Analysis of risk estimates across geographical regions and host factors suggests the acral melanoma subtype is uniquely unrelated to pigmentation. Combining this meta-analysis with GWAS of nevus count and hair color, and transcriptome association approaches, uncovered 31 potential secondary loci for a total of 85 cutaneous melanoma susceptibility loci. These findings provide insights into cutaneous melanoma genetic architecture, reinforcing the importance of nevogenesis, pigmentation and telomere maintenance, together with identifying potential new pathways for cutaneous melanoma pathogenesis. © 2020, This is a U.S. government work and not under copyright protection in the U.S.; foreign copyright protection may apply.

Published
2020

78. From GWAS to genome sequencing: complementary approaches to identify melanoma predisposition genes

Author

MacGregor S, Brown KM, Stark M, Gartside M, Woods S, Bonazzi V, Aoude L, Dutton-Regester K, Tyagi S, Liu J, Duffy DL, Palmer J, Cust A, Schmid H, Symmons J, Holland E, Agha-Hamilton C, Holohan K, Youngkin D, Gillanders E, Jenkins MA, Kelly J, Whiteman DC, Kefford R, Giles G, Armstrong B, Aitken J, Hopper J, Montgomery G, Schmidt C, Trent JM, Martin NG, Mann GJ, and Hayward NK

Subjects
Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282, Genetics, QH426-470
Published
2012
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79. Multitrait analysis of glaucoma identifies new risk loci and enables polygenic prediction of disease susceptibility and progression

Author

Craig, J.E., Han, X., Qassim, A., Hassall, M., Bailey, J.N., Kinzy, T.G., Khawaja, A.P., An, J., Marshall, H., Gharahkhani, P., Igo, R.P., Jr., Graham, S.L., Healey, P.R., Ong, J.S., Zhou, T., Siggs, O., Law, M.H., Souzeau, E., Ridge, B., Hysi, P.G., Burdon, K.P., Mills, R.A., Landers, J., Ruddle, J.B., Agar, A., Galanopoulos, A., White, A.J.R., Willoughby, C.E., Andrew, N.H., Best, S., Vincent, A.L., Goldberg, I., Radford-Smith, G., Martin, N.G., Montgomery, G.W., Vitart, V., Hoehn, R., Wojciechowski, R., Jonas, J.B., Aung, T., Pasquale, L.R., Cree, A.J., Sivaprasad, S., Vallabh, N.A., Viswanathan, A.C., Pasutto, F., Haines, J.L., Klaver, C.C.W., Duijn, C.M. van, Casson, R.J., Foster, P.J., Khaw, P.T., Hammond, C.J., Mackey, D.A., Mitchell, P., Lotery, A.J., Wiggs, J.L., Hewitt, A.W., MacGregor, S., Craig, J.E., Han, X., Qassim, A., Hassall, M., Bailey, J.N., Kinzy, T.G., Khawaja, A.P., An, J., Marshall, H., Gharahkhani, P., Igo, R.P., Jr., Graham, S.L., Healey, P.R., Ong, J.S., Zhou, T., Siggs, O., Law, M.H., Souzeau, E., Ridge, B., Hysi, P.G., Burdon, K.P., Mills, R.A., Landers, J., Ruddle, J.B., Agar, A., Galanopoulos, A., White, A.J.R., Willoughby, C.E., Andrew, N.H., Best, S., Vincent, A.L., Goldberg, I., Radford-Smith, G., Martin, N.G., Montgomery, G.W., Vitart, V., Hoehn, R., Wojciechowski, R., Jonas, J.B., Aung, T., Pasquale, L.R., Cree, A.J., Sivaprasad, S., Vallabh, N.A., Viswanathan, A.C., Pasutto, F., Haines, J.L., Klaver, C.C.W., Duijn, C.M. van, Casson, R.J., Foster, P.J., Khaw, P.T., Hammond, C.J., Mackey, D.A., Mitchell, P., Lotery, A.J., Wiggs, J.L., Hewitt, A.W., and MacGregor, S.

Abstract

Contains fulltext : 218893.pdf (Publisher’s version ) (Closed access), Glaucoma, a disease characterized by progressive optic nerve degeneration, can be prevented through timely diagnosis and treatment. We characterize optic nerve photographs of 67,040 UK Biobank participants and use a multitrait genetic model to identify risk loci for glaucoma. A glaucoma polygenic risk score (PRS) enables effective risk stratification in unselected glaucoma cases and modifies penetrance of the MYOC variant encoding p.Gln368Ter, the most common glaucoma-associated myocilin variant. In the unselected glaucoma population, individuals in the top PRS decile reach an absolute risk for glaucoma 10 years earlier than the bottom decile and are at 15-fold increased risk of developing advanced glaucoma (top 10% versus remaining 90%, odds ratio = 4.20). The PRS predicts glaucoma progression in prospectively monitored, early manifest glaucoma cases (P = 0.004) and surgical intervention in advanced disease (P = 3.6 x 10(-)(6)). This glaucoma PRS will facilitate the development of a personalized approach for earlier treatment of high-risk individuals, with less intensive monitoring and treatment being possible for lower-risk groups.

Published
2020

80. Genome-wide association meta-analysis of corneal curvature identifies novel loci and shared genetic influences across axial length and refractive error

Author

Fan, Q., Pozarickij, A., Tan, N.Y.Q., Guo, X., Verhoeven, V.J.M., Vitart, V., Guggenheim, J.A., Miyake, M., Tideman, J.W.L., Khawaja, A.P., Zhang, L., MacGregor, S., Hohn, R., Chen, P., Biino, G., Wedenoja, J., Saffari, S.E., Tedja, M.S., Xie, J, Lanca, C., Wang, Y.X., Sahebjada, S., Mazur, J., Mirshahi, A., Martin, N.G., Yazar, S., Pennell, C.E., Yap, M., Haarman, A.E.G., Enthoven, C.A., Polling, J., Hewitt, A.W., Jaddoe, V.W.V., Duijn, C.M. van, Hayward, C., Polasek, O., Tai, E.S., Yoshikatsu, H., Hysi, P.G., Young, T.L., Tsujikawa, A., Wang, J.J., Mitchell, P., Pfeiffer, N., Parssinen, O., Foster, P.J., Fossarello, M., Yip, S.P., Williams, C., Hammond, C.J., Jonas, J.B., He, M., Mackey, D.A., Wong, T.Y., Klaver, C.C.W., Saw, S.M., Baird, P.N., Cheng, C.Y., Fan, Q., Pozarickij, A., Tan, N.Y.Q., Guo, X., Verhoeven, V.J.M., Vitart, V., Guggenheim, J.A., Miyake, M., Tideman, J.W.L., Khawaja, A.P., Zhang, L., MacGregor, S., Hohn, R., Chen, P., Biino, G., Wedenoja, J., Saffari, S.E., Tedja, M.S., Xie, J, Lanca, C., Wang, Y.X., Sahebjada, S., Mazur, J., Mirshahi, A., Martin, N.G., Yazar, S., Pennell, C.E., Yap, M., Haarman, A.E.G., Enthoven, C.A., Polling, J., Hewitt, A.W., Jaddoe, V.W.V., Duijn, C.M. van, Hayward, C., Polasek, O., Tai, E.S., Yoshikatsu, H., Hysi, P.G., Young, T.L., Tsujikawa, A., Wang, J.J., Mitchell, P., Pfeiffer, N., Parssinen, O., Foster, P.J., Fossarello, M., Yip, S.P., Williams, C., Hammond, C.J., Jonas, J.B., He, M., Mackey, D.A., Wong, T.Y., Klaver, C.C.W., Saw, S.M., Baird, P.N., and Cheng, C.Y.

Abstract

Contains fulltext : 218869.pdf (publisher's version ) (Open Access), Corneal curvature, a highly heritable trait, is a key clinical endophenotype for myopia - a major cause of visual impairment and blindness in the world. Here we present a trans-ethnic meta-analysis of corneal curvature GWAS in 44,042 individuals of Caucasian and Asian with replication in 88,218 UK Biobank data. We identified 47 loci (of which 26 are novel), with population-specific signals as well as shared signals across ethnicities. Some identified variants showed precise scaling in corneal curvature and eye elongation (i.e. axial length) to maintain eyes in emmetropia (i.e. HDAC11/FBLN2 rs2630445, RBP3 rs11204213); others exhibited association with myopia with little pleiotropic effects on eye elongation. Implicated genes are involved in extracellular matrix organization, developmental process for body and eye, connective tissue cartilage and glycosylation protein activities. Our study provides insights into population-specific novel genes for corneal curvature, and their pleiotropic effect in regulating eye size or conferring susceptibility to myopia.

Published
2020

81. Investigating the genetic and causal relationship between initiation or use of alcohol, caffeine, cannabis and nicotine

Author

Chang, L.H., Ong, J.S., An, J., Verweij, K.J.H., Vink, J.M., Pasman, J.A., Liu, M., MacGregor, S., Cornelis, M.C., Martin, N.G., Derks, E.M., Chang, L.H., Ong, J.S., An, J., Verweij, K.J.H., Vink, J.M., Pasman, J.A., Liu, M., MacGregor, S., Cornelis, M.C., Martin, N.G., and Derks, E.M.

Abstract

Contains fulltext : 217711.pdf (Publisher’s version ) (Closed access), Background: Caffeine, alcohol, nicotine and cannabis are commonly used psychoactive substances. While the use of these substances has been previously shown to be genetically correlated, causality between these substance use traits remains unclear. We aimed to revisit the genetic relationships among different measures of SU using genome-wide association study (GWAS) summary statistics from the UK Biobank, International Cannabis Consortium, and GWAS & Sequencing Consortium of Alcohol and Nicotine use. Methods: We obtained GWAS summary statistics from the aforementioned consortia for ten substance use traits including various measures of alcohol consumption, caffeine consumption, cannabis initiation and smoking behaviours. We then conducted SNP-heritability (h2) estimation for individual SU traits, followed by genetic correlation analyses and two-sample Mendelian randomisation (MR) studies between substance use trait pairs. Results: SNP h2 of the ten traits ranged from 0.03 to 0.11. After multiple testing correction, 29 of the 45 trait pairs showed evidence of being genetically correlated. MR analyses revealed that most SU traits were not causally associated with each other. However, we found evidence for an MR association between regular smoking initiation and caffeine consumption 40.17 mg; 95% CI: [ 24.01, 56.33] increase in caffeine intake per doubling of odds in smoking initiation). Our findings were robust against horizontal pleiotropy, SNP-outliers, and the direction of causality was consistent in all MR analyses. Conclusions: Most of the substance traits were genetically correlated but there is little evidence to establish causality apart from the relationship between smoking initiation and caffeine consumption.

Published
2020

82. Genome-wide association meta-analysis of single-nucleotide polymorphisms and symptomatic venous thromboembolism during therapy for acute lymphoblastic leukemia and lymphoma in caucasian children

Author

Mateos, MK, Tulstrup, M, Quinn, MCJ, Tuckuviene, R, Marshall, GM, Gupta, R, Mayoh, C, Wolthers, BO, Barbaro, PM, Ruud, E, Sutton, R, Huttunen, P, Revesz, T, Trakymiene, SS, Barbaric, D, Tedgård, U, Giles, JE, Alvaro, F, Jonsson, OG, Mechinaud, F, Saks, K, Catchpoole, D, Kotecha, RS, Dalla-Pozza, L, Chenevix-Trench, G, Trahair, TN, Macgregor, S, Schmiegelow, K, Mateos, MK, Tulstrup, M, Quinn, MCJ, Tuckuviene, R, Marshall, GM, Gupta, R, Mayoh, C, Wolthers, BO, Barbaro, PM, Ruud, E, Sutton, R, Huttunen, P, Revesz, T, Trakymiene, SS, Barbaric, D, Tedgård, U, Giles, JE, Alvaro, F, Jonsson, OG, Mechinaud, F, Saks, K, Catchpoole, D, Kotecha, RS, Dalla-Pozza, L, Chenevix-Trench, G, Trahair, TN, Macgregor, S, and Schmiegelow, K

Abstract

Symptomatic venous thromboembolism (VTE) occurs in five percent of children treated for acute lymphoblastic leukemia (ALL), but whether a genetic predisposition exists across different ALL treatment regimens has not been well studied. Methods: We undertook a genome-wide association study (GWAS) meta-analysis for VTE in consecutively treated children in the Nordic/Baltic acute lymphoblastic leukemia 2008 (ALL2008) cohort and the Australian Evaluation of Risk of ALL Treatment-Related Side-Effects (ERASE) cohort. A total of 92 cases and 1481 controls of European ancestry were included. Results: No SNPs reached genome-wide significance (p < 5 × 10−8) in either cohort. Among the top 34 single-nucleotide polymorphisms (SNPs) (p < 1 × 10−6), two loci had concordant effects in both cohorts: ALOX15B (rs1804772) (MAF: 1%; p = 3.95 × 10−7) that influences arachidonic acid metabolism and thus platelet aggregation, and KALRN (rs570684) (MAF: 1%; p = 4.34 × 10−7) that has been previously associated with risk of ischemic stroke, atherosclerosis, and early-onset coronary artery disease. Conclusion: This represents the largest GWAS meta-analysis conducted to date associating SNPs to VTE in children and adolescents treated on childhood ALL protocols. Validation of these findings is needed and may then lead to patient stratification for VTE preventive interventions. As VTE hemostasis involves multiple pathways, a more powerful GWAS is needed to detect combination of variants associated with VTE.

Published
2020

83. Assessment of polygenic architecture and risk prediction based on common variants across fourteen cancers.

Author

Houlston R., Choudhury P.P., Easton D.F., Milne R.L., Simard J., Hall P., Michailidou K., Dennis J., Schmidt M.K., Chang-Claude J., Gharahkhani P., Whiteman D., O'Mara T.A., Spurdle A.B., Thompson D.J., Tomlinson I., De Vivo I., Campbell P.T., Hoffmeister M., Jenkins M., Peters U., Hsu L., Gruber S.B., Casey G., Schmit S.L., Landi M.T., Law M.H., Iles M.M., Demenais F., Kumar R., MacGregor S., Bishop D.T., Ward S.V., Bondy M.L., Wiencke J.K., Melin B., Barnholtz-Sloan J., Kinnersley B., Wrensch M.R., Hung R.J., Caporaso N.E., Berndt S.I., Birmann B.M., Camp N.J., Kraft P., Rothman N., Slager S.L., Berchuck A., Pharoah P.D.P., Sellers T.A., Gayther S.A., Pearce C.L., Goode E.L., Schildkraut J.M., Moysich K.B., Amos C.I., Brennan P., McKay J., Amundadottir L.T., Jacobs E.J., Klein A.P., Petersen G.M., Risch H.A., Stolzenberg-Solomon R.Z., Wolpin B.M., Li D., Eeles R.A., Haiman C.A., Kote-Jarai Z., Schumacher F.R., Al Olama A.A., Purdue M.P., Scelo G., Dalgaard M.D., Greene M.H., Grotmol T., Kanetsky P.A., McGlynn K.A., Nathanson K.L., Turnbull C., Wiklund F., Chanock S.J., Chatterjee N., Garcia-Closas M., Zhang Y.D., Hurson A.N., Zhang H., Houlston R., Choudhury P.P., Easton D.F., Milne R.L., Simard J., Hall P., Michailidou K., Dennis J., Schmidt M.K., Chang-Claude J., Gharahkhani P., Whiteman D., O'Mara T.A., Spurdle A.B., Thompson D.J., Tomlinson I., De Vivo I., Campbell P.T., Hoffmeister M., Jenkins M., Peters U., Hsu L., Gruber S.B., Casey G., Schmit S.L., Landi M.T., Law M.H., Iles M.M., Demenais F., Kumar R., MacGregor S., Bishop D.T., Ward S.V., Bondy M.L., Wiencke J.K., Melin B., Barnholtz-Sloan J., Kinnersley B., Wrensch M.R., Hung R.J., Caporaso N.E., Berndt S.I., Birmann B.M., Camp N.J., Kraft P., Rothman N., Slager S.L., Berchuck A., Pharoah P.D.P., Sellers T.A., Gayther S.A., Pearce C.L., Goode E.L., Schildkraut J.M., Moysich K.B., Amos C.I., Brennan P., McKay J., Amundadottir L.T., Jacobs E.J., Klein A.P., Petersen G.M., Risch H.A., Stolzenberg-Solomon R.Z., Wolpin B.M., Li D., Eeles R.A., Haiman C.A., Kote-Jarai Z., Schumacher F.R., Al Olama A.A., Purdue M.P., Scelo G., Dalgaard M.D., Greene M.H., Grotmol T., Kanetsky P.A., McGlynn K.A., Nathanson K.L., Turnbull C., Wiklund F., Chanock S.J., Chatterjee N., Garcia-Closas M., Zhang Y.D., Hurson A.N., and Zhang H.

Abstract

Genome-wide association studies (GWAS) have led to the identification of hundreds of susceptibility loci across cancers, but the impact of further studies remains uncertain. Here we analyse summary-level data from GWAS of European ancestry across fourteen cancer sites to estimate the number of common susceptibility variants (polygenicity) and underlying effect-size distribution. All cancers show a high degree of polygenicity, involving at a minimum of thousands of loci. We project that sample sizes required to explain 80% of GWAS heritability vary from 60,000 cases for testicular to over 1,000,000 cases for lung cancer. The maximum relative risk achievable for subjects at the 99th risk percentile of underlying polygenic risk scores (PRS), compared to average risk, ranges from 12 for testicular to 2.5 for ovarian cancer. We show that PRS have potential for risk stratification for cancers of breast, colon and prostate, but less so for others because of modest heritability and lower incidence.Copyright © 2020, This is a U.S. government work and not under copyright protection in the U.S.; foreign copyright protection may apply.

Published
2020

84. Genome-wide association meta-analysis of corneal curvature identifies novel loci and shared genetic influences across axial length and refractive error

Author

Fan, Q. (Qiao), Pozarickij, A. (Alfred), Tan, N.Y.Q. (Nicholas Y. Q.), Guo, X. (Xiaobo), Verhoeven, V.J.M. (Virginie), Vitart, V. (Veronique), Guggenheim, J. (Jean), Miyake, M. (Masahiro), Tideman, J.W.L. (Willem), Khawaja, A.P. (Anthony), Zhang, L. (Liang), MacGregor, S. (Stuart), Höhn, R. (René), Chen, P. (Peng), Biino, G. (Ginevra), Wedenoja, J. (Juho), Saffari, S.E. (Seyed Ehsan), Tedja, M. (Milly), Xie, J. (Jing), Lanca, C. (Carla), Wang, Y.X. (Ya Xing), Sahebjada, S. (Srujana), Mazur, J. (Johanna), Mirshahi, A. (Alireza), Martin, N.G. (Nicholas), Yazar, S. (Seyhan), Pennell, C.E. (Craig), Yap, M.K.H. (Maurice K. H.), Haarman, A.E.G. (Annechien E. G.), Enthoven, C.A. (Clair A.), Polling, J.R. (Jan Roelof), Bailey-Wilson, J.E. (Joan E.), Veluchamy, A.B. (Amutha Barathi), Burdon, K.P. (Kathryn P.), Campbell, H. (Harry), Chen, L.J. (Li Jia), Chew, E.Y. (Emily Y.), Craig, J.E. (Jamie), Cumberland, P.M. (Phillippa M.), DeAngelis, M.M. (Margaret), Delcourt, C. (Cécile), Ding, X. (Xiaohu), Evans, D.M. (David M.), Gharahkhani, P. (Puya), Iglesias, A.I. (Adriana I.), Haller, T. (Toomas), Han, X. (Xikun), Hoang, Q. (Quan), Igo Jr., R.P. (Robert), Iyengar, S.K. (Sudha), Kähönen, M. (Mika), Kaprio, J. (Jaakko), Klein, B.E. (Barbara E.), Klein, R. (Ronald), Lass Jr., J.H. (Jonathan), Lee, K. (Kris), Lehtimäki, T. (Terho), Lewis, D.D. (Deyana D.), Li, Q. (Qing), Li, S.-M. (Shi-Ming), Lyytikäinen, L.-P. (Leo-Pekka), Meguro, A. (Akira), Metspalu, A. (Andres), Middlebrooks, C.D. (Candace D.), Mizuki, N. (Nobuhisa), Musolf, A.M. (Anthony M.), Nickels, S. (Stefan), Oexle, K. (Konrad), Pang, C.P. (Chi Pui), Paterson, A.D. (Andrew), Rahi, J.S. (Jugnoo S.), Raitakari, O. (Olli), Rudan, I. (Igor), Stambolian, D.E. (Dwight), Simpson, C.L. (Claire), Wang, N. (Ningli), Bin Wei, W. (Wen), Williams, K.M. (Katie M.), Wilson, J.F. (James), Wojciechowski, R. (Robert), Yamashiro, K. (Kenji), Yam, J.C.S. (Jason C. S.), Zhou, X. (Xiangtian), Aslam, T. (Tariq), Barman, S.A. (Sarah A.), Barrett, J.H. (Jenny H.), Bishop, P.N. (Paul), Blows, P. (Peter), Bunce, C. (Catey), Carare, R.O. (Roxana O.), Chakravarthy, U. (Usha), Chan, M. (Michelle), Chua, S.Y.L. (Sharon Y. L.), Crabb, D.P. (David), Cumberland, P.M. (Philippa M.), Day, A. (Alexander), Desai, P. (Parul), Dhillon, B. (Bal), Dick, A.D. (Andrew D.), Egan, C. (Cathy), Ennis, S. (Sarah), Fruttiger, M. (Marcus), Gallacher, J. (John), Garway-Heath, D.F. (David F.), Gibson, J. (Jane), Gore, D. (Dan), Hardcastle, A. (Alison), Harding, S.P. (Simon), Hogg, R. (Ruth), Keane, P.A. (Pearse A.), Khaw, S.P.T. (Sir Peng T.), Lascaratos, G. (Gerassimos), Lotery, A.J. (Andrew), Macgillivray, T. (Tom), Mackie, S. (Sarah), Martin, K. (Keith), McGaughey, M. (Michelle), McGuinness, B. (Bernadette), McKay, G.J. (Gareth), McKibbin, M. (Martin), Mitry, D. (Danny), Moore, T. (Tony), Morgan, J.E. (James E.), Muthy, Z.A. (Zaynah A.), O’Sullivan, E. (Eoin), Owen, C.G. (Chris G.), Patel, P. (Praveen), Paterson, E. (Euan), Peto, T. (Tünde), Petzold, A. (Axel), Rudnikca, A.R. (Alicja R.), Self, J. (Jay), Sivaprasad, S., Steel, D. (David), Stratton, I. (Irene), Strouthidis, N. (Nicholas), Sudlow, C. (Cathie), Thomas, D. (Dhanes), Trucco, E. (Emanuele), Tufail, A. (Adnan), Vernon, S.A. (Stephen A.), Viswanathan, A.C. (Ananth C.), Williams, K. (Katie), Woodside, J.V. (J.), Yates, M.M. (Max M.), Yip, J. (Jennifer), Zheng, Y. (Yalin), Hewit, A.W. (Alex), Jaddoe, V.W.V. (Vincent), Duijn, C.M. (Cornelia) van, Hayward, C. (Caroline), Polasek, O. (Ozren), Tai, E.S. (Shyong), Yoshikatsu, H. (Hosoda), Hysi, P.G. (Pirro G.), Young, T.L. (Terri L.), Tsujikawa, A. (Akitaka), Wang, J.J. (Jie Jing), Mitchell, P. (Paul), Pfeiffer, A.F.H. (Andreas), Pärssinen, O. (Olavi), Foster, P.J. (Paul), Fossarello, M. (Maurizio), Yip, S.P. (Shea Ping), Williams, C. (Cathy), Hammond, C.J. (Christopher), Jonas, J.B., He, M. (Mingguang), Mackey, D.A. (David), Wong, T.-Y. (Tien-Yin), Klaver, C.C.W. (Caroline), Saw, S-M. (Seang-Mei), Baird, P.N. (Paul), Cheng, C.-Y. (Ching-Yu), Fan, Q. (Qiao), Pozarickij, A. (Alfred), Tan, N.Y.Q. (Nicholas Y. Q.), Guo, X. (Xiaobo), Verhoeven, V.J.M. (Virginie), Vitart, V. (Veronique), Guggenheim, J. (Jean), Miyake, M. (Masahiro), Tideman, J.W.L. (Willem), Khawaja, A.P. (Anthony), Zhang, L. (Liang), MacGregor, S. (Stuart), Höhn, R. (René), Chen, P. (Peng), Biino, G. (Ginevra), Wedenoja, J. (Juho), Saffari, S.E. (Seyed Ehsan), Tedja, M. (Milly), Xie, J. (Jing), Lanca, C. (Carla), Wang, Y.X. (Ya Xing), Sahebjada, S. (Srujana), Mazur, J. (Johanna), Mirshahi, A. (Alireza), Martin, N.G. (Nicholas), Yazar, S. (Seyhan), Pennell, C.E. (Craig), Yap, M.K.H. (Maurice K. H.), Haarman, A.E.G. (Annechien E. G.), Enthoven, C.A. (Clair A.), Polling, J.R. (Jan Roelof), Bailey-Wilson, J.E. (Joan E.), Veluchamy, A.B. (Amutha Barathi), Burdon, K.P. (Kathryn P.), Campbell, H. (Harry), Chen, L.J. (Li Jia), Chew, E.Y. (Emily Y.), Craig, J.E. (Jamie), Cumberland, P.M. (Phillippa M.), DeAngelis, M.M. (Margaret), Delcourt, C. (Cécile), Ding, X. (Xiaohu), Evans, D.M. (David M.), Gharahkhani, P. (Puya), Iglesias, A.I. (Adriana I.), Haller, T. (Toomas), Han, X. (Xikun), Hoang, Q. (Quan), Igo Jr., R.P. (Robert), Iyengar, S.K. (Sudha), Kähönen, M. (Mika), Kaprio, J. (Jaakko), Klein, B.E. (Barbara E.), Klein, R. (Ronald), Lass Jr., J.H. (Jonathan), Lee, K. (Kris), Lehtimäki, T. (Terho), Lewis, D.D. (Deyana D.), Li, Q. (Qing), Li, S.-M. (Shi-Ming), Lyytikäinen, L.-P. (Leo-Pekka), Meguro, A. (Akira), Metspalu, A. (Andres), Middlebrooks, C.D. (Candace D.), Mizuki, N. (Nobuhisa), Musolf, A.M. (Anthony M.), Nickels, S. (Stefan), Oexle, K. (Konrad), Pang, C.P. (Chi Pui), Paterson, A.D. (Andrew), Rahi, J.S. (Jugnoo S.), Raitakari, O. (Olli), Rudan, I. (Igor), Stambolian, D.E. (Dwight), Simpson, C.L. (Claire), Wang, N. (Ningli), Bin Wei, W. (Wen), Williams, K.M. (Katie M.), Wilson, J.F. (James), Wojciechowski, R. (Robert), Yamashiro, K. (Kenji), Yam, J.C.S. (Jason C. S.), Zhou, X. (Xiangtian), Aslam, T. (Tariq), Barman, S.A. (Sarah A.), Barrett, J.H. (Jenny H.), Bishop, P.N. (Paul), Blows, P. (Peter), Bunce, C. (Catey), Carare, R.O. (Roxana O.), Chakravarthy, U. (Usha), Chan, M. (Michelle), Chua, S.Y.L. (Sharon Y. L.), Crabb, D.P. (David), Cumberland, P.M. (Philippa M.), Day, A. (Alexander), Desai, P. (Parul), Dhillon, B. (Bal), Dick, A.D. (Andrew D.), Egan, C. (Cathy), Ennis, S. (Sarah), Fruttiger, M. (Marcus), Gallacher, J. (John), Garway-Heath, D.F. (David F.), Gibson, J. (Jane), Gore, D. (Dan), Hardcastle, A. (Alison), Harding, S.P. (Simon), Hogg, R. (Ruth), Keane, P.A. (Pearse A.), Khaw, S.P.T. (Sir Peng T.), Lascaratos, G. (Gerassimos), Lotery, A.J. (Andrew), Macgillivray, T. (Tom), Mackie, S. (Sarah), Martin, K. (Keith), McGaughey, M. (Michelle), McGuinness, B. (Bernadette), McKay, G.J. (Gareth), McKibbin, M. (Martin), Mitry, D. (Danny), Moore, T. (Tony), Morgan, J.E. (James E.), Muthy, Z.A. (Zaynah A.), O’Sullivan, E. (Eoin), Owen, C.G. (Chris G.), Patel, P. (Praveen), Paterson, E. (Euan), Peto, T. (Tünde), Petzold, A. (Axel), Rudnikca, A.R. (Alicja R.), Self, J. (Jay), Sivaprasad, S., Steel, D. (David), Stratton, I. (Irene), Strouthidis, N. (Nicholas), Sudlow, C. (Cathie), Thomas, D. (Dhanes), Trucco, E. (Emanuele), Tufail, A. (Adnan), Vernon, S.A. (Stephen A.), Viswanathan, A.C. (Ananth C.), Williams, K. (Katie), Woodside, J.V. (J.), Yates, M.M. (Max M.), Yip, J. (Jennifer), Zheng, Y. (Yalin), Hewit, A.W. (Alex), Jaddoe, V.W.V. (Vincent), Duijn, C.M. (Cornelia) van, Hayward, C. (Caroline), Polasek, O. (Ozren), Tai, E.S. (Shyong), Yoshikatsu, H. (Hosoda), Hysi, P.G. (Pirro G.), Young, T.L. (Terri L.), Tsujikawa, A. (Akitaka), Wang, J.J. (Jie Jing), Mitchell, P. (Paul), Pfeiffer, A.F.H. (Andreas), Pärssinen, O. (Olavi), Foster, P.J. (Paul), Fossarello, M. (Maurizio), Yip, S.P. (Shea Ping), Williams, C. (Cathy), Hammond, C.J. (Christopher), Jonas, J.B., He, M. (Mingguang), Mackey, D.A. (David), Wong, T.-Y. (Tien-Yin), Klaver, C.C.W. (Caroline), Saw, S-M. (Seang-Mei), Baird, P.N. (Paul), and Cheng, C.-Y. (Ching-Yu)

Abstract

Corneal curvature, a highly heritable trait, is a key clinical endophenotype for myopia - a major cause of visual impairment and blindness in the world. Here we present a trans-ethnic meta-analysis of corneal curvature GWAS in 44,042 individuals of Caucasian and Asian with replication in 88,218 UK Biobank data. We identified 47 loci (of which 26 are novel), with population-specific signals as well as shared signals across ethnicities. Some identified variants showed precise scaling in corneal curvature and eye elongation (i.e. axial length) to maintain eyes in emmetropia (i.e. HDAC11/FBLN2 rs2630445, RBP3 rs11204213); others exhibited association with myopia with little pleiotropic effects on eye elongation. Implicated genes are involved in extracellular matrix organization, developmental process for body and eye, connective tissue cartilage and glycosylation protein activities. Our study provides insights into population-specific novel genes for corneal curvature, and their pleiotropic effect in regulating eye size or conferring susceptibility to myopia.

Published
2020
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85. Overlapping genetic architecture between Parkinson disease and melanoma

Author

Dube, Umber, Ibanez, Laura, Budde, John P., Benitez, Bruno A., Davis, Albert A., Harari, Oscar, Iles, M. M., Law, Matthew H., Brown, Kevin M., Agee, Michelle, Alipanahi, Babak, Auton, Adam, Bell, Robert K., Bryc, Katarzyna, Elson, Sarah L., Fontanillas, Pierre, Furlotte, Nicholas A., Hinds, David A., Huber, Karen E., Kleinman, Aaron, Litterman, Nadia K., McCreight, Jennifer C., McIntyre, Matthew H., Mountain, Joanna L., Noblin, Elizabeth S., Northover, Carrie A.M., Pitts, Steven J., Sathirapongsasuti, J. Fah, Sazonova, Olga V., Shelton, Janie F., Shringarpure, Suyash, Tian, Chao, Tung, Joyce Y., Vacic, Vladimir, Wilson, Catherine H., Bishop, D. T., Lee, J. E., Brossard, M., Martin, N. G., Moses, E. K., Song, F., Barrett, J. H., Kumar, R., Easton, D. F., Pharoah, P. D., Swerdlow, A. J., Kypreou, K. P., Taylor, J. C., Harland, M., Randerson-Moor, J., Akslen, L. A., Andresen, P. A., Avril, M. F., Azizi, E., Scarrà, G. B., Brown, K. M., Debniak, T., Duffy, D. L., Elder, D. E., Fang, S., Friedman, E., Galan, P., Ghiorzo, P., Gillanders, E. M., Goldstein, A. M., Gruis, N. A., Hansson, J., Helsing, P., Hočevar, M., Höiom, V., Ingvar, C., Kanetsky, P. A., Chen, W. V., Landi, M. T., Lang, J., Lathrop, G. M., Lubiński, J., Mackie, R. M., Mann, G. J., Molven, A., Montgomery, G. W., Novaković, S., Olsson, H., Puig, S., Puig-Butille, J. A., Wu, W., Qureshi, A. A., Radford-Smith, G. L., van der Stoep, N., van Doorn, R., Whiteman, D. C., Craig, J. E., Schadendorf, E., Simms, L. A., Burdon, K. P., Nyholt, D. R., Pooley, K. A., Orr, N., Stratigos, A. J., Cust, A. E., Ward, S. V., Hayward, N. K., Han, J., Schulze, H. J., Dunning, A. M., Bishop, J. A., Demenais, F., Amos, C. I., MacGregor, S., Cruchaga, Carlos, other, and, Dube, Umber, Ibanez, Laura, Budde, John P., Benitez, Bruno A., Davis, Albert A., Harari, Oscar, Iles, M. M., Law, Matthew H., Brown, Kevin M., Agee, Michelle, Alipanahi, Babak, Auton, Adam, Bell, Robert K., Bryc, Katarzyna, Elson, Sarah L., Fontanillas, Pierre, Furlotte, Nicholas A., Hinds, David A., Huber, Karen E., Kleinman, Aaron, Litterman, Nadia K., McCreight, Jennifer C., McIntyre, Matthew H., Mountain, Joanna L., Noblin, Elizabeth S., Northover, Carrie A.M., Pitts, Steven J., Sathirapongsasuti, J. Fah, Sazonova, Olga V., Shelton, Janie F., Shringarpure, Suyash, Tian, Chao, Tung, Joyce Y., Vacic, Vladimir, Wilson, Catherine H., Bishop, D. T., Lee, J. E., Brossard, M., Martin, N. G., Moses, E. K., Song, F., Barrett, J. H., Kumar, R., Easton, D. F., Pharoah, P. D., Swerdlow, A. J., Kypreou, K. P., Taylor, J. C., Harland, M., Randerson-Moor, J., Akslen, L. A., Andresen, P. A., Avril, M. F., Azizi, E., Scarrà, G. B., Brown, K. M., Debniak, T., Duffy, D. L., Elder, D. E., Fang, S., Friedman, E., Galan, P., Ghiorzo, P., Gillanders, E. M., Goldstein, A. M., Gruis, N. A., Hansson, J., Helsing, P., Hočevar, M., Höiom, V., Ingvar, C., Kanetsky, P. A., Chen, W. V., Landi, M. T., Lang, J., Lathrop, G. M., Lubiński, J., Mackie, R. M., Mann, G. J., Molven, A., Montgomery, G. W., Novaković, S., Olsson, H., Puig, S., Puig-Butille, J. A., Wu, W., Qureshi, A. A., Radford-Smith, G. L., van der Stoep, N., van Doorn, R., Whiteman, D. C., Craig, J. E., Schadendorf, E., Simms, L. A., Burdon, K. P., Nyholt, D. R., Pooley, K. A., Orr, N., Stratigos, A. J., Cust, A. E., Ward, S. V., Hayward, N. K., Han, J., Schulze, H. J., Dunning, A. M., Bishop, J. A., Demenais, F., Amos, C. I., MacGregor, S., Cruchaga, Carlos, and other, and

Abstract

Epidemiologic studies have reported inconsistent results regarding an association between Parkinson disease (PD) and cutaneous melanoma (melanoma). Identifying shared genetic architecture between these diseases can support epidemiologic findings and identify common risk genes and biological pathways. Here, we apply polygenic, linkage disequilibrium-informed methods to the largest available case–control, genome-wide association study summary statistic data for melanoma and PD. We identify positive and significant genetic correlation (correlation: 0.17, 95% CI 0.10–0.24; P = 4.09 × 10−06) between melanoma and PD. We further demonstrate melanoma and PD-inferred gene expression to overlap across tissues (correlation: 0.14, 95% CI 0.06 to 0.22; P = 7.87 × 10−04) and highlight seven genes including PIEZO1, TRAPPC2L, and SOX6 as potential mediators of the genetic correlation between melanoma and PD. These findings demonstrate specific, shared genetic architecture between PD and melanoma that manifests at the level of gene expression.

Published
2020

86. Genome-wide association meta-analysis of corneal curvature identifies novel loci and shared genetic influences across axial length and refractive error

Author

Fan, Q, Pozarickij, A, Tan, NYQ, Guo, X, Verhoeven, VJM, Vitart, V, Guggenheim, JA, Miyake, M, Tideman, JWL, Khawaja, AP, Zhang, L, MacGregor, S, Hoehn, R, Chen, P, Biino, G, Wedenoja, J, Saffari, SE, Tedja, MS, Xie, J, Lanca, C, Wang, YX, Sahebjada, S, Mazur, J, Mirshahi, A, Martin, NG, Yazar, S, Pennell, CE, Yap, M, Haarman, AEG, Enthoven, CA, Polling, J, Hewitt, AW, Jaddoe, VWV, van Duijn, CM, Hayward, C, Polasek, O, Tai, E-S, Yoshikatsu, H, Hysi, PG, Young, TL, Tsujikawa, A, Wang, JJ, Mitchell, P, Pfeiffer, N, Parssinen, O, Foster, PJ, Fossarello, M, Yip, SP, Williams, C, Hammond, CJ, Jonas, JB, He, M, Mackey, DA, Wong, T-Y, Klaver, CCW, Saw, S-M, Baird, PN, Cheng, C-Y, Fan, Q, Pozarickij, A, Tan, NYQ, Guo, X, Verhoeven, VJM, Vitart, V, Guggenheim, JA, Miyake, M, Tideman, JWL, Khawaja, AP, Zhang, L, MacGregor, S, Hoehn, R, Chen, P, Biino, G, Wedenoja, J, Saffari, SE, Tedja, MS, Xie, J, Lanca, C, Wang, YX, Sahebjada, S, Mazur, J, Mirshahi, A, Martin, NG, Yazar, S, Pennell, CE, Yap, M, Haarman, AEG, Enthoven, CA, Polling, J, Hewitt, AW, Jaddoe, VWV, van Duijn, CM, Hayward, C, Polasek, O, Tai, E-S, Yoshikatsu, H, Hysi, PG, Young, TL, Tsujikawa, A, Wang, JJ, Mitchell, P, Pfeiffer, N, Parssinen, O, Foster, PJ, Fossarello, M, Yip, SP, Williams, C, Hammond, CJ, Jonas, JB, He, M, Mackey, DA, Wong, T-Y, Klaver, CCW, Saw, S-M, Baird, PN, and Cheng, C-Y

Abstract

Corneal curvature, a highly heritable trait, is a key clinical endophenotype for myopia - a major cause of visual impairment and blindness in the world. Here we present a trans-ethnic meta-analysis of corneal curvature GWAS in 44,042 individuals of Caucasian and Asian with replication in 88,218 UK Biobank data. We identified 47 loci (of which 26 are novel), with population-specific signals as well as shared signals across ethnicities. Some identified variants showed precise scaling in corneal curvature and eye elongation (i.e. axial length) to maintain eyes in emmetropia (i.e. HDAC11/FBLN2 rs2630445, RBP3 rs11204213); others exhibited association with myopia with little pleiotropic effects on eye elongation. Implicated genes are involved in extracellular matrix organization, developmental process for body and eye, connective tissue cartilage and glycosylation protein activities. Our study provides insights into population-specific novel genes for corneal curvature, and their pleiotropic effect in regulating eye size or conferring susceptibility to myopia.

Published
2020

87. Multitrait analysis of glaucoma identifies new risk loci and enables polygenic prediction of disease susceptibility and progression

Author

Craig, JE, Han, X, Qassim, A, Hassall, M, Bailey, JNC, Kinzy, TG, Khawaja, AP, An, J, Marshall, H, Gharahkhani, P, Igo, RP, Graham, SL, Healey, PR, Ong, J-S, Zhou, T, Siggs, O, Law, MH, Souzeau, E, Ridge, B, Hysi, PG, Burdon, KP, Mills, RA, Landers, J, Ruddle, JB, Agar, A, Galanopoulos, A, White, AJR, Willoughby, CE, Andrew, NH, Best, S, Vincent, AL, Goldberg, I, Radford-Smith, G, Martin, NG, Montgomery, GW, Vitart, V, Hoehn, R, Wojciechowski, R, Jonas, JB, Aung, T, Pasquale, LR, Cree, AJ, Sivaprasad, S, Vallabh, NA, Viswanathan, AC, Pasutto, F, Haines, JL, Klaver, CCW, van Duijn, CM, Casson, RJ, Foster, PJ, Khaw, PT, Hammond, CJ, Mackey, DA, Mitchell, P, Lotery, AJ, Wiggs, JL, Hewitt, AW, MacGregor, S, Craig, JE, Han, X, Qassim, A, Hassall, M, Bailey, JNC, Kinzy, TG, Khawaja, AP, An, J, Marshall, H, Gharahkhani, P, Igo, RP, Graham, SL, Healey, PR, Ong, J-S, Zhou, T, Siggs, O, Law, MH, Souzeau, E, Ridge, B, Hysi, PG, Burdon, KP, Mills, RA, Landers, J, Ruddle, JB, Agar, A, Galanopoulos, A, White, AJR, Willoughby, CE, Andrew, NH, Best, S, Vincent, AL, Goldberg, I, Radford-Smith, G, Martin, NG, Montgomery, GW, Vitart, V, Hoehn, R, Wojciechowski, R, Jonas, JB, Aung, T, Pasquale, LR, Cree, AJ, Sivaprasad, S, Vallabh, NA, Viswanathan, AC, Pasutto, F, Haines, JL, Klaver, CCW, van Duijn, CM, Casson, RJ, Foster, PJ, Khaw, PT, Hammond, CJ, Mackey, DA, Mitchell, P, Lotery, AJ, Wiggs, JL, Hewitt, AW, and MacGregor, S

Abstract

Glaucoma, a disease characterized by progressive optic nerve degeneration, can be prevented through timely diagnosis and treatment. We characterize optic nerve photographs of 67,040 UK Biobank participants and use a multitrait genetic model to identify risk loci for glaucoma. A glaucoma polygenic risk score (PRS) enables effective risk stratification in unselected glaucoma cases and modifies penetrance of the MYOC variant encoding p.Gln368Ter, the most common glaucoma-associated myocilin variant. In the unselected glaucoma population, individuals in the top PRS decile reach an absolute risk for glaucoma 10 years earlier than the bottom decile and are at 15-fold increased risk of developing advanced glaucoma (top 10% versus remaining 90%, odds ratio = 4.20). The PRS predicts glaucoma progression in prospectively monitored, early manifest glaucoma cases (P = 0.004) and surgical intervention in advanced disease (P = 3.6 × 10-6). This glaucoma PRS will facilitate the development of a personalized approach for earlier treatment of high-risk individuals, with less intensive monitoring and treatment being possible for lower-risk groups.

Published
2020

88. Assessment of polygenic architecture and risk prediction based on common variants across fourteen cancers

Author

Zhang, YD, Hurson, AN, Zhang, H, Choudhury, PP, Easton, DF, Milne, RL, Simard, J, Hall, P, Michailidou, K, Dennis, J, Schmidt, MK, Chang-Claude, J, Gharahkhani, P, Whiteman, D, Campbell, PT, Hoffmeister, M, Jenkins, M, Peters, U, Hsu, L, Gruber, SB, Casey, G, Schmit, SL, O'Mara, TA, Spurdle, AB, Thompson, DJ, Tomlinson, I, De Vivo, I, Landi, MT, Law, MH, Iles, MM, Demenais, F, Kumar, R, MacGregor, S, Bishop, DT, Ward, SV, Bondy, ML, Houlston, R, Wiencke, JK, Melin, B, Barnholtz-Sloan, J, Kinnersley, B, Wrensch, MR, Amos, CI, Hung, RJ, Brennan, P, McKay, J, Caporaso, NE, Berndt, SI, Birmann, BM, Camp, NJ, Kraft, P, Rothman, N, Slager, SL, Berchuck, A, Pharoah, PDP, Sellers, TA, Gayther, SA, Pearce, CL, Goode, EL, Schildkraut, JM, Moysich, KB, Amundadottir, LT, Jacobs, EJ, Klein, AP, Petersen, GM, Risch, HA, Stolzenberg-Solomon, RZ, Wolpin, BM, Li, D, Eeles, RA, Haiman, CA, Kote-Jarai, Z, Schumacher, FR, Al Olama, AA, Purdue, MP, Scelo, G, Dalgaard, MD, Greene, MH, Grotmol, T, Kanetsky, PA, McGlynn, KA, Nathanson, KL, Turnbull, C, Wiklund, F, Chanock, SJ, Chatterjee, N, Garcia-Closas, M, Zhang, YD, Hurson, AN, Zhang, H, Choudhury, PP, Easton, DF, Milne, RL, Simard, J, Hall, P, Michailidou, K, Dennis, J, Schmidt, MK, Chang-Claude, J, Gharahkhani, P, Whiteman, D, Campbell, PT, Hoffmeister, M, Jenkins, M, Peters, U, Hsu, L, Gruber, SB, Casey, G, Schmit, SL, O'Mara, TA, Spurdle, AB, Thompson, DJ, Tomlinson, I, De Vivo, I, Landi, MT, Law, MH, Iles, MM, Demenais, F, Kumar, R, MacGregor, S, Bishop, DT, Ward, SV, Bondy, ML, Houlston, R, Wiencke, JK, Melin, B, Barnholtz-Sloan, J, Kinnersley, B, Wrensch, MR, Amos, CI, Hung, RJ, Brennan, P, McKay, J, Caporaso, NE, Berndt, SI, Birmann, BM, Camp, NJ, Kraft, P, Rothman, N, Slager, SL, Berchuck, A, Pharoah, PDP, Sellers, TA, Gayther, SA, Pearce, CL, Goode, EL, Schildkraut, JM, Moysich, KB, Amundadottir, LT, Jacobs, EJ, Klein, AP, Petersen, GM, Risch, HA, Stolzenberg-Solomon, RZ, Wolpin, BM, Li, D, Eeles, RA, Haiman, CA, Kote-Jarai, Z, Schumacher, FR, Al Olama, AA, Purdue, MP, Scelo, G, Dalgaard, MD, Greene, MH, Grotmol, T, Kanetsky, PA, McGlynn, KA, Nathanson, KL, Turnbull, C, Wiklund, F, Chanock, SJ, Chatterjee, N, and Garcia-Closas, M

Abstract

Genome-wide association studies (GWAS) have led to the identification of hundreds of susceptibility loci across cancers, but the impact of further studies remains uncertain. Here we analyse summary-level data from GWAS of European ancestry across fourteen cancer sites to estimate the number of common susceptibility variants (polygenicity) and underlying effect-size distribution. All cancers show a high degree of polygenicity, involving at a minimum of thousands of loci. We project that sample sizes required to explain 80% of GWAS heritability vary from 60,000 cases for testicular to over 1,000,000 cases for lung cancer. The maximum relative risk achievable for subjects at the 99th risk percentile of underlying polygenic risk scores (PRS), compared to average risk, ranges from 12 for testicular to 2.5 for ovarian cancer. We show that PRS have potential for risk stratification for cancers of breast, colon and prostate, but less so for others because of modest heritability and lower incidence.

Published
2020

89. Meta-analysis of 542,934 subjects of European ancestry identifies new genes and mechanisms predisposing to refractive error and myopia

Author

Hysi, PG, Choquet, H, Khawaja, AP, Wojciechowski, R, Tedja, MS, Yin, J, Simcoe, MJ, Patasova, K, Mahroo, OA, Thai, KK, Cumberland, PM, Melles, RB, Verhoeven, VJM, Vitart, V, Segre, A, Stone, RA, Wareham, N, Hewitt, AW, Mackey, DA, Klaver, CCW, MacGregor, S, Khaw, PT, Foster, PJ, Guggenheim, JA, Rahi, JS, Jorgenson, E, Hammond, CJ, Hysi, PG, Choquet, H, Khawaja, AP, Wojciechowski, R, Tedja, MS, Yin, J, Simcoe, MJ, Patasova, K, Mahroo, OA, Thai, KK, Cumberland, PM, Melles, RB, Verhoeven, VJM, Vitart, V, Segre, A, Stone, RA, Wareham, N, Hewitt, AW, Mackey, DA, Klaver, CCW, MacGregor, S, Khaw, PT, Foster, PJ, Guggenheim, JA, Rahi, JS, Jorgenson, E, and Hammond, CJ

Abstract

Refractive errors, in particular myopia, are a leading cause of morbidity and disability worldwide. Genetic investigation can improve understanding of the molecular mechanisms that underlie abnormal eye development and impaired vision. We conducted a meta-analysis of genome-wide association studies (GWAS) that involved 542,934 European participants and identified 336 novel genetic loci associated with refractive error. Collectively, all associated genetic variants explain 18.4% of heritability and improve the accuracy of myopia prediction (area under the curve (AUC) = 0.75). Our results suggest that refractive error is genetically heterogeneous, driven by genes that participate in the development of every anatomical component of the eye. In addition, our analyses suggest that genetic factors controlling circadian rhythm and pigmentation are also involved in the development of myopia and refractive error. These results may enable the prediction of refractive error and the development of personalized myopia prevention strategies in the future.

Published
2020

90. Rationale and protocol for the 7-and 8-year longitudinal assessments of eye health in a cohort of young adults in the Raine Study

Author

Lee, SS-Y, Lingham, G, Yazar, S, Sanfilippo, PG, Charng, J, Chen, FK, Hewitt, AW, Ng, F, Hammond, C, Straker, LM, Eastwood, PR, MacGregor, S, Rose, KA, Lucas, RM, Guggenheim, JA, Saw, S-M, Coroneo, MT, He, M, Mackey, DA, Lee, SS-Y, Lingham, G, Yazar, S, Sanfilippo, PG, Charng, J, Chen, FK, Hewitt, AW, Ng, F, Hammond, C, Straker, LM, Eastwood, PR, MacGregor, S, Rose, KA, Lucas, RM, Guggenheim, JA, Saw, S-M, Coroneo, MT, He, M, and Mackey, DA

Abstract

INTRODUCTION: Eye diseases and visual impairment more commonly affect elderly adults, thus, the majority of ophthalmic cohort studies have focused on older adults. Cohort studies on the ocular health of younger adults, on the other hand, have been few. The Raine Study is a longitudinal study that has been following a cohort since their birth in 1989-1991. As part of the 20-year follow-up of the Raine Study, participants underwent a comprehensive eye examination. As part of the 27- and 28-year follow-ups, eye assessments are being conducted and the data collected will be compared with those of the 20-year follow-up. This will provide an estimate of population incidence and updated prevalence of ocular conditions such as myopia and keratoconus, as well as longitudinal change in ocular parameters in young Australian adults. Additionally, the data will allow exploration of the environmental, health and genetic factors underlying inter-subject differential long-term ocular changes. METHODS AND ANALYSIS: Participants are being contacted via telephone, email and/or social media and invited to participate in the eye examination. At the 27-year follow-up, participants completed a follow-up eye screening, which assessed visual acuity, autorefraction, ocular biometry and ocular sun exposure. Currently, at the 28-year follow-up, a comprehensive eye examination is being conducted which, in addition to all the eye tests performed at the 27-year follow-up visit, includes tonometry, optical coherence tomography, funduscopy and anterior segment topography, among others. Outcome measures include the incidence of refractive error and pterygium, an updated prevalence of these conditions, and the 8-year change in ocular parameters. ETHICS AND DISSEMINATION: The Raine Study is registered in the Australian New Zealand Clinical Trials Registry. The Gen2 20-year, 27-year and 28-year follow-ups are approved by the Human Research Ethics Committee of the University of Western Australia. Findin

Published
2020

91. Rationale and protocol for the 7- And 8-year longitudinal assessments of eye health in a cohort of young adults in the Raine Study

Author

Lee, S.S.Y., Lingham, G., Yazar, S., Sanfilippo, P.G., Charng, J., Chen, F.K., Hewitt, A.W., Ng, F., Hammond, C., Straker, Leon, Eastwood, Peter, MacGregor, S., Rose, K.A., Lucas, R.M., Guggenheim, J.A., Saw, S.M., Coroneo, M.T., He, M., MacKey, D.A., Lee, S.S.Y., Lingham, G., Yazar, S., Sanfilippo, P.G., Charng, J., Chen, F.K., Hewitt, A.W., Ng, F., Hammond, C., Straker, Leon, Eastwood, Peter, MacGregor, S., Rose, K.A., Lucas, R.M., Guggenheim, J.A., Saw, S.M., Coroneo, M.T., He, M., and MacKey, D.A.

Abstract

Introduction Eye diseases and visual impairment more commonly affect elderly adults, thus, the majority of ophthalmic cohort studies have focused on older adults. Cohort studies on the ocular health of younger adults, on the other hand, have been few. The Raine Study is a longitudinal study that has been following a cohort since their birth in 1989-1991. As part of the 20-year follow-up of the Raine Study, participants underwent a comprehensive eye examination. As part of the 27- and 28-year follow-ups, eye assessments are being conducted and the data collected will be compared with those of the 20-year follow-up. This will provide an estimate of population incidence and updated prevalence of ocular conditions such as myopia and keratoconus, as well as longitudinal change in ocular parameters in young Australian adults. Additionally, the data will allow exploration of the environmental, health and genetic factors underlying inter-subject differential long-term ocular changes. Methods and analysis Participants are being contacted via telephone, email and/or social media and invited to participate in the eye examination. At the 27-year follow-up, participants completed a follow-up eye screening, which assessed visual acuity, autorefraction, ocular biometry and ocular sun exposure. Currently, at the 28-year follow-up, a comprehensive eye examination is being conducted which, in addition to all the eye tests performed at the 27-year follow-up visit, includes tonometry, optical coherence tomography, funduscopy and anterior segment topography, among others. Outcome measures include the incidence of refractive error and pterygium, an updated prevalence of these conditions, and the 8-year change in ocular parameters. Ethics and dissemination The Raine Study is registered in the Australian New Zealand Clinical Trials Registry. The Gen2 20-year, 27-year and 28-year follow-ups are approved by the Human Research Ethics Committee of the University of Western Australia. Findings

Published
2020

94. Web-based learning: how task scaffolding and web site design support knowledge acquisition

Author

MacGregor, S. Kim and Lou, Yiping

Subjects
Online education -- Research, Online education -- Analysis, Children
Abstract

Abstract Using WebQuests for inquiry-based learning represents a higher-order use of technology requiring students to exercise information seeking, analyzing, and synthesizing strategies. This research was designed to obtain a better […]

Published
2004

96. A genome scan for quantitative trait loci in a wild population of red deer (Cervus elaphus)

Author

Slate, J., Visscher, P.M., MacGregor, S., Stevens, D., Tate, M.L., and Pemberton, J.M.

Subjects
Genetic research, Red deer -- Genetic aspects, Biological sciences
Abstract

Recent empirical evidence indicates that although fitness and fitness components tend to have low heritability in natural populations, they may nonetheless have relatively large components of additive genetic variance. The molecular basis of additive genetic variation has been investigated in model organisms but never in the wild. In this article we describe an attempt to map quantitative trait loci (QTL) for birth weight (a trait positively associated with overall fitness) in an unmanipulated, wild population of red deer (Cervus elaphus). Two approaches were used: interval mapping by linear regression within half-sib families and a variance components analysis of a six-generation pedigree of >350 animals. Evidence for segregating QTL was found on three linkage groups, one of which was significant at the genome-wide suggestive linkage threshold. To our knowledge this is the first time that a QTL for any trait has been mapped in a wild mammal population. It is hoped that this study will stimulate further investigations of the genetic architecture of fitness traits in the wild.

Published
2002

98. Genome-wide association study of major depressive disorder: new results, meta-analysis, and lessons learned

Author

Wray, N R, Pergadia, M L, Blackwood, D HR, Penninx, B WJH, Gordon, S D, Nyholt, D R, Ripke, S, MacIntyre, D J, McGhee, K A, Maclean, A W, Smit, J H, Hottenga, J J, Willemsen, G, Middeldorp, C M, de Geus, E JC, Lewis, C M, McGuffin, P, Hickie, I B, van den Oord, E JCG, Liu, J Z, Macgregor, S, McEvoy, B P, Byrne, E M, Medland, S E, Statham, D J, Henders, A K, Heath, A C, Montgomery, G W, Martin, N G, Boomsma, D I, Madden, P AF, and Sullivan, P F

Published
2012
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