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1. Germline MBD4 deficiency causes a multi-tumor predisposition syndrome

Author: Palles, C, West, HD, Chew, E, Galavotti, S, Flensburg, C, Grolleman, JE, Jansen, EAM, Curley, H, Chegwidden, L, Arbe-Barnes, EH, Lander, N, Truscott, R, Pagan, J, Bajel, A, Sherwood, K, Martin, L, Thomas, H, Georgiou, D, Fostira, F, Goldberg, Y, Adams, DJ, van der Biezen, SAM, Christie, M, Clendenning, M, Thomas, LE, Deltas, C, Dimovski, AJ, Dymerska, D, Lubinski, J, Mahmood, K, van der Post, RS, Sanders, M, Weitz, J, Taylor, JC, Turnbull, C, Vreede, L, van Wezel, T, Whalley, C, Arnedo-Pac, C, Caravagna, G, Cross, W, Chubb, D, Frangou, A, Gruber, AJ, Kinnersley, B, Noyvert, B, Church, D, Graham, T, Houlston, R, Lopez-Bigas, N, Sottoriva, A, Wedge, D, Jenkins, MA, Kuiper, RP, Roberts, AW, Cheadle, JP, Ligtenberg, MJL, Hoogerbrugge, N, Koelzer, VH, Rivas, AD, Winship, IM, Ponte, CR, Buchanan, DD, Power, DG, Green, A, Tomlinson, IPM, Sampson, JR, Majewski, IJ, de Voer, RM, Palles, C, West, HD, Chew, E, Galavotti, S, Flensburg, C, Grolleman, JE, Jansen, EAM, Curley, H, Chegwidden, L, Arbe-Barnes, EH, Lander, N, Truscott, R, Pagan, J, Bajel, A, Sherwood, K, Martin, L, Thomas, H, Georgiou, D, Fostira, F, Goldberg, Y, Adams, DJ, van der Biezen, SAM, Christie, M, Clendenning, M, Thomas, LE, Deltas, C, Dimovski, AJ, Dymerska, D, Lubinski, J, Mahmood, K, van der Post, RS, Sanders, M, Weitz, J, Taylor, JC, Turnbull, C, Vreede, L, van Wezel, T, Whalley, C, Arnedo-Pac, C, Caravagna, G, Cross, W, Chubb, D, Frangou, A, Gruber, AJ, Kinnersley, B, Noyvert, B, Church, D, Graham, T, Houlston, R, Lopez-Bigas, N, Sottoriva, A, Wedge, D, Jenkins, MA, Kuiper, RP, Roberts, AW, Cheadle, JP, Ligtenberg, MJL, Hoogerbrugge, N, Koelzer, VH, Rivas, AD, Winship, IM, Ponte, CR, Buchanan, DD, Power, DG, Green, A, Tomlinson, IPM, Sampson, JR, Majewski, IJ, and de Voer, RM
Abstract: We report an autosomal recessive, multi-organ tumor predisposition syndrome, caused by bi-allelic loss-of-function germline variants in the base excision repair (BER) gene MBD4. We identified five individuals with bi-allelic MBD4 variants within four families and these individuals had a personal and/or family history of adenomatous colorectal polyposis, acute myeloid leukemia, and uveal melanoma. MBD4 encodes a glycosylase involved in repair of G:T mismatches resulting from deamination of 5'-methylcytosine. The colorectal adenomas from MBD4-deficient individuals showed a mutator phenotype attributable to mutational signature SBS1, consistent with the function of MBD4. MBD4-deficient polyps harbored somatic mutations in similar driver genes to sporadic colorectal tumors, although AMER1 mutations were more common and KRAS mutations less frequent. Our findings expand the role of BER deficiencies in tumor predisposition. Inclusion of MBD4 in genetic testing for polyposis and multi-tumor phenotypes is warranted to improve disease management.
Published: 2022

2. Germline MBD4 deficiency causes a multi-tumor predisposition syndrome

Author: Palles, C., West, H.D., Chew, E., Galavotti, S., Flensburg, C., Grolleman, J.E., Jansen, E.A.M., Curley, H., Chegwidden, L., Arbe-Barnes, E.H., Lander, N., Truscott, R., Pagan, J., Bajel, A., Sherwood, K., Martin, L., Thomas, H, Georgiou, D., Fostira, F., Goldberg, Y., Adams, D.J., Biezen, S.A.M. van der, Christie, M., Clendenning, M., Thomas, L.E., Deltas, C., Dimovski, A.J., Dymerska, D., Lubinski, J., Mahmood, K., Post, R.S. van der, Sanders, M., Weitz, J., Taylor, J.C., Turnbull, C., Vreede, L., Wezel, T. van, Whalley, C., Arnedo-Pac, C., Caravagna, G., Cross, W., Chubb, D., Frangou, A., Gruber, A.J., Kinnersley, B., Noyvert, B., Church, D., Graham, T., Houlston, R., Lopez-Bigas, N., Sottoriva, A., Wedge, D., Jenkins, Mark A., Kuiper, R.P., Roberts, A.W., Cheadle, J.P., Ligtenberg, M.J.L., Hoogerbrugge, N., Koelzer, V.H., Rivas, A.D., Winship, I.M., Ponte, C.R., Buchanan, D.D., Power, D.G., Green, A., Tomlinson, I.P., Sampson, J.R., Majewski, I.J., Voer, R.M. de, Palles, C., West, H.D., Chew, E., Galavotti, S., Flensburg, C., Grolleman, J.E., Jansen, E.A.M., Curley, H., Chegwidden, L., Arbe-Barnes, E.H., Lander, N., Truscott, R., Pagan, J., Bajel, A., Sherwood, K., Martin, L., Thomas, H, Georgiou, D., Fostira, F., Goldberg, Y., Adams, D.J., Biezen, S.A.M. van der, Christie, M., Clendenning, M., Thomas, L.E., Deltas, C., Dimovski, A.J., Dymerska, D., Lubinski, J., Mahmood, K., Post, R.S. van der, Sanders, M., Weitz, J., Taylor, J.C., Turnbull, C., Vreede, L., Wezel, T. van, Whalley, C., Arnedo-Pac, C., Caravagna, G., Cross, W., Chubb, D., Frangou, A., Gruber, A.J., Kinnersley, B., Noyvert, B., Church, D., Graham, T., Houlston, R., Lopez-Bigas, N., Sottoriva, A., Wedge, D., Jenkins, Mark A., Kuiper, R.P., Roberts, A.W., Cheadle, J.P., Ligtenberg, M.J.L., Hoogerbrugge, N., Koelzer, V.H., Rivas, A.D., Winship, I.M., Ponte, C.R., Buchanan, D.D., Power, D.G., Green, A., Tomlinson, I.P., Sampson, J.R., Majewski, I.J., and Voer, R.M. de
Abstract: Contains fulltext : 251996.pdf (Publisher’s version ) (Open Access), We report an autosomal recessive, multi-organ tumor predisposition syndrome, caused by bi-allelic loss-of-function germline variants in the base excision repair (BER) gene MBD4. We identified five individuals with bi-allelic MBD4 variants within four families and these individuals had a personal and/or family history of adenomatous colorectal polyposis, acute myeloid leukemia, and uveal melanoma. MBD4 encodes a glycosylase involved in repair of G:T mismatches resulting from deamination of 5'-methylcytosine. The colorectal adenomas from MBD4-deficient individuals showed a mutator phenotype attributable to mutational signature SBS1, consistent with the function of MBD4. MBD4-deficient polyps harbored somatic mutations in similar driver genes to sporadic colorectal tumors, although AMER1 mutations were more common and KRAS mutations less frequent. Our findings expand the role of BER deficiencies in tumor predisposition. Inclusion of MBD4 in genetic testing for polyposis and multi-tumor phenotypes is warranted to improve disease management.
Published: 2022

3. 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

4. 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

5. Diffuse gliomas classified by 1p/19q co-deletion, TERT promoter and IDH mutation status are associated with specific genetic risk loci

Author: Labreche K., Kinnersley B., Berzero G., Di Stefano A. L., Rahimian A., Detrait I., Marie Y., Grenier-Boley B., Hoang-Xuan K., Delattre J. -Y., Idbaih A., Houlston R. S., Sanson M., Labreche, K., Kinnersley, B., Berzero, G., Di Stefano, A. L., Rahimian, A., Detrait, I., Marie, Y., Grenier-Boley, B., Hoang-Xuan, K., Delattre, J. -Y., Idbaih, A., Houlston, R. S., and Sanson, M.
Abstract: Recent genome-wide association studies of glioma have led to the discovery of single nucleotide polymorphisms (SNPs) at 25 loci influencing risk. Gliomas are heterogeneous, hence to investigate the relationship between risk SNPs and glioma subtype we analysed 1659 tumours profiled for IDH mutation, TERT promoter mutation and 1p/19q co-deletion. These data allowed definition of five molecular subgroups of glioma: triple-positive (IDH mutated, 1p/19q co-deletion, TERT promoter mutated); TERT-IDH (IDH mutated, TERT promoter mutated, 1p/19q-wild-type); IDH-only (IDH mutated, 1p/19q wild-type, TERT promoter wild-type); triple-negative (IDH wild-type, 1p/19q wild-type, TERT promoter wild-type) and TERT-only (TERT promoter mutated, IDH wild-type, 1p/19q wild-type). Most glioma risk loci showed subtype specificity: (1) the 8q24.21 SNP for triple-positive glioma; (2) 5p15.33, 9p21.3, 17p13.1 and 20q13.33 SNPs for TERT-only glioma; (3) 1q44, 2q33.3, 3p14.1, 11q21, 11q23.3, 14q12, and 15q24.2 SNPs for IDH mutated glioma. To link risk SNPs to target candidate genes we analysed Hi-C and gene expression data, highlighting the potential role of IDH1 at 2q33.3, MYC at 8q24.21 and STMN3 at 20q13.33. Our observations provide further insight into the nature of susceptibility to glioma.
Published: 2018

6. Genome-wide association study identifies susceptibility loci for B-cell childhood acute lymphoblastic leukemia

Author: Vijayakrishnan, J, Studd, J, Broderick, P, Kinnersley, B, Holroyd, A, Law, PJ, Kumar, R, Allan, JM, Harrison, CJ, Moorman, AV, Vora, A, Roman, E, Rachakonda, S, Kinsey, SE, Sheridan, E, Thompson, PD, Irving, JA, Koehler, R, Hoffmann, P, Nöthen, MM, Heilmann-Heimbach, S, Jöckel, KH, Easton, DF, Pharaoh, PDP, Dunning, AM, Peto, J, Canzian, F, Swerdlow, A, Eeles, RA, Kote-Jarai, Z, Muir, K, Pashayan, N, Greaves, M, Zimmerman, M, Bartram, CR, Schrappe, M, Stanulla, M, Hemminki, K, Houlston, RS, Henderson, BE, Haiman, CA, Benlloch, S, Schumacher, FR, Olama, AAA, Berndt, SI, Conti, DV, Wiklund, F, Chanock, S, Stevens, VL, Tangen, CM, Batra, J, Clements, J, Gronberg, H, Schleutker, J, Albanes, D, Weinstein, S, Wolk, A, West, C, Mucci, L, Cancel-Tassin, G, Koutros, S, Sorensen, KD, Maehle, L, Neal, DE, Travis, RC, Hamilton, RJ, Ingles, SA, Rosenstein, B, Lu, YJ, Giles, GG, Kibel, AS, Vega, A, Kogevinas, M, Penney, KL, Park, JY, Stanford, JL, The PRACTICAL Consortium, and Claessens, Frank
Subjects: Male, Oncogene Proteins, Fusion, Glycosyltransferases, Prognosis, Polymorphism, Single Nucleotide, HLA Antigens, Risk Factors, Child, Preschool, Precursor B-Cell Lymphoblastic Leukemia-Lymphoma, Core Binding Factor Alpha 2 Subunit, Humans, Female, Genetic Predisposition to Disease, Child, Genome-Wide Association Study
Abstract: © 2018 The Author(s). Genome-wide association studies (GWAS) have advanced our understanding of susceptibility to B-cell precursor acute lymphoblastic leukemia (BCP-ALL); however, much of the heritable risk remains unidentified. Here, we perform a GWAS and conduct a meta-analysis with two existing GWAS, totaling 2442 cases and 14,609 controls. We identify risk loci for BCP-ALL at 8q24.21 (rs28665337, P = 3.86 × 10-9, odds ratio (OR) = 1.34) and for ETV6-RUNX1 fusion-positive BCP-ALL at 2q22.3 (rs17481869, P = 3.20 × 10-8, OR = 2.14). Our findings provide further insights into genetic susceptibility to ALL and its biology. ispartof: Nature Communications vol:9 issue:1 ispartof: location:England status: published
Published: 2018

7. Transcriptome-wide association study of multiple myeloma identifies candidate susceptibility genes

Author: Went, M., Kinnersley, B., Sud, A., Johnson, D.C. (David), Weinhold, N, Försti, A. (Asta), Duin, M. (Mark) van, Orlando, G., Mitchell, JS, de Kuiper, R., Walker, BA, Gregory, WM, Hoffmann, P. (Per), Jackson, G. (Graham), Nöthen, M.M. (Markus), da Silva, MI, Thomsen, H, Broyl, A. (Annemiek), Davies, F.E., Thorsteinsdottir, U. (Unnur), Hansson, M, Kaiser, M, Sonneveld, P. (Pieter), Goldschmidt, H. (Hartmut), Zwart, J-A. (John-Anker), Hemminki, K. (Kari), Nilsson, B, Morgan, G.J., Houlston, R. (Richard), Went, M., Kinnersley, B., Sud, A., Johnson, D.C. (David), Weinhold, N, Försti, A. (Asta), Duin, M. (Mark) van, Orlando, G., Mitchell, JS, de Kuiper, R., Walker, BA, Gregory, WM, Hoffmann, P. (Per), Jackson, G. (Graham), Nöthen, M.M. (Markus), da Silva, MI, Thomsen, H, Broyl, A. (Annemiek), Davies, F.E., Thorsteinsdottir, U. (Unnur), Hansson, M, Kaiser, M, Sonneveld, P. (Pieter), Goldschmidt, H. (Hartmut), Zwart, J-A. (John-Anker), Hemminki, K. (Kari), Nilsson, B, Morgan, G.J., and Houlston, R. (Richard)
Abstract: Background: While genome-wide association studies (GWAS) of multiple myeloma (MM) have identified variants at 23 regions influencing risk, the genes underlying these associations are largely unknown. To identify candidate causal genes at these regions and search for novel risk regions, we performed a multi-tissue transcriptome-wide association study (TWAS). Results: GWAS data on 7319 MM cases and 234,385 controls was integrated with Genotype-Tissue Expression Project (GTEx) data assayed in 48 tissues (sample sizes, N = 80–491), including lymphocyte cell lines and whole blood, to predict gene expression. We identified 108 genes at 13 independent regions associated with MM risk, all of which were in 1 Mb of known MM GWAS risk variants. Of these, 94 genes, located in eight regions, had not previously been considered as a candidate gene for that locus. Conclusions: Our findings highlight the value of leveraging expression data from multiple tissues to identify candidate genes responsible for GWAS associations which provide insight into MM tumorigenesis. Among the genes identified, a number have plausible roles in MM biology, notably APOBEC3C, APOBEC3H, APOBEC3D, APOBEC3F, APOBEC3G, or have been previously implicated in other malignancies. The genes identified in this TWAS can be explored for follow-up and validation to further understand their role in MM biology.
Published: 2019
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8. Genome-wide association study identifies susceptibility loci for B-cell childhood acute lymphoblastic leukemia (vol 9, 1340, 2018)

Author: Vijayakrishnan, J, Studd, J, Broderick, P, Kinnersley, B, Holroyd, A, Law, PJ, Kumar, R, Allan, JM, Harrison, CJ, Moorman, AV, Vora, A, Roman, E, Rachakonda, S, Kinsey, SE, Sheridan, E, Thompson, PD, Irving, JA, Koehler, R, Hoffmann, P, Noethen, MM, Heilmann-Heimbach, S, Joeckel, K-H, Easton, DF, Pharaoh, PDP, Dunning, AM, Peto, J, Canzian, F, Swerdlow, A, Eeles, RA, Kote-Jarai, Z, Muir, K, Pashayan, N, Henderson, BE, Haiman, CA, Benlloch, S, Schumacher, FR, Al Olama, AA, Berndt, SI, Conti, DV, Wiklund, F, Chanock, S, Stevens, VL, Tangen, CM, Batra, J, Clements, J, Gronberg, H, Schleutker, J, Albanes, D, Weinstein, S, Wolk, A, West, C, Mucci, L, Cancel-Tassin, G, Koutros, S, Sorensen, KD, Maehle, L, Neal, DE, Travis, RC, Hamilton, RJ, Ingles, SA, Rosenstein, B, Lu, Y-J, Giles, GG, Kibel, AS, Vega, A, Kogevinas, M, Penney, KL, Park, JY, Stanford, JL, Cybulski, C, Nordestgaard, BG, Brenner, H, Maier, C, Kim, J, John, EM, Teixeira, MR, Neuhausen, SL, De Ruyck, K, Razack, A, Newcomb, LF, Lessel, D, Kaneva, R, Usmani, N, Claessens, F, Townsend, PA, Gago-Dominguez, M, Roobol, MJ, Menegaux, F, Greaves, M, Zimmerman, M, Bartram, CR, Schrappe, M, Stanulla, M, Hemminki, K, Houlston, RS, Vijayakrishnan, J, Studd, J, Broderick, P, Kinnersley, B, Holroyd, A, Law, PJ, Kumar, R, Allan, JM, Harrison, CJ, Moorman, AV, Vora, A, Roman, E, Rachakonda, S, Kinsey, SE, Sheridan, E, Thompson, PD, Irving, JA, Koehler, R, Hoffmann, P, Noethen, MM, Heilmann-Heimbach, S, Joeckel, K-H, Easton, DF, Pharaoh, PDP, Dunning, AM, Peto, J, Canzian, F, Swerdlow, A, Eeles, RA, Kote-Jarai, Z, Muir, K, Pashayan, N, Henderson, BE, Haiman, CA, Benlloch, S, Schumacher, FR, Al Olama, AA, Berndt, SI, Conti, DV, Wiklund, F, Chanock, S, Stevens, VL, Tangen, CM, Batra, J, Clements, J, Gronberg, H, Schleutker, J, Albanes, D, Weinstein, S, Wolk, A, West, C, Mucci, L, Cancel-Tassin, G, Koutros, S, Sorensen, KD, Maehle, L, Neal, DE, Travis, RC, Hamilton, RJ, Ingles, SA, Rosenstein, B, Lu, Y-J, Giles, GG, Kibel, AS, Vega, A, Kogevinas, M, Penney, KL, Park, JY, Stanford, JL, Cybulski, C, Nordestgaard, BG, Brenner, H, Maier, C, Kim, J, John, EM, Teixeira, MR, Neuhausen, SL, De Ruyck, K, Razack, A, Newcomb, LF, Lessel, D, Kaneva, R, Usmani, N, Claessens, F, Townsend, PA, Gago-Dominguez, M, Roobol, MJ, Menegaux, F, Greaves, M, Zimmerman, M, Bartram, CR, Schrappe, M, Stanulla, M, Hemminki, K, and Houlston, RS
Abstract: The original version of this Article contained an error in the spelling of a member of the PRACTICAL Consortium, Manuela Gago-Dominguez, which was incorrectly given as Manuela Gago Dominguez. This has now been corrected in both the PDF and HTML versions of the Article. Furthermore, in the original HTML version of this Article, the order of authors within the author list was incorrect. The PRACTICAL consortium was incorrectly listed after Richard S. Houlston and should have been listed after Nora Pashayan. This error has been corrected in the HTML version of the Article; the PDF version was correct at the time of publication.
Published: 2019

9. Transcriptome-wide association study of multiple myeloma identifies candidate susceptibility genes

Author: Went, M, Kinnersley, B, Sud, A, Johnson, DC, Weinhold, N, Forsti, A, van Duin, Mark, Orlando, G, Mitchell, JS, Kuiper, Ronella, Walker, BA, Gregory, WM, Hoffmann, P, Jackson, GH, Nothen, MM, da Silva, MI, Thomsen, H, Broijl, A., Davies, FE, Thorsteinsdottir, U, Hansson, M, Kaiser, M, Sonneveld, Pieter, Goldschmidt, H, Stefansson, K, Hemminki, K, Nilsson, B, Morgan, GJ, Houlston, RS, Went, M, Kinnersley, B, Sud, A, Johnson, DC, Weinhold, N, Forsti, A, van Duin, Mark, Orlando, G, Mitchell, JS, Kuiper, Ronella, Walker, BA, Gregory, WM, Hoffmann, P, Jackson, GH, Nothen, MM, da Silva, MI, Thomsen, H, Broijl, A., Davies, FE, Thorsteinsdottir, U, Hansson, M, Kaiser, M, Sonneveld, Pieter, Goldschmidt, H, Stefansson, K, Hemminki, K, Nilsson, B, Morgan, GJ, and Houlston, RS
Published: 2019

10. Testicular cancer genomics England Clinical Interpretation Partnership (GECIP): A genomic exploration of testicular germ cell tumours

Author: Frangou, A.M., primary, Cornish, A., additional, Kinnersley, B., additional, Wedge, D.C., additional, Protheroe, A., additional, Murray, M.J., additional, and Verrill, C., additional
Published: 2019
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11. Genome-wide association study identifies susceptibility loci for B-cell childhood acute lymphoblastic leukemia

Author: Vijayakrishnan, J. (Jayaram), Studd, J. (James), Broderick, P. (Peter), Kinnersley, B. (Ben), Holroyd, A. (Amy), Law, P.J. (Philip J.), Kumar, R., Allan, J.M. (James M.), Harrison, C.J. (Christine), Moorman, A.V. (Anthony), Vora, A. (Ajay), Roman, E. (Eve), Rachakonda, S. (Sivaramakrishna), Kinsey, S.E. (Sally E.), Sheridan, E. (Eamonn), Thompson, P.D. (Pamela D.), Irving, J. (Julie), Koehler, R. (Rolf), Hoffmann, P. (Per), Nöthen, M.M. (Markus), Heilmann-Heimbach, S. (Stefanie), JöCkel, K.-H. (Karl-Heinz), Easton, D.F. (Douglas), Pharaoh, P.D.P. (Paul), Dunning, A.M. (Alison), Peto, J. (Julian), Canzian, F. (Frederico), Swerdlow, A.J. (Anthony ), Eeles, R.A. (Rosalind A.), Kote-Jarai, Z., Muir, K. (Kenneth), Pashayan, N. (Nora), Greaves, M.F. (Mel), Zimmerman, M. (Martin), Bartram, C.R. (Claus), Schrappe, M. (Martin), Stanulla, M. (Martin), Hemminki, K. (Kari), Houlston, R.S. (Richard S.), Vijayakrishnan, J. (Jayaram), Studd, J. (James), Broderick, P. (Peter), Kinnersley, B. (Ben), Holroyd, A. (Amy), Law, P.J. (Philip J.), Kumar, R., Allan, J.M. (James M.), Harrison, C.J. (Christine), Moorman, A.V. (Anthony), Vora, A. (Ajay), Roman, E. (Eve), Rachakonda, S. (Sivaramakrishna), Kinsey, S.E. (Sally E.), Sheridan, E. (Eamonn), Thompson, P.D. (Pamela D.), Irving, J. (Julie), Koehler, R. (Rolf), Hoffmann, P. (Per), Nöthen, M.M. (Markus), Heilmann-Heimbach, S. (Stefanie), JöCkel, K.-H. (Karl-Heinz), Easton, D.F. (Douglas), Pharaoh, P.D.P. (Paul), Dunning, A.M. (Alison), Peto, J. (Julian), Canzian, F. (Frederico), Swerdlow, A.J. (Anthony ), Eeles, R.A. (Rosalind A.), Kote-Jarai, Z., Muir, K. (Kenneth), Pashayan, N. (Nora), Greaves, M.F. (Mel), Zimmerman, M. (Martin), Bartram, C.R. (Claus), Schrappe, M. (Martin), Stanulla, M. (Martin), Hemminki, K. (Kari), and Houlston, R.S. (Richard S.)
Abstract: Genome-wide association studies (GWAS) have advanced our understanding of susceptibility to B-cell precursor acute lymphoblastic leukemia (BCP-ALL); however, much of the heritable risk remains unidentified. Here, we perform a GWAS and conduct a meta-analysis with two existing GWAS, totaling 2442 cases and 14,609 controls. We identify risk loci for BCP-ALL at 8q24.21 (rs28665337, P = 3.86 × 10-9, odds ratio (OR) = 1.34) and for ETV6-RUNX1 fusion-positive BCP-ALL at 2q22.3 (rs17481869, P = 3.20 × 10-8, OR = 2.14). Our findings provide further insights into genetic susceptibility to ALL and its biology.
Published: 2018
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12. Sex-specific glioma genome-wide association study identifies new risk locus at 3p21.31 in females, and finds sex-differences in risk at 8q24.21.

Author: Ostrom, QT, Kinnersley, B, Wrensch, MR, Eckel-Passow, JE, Armstrong, G, Rice, T, Chen, Y, Wiencke, JK, McCoy, LS, Hansen, HM, Amos, CI, Bernstein, JL, Claus, EB, Il'yasova, D, Johansen, C, Lachance, DH, Lai, RK, Merrell, RT, Olson, SH, Sadetzki, S, Schildkraut, JM, Shete, S, Rubin, JB, Lathia, JD, Berens, ME, Andersson, U, Rajaraman, P, Chanock, SJ, Linet, MS, Wang, Z, Yeager, M, GliomaScan consortium, Houlston, RS, Jenkins, RB, Melin, B, Bondy, ML, Barnholtz-Sloan, JS, Ostrom, QT, Kinnersley, B, Wrensch, MR, Eckel-Passow, JE, Armstrong, G, Rice, T, Chen, Y, Wiencke, JK, McCoy, LS, Hansen, HM, Amos, CI, Bernstein, JL, Claus, EB, Il'yasova, D, Johansen, C, Lachance, DH, Lai, RK, Merrell, RT, Olson, SH, Sadetzki, S, Schildkraut, JM, Shete, S, Rubin, JB, Lathia, JD, Berens, ME, Andersson, U, Rajaraman, P, Chanock, SJ, Linet, MS, Wang, Z, Yeager, M, GliomaScan consortium, Houlston, RS, Jenkins, RB, Melin, B, Bondy, ML, and Barnholtz-Sloan, JS
Abstract: Incidence of glioma is approximately 50% higher in males. Previous analyses have examined exposures related to sex hormones in women as potential protective factors for these tumors, with inconsistent results. Previous glioma genome-wide association studies (GWAS) have not stratified by sex. Potential sex-specific genetic effects were assessed in autosomal SNPs and sex chromosome variants for all glioma, GBM and non-GBM patients using data from four previous glioma GWAS. Datasets were analyzed using sex-stratified logistic regression models and combined using meta-analysis. There were 4,831 male cases, 5,216 male controls, 3,206 female cases and 5,470 female controls. A significant association was detected at rs11979158 (7p11.2) in males only. Association at rs55705857 (8q24.21) was stronger in females than in males. A large region on 3p21.31 was identified with significant association in females only. The identified differences in effect of risk variants do not fully explain the observed incidence difference in glioma by sex.
Published: 2018

13. Genome-wide association study identifies multiple susceptibility loci for glioma

Author: Kinnersley, B, Labussière, M, Holroyd, A, Di Stefano, A-L, Broderick, P, Vijayakrishnan, J, Mokhtari, K, Delattre, J-Y, Gousias, K, Schramm, J, Schoemaker, MJ, Fleming, SJ, Herms, S, Heilmann, S, Schreiber, S, Wichmann, H-E, Nöthen, MM, Swerdlow, A, Lathrop, M, Simon, M, Bondy, M, Sanson, M, and Houlston, RS
Abstract: Previous genome-wide association studies (GWASs) have shown that common genetic variation contributes to the heritable risk of glioma. To identify new glioma susceptibility loci, we conducted a meta-analysis of four GWAS (totalling 4,147 cases and 7,435 controls), with imputation using 1000 Genomes and UK10K Project data as reference. After genotyping an additional 1,490 cases and 1,723 controls we identify new risk loci for glioblastoma (GBM) at 12q23.33 (rs3851634, near POLR3B, P=3.02 × 10−9) and non-GBM at 10q25.2 (rs11196067, near VTI1A, P=4.32 × 10−8), 11q23.2 (rs648044, near ZBTB16, P=6.26 × 10−11), 12q21.2 (rs12230172, P=7.53 × 10−11) and 15q24.2 (rs1801591, near ETFA, P=5.71 × 10−9). Our findings provide further insights into the genetic basis of the different glioma subtypes.
Published: 2015

14. Meta-analysis of genome-wide association studies identifies common susceptibility polymorphisms for colorectal and endometrial cancer near SH2B3 and TSHZ1

Author: Cheng, T.H.T., Thompson, D., Painter, J., O'Mara, T., Gorman, M., Martin, L., Palles, C., Jones, A., Buchanan, D.D., Win, A.K., Hopper, J., Jenkins, M., Lindor, N.M., Newcomb, P.A., Gallinger, S., Conti, D., Schumacher, F., Casey, G., Giles, G.G., Pharoah, P., Peto, J., Cox, A., Swerdlow, A., Couch, F., Cunningham, J.M., Goode, E.L., Winham, S.J., Lambrechts, D., Fasching, P., Burwinkel, B., Brenner, H., Brauch, H., Chang-Claude, J., Salvesen, H.B., Kristensen, V., Darabi, H., Li, J., Liu, T., Lindblom, A., Hall, P., Echeverry de Polanco, M., Sans, M., Carracedo, A., Castellvi-Bel, S., Rojas-Martinez, A., Jr, A.S., Teixeira, M.R., Dunning, A.M., Dennis, J., Otton, G., Proietto, T., Holliday, E., Attia, J., Ashton, K., Scott, R.J., McEvoy, M., Dowdy, S.C., Fridley, B.L., Werner, H.M.J., Trovik, J., Njolstad, T.S., Tham, E., Mints, M., Runnebaum, I., Hillemanns, P., Doerk, T., Amant, F., Schrauwen, S., Hein, A., Beckmann, M.W., Ekici, A., Czene, K., Meindl, A., Bolla, M.K., Michailidou, K., Tyrer, J.P., Wang, Q., Ahmed, S., Healey, C.S., Shah, M., Annibali, D., Depreeuw, J., Al-Tassan, N.A., Harris, R., Meyer, B.F., Whiffin, N., Hosking, F.J., Kinnersley, B., Farrington, S.M., Timofeeva, M., Tenesa, A., Campbell, H., Haile, R.W., Hodgson, S., Carvajal-Carmona, L., Cheadle, J.P., Easton, D., Dunlop, M., Houlston, R., Spurdle, A., Tomlinson, I., and Other departments
Subjects: Male, CARCINOMA, MICROSATELLITE INSTABILITY, DNA-POLYMERASE, LOCI, MTHFR C677T, VARIANTS, LYNCH-SYNDROME, Article, BREAST-CANCER, Humans, Genetic Predisposition to Disease, Alleles, Adaptor Proteins, Signal Transducing, RISK, Homeodomain Proteins, Science & Technology, Polymorphism, Genetic, MUTATIONS, Intracellular Signaling Peptides and Proteins, Proteins, Endometrial Neoplasms, Neoplasm Proteins, Multidisciplinary Sciences, Repressor Proteins, Science & Technology - Other Topics, Female, Colorectal Neoplasms, Genome-Wide Association Study
Abstract: High-risk mutations in several genes predispose to both colorectal cancer (CRC) and endometrial cancer (EC). We therefore hypothesised that some lower-risk genetic variants might also predispose to both CRC and EC. Using CRC and EC genome-wide association series, totalling 13,265 cancer cases and 40,245 controls, we found that the protective allele [G] at one previously-identified CRC polymorphism, rs2736100 near TERT, was associated with EC risk (odds ratio (OR) = 1.08, P = 0.000167); this polymorphism influences the risk of several other cancers. A further CRC polymorphism near TERC also showed evidence of association with EC (OR = 0.92; P = 0.03). Overall, however, there was no good evidence that the set of CRC polymorphisms was associated with EC risk, and neither of two previously-reported EC polymorphisms was associated with CRC risk. A combined analysis revealed one genome-wide significant polymorphism, rs3184504, on chromosome 12q24 (OR = 1.10, P = 7.23 × 10(-9)) with shared effects on CRC and EC risk. This polymorphism, a missense variant in the gene SH2B3, is also associated with haematological and autoimmune disorders, suggesting that it influences cancer risk through the immune response. Another polymorphism, rs12970291 near gene TSHZ1, was associated with both CRC and EC (OR = 1.26, P = 4.82 × 10(-8)), with the alleles showing opposite effects on the risks of the two cancers. ispartof: Scientific Reports vol:5 pages:17369- ispartof: location:England status: published
Published: 2015

15. Quantifying the heritability of glioma using genome-wide complex trait analysis

Author: Kinnersley, B., Mitchell, J.S., Gousias, K., Schramm, J., Idbaih, A., Labussière, M., Marie, Y., Rahimian, A., Wichmann, H.-E., Schreiber, S., Hoang-Xuan, K., Delattre, J.Y., Nöthen, M.M., Mokhtari, K., Lathrop, M, Bondy, M., Simon, M., and Houlston, R.S.
Abstract: Genome-wide association studies (GWAS) have successfully identified a number of common single-nucleotide polymorphisms (SNPs) influencing glioma risk. While these SNPs only explain a small proportion of the genetic risk it is unclear how much is left to be detected by other, yet to be identified, common SNPs. Therefore, we applied Genome-Wide Complex Trait Analysis (GCTA) to three GWAS datasets totalling 3,373 cases and 4,571 controls and performed a meta-analysis to estimate the heritability of glioma. Our results identify heritability estimates of 25% (95% CI: 20-31%, P = 1.15 × 10-17) for all forms of glioma - 26% (95% CI: 17-35%, P = 1.05 × 10-8) for glioblastoma multiforme (GBM) and 25% (95% CI: 17-32%, P = 1.26 × 10-10) for non-GBM tumors. This is a substantial increase from the genetic variance identified by the currently identified GWAS risk loci (∼6% of common heritability), indicating that most of the heritable risk attributable to common genetic variants remains to be identified.
Published: 2015

16. Correspondence: SEMA4A variation and risk of colorectal cancer

Author: Kinnersley, B. (Ben), Chubb, D. (Daniel), Dobbins, S.E. (Sara E.), Frampton, M. (Matthew), Buch, T. (Thorsten), Timofeeva, M.N. (Maria N.), Castellví-Bel, S., Farrington, S.M. (Susan), Försti, A. (Asta), Hampe, J. (Jochen), Hemminki, K. (Kari), Hofstra, R.M.W. (Robert), Northwood, J.B. (John Blackman), Palles, C. (Claire), Pinheiro, M. (Manuela), Ruiz-Ponte, C. (Clara), Schafmayer, C. (Clemens), Teixeira, M.R. (Manuel R.), Westers, H. (Helga), Wezel, T. (Tom) van, Bishop, D.T. (David Timothy), Tomlinson, I. (Ian), Dunlop, M. (Malcolm), Houlston, R. (Richard), Kinnersley, B. (Ben), Chubb, D. (Daniel), Dobbins, S.E. (Sara E.), Frampton, M. (Matthew), Buch, T. (Thorsten), Timofeeva, M.N. (Maria N.), Castellví-Bel, S., Farrington, S.M. (Susan), Försti, A. (Asta), Hampe, J. (Jochen), Hemminki, K. (Kari), Hofstra, R.M.W. (Robert), Northwood, J.B. (John Blackman), Palles, C. (Claire), Pinheiro, M. (Manuela), Ruiz-Ponte, C. (Clara), Schafmayer, C. (Clemens), Teixeira, M.R. (Manuel R.), Westers, H. (Helga), Wezel, T. (Tom) van, Bishop, D.T. (David Timothy), Tomlinson, I. (Ian), Dunlop, M. (Malcolm), and Houlston, R. (Richard)
Published: 2016
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17. Correspondence: SEMA4A variation and risk of colorectal cancer

Author: Kinnersley, B, Chubb, D, Dobbins, S E, Frampton, M, Buch, S, Timofeeva, MN, Castellvi-Bel, S, Farrington, SM, Forsti, A, Hampe, J, Hemminki, K, Hofstra, Robert, Northwood, E, Palles, C, Pinheiro, M, Ruiz-Ponte, C, Schafmayer, C, Teixeira, MR, Westers, H, van Wezel, T, Bishop, DT, Tomlinson, I, Dunlop, MG, Houlston, RS, Kinnersley, B, Chubb, D, Dobbins, S E, Frampton, M, Buch, S, Timofeeva, MN, Castellvi-Bel, S, Farrington, SM, Forsti, A, Hampe, J, Hemminki, K, Hofstra, Robert, Northwood, E, Palles, C, Pinheiro, M, Ruiz-Ponte, C, Schafmayer, C, Teixeira, MR, Westers, H, van Wezel, T, Bishop, DT, Tomlinson, I, Dunlop, MG, and Houlston, RS
Published: 2016

18. GCT-21 - Testicular cancer genomics England Clinical Interpretation Partnership (GECIP): A genomic exploration of testicular germ cell tumours

Author: Frangou, A.M., Cornish, A., Kinnersley, B., Wedge, D.C., Protheroe, A., Murray, M.J., and Verrill, C.
Published: 2019
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19. Recurrent Coding Sequence Variation Explains only A Small Fraction of the Genetic Architecture of Colorectal Cancer

Author: Timofeeva, M.N. (Maria N.), Kinnersley, B. (Ben), Farrington, S.M. (Susan M.), Whiffin, N. (Nicola), Palles, C. (Claire), Svinti, V. (Victoria), Lloyd, A. (Amy), Gorman, M. (Maggie), Ooi, L.-Y. (Li-Yin), Hosking, F. (Fay), Barclay, E. (Ella), Zgaga, L. (Lina), Dobbins, S.E. (Sara E.), Martin, L. (Lynn), Theodoratou, E. (Evropi), Broderick, P. (Peter), Tenesa, A. (Albert), Smillie, C. (Claire), Grimes, G. (Graeme), Hayward, C. (Caroline), Campbell, A. (Archie), Porteous, D. (David), Deary, I.J. (Ian), Harris, S.E. (Sarah), Northwood, J.B. (John Blackman), Barrett, J.H. (Jennifer H.), Smith, G. (Gillian), Wolf, R. (Roland), Forman, D. (David), Morreau, H. (Hans), Ruano, D. (Dina), Tops, C. (Carli), Wijnen, J.T. (Juul), Schrumpf, M. (Melanie), Boot, A. (Arnoud), Vasen, H. (Hans), Hes, F.J. (Frederik), Wezel, T. (Tom) van, Franke, A. (Andre), Lieb, W. (Wolgang), Schafmayer, C. (Clemens), Hampe, J. (Jochen), Buch, T. (Thorsten), Propping, P. (Peter), Hemminki, K. (Kari), Försti, A. (Asta), Westers, H. (Helga), Hofstra, R.M.W. (Robert), Pinheiro, M. (Manuela), Pinto, C. (Carla), Teixeira, P.J., Ruiz-Ponte, C. (Clara), Fernández-Rozadilla, C. (Ceres), Carracedo, A. (Angel), Castells, A., Castellví-Bel, S., Campbell, H. (Harry), Bishop, D.T. (David Timothy), Tomlinson, I. (Ian), Dunlop, M.G. (Malcolm), Houlston, R. (Richard), Timofeeva, M.N. (Maria N.), Kinnersley, B. (Ben), Farrington, S.M. (Susan M.), Whiffin, N. (Nicola), Palles, C. (Claire), Svinti, V. (Victoria), Lloyd, A. (Amy), Gorman, M. (Maggie), Ooi, L.-Y. (Li-Yin), Hosking, F. (Fay), Barclay, E. (Ella), Zgaga, L. (Lina), Dobbins, S.E. (Sara E.), Martin, L. (Lynn), Theodoratou, E. (Evropi), Broderick, P. (Peter), Tenesa, A. (Albert), Smillie, C. (Claire), Grimes, G. (Graeme), Hayward, C. (Caroline), Campbell, A. (Archie), Porteous, D. (David), Deary, I.J. (Ian), Harris, S.E. (Sarah), Northwood, J.B. (John Blackman), Barrett, J.H. (Jennifer H.), Smith, G. (Gillian), Wolf, R. (Roland), Forman, D. (David), Morreau, H. (Hans), Ruano, D. (Dina), Tops, C. (Carli), Wijnen, J.T. (Juul), Schrumpf, M. (Melanie), Boot, A. (Arnoud), Vasen, H. (Hans), Hes, F.J. (Frederik), Wezel, T. (Tom) van, Franke, A. (Andre), Lieb, W. (Wolgang), Schafmayer, C. (Clemens), Hampe, J. (Jochen), Buch, T. (Thorsten), Propping, P. (Peter), Hemminki, K. (Kari), Försti, A. (Asta), Westers, H. (Helga), Hofstra, R.M.W. (Robert), Pinheiro, M. (Manuela), Pinto, C. (Carla), Teixeira, P.J., Ruiz-Ponte, C. (Clara), Fernández-Rozadilla, C. (Ceres), Carracedo, A. (Angel), Castells, A., Castellví-Bel, S., Campbell, H. (Harry), Bishop, D.T. (David Timothy), Tomlinson, I. (Ian), Dunlop, M.G. (Malcolm), and Houlston, R. (Richard)
Abstract: Whilst common genetic variation in many non-coding genomic regulatory regions are known to impart risk of colorectal cancer (CRC), much of the heritability of CRC remains unexplained. To examine the role of recurrent coding sequence variation in CRC aetiology, we genotyped 12,638 CRCs cases and 29,045 controls from six European populations. Single-variant analysis identified a coding variant (rs3184504) in SH2B3 (12q24) associated with CRC risk (OR = 1.08, P = 3.9 × 10-7), and novel damaging coding variants in 3 genes previously tagged by GWAS efforts; rs16888728 (8q24) in UTP23 (OR = 1.15, P = 1.4 × 10-7); rs6580742 and rs12303082 (12q13) in FAM186A (OR = 1.11, P = 1.2 × 10-7
Published: 2015
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20. A new GWAS and meta-analysis with 1000Genomes imputation identifies novel risk variants for colorectal cancer

Author: Al-Tassan, NA, Whiffin, N, Hosking, FJ, Palles, C, Farrington, SM, Dobbins, SE, Harris, R, Gorman, M, Tenesa, A, Meyer, BF, Wakil, SM, Kinnersley, B, Campbell, H, Martin, L, Smith, CG, Idziaszczyk, S, Barclay, E, Maughan, TS, Kaplan, R, Kerr, R, Kerr, D, Buchannan, DD, Win, AK, Hopper, J, Jenkins, M, Lindor, NM, Newcomb, PA, Gallinger, S, Conti, D, Schumacher, F, Casey, G, Dunlop, MG, Tomlinson, IP, Cheadle, JP, Houlston, RS, Al-Tassan, NA, Whiffin, N, Hosking, FJ, Palles, C, Farrington, SM, Dobbins, SE, Harris, R, Gorman, M, Tenesa, A, Meyer, BF, Wakil, SM, Kinnersley, B, Campbell, H, Martin, L, Smith, CG, Idziaszczyk, S, Barclay, E, Maughan, TS, Kaplan, R, Kerr, R, Kerr, D, Buchannan, DD, Win, AK, Hopper, J, Jenkins, M, Lindor, NM, Newcomb, PA, Gallinger, S, Conti, D, Schumacher, F, Casey, G, Dunlop, MG, Tomlinson, IP, Cheadle, JP, and Houlston, RS
Abstract: Genome-wide association studies (GWAS) of colorectal cancer (CRC) have identified 23 susceptibility loci thus far. Analyses of previously conducted GWAS indicate additional risk loci are yet to be discovered. To identify novel CRC susceptibility loci, we conducted a new GWAS and performed a meta-analysis with five published GWAS (totalling 7,577 cases and 9,979 controls of European ancestry), imputing genotypes utilising the 1000 Genomes Project. The combined analysis identified new, significant associations with CRC at 1p36.2 marked by rs72647484 (minor allele frequency [MAF] = 0.09) near CDC42 and WNT4 (P = 1.21 × 10(-8), odds ratio [OR] = 1.21 ) and at 16q24.1 marked by rs16941835 (MAF = 0.21, P = 5.06 × 10(-8); OR = 1.15) within the long non-coding RNA (lncRNA) RP11-58A18.1 and ~500 kb from the nearest coding gene FOXL1. Additionally we identified a promising association at 10p13 with rs10904849 intronic to CUBN (MAF = 0.32, P = 7.01 × 10(-8); OR = 1.14). These findings provide further insights into the genetic and biological basis of inherited genetic susceptibility to CRC. Additionally, our analysis further demonstrates that imputation can be used to exploit GWAS data to identify novel disease-causing variants.
Published: 2015

21. A new GWAS and meta-analysis with 1000Genomes imputation identifies novel risk variants for colorectal cancer (vol 5, 10442, 2015)

Author: Al-Tassan, NA, Whiffin, N, Hosking, FJ, Palles, C, Farrington, SM, Dobbins, SE, Harris, R, Gorman, M, Tenesa, A, Meyer, BF, Wakil, SM, Kinnersley, B, Campbell, H, Martin, L, Smith, CG, Idziaszczyk, S, Barclay, E, Maughan, TS, Kaplan, R, Kerr, R, Kerr, D, Buchanan, DD, Win, AK, Hopper, J, Jenkins, M, Lindor, NM, Newcomb, PA, Gallinger, S, Conti, D, Schumacher, F, Casey, G, Dunlop, MG, Tomlinson, IP, Cheadle, JP, Houlston, RS, Al-Tassan, NA, Whiffin, N, Hosking, FJ, Palles, C, Farrington, SM, Dobbins, SE, Harris, R, Gorman, M, Tenesa, A, Meyer, BF, Wakil, SM, Kinnersley, B, Campbell, H, Martin, L, Smith, CG, Idziaszczyk, S, Barclay, E, Maughan, TS, Kaplan, R, Kerr, R, Kerr, D, Buchanan, DD, Win, AK, Hopper, J, Jenkins, M, Lindor, NM, Newcomb, PA, Gallinger, S, Conti, D, Schumacher, F, Casey, G, Dunlop, MG, Tomlinson, IP, Cheadle, JP, and Houlston, RS
Published: 2015

22. Meta-analysis of genome-wide association studies identifies common susceptibility polymorphisms for colorectal and endometrial cancer near SH2B3 and TSHZ1

Author: Cheng, THT, Thompson, D, Painter, J, O'Mara, T, Gorman, M, Martin, L, Palles, C, Jones, A, Buchanan, DD, Win, AK, Hopper, J, Jenkins, M, Lindor, NM, Newcomb, PA, Gallinger, S, Conti, D, Schumacher, F, Casey, G, Giles, GG, Pharoah, P, Peto, J, Cox, A, Swerdlow, A, Couch, F, Cunningham, JM, Goode, EL, Winham, SJ, Lambrechts, D, Fasching, P, Burwinkel, B, Brenner, H, Brauch, H, Chang-Claude, J, Salvesen, HB, Kristensen, V, Darabi, H, Li, J, Liu, T, Lindblom, A, Hall, P, Echeverry de Polanco, M, Sans, M, Carracedo, A, Castellvi-Bel, S, Rojas-Martinez, A, Aguiar, S, Teixeira, MR, Dunning, AM, Dennis, J, Otton, G, Proietto, T, Holliday, E, Attia, J, Ashton, K, Scott, RJ, McEvoy, M, Dowdy, SC, Fridley, BL, Werner, HMJ, Trovik, J, Njolstad, TS, Tham, E, Mints, M, Runnebaum, I, Hillemanns, P, Doerk, T, Amant, F, Schrauwen, S, Hein, A, Beckmann, MW, Ekici, A, Czene, K, Meindl, A, Bolla, MK, Michailidou, K, Tyrer, JP, Wang, Q, Ahmed, S, Healey, CS, Shah, M, Annibali, D, Depreeuw, J, Al-Tassan, NA, Harris, R, Meyer, BF, Whiffin, N, Hosking, FJ, Kinnersley, B, Farrington, SM, Timofeeva, M, Tenesa, A, Campbell, H, Haile, RW, Hodgson, S, Carvajal-Carmona, L, Cheadle, JP, Easton, D, Dunlop, M, Houlston, R, Spurdle, A, Tomlinson, I, Cheng, THT, Thompson, D, Painter, J, O'Mara, T, Gorman, M, Martin, L, Palles, C, Jones, A, Buchanan, DD, Win, AK, Hopper, J, Jenkins, M, Lindor, NM, Newcomb, PA, Gallinger, S, Conti, D, Schumacher, F, Casey, G, Giles, GG, Pharoah, P, Peto, J, Cox, A, Swerdlow, A, Couch, F, Cunningham, JM, Goode, EL, Winham, SJ, Lambrechts, D, Fasching, P, Burwinkel, B, Brenner, H, Brauch, H, Chang-Claude, J, Salvesen, HB, Kristensen, V, Darabi, H, Li, J, Liu, T, Lindblom, A, Hall, P, Echeverry de Polanco, M, Sans, M, Carracedo, A, Castellvi-Bel, S, Rojas-Martinez, A, Aguiar, S, Teixeira, MR, Dunning, AM, Dennis, J, Otton, G, Proietto, T, Holliday, E, Attia, J, Ashton, K, Scott, RJ, McEvoy, M, Dowdy, SC, Fridley, BL, Werner, HMJ, Trovik, J, Njolstad, TS, Tham, E, Mints, M, Runnebaum, I, Hillemanns, P, Doerk, T, Amant, F, Schrauwen, S, Hein, A, Beckmann, MW, Ekici, A, Czene, K, Meindl, A, Bolla, MK, Michailidou, K, Tyrer, JP, Wang, Q, Ahmed, S, Healey, CS, Shah, M, Annibali, D, Depreeuw, J, Al-Tassan, NA, Harris, R, Meyer, BF, Whiffin, N, Hosking, FJ, Kinnersley, B, Farrington, SM, Timofeeva, M, Tenesa, A, Campbell, H, Haile, RW, Hodgson, S, Carvajal-Carmona, L, Cheadle, JP, Easton, D, Dunlop, M, Houlston, R, Spurdle, A, and Tomlinson, I
Abstract: High-risk mutations in several genes predispose to both colorectal cancer (CRC) and endometrial cancer (EC). We therefore hypothesised that some lower-risk genetic variants might also predispose to both CRC and EC. Using CRC and EC genome-wide association series, totalling 13,265 cancer cases and 40,245 controls, we found that the protective allele [G] at one previously-identified CRC polymorphism, rs2736100 near TERT, was associated with EC risk (odds ratio (OR) = 1.08, P = 0.000167); this polymorphism influences the risk of several other cancers. A further CRC polymorphism near TERC also showed evidence of association with EC (OR = 0.92; P = 0.03). Overall, however, there was no good evidence that the set of CRC polymorphisms was associated with EC risk, and neither of two previously-reported EC polymorphisms was associated with CRC risk. A combined analysis revealed one genome-wide significant polymorphism, rs3184504, on chromosome 12q24 (OR = 1.10, P = 7.23 × 10(-9)) with shared effects on CRC and EC risk. This polymorphism, a missense variant in the gene SH2B3, is also associated with haematological and autoimmune disorders, suggesting that it influences cancer risk through the immune response. Another polymorphism, rs12970291 near gene TSHZ1, was associated with both CRC and EC (OR = 1.26, P = 4.82 × 10(-8)), with the alleles showing opposite effects on the risks of the two cancers.
Published: 2015

23. Re: Role of the oxidative DNA damage repair gene OGG1 in colorectal tumorigenesis

Author: Kinnersley, B. (Ben), Buch, T. (Thorsten), Castellví-Bel, S., Farrington, S.M. (Susan), Försti, A. (Asta), Hampe, J. (Jochen), Hemminki, K. (Kari), Hofstra, R.M.W. (Robert), Northwood, J.B. (John Blackman), Palles, C. (Claire), Pinheiro, M.A. (Magda Avelar), Ruiz-Ponte, C. (Clara), Schafmayer, C. (Clemens), Teixeira, P.J., Westers, H. (Helga), Wezel, T. (Tom) van, Bishop, D.T. (David Timothy), Tomlinson, I.P. (Ian), Dunlop, M.G. (Malcolm), Houlston, R. (Richard), Kinnersley, B. (Ben), Buch, T. (Thorsten), Castellví-Bel, S., Farrington, S.M. (Susan), Försti, A. (Asta), Hampe, J. (Jochen), Hemminki, K. (Kari), Hofstra, R.M.W. (Robert), Northwood, J.B. (John Blackman), Palles, C. (Claire), Pinheiro, M.A. (Magda Avelar), Ruiz-Ponte, C. (Clara), Schafmayer, C. (Clemens), Teixeira, P.J., Westers, H. (Helga), Wezel, T. (Tom) van, Bishop, D.T. (David Timothy), Tomlinson, I.P. (Ian), Dunlop, M.G. (Malcolm), and Houlston, R. (Richard)
Published: 2014
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24. Identification of susceptibility loci for colorectal cancer in a genome-wide meta-analysis

Author: Whiffin, N, Hosking, FJ, Farrington, SM, Palles, C, Dobbins, SE, Zgaga, L, Lloyd, A, Kinnersley, B, Gorman, M, Tenesa, A, Broderick, P, Wang, Y, Barclay, E, Hayward, C, Martin, L, Buchanan, DD, Win, AK, Hopper, J, Jenkins, M, Lindor, NM, Newcomb, PA, Gallinger, S, Conti, D, Schumacher, F, Casey, G, Liu, T, Campbell, H, Lindblom, A, Houlston, RS, Tomlinson, IP, Dunlop, MG, Whiffin, N, Hosking, FJ, Farrington, SM, Palles, C, Dobbins, SE, Zgaga, L, Lloyd, A, Kinnersley, B, Gorman, M, Tenesa, A, Broderick, P, Wang, Y, Barclay, E, Hayward, C, Martin, L, Buchanan, DD, Win, AK, Hopper, J, Jenkins, M, Lindor, NM, Newcomb, PA, Gallinger, S, Conti, D, Schumacher, F, Casey, G, Liu, T, Campbell, H, Lindblom, A, Houlston, RS, Tomlinson, IP, and Dunlop, MG
Abstract: To identify common variants influencing colorectal cancer (CRC) risk, we performed a meta-analysis of five genome-wide association studies, comprising 5626 cases and 7817 controls of European descent. We conducted replication of top ranked single nucleotide polymorphisms (SNPs) in additional series totalling 14 037 cases and 15 937 controls, identifying a new CRC risk locus at 10q24.2 [rs1035209; odds ratio (OR) = 1.13, P = 4.54 × 10(-11)]. We also performed meta-analysis of our studies, with previously published data, of several recently purported CRC risk loci. We failed to find convincing evidence for a previously reported genome-wide association at rs11903757 (2q32.3). Of the three additional loci for which evidence of an association in Europeans has been previously described we failed to show an association between rs59336 (12q24.21) and CRC risk. However, for the other two SNPs, our analyses demonstrated new, formally significant associations with CRC. These are rs3217810 intronic in CCND2 (12p13.32; OR = 1.19, P = 2.16 × 10(-10)) and rs10911251 near LAMC1 (1q25.3; OR = 1.09, P = 1.75 × 10(-8)). Additionally, we found some evidence to support a relationship between, rs647161, rs2423297 and rs10774214 and CRC risk originally identified in East Asians in our European datasets. Our findings provide further insights into the genetic and biological basis of inherited genetic susceptibility to CRC.
Published: 2014

25. The TERT variant rs2736100 is associated with colorectal cancer risk

Author: Kinnersley, B, Migliorini, G, Broderick, P, Whiffin, N, Dobbins, SE, Casey, G, Hopper, J, Sieber, O, Lipton, L, Kerr, DJ, Dunlop, MG, Tomlinson, IPM, Houlston, RS, Kinnersley, B, Migliorini, G, Broderick, P, Whiffin, N, Dobbins, SE, Casey, G, Hopper, J, Sieber, O, Lipton, L, Kerr, DJ, Dunlop, MG, Tomlinson, IPM, and Houlston, RS
Abstract: BACKGROUND: Polymorphic variation at the 5p15.33 (TERT-CLPTM1L) locus is associated with the risk of many cancers but a relationship with colorectal cancer (CRC) risk has yet to be defined. METHODS: We used data from six genome-wide association studies (GWAS) of CRC, linkage disequilibrium mapping and imputation, to examine the relationship between 73 single-nucleotide polymorphisms at 5p15.33 and CRC risk in detail. RESULTS: rs2736100, which localises to intron 2 of TERT, provided the strongest evidence of an association with CRC (P=2.28 × 10⁻⁴). The association was also shown in an independent series of 10 047 CRC cases and 6918 controls (P=0.02). A meta-analysis of all seven studies (totalling 16 039 cases, 16 430 controls) provided increased evidence of association (P=2.49 × 10⁻⁵; per allele odds ratio=1.07). The association of rs2736100 on CRC risk was shown to be independent of 15 low-penetrance variants previously identified. CONCLUSION: The rs2736100 association demonstrates an influence of variation at 5p15.33 on CRC risk and further evidence that the 5p15.33 (TERT-CLPTM1L) locus has pleiotropic effects (reflecting generic or lineage-specific effects) on cancer risk.
Published: 2012

26. Cumulative incidence and risk factors for radiation induced leukoencephalopathy in high grade glioma long term survivors

Author: Ben Kinnersley, Julian Jacob, Wolf Mueller, Flavie Bompaire, Giulia Berzero, Yannick Marie, Robert Terziev, Damien Ricard, Caroline Dehais, Marc Sanson, Loïc Feuvret, Ahmed Idbaih, Khê Hoang-Xuan, Jean-Yves Delattre, Dimitri Psimaras, Terziev, R., Psimaras, D., Marie, Y., Feuvret, L., Berzero, G., Jacob, J., Dehais, C., Bompaire, F., Mueller, W., Kinnersley, B., Delattre, J. -Y., Idbaih, A., Hoang-Xuan, K., Sanson, M., Ricard, D., Sorbonne Université - Département de neurologie 2 - Mazarin, Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Leipzig University, University hospital of Zurich [Zurich], Hôpital d'instruction des Armées Percy, Service de Santé des Armées, Institut du Cerveau et de la Moëlle Epinière = Brain and Spine Institute (ICM), Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Service de Radiothérapie [CHU Pitié-Salpêtrière], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Sorbonne Université (SU), CB - Centre Borelli - UMR 9010 (CB), Service de Santé des Armées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Ecole Normale Supérieure Paris-Saclay (ENS Paris Saclay)-Université de Paris (UP), The institute of cancer research [London], École du Val de Grâce (EVDG), CHU Pitié-Salpêtrière [AP-HP], Gestionnaire, Hal Sorbonne Université, Service d'Onco-neurologie = Département de neurologie 2 [CHU Pitié Salpêtrière], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Institut du Cerveau = Paris Brain Institute (ICM), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Sorbonne Université (SU)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Service d'Oncologie Radiothérapie [CHU Pitié Salpétrière], and Service de Santé des Armées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Ecole Normale Supérieure Paris-Saclay (ENS Paris Saclay)-Université Paris Cité (UPCité)
Subjects: Oncology, Male, Cancer therapy, medicine.medical_treatment, [SDV]Life Sciences [q-bio], Urinary incontinence, Leukoencephalopathy, 0302 clinical medicine, Cancer Survivors, Leukoencephalopathies, Risk Factors, White matter disease, Cumulative incidence, Survivors, Multidisciplinary, Molecular medicine, Brain Neoplasms, Incidence (epidemiology), Medical record, Incidence, Smoking, Age Factors, Glioma, Middle Aged, Magnetic Resonance Imaging, Progression-Free Survival, 3. Good health, [SDV] Life Sciences [q-bio], 030220 oncology & carcinogenesis, Medicine, Female, medicine.symptom, Adult, medicine.medical_specialty, Adolescent, Science, Single-nucleotide polymorphism, Polymorphism, Single Nucleotide, Article, 03 medical and health sciences, Young Adult, Neurotoxicity syndromes, Internal medicine, medicine, Humans, Radiation Injuries, Aged, Retrospective Studies, Radiotherapy, business.industry, medicine.disease, Radiation therapy, CNS cancer, business, 030217 neurology & neurosurgery
Abstract: The incidence and risk factors associated with radiation-induced leukoencephalopathy (RIL) in long-term survivors of high-grade glioma (HGG) are still poorly investigated. We performed a retrospective research in our institutional database for patients with supratentorial HGG treated with focal radiotherapy, having a progression-free overall survival > 30 months and available germline DNA. We reviewed MRI scans for signs of leukoencephalopathy on T2/FLAIR sequences, and medical records for information on cerebrovascular risk factors and neurological symptoms. We investigated a panel of candidate single nucleotide polymorphisms (SNPs) to assess genetic risk. Eighty-one HGG patients (18 grade IV and 63 grade III, 50M/31F) were included in the study. The median age at the time of radiotherapy was 48 years old (range 18–69). The median follow-up after the completion of radiotherapy was 79 months. A total of 44 patients (44/81, 54.3%) developed RIL during follow-up. Twenty-nine of the 44 patients developed consistent symptoms such as subcortical dementia (n = 28), gait disturbances (n = 12), and urinary incontinence (n = 9). The cumulative incidence of RIL was 21% at 12 months, 42% at 36 months, and 48% at 60 months. Age > 60 years, smoking, and the germline SNP rs2120825 (PPARg locus) were associated with an increased risk of RIL. Our study identified potential risk factors for the development of RIL (age, smoking, and the germline SNP rs2120825) and established the rationale for testing PPARg agonists in the prevention and management of late-delayed radiation-induced neurotoxicity.
Published: 2021

27. The genomic landscape of 2,023 colorectal cancers.

Author: Cornish AJ, Gruber AJ, Kinnersley B, Chubb D, Frangou A, Caravagna G, Noyvert B, Lakatos E, Wood HM, Thorn S, Culliford R, Arnedo-Pac C, Househam J, Cross W, Sud A, Law P, Leathlobhair MN, Hawari A, Woolley C, Sherwood K, Feeley N, Gül G, Fernandez-Tajes J, Zapata L, Alexandrov LB, Murugaesu N, Sosinsky A, Mitchell J, Lopez-Bigas N, Quirke P, Church DN, Tomlinson IPM, Sottoriva A, Graham TA, Wedge DC, and Houlston RS
Subjects: Adult, Aged, Aged, 80 and over, Female, Humans, Male, Middle Aged, Young Adult, Chromosomal Instability genetics, Diet adverse effects, DNA Copy Number Variations genetics, HLA Antigens genetics, Microsatellite Instability, Prognosis, Smoking adverse effects, United Kingdom epidemiology, Whole Genome Sequencing, Colorectal Neoplasms classification, Colorectal Neoplasms genetics, Colorectal Neoplasms immunology, Genetic Predisposition to Disease genetics, Genome, Human genetics, Genomics, Mutation
Abstract: Colorectal carcinoma (CRC) is a common cause of mortality 1 , but a comprehensive description of its genomic landscape is lacking 2-9 . Here we perform whole-genome sequencing of 2,023 CRC samples from participants in the UK 100,000 Genomes Project, thereby providing a highly detailed somatic mutational landscape of this cancer. Integrated analyses identify more than 250 putative CRC driver genes, many not previously implicated in CRC or other cancers, including several recurrent changes outside the coding genome. We extend the molecular pathways involved in CRC development, define four new common subgroups of microsatellite-stable CRC based on genomic features and show that these groups have independent prognostic associations. We also characterize several rare molecular CRC subgroups, some with potential clinical relevance, including cancers with both microsatellite and chromosomal instability. We demonstrate a spectrum of mutational profiles across the colorectum, which reflect aetiological differences. These include the role of Escherichia coli pks+ colibactin in rectal cancers 10 and the importance of the SBS93 signature 11-13 , which suggests that diet or smoking is a risk factor. Immune-escape driver mutations 14 are near-ubiquitous in hypermutant tumours and occur in about half of microsatellite-stable CRCs, often in the form of HLA copy number changes. Many driver mutations are actionable, including those associated with rare subgroups (for example, BRCA1 and IDH1), highlighting the role of whole-genome sequencing in optimizing patient care., (© 2024. The Author(s).)
Published: 2024
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28. Analysis of 10,478 cancer genomes identifies candidate driver genes and opportunities for precision oncology.

Author: Kinnersley B, Sud A, Everall A, Cornish AJ, Chubb D, Culliford R, Gruber AJ, Lärkeryd A, Mitsopoulos C, Wedge D, and Houlston R
Subjects: Humans, Genome, Human, Genomics methods, Medical Oncology methods, Neoplasms genetics, Precision Medicine methods, Mutation, Whole Genome Sequencing
Abstract: Tumor genomic profiling is increasingly seen as a prerequisite to guide the treatment of patients with cancer. To explore the value of whole-genome sequencing (WGS) in broadening the scope of cancers potentially amenable to a precision therapy, we analysed whole-genome sequencing data on 10,478 patients spanning 35 cancer types recruited to the UK 100,000 Genomes Project. We identified 330 candidate driver genes, including 74 that are new to any cancer. We estimate that approximately 55% of patients studied harbor at least one clinically relevant mutation, predicting either sensitivity or resistance to certain treatments or clinical trial eligibility. By performing computational chemogenomic analysis of cancer mutations we identify additional targets for compounds that represent attractive candidates for future clinical trials. This study represents one of the most comprehensive efforts thus far to identify cancer driver genes in the real world setting and assess their impact on informing precision oncology., (© 2024. The Author(s).)
Published: 2024
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29. Whole genome sequencing refines stratification and therapy of patients with clear cell renal cell carcinoma.

Author: Culliford R, Lawrence SED, Mills C, Tippu Z, Chubb D, Cornish AJ, Browning L, Kinnersley B, Bentham R, Sud A, Pallikonda H, Frangou A, Gruber AJ, Litchfield K, Wedge D, Larkin J, Turajlic S, and Houlston RS
Subjects: Humans, Prognosis, Male, Female, DNA Copy Number Variations, Middle Aged, Epigenesis, Genetic, Aged, Gene Expression Regulation, Neoplastic, Immunotherapy methods, Carcinoma, Renal Cell genetics, Carcinoma, Renal Cell therapy, Carcinoma, Renal Cell mortality, Carcinoma, Renal Cell pathology, Kidney Neoplasms genetics, Kidney Neoplasms therapy, Whole Genome Sequencing, Mutation, Von Hippel-Lindau Tumor Suppressor Protein genetics
Abstract: Clear cell renal cell carcinoma (ccRCC) is the most common form of kidney cancer, but a comprehensive description of its genomic landscape is lacking. We report the whole genome sequencing of 778 ccRCC patients enrolled in the 100,000 Genomes Project, providing for a detailed description of the somatic mutational landscape of ccRCC. We identify candidate driver genes, which as well as emphasising the major role of epigenetic regulation in ccRCC highlight additional biological pathways extending opportunities for therapeutic interventions. Genomic characterisation identified patients with divergent clinical outcome; higher number of structural copy number alterations associated with poorer prognosis, whereas VHL mutations were independently associated with a better prognosis. The observations that higher T-cell infiltration is associated with better overall survival and that genetically predicted immune evasion is not common supports the rationale for immunotherapy. These findings should inform personalised surveillance and treatment strategies for ccRCC patients., (© 2024. The Author(s).)
Published: 2024
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30. Genetic landscape of interval and screen detected breast cancer.

Author: Mills C, Sud A, Everall A, Chubb D, Lawrence SED, Kinnersley B, Cornish AJ, Bentham R, and Houlston RS
Abstract: Interval breast cancers (IBCs) are cancers diagnosed between screening episodes. Understanding the biological differences between IBCs and screen-detected breast-cancers (SDBCs) has the potential to improve mammographic screening and patient management. We analysed and compared the genomic landscape of 288 IBCs and 473 SDBCs by whole genome sequencing of paired tumour-normal patient samples collected as part of the UK 100,000 Genomes Project. Compared to SDBCs, IBCs were more likely to be lobular, higher grade, and triple negative. A more aggressive clinical phenotype was reflected in IBCs displaying features of genomic instability including a higher mutation rate and number of chromosomal structural abnormalities, defective homologous recombination and TP53 mutations. We did not however, find evidence to indicate that IBCs are associated with a significantly different immune response. While IBCs do not represent a unique molecular class of invasive breast cancer they exhibit a more aggressive phenotype, which is likely to be a consequence of the timing of tumour initiation. This information is relevant both with respect to treatment as well as informing the screening interval for mammography., (© 2024. The Author(s).)
Published: 2024
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31. Radiogenomic biomarkers for immunotherapy in glioblastoma: A systematic review of magnetic resonance imaging studies.

Author: Ghimire P, Kinnersley B, Karami G, Arumugam P, Houlston R, Ashkan K, Modat M, and Booth TC
Abstract: Background: Immunotherapy is an effective "precision medicine" treatment for several cancers. Imaging signatures of the underlying genome (radiogenomics) in glioblastoma patients may serve as preoperative biomarkers of the tumor-host immune apparatus. Validated biomarkers would have the potential to stratify patients during immunotherapy clinical trials, and if trials are beneficial, facilitate personalized neo-adjuvant treatment. The increased use of whole genome sequencing data, and the advances in bioinformatics and machine learning make such developments plausible. We performed a systematic review to determine the extent of development and validation of immune-related radiogenomic biomarkers for glioblastoma., Methods: A systematic review was performed following PRISMA guidelines using the PubMed, Medline, and Embase databases. Qualitative analysis was performed by incorporating the QUADAS 2 tool and CLAIM checklist. PROSPERO registered: CRD42022340968. Extracted data were insufficiently homogenous to perform a meta-analysis., Results: Nine studies, all retrospective, were included. Biomarkers extracted from magnetic resonance imaging volumes of interest included apparent diffusion coefficient values, relative cerebral blood volume values, and image-derived features. These biomarkers correlated with genomic markers from tumor cells or immune cells or with patient survival. The majority of studies had a high risk of bias and applicability concerns regarding the index test performed., Conclusions: Radiogenomic immune biomarkers have the potential to provide early treatment options to patients with glioblastoma. Targeted immunotherapy, stratified by these biomarkers, has the potential to allow individualized neo-adjuvant precision treatment options in clinical trials. However, there are no prospective studies validating these biomarkers, and interpretation is limited due to study bias with little evidence of generalizability., Competing Interests: None., (© The Author(s) 2024. Published by Oxford University Press, the Society for Neuro-Oncology and the European Association of Neuro-Oncology.)
Published: 2024
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32. Therapeutic Targeting of Glioblastoma and the Interactions with Its Microenvironment.

Author: Genoud V, Kinnersley B, Brown NF, Ottaviani D, and Mulholland P
Abstract: Glioblastoma (GBM) is the most common primary malignant brain tumour, and it confers a dismal prognosis despite intensive multimodal treatments. Whilst historically, research has focussed on the evolution of GBM tumour cells themselves, there is growing recognition of the importance of studying the tumour microenvironment (TME). Improved characterisation of the interaction between GBM cells and the TME has led to a better understanding of therapeutic resistance and the identification of potential targets to block these escape mechanisms. This review describes the network of cells within the TME and proposes treatment strategies for simultaneously targeting GBM cells, the surrounding immune cells, and the crosstalk between them.
Published: 2023
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33. Whole genome sequencing refines stratification and therapy of patients with clear cell renal cell carcinoma.

Author: Houlston R, Culliford R, Lawrence S, Mills C, Tippu Z, Chubb D, Cornish A, Browining L, Kinnersley B, Bentham R, Sud A, Pallikonda H, Frangou A, Gruber A, Litchfield K, Wedge D, Larkin J, and Turajlic S
Abstract: Clear cell renal cell carcinoma (ccRCC) is the most common form of kidney cancer, but a comprehensive description of its genomic landscape is lacking. We report the whole genome sequencing of 778 ccRCC patients enrolled in the 100,000 Genomes Project, providing the most detailed somatic mutational landscape to date. We identify new driver genes, which as well as emphasising the major role of epigenetic regulation in ccRCC highlight additional biological pathways extending opportunities for drug repurposing. Genomic characterisation identified patients with divergent clinical outcome; higher number of structural copy number alterations associated with poorer prognosis, whereas VHL mutations were independently associated with a better prognosis. The twin observations that higher T-cell infiltration is associated with better outcome and that genetically predicted immune evasion is not common supports the rationale for immunotherapy. These findings should inform personalised surveillance and treatment strategies for ccRCC patients., Competing Interests: DECLARATION OF INTERESTS S.T. has received speaking fees from Roche, AstraZeneca, Novartis and Ipsen. ST has the following patents filed: Indel mutations as a therapeutic target and predictive biomarker PCTGB2018/051892 and PCTGB2018/051893 and Clear Cell Renal Cell Carcinoma Biomarkers P113326GB. None of the other authors have a conflict of interest.
Published: 2023
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34. Algorithmic considerations when analysing capture Hi-C data.

Author: Disney-Hogg L, Kinnersley B, and Houlston R
Abstract: Chromosome conformation capture methodologies have provided insight into the effect of 3D genomic architecture on gene regulation. Capture Hi-C (CHi-C) is a recent extension of Hi-C that improves the effective resolution of chromatin interactions by enriching for defined regions of biological relevance. The varying targeting efficiency between capture regions, however, introduces bias not present in conventional Hi-C, making analysis more complicated. Here we consider salient features of an algorithm that should be considered in evaluating the performance of a program used to analyse CHi-C data in order to infer meaningful interactions. We use the program CHICAGO to analyse promoter capture Hi-C data generated on 28 different cell lines as a case study., Competing Interests: No competing interests were disclosed., (Copyright: © 2022 Disney-Hogg L et al.)
Published: 2022
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35. Whole-genome sequencing of chronic lymphocytic leukemia identifies subgroups with distinct biological and clinical features.

Author: Robbe P, Ridout KE, Vavoulis DV, Dréau H, Kinnersley B, Denny N, Chubb D, Appleby N, Cutts A, Cornish AJ, Lopez-Pascua L, Clifford R, Burns A, Stamatopoulos B, Cabes M, Alsolami R, Antoniou P, Oates M, Cavalieri D, Gibson J, Prabhu AV, Schwessinger R, Jennings D, James T, Maheswari U, Duran-Ferrer M, Carninci P, Knight SJL, Månsson R, Hughes J, Davies J, Ross M, Bentley D, Strefford JC, Devereux S, Pettitt AR, Hillmen P, Caulfield MJ, Houlston RS, Martín-Subero JI, and Schuh A
Subjects: Humans, Whole Genome Sequencing, Mutation, Genomics, Prognosis, Leukemia, Lymphocytic, Chronic, B-Cell genetics
Abstract: The value of genome-wide over targeted driver analyses for predicting clinical outcomes of cancer patients is debated. Here, we report the whole-genome sequencing of 485 chronic lymphocytic leukemia patients enrolled in clinical trials as part of the United Kingdom's 100,000 Genomes Project. We identify an extended catalog of recurrent coding and noncoding genetic mutations that represents a source for future studies and provide the most complete high-resolution map of structural variants, copy number changes and global genome features including telomere length, mutational signatures and genomic complexity. We demonstrate the relationship of these features with clinical outcome and show that integration of 186 distinct recurrent genomic alterations defines five genomic subgroups that associate with response to therapy, refining conventional outcome prediction. While requiring independent validation, our findings highlight the potential of whole-genome sequencing to inform future risk stratification in chronic lymphocytic leukemia., (© 2022. The Author(s).)
Published: 2022
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36. Germline MBD4 deficiency causes a multi-tumor predisposition syndrome.

Author: Palles C, West HD, Chew E, Galavotti S, Flensburg C, Grolleman JE, Jansen EAM, Curley H, Chegwidden L, Arbe-Barnes EH, Lander N, Truscott R, Pagan J, Bajel A, Sherwood K, Martin L, Thomas H, Georgiou D, Fostira F, Goldberg Y, Adams DJ, van der Biezen SAM, Christie M, Clendenning M, Thomas LE, Deltas C, Dimovski AJ, Dymerska D, Lubinski J, Mahmood K, van der Post RS, Sanders M, Weitz J, Taylor JC, Turnbull C, Vreede L, van Wezel T, Whalley C, Arnedo-Pac C, Caravagna G, Cross W, Chubb D, Frangou A, Gruber AJ, Kinnersley B, Noyvert B, Church D, Graham T, Houlston R, Lopez-Bigas N, Sottoriva A, Wedge D, Jenkins MA, Kuiper RP, Roberts AW, Cheadle JP, Ligtenberg MJL, Hoogerbrugge N, Koelzer VH, Rivas AD, Winship IM, Ponte CR, Buchanan DD, Power DG, Green A, Tomlinson IPM, Sampson JR, Majewski IJ, and de Voer RM
Subjects: Endodeoxyribonucleases genetics, Genetic Predisposition to Disease, Germ Cells pathology, Germ-Line Mutation genetics, Humans, Adenomatous Polyposis Coli genetics, Colorectal Neoplasms genetics, Colorectal Neoplasms pathology, Uveal Neoplasms genetics
Abstract: We report an autosomal recessive, multi-organ tumor predisposition syndrome, caused by bi-allelic loss-of-function germline variants in the base excision repair (BER) gene MBD4. We identified five individuals with bi-allelic MBD4 variants within four families and these individuals had a personal and/or family history of adenomatous colorectal polyposis, acute myeloid leukemia, and uveal melanoma. MBD4 encodes a glycosylase involved in repair of G:T mismatches resulting from deamination of 5'-methylcytosine. The colorectal adenomas from MBD4-deficient individuals showed a mutator phenotype attributable to mutational signature SBS1, consistent with the function of MBD4. MBD4-deficient polyps harbored somatic mutations in similar driver genes to sporadic colorectal tumors, although AMER1 mutations were more common and KRAS mutations less frequent. Our findings expand the role of BER deficiencies in tumor predisposition. Inclusion of MBD4 in genetic testing for polyposis and multi-tumor phenotypes is warranted to improve disease management., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2022 The Author(s). Published by Elsevier Inc. All rights reserved.)
Published: 2022
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37. Relationship between genetically determined telomere length and glioma risk.

Author: Saunders CN, Kinnersley B, Culliford R, Cornish AJ, Law PJ, and Houlston RS
Subjects: Humans, Leukocytes metabolism, Polymorphism, Single Nucleotide, Risk Factors, Telomere genetics, Telomere Homeostasis genetics, Genome-Wide Association Study, Glioma genetics, Glioma metabolism
Abstract: Background: Telomere maintenance is increasingly recognized as being fundamental to glioma oncogenesis with longer leukocyte telomere length (LTL) reported to increase risk of glioma. To gain further insight into the relationship between telomere genetics and risk of glioma, we conducted several complementary analyses, using genome-wide association studies data on LTL (78 592 individuals) and glioma (12 488 cases and 18 169 controls)., Methods: We performed both classical and summary Mendelian randomization (SMR), coupled with heterogeneity in dependent instruments tests, at genome-wide significant LTL loci to examine if an association was mediated by the same causal variant in glioma. To prioritize genes underscoring glioma-LTL associations, we analyzed gene expression and DNA methylation data., Results: Genetically increased LTL was significantly associated with increased glioma risk, random-effects inverse variance weighted ORs per 1 SD unit increase in the putative risk factor (odds ratio [OR]SD) 4.79 (95% confidence interval: 2.11-10.85; P = 1.76 × 10-4). SMR confirmed the previously reported LTL associations at 3q26.2 (TERC; PSMR = 1.33 × 10-5), 5p15.33 (TERT; PSMR = 9.80 × 10-27), 10q24.33 (STN1 alias OBFC1; PSMR = 4.31 × 10-5), and 20q13.3 (STMN3/RTEL1; PSMR = 2.47 × 10-4) glioma risk loci. Our analysis implicates variation at 1q42.12 (PSMR = 1.55 × 10-2), 6p21.3 (PSMR = 9.76 × 10-3), 6p22.2 (PSMR = 5.45 × 10-3), 7q31.33 (PSMR = 6.52 × 10-3), and 11q22.3 (PSMR = 8.89 × 10-4) as risk factors for glioma risk. While complicated by patterns of linkage disequilibrium, genetic variation involving PARP1, PRRC2A, CARMIL1, POT1, and ATM-NPAT1 was implicated in the etiology of glioma., Conclusions: These observations extend the role of telomere-related genes in the development of glioma., (© The Author(s) 2021. Published by Oxford University Press on behalf of the Society for Neuro-Oncology.)
Published: 2022
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38. Cancer drivers and clonal dynamics in acute lymphoblastic leukaemia subtypes.

Author: Studd JB, Cornish AJ, Hoang PH, Law P, Kinnersley B, and Houlston R
Subjects: Female, Genome-Wide Association Study, Humans, Male, Multigene Family, Mutation, Neoplasm Proteins genetics, Precursor B-Cell Lymphoblastic Leukemia-Lymphoma genetics
Abstract: To obtain a comprehensive picture of composite genetic driver events and clonal dynamics in subtypes of paediatric acute lymphoblastic leukaemia (ALL) we analysed tumour-normal whole genome sequencing and expression data from 361 newly diagnosed patients. We report the identification of both structural drivers, as well as recurrent non-coding variation in promoters. Additionally we found the transcriptional profile of histone gene cluster 1 and CTCF altered tumours shared hallmarks of hyperdiploid ALL suggesting a 'hyperdiploid like' subtype. ALL subtypes are driven by distinct mutational processes with AID mutagenesis being confined to ETV6-RUNX1 tumours. Subclonality is a ubiquitous feature of ALL, consistent with Darwinian evolution driving selection and expansion of tumours. Driver mutations in B-cell developmental genes (IKZF1, PAX5, ZEB2) tend to be clonal and RAS/RTK mutations subclonal. In addition to identifying new avenues for therapeutic exploitation, this analysis highlights that targeted therapies should take into account composite mutational profile and clonality., (© 2021. The Author(s).)
Published: 2021
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39. Partitioned glioma heritability shows subtype-specific enrichment in immune cells.

Author: Ostrom QT, Edelson J, Byun J, Han Y, Kinnersley B, Melin B, Houlston RS, Monje M, Walsh KM, Amos CI, and Bondy ML
Subjects: Adult, Genetic Predisposition to Disease, Humans, Linkage Disequilibrium, Polymorphism, Single Nucleotide, Genome-Wide Association Study, Glioma genetics
Abstract: Background: Epidemiological studies of adult glioma have identified genetic syndromes and 25 heritable risk loci that modify individual risk for glioma, as well increased risk in association with exposure to ionizing radiation and decreased risk in association with allergies. In this analysis, we assess whether there is a shared genome-wide genetic architecture between glioma and atopic/autoimmune diseases., Methods: Using summary statistics from a glioma genome-wide association studies (GWAS) meta-analysis, we identified significant enrichment for risk variants associated with gene expression changes in immune cell populations. We also estimated genetic correlations between glioma and autoimmune, atopic, and hematologic traits using linkage disequilibrium score regression (LDSC), which leverages genome-wide single-nucleotide polymorphism (SNP) associations and patterns of linkage disequilibrium., Results: Nominally significant negative correlations were observed for glioblastoma (GB) and primary biliary cirrhosis (rg = -0.26, P = .0228), and for non-GB gliomas and celiac disease (rg = -0.32, P = .0109). Our analyses implicate dendritic cells (GB pHM = 0.0306 and non-GB pHM = 0.0186) in mediating both GB and non-GB genetic predisposition, with GB-specific associations identified in natural killer (NK) cells (pHM = 0.0201) and stem cells (pHM = 0.0265)., Conclusions: This analysis identifies putative new associations between glioma and autoimmune conditions with genomic architecture that is inversely correlated with that of glioma and that T cells, NK cells, and myeloid cells are involved in mediating glioma predisposition. This provides further evidence that increased activation of the acquired immune system may modify individual susceptibility to glioma., (© The Author(s) 2021. Published by Oxford University Press on behalf of the Society for Neuro-Oncology. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)
Published: 2021
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40. Cumulative incidence and risk factors for radiation induced leukoencephalopathy in high grade glioma long term survivors.

Author: Terziev R, Psimaras D, Marie Y, Feuvret L, Berzero G, Jacob J, Dehais C, Bompaire F, Mueller W, Kinnersley B, Delattre JY, Idbaih A, Hoang-Xuan K, Sanson M, and Ricard D
Subjects: Adolescent, Adult, Age Factors, Aged, Brain Neoplasms genetics, Cancer Survivors, Female, Glioma genetics, Humans, Incidence, Leukoencephalopathies diagnostic imaging, Leukoencephalopathies etiology, Leukoencephalopathies genetics, Magnetic Resonance Imaging, Male, Middle Aged, Polymorphism, Single Nucleotide, Progression-Free Survival, Radiation Injuries, Radiotherapy adverse effects, Retrospective Studies, Risk Factors, Smoking, Survivors, Young Adult, Brain Neoplasms epidemiology, Brain Neoplasms radiotherapy, Glioma epidemiology, Glioma radiotherapy, Leukoencephalopathies epidemiology
Abstract: The incidence and risk factors associated with radiation-induced leukoencephalopathy (RIL) in long-term survivors of high-grade glioma (HGG) are still poorly investigated. We performed a retrospective research in our institutional database for patients with supratentorial HGG treated with focal radiotherapy, having a progression-free overall survival > 30 months and available germline DNA. We reviewed MRI scans for signs of leukoencephalopathy on T2/FLAIR sequences, and medical records for information on cerebrovascular risk factors and neurological symptoms. We investigated a panel of candidate single nucleotide polymorphisms (SNPs) to assess genetic risk. Eighty-one HGG patients (18 grade IV and 63 grade III, 50M/31F) were included in the study. The median age at the time of radiotherapy was 48 years old (range 18-69). The median follow-up after the completion of radiotherapy was 79 months. A total of 44 patients (44/81, 54.3%) developed RIL during follow-up. Twenty-nine of the 44 patients developed consistent symptoms such as subcortical dementia (n = 28), gait disturbances (n = 12), and urinary incontinence (n = 9). The cumulative incidence of RIL was 21% at 12 months, 42% at 36 months, and 48% at 60 months. Age > 60 years, smoking, and the germline SNP rs2120825 (PPARg locus) were associated with an increased risk of RIL. Our study identified potential risk factors for the development of RIL (age, smoking, and the germline SNP rs2120825) and established the rationale for testing PPARg agonists in the prevention and management of late-delayed radiation-induced neurotoxicity.
Published: 2021
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41. Searching for causal relationships of glioma: a phenome-wide Mendelian randomisation study.

Author: Saunders CN, Cornish AJ, Kinnersley B, Law PJ, and Houlston RS
Subjects: Genetic Variation, Humans, Mendelian Randomization Analysis, Risk Factors, Brain Neoplasms genetics, Brain Neoplasms pathology, Genome-Wide Association Study, Glioma genetics, Glioma pathology
Abstract: Background: The aetiology of glioma is poorly understood. Summary data from genome-wide association studies (GWAS) can be used in a Mendelian randomisation (MR) phenome-wide association study (PheWAS) to search for glioma risk factors., Methods: We performed an MR-PheWAS analysing 316 phenotypes, proxied by 8387 genetic variants, and summary genetic data from a GWAS of 12,488 glioma cases and 18,169 controls. Causal effects were estimated under a random-effects inverse-variance-weighted (IVW-RE) model, with robust adjusted profile score (MR-RAPS), weighted median and mode-based estimates computed to assess the robustness of findings. Odds ratios per one standard deviation increase in each phenotype were calculated for all glioma, glioblastoma (GBM) and non-GBM tumours., Results: No significant associations (P < 1.58 × 10 -4 ) were observed between phenotypes and glioma under the IVW-RE model. Suggestive associations (1.58 × 10 -4 < P < 0.05) were observed between leukocyte telomere length (LTL) with all glioma (OR SD = 3.91, P = 9.24 × 10 -3 ) and GBM (OR SD = 4.86, P = 3.23 × 10 -2 ), but the association was primarily driven by the TERT variant rs2736100. Serum low-density lipoprotein cholesterol and plasma HbA1C showed suggestive associations with glioma (OR SD = 1.11, P = 1.39 × 10 -2 and OR SD = 1.28, P = 1.73 × 10 -2 , respectively), both associations being reliant on single genetic variants., Conclusions: Our study provides further insight into the aetiological basis of glioma for which published data have been mixed.
Published: 2021
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42. Algorithmic considerations when analysing capture Hi-C data.

Author: Disney-Hogg L, Kinnersley B, and Houlston R
Abstract: Chromosome conformation capture methodologies have provided insight into the effect of 3D genomic architecture on gene regulation. Capture Hi-C (CHi-C) is a recent extension of Hi-C that improves the effective resolution of chromatin interactions by enriching for defined regions of biological relevance. The varying targeting efficiency between capture regions, however, introduces bias not present in conventional Hi-C, making analysis more complicated. Here we consider salient features of an algorithm that should be considered in evaluating the performance of a program used to analyse CHi-C data in order to infer meaningful interactions. We use the program CHICAGO to analyse promotor capture Hi-C data generated on 28 different cell lines as a case study., Competing Interests: No competing interests were disclosed., (Copyright: © 2020 Disney-Hogg L et al.)
Published: 2020
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43. An enhanced genetic model of relapsed IGH-translocated multiple myeloma evolutionary dynamics.

Author: Hoang PH, Cornish AJ, Sherborne AL, Chubb D, Kimber S, Jackson G, Morgan GJ, Cook G, Kinnersley B, Kaiser M, and Houlston RS
Subjects: Adult, Aged, Aged, 80 and over, Female, Humans, Male, Middle Aged, Recurrence, Chromosome Deletion, Chromosomes, Human, Pair 17 genetics, Models, Genetic, Multiple Myeloma genetics, Neoplasm Proteins genetics, Point Mutation, Translocation, Genetic
Abstract: Most patients with multiple myeloma (MM) die from progressive disease after relapse. To advance our understanding of MM evolution mechanisms, we performed whole-genome sequencing of 80 IGH-translocated tumour-normal newly diagnosed pairs and 24 matched relapsed tumours from the Myeloma XI trial. We identify multiple events as potentially important for survival and therapy-resistance at relapse including driver point mutations (e.g., TET2), translocations (MAP3K14), lengthened telomeres, and increased genomic instability (e.g., 17p deletions). Despite heterogeneous mutational processes contributing to relapsed mutations across MM subtypes, increased AID/APOBEC activity is particularly associated with shorter progression time to relapse, and contributes to higher mutational burden at relapse. In addition, we identify three enhanced major clonal evolution patterns of MM relapse, independent of treatment strategies and molecular karyotypes, questioning the viability of "evolutionary herding" approach in treating drug-resistant MM. Our data show that MM relapse is associated with acquisition of new mutations and clonal selection, and suggest APOBEC enzymes among potential targets for therapy-resistant MM.
Published: 2020
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44. 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, and Garcia-Closas M
Subjects: Animals, Female, Genome-Wide Association Study, Humans, Incidence, Male, Neoplasms genetics, Polymorphism, Single Nucleotide, Risk Assessment methods, Risk Factors, Genetic Predisposition to Disease, Models, Genetic, Multifactorial Inheritance, Neoplasms epidemiology
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
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45. Search for multiple myeloma risk factors using Mendelian randomization.

Author: Went M, Cornish AJ, Law PJ, Kinnersley B, van Duin M, Weinhold N, Försti A, Hansson M, Sonneveld P, Goldschmidt H, Morgan GJ, Hemminki K, Nilsson B, Kaiser M, and Houlston RS
Subjects: Humans, Mendelian Randomization Analysis, Polymorphism, Single Nucleotide, Risk Factors, Genome-Wide Association Study, Multiple Myeloma epidemiology, Multiple Myeloma genetics
Abstract: The etiology of multiple myeloma (MM) is poorly understood. Summary data from genome-wide association studies (GWASs) of multiple phenotypes can be exploited in a Mendelian randomization (MR) phenome-wide association study (PheWAS) to search for factors influencing MM risk. We performed an MR-PheWAS analyzing 249 phenotypes, proxied by 10 225 genetic variants, and summary genetic data from a GWAS of 7717 MM cases and 29 304 controls. Odds ratios (ORs) per 1 standard deviation increase in each phenotype were estimated under an inverse variance weighted random effects model. A Bonferroni-corrected threshold of P = 2 × 10-4 was considered significant, whereas P < .05 was considered suggestive of an association. Although no significant associations with MM risk were observed among the 249 phenotypes, 28 phenotypes showed evidence suggestive of association, including increased levels of serum vitamin B6 and blood carnitine (P = 1.1 × 10-3) with greater MM risk and ω-3 fatty acids (P = 5.4 × 10-4) with reduced MM risk. A suggestive association between increased telomere length and reduced MM risk was also noted; however, this association was primarily driven by the previously identified risk variant rs10936599 at 3q26 (TERC). Although not statistically significant, increased body mass index was associated with increased risk (OR, 1.10; 95% confidence interval, 0.99-1.22), supporting findings from a previous meta-analysis of prospective observational studies. Our study did not provide evidence supporting any modifiable factors examined as having a major influence on MM risk; however, it provides insight into factors for which the evidence has previously been mixed., (© 2020 by The American Society of Hematology.)
Published: 2020
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46. Lack of association between modifiable exposures and glioma risk: a Mendelian randomization analysis.

Author: Saunders CN, Cornish AJ, Kinnersley B, Law PJ, Claus EB, Il'yasova D, Schildkraut J, Barnholtz-Sloan JS, Olson SH, Bernstein JL, Lai RK, Chanock S, Rajaraman P, Johansen C, Jenkins RB, Melin BS, Wrensch MR, Sanson M, Bondy ML, and Houlston RS
Subjects: Diet adverse effects, Humans, Inflammation complications, Life Style, Mendelian Randomization Analysis, Metabolism genetics, Risk Factors, Brain Neoplasms, Glioma
Abstract: Background: The etiological basis of glioma is poorly understood. We have used genetic markers in a Mendelian randomization (MR) framework to examine if lifestyle, cardiometabolic, and inflammatory factors influence the risk of glioma. This methodology reduces bias from confounding and is not affected by reverse causation., Methods: We identified genetic instruments for 37 potentially modifiable risk factors and evaluated their association with glioma risk using data from a genome-wide association study of 12 488 glioma patients and 18 169 controls. We used the estimated odds ratio of glioma associated with each of the genetically defined traits to infer evidence for a causal relationship with the following exposures:Lifestyle and dietary factors-height, plasma insulin-like growth factor 1, blood carnitine, blood methionine, blood selenium, blood zinc, circulating adiponectin, circulating carotenoids, iron status, serum calcium, vitamins (A1, B12, B6, E, and 25-hydroxyvitamin D), fatty acid levels (monounsaturated, omega-3, and omega-6) and circulating fetuin-A;Cardiometabolic factors-birth weight, high density lipoprotein cholesterol, low density lipoprotein cholesterol, total cholesterol, total triglycerides, basal metabolic rate, body fat percentage, body mass index, fasting glucose, fasting proinsulin, glycated hemoglobin levels, diastolic and systolic blood pressure, waist circumference, waist-to-hip ratio; andInflammatory factors- C-reactive protein, plasma interleukin-6 receptor subunit alpha and serum immunoglobulin E., Results: After correction for the testing of multiple potential risk factors and excluding associations driven by one single nucleotide polymorphism, no significant association with glioma risk was observed (ie, PCorrected > 0.05)., Conclusions: This study did not provide evidence supporting any of the 37 factors examined as having a significant influence on glioma risk., (© The Author(s) 2019. Published by Oxford University Press on behalf of the Society for Neuro-Oncology.)
Published: 2020
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47. Identification of four novel associations for B-cell acute lymphoblastic leukaemia risk.

Author: Vijayakrishnan J, Qian M, Studd JB, Yang W, Kinnersley B, Law PJ, Broderick P, Raetz EA, Allan J, Pui CH, Vora A, Evans WE, Moorman A, Yeoh A, Yang W, Li C, Bartram CR, Mullighan CG, Zimmerman M, Hunger SP, Schrappe M, Relling MV, Stanulla M, Loh ML, Houlston RS, and Yang JJ
Subjects: Child, Epigenomics, Genome-Wide Association Study, Humans, Precursor B-Cell Lymphoblastic Leukemia-Lymphoma pathology, Risk Factors, Transcriptome, Core Binding Factor Alpha 2 Subunit genetics, Genetic Predisposition to Disease genetics, Oncogene Proteins, Fusion genetics, Polymorphism, Single Nucleotide, Precursor B-Cell Lymphoblastic Leukemia-Lymphoma genetics, RNA-Binding Proteins genetics, bcl-2 Homologous Antagonist-Killer Protein genetics
Abstract: There is increasing evidence for a strong inherited genetic basis of susceptibility to acute lymphoblastic leukaemia (ALL) in children. To identify new risk variants for B-cell ALL (B-ALL) we conducted a meta-analysis with four GWAS (genome-wide association studies), totalling 5321 cases and 16,666 controls of European descent. We herein describe novel risk loci for B-ALL at 9q21.31 (rs76925697, P = 2.11 × 10 -8 ), for high-hyperdiploid ALL at 5q31.1 (rs886285, P = 1.56 × 10 -8 ) and 6p21.31 (rs210143 in BAK1, P = 2.21 × 10 -8 ), and ETV6-RUNX1 ALL at 17q21.32 (rs10853104 in IGF2BP1, P = 1.82 × 10 -8 ). Particularly notable are the pleiotropic effects of the BAK1 variant on multiple haematological malignancies and specific effects of IGF2BP1 on ETV6-RUNX1 ALL evidenced by both germline and somatic genomic analyses. Integration of GWAS signals with transcriptomic/epigenomic profiling and 3D chromatin interaction data for these leukaemia risk loci suggests deregulation of B-cell development and the cell cycle as central mechanisms governing genetic susceptibility to ALL.
Published: 2019
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48. Genetic predisposition to mosaic Y chromosome loss in blood.

Author: Thompson DJ, Genovese G, Halvardson J, Ulirsch JC, Wright DJ, Terao C, Davidsson OB, Day FR, Sulem P, Jiang Y, Danielsson M, Davies H, Dennis J, Dunlop MG, Easton DF, Fisher VA, Zink F, Houlston RS, Ingelsson M, Kar S, Kerrison ND, Kinnersley B, Kristjansson RP, Law PJ, Li R, Loveday C, Mattisson J, McCarroll SA, Murakami Y, Murray A, Olszewski P, Rychlicka-Buniowska E, Scott RA, Thorsteinsdottir U, Tomlinson I, Moghadam BT, Turnbull C, Wareham NJ, Gudbjartsson DF, Kamatani Y, Hoffmann ER, Jackson SP, Stefansson K, Auton A, Ong KK, Machiela MJ, Loh PR, Dumanski JP, Chanock SJ, Forsberg LA, and Perry JRB
Subjects: Adult, Aged, Computational Biology, Databases, Genetic, Female, Genetic Markers genetics, Humans, Male, Middle Aged, Neoplasms genetics, United Kingdom, Chromosome Deletion, Chromosomes, Human, Y genetics, Genetic Predisposition to Disease genetics, Genomic Instability genetics, Leukocytes pathology, Mosaicism
Abstract: Mosaic loss of chromosome Y (LOY) in circulating white blood cells is the most common form of clonal mosaicism 1-5 , yet our knowledge of the causes and consequences of this is limited. Here, using a computational approach, we estimate that 20% of the male population represented in the UK Biobank study (n = 205,011) has detectable LOY. We identify 156 autosomal genetic determinants of LOY, which we replicate in 757,114 men of European and Japanese ancestry. These loci highlight genes that are involved in cell-cycle regulation and cancer susceptibility, as well as somatic drivers of tumour growth and targets of cancer therapy. We demonstrate that genetic susceptibility to LOY is associated with non-haematological effects on health in both men and women, which supports the hypothesis that clonal haematopoiesis is a biomarker of genomic instability in other tissues. Single-cell RNA sequencing identifies dysregulated expression of autosomal genes in leukocytes with LOY and provides insights into why clonal expansion of these cells may occur. Collectively, these data highlight the value of studying clonal mosaicism to uncover fundamental mechanisms that underlie cancer and other ageing-related diseases.
Published: 2019
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49. Phenome-wide association analysis of LDL-cholesterol lowering genetic variants in PCSK9.

Author: Schmidt AF, Holmes MV, Preiss D, Swerdlow DI, Denaxas S, Fatemifar G, Faraway R, Finan C, Valentine D, Fairhurst-Hunter Z, Hartwig FP, Horta BL, Hypponen E, Power C, Moldovan M, van Iperen E, Hovingh K, Demuth I, Norman K, Steinhagen-Thiessen E, Demuth J, Bertram L, Lill CM, Coassin S, Willeit J, Kiechl S, Willeit K, Mason D, Wright J, Morris R, Wanamethee G, Whincup P, Ben-Shlomo Y, McLachlan S, Price JF, Kivimaki M, Welch C, Sanchez-Galvez A, Marques-Vidal P, Nicolaides A, Panayiotou AG, Onland-Moret NC, van der Schouw YT, Matullo G, Fiorito G, Guarrera S, Sacerdote C, Wareham NJ, Langenberg C, Scott RA, Luan J, Bobak M, Malyutina S, Pająk A, Kubinova R, Tamosiunas A, Pikhart H, Grarup N, Pedersen O, Hansen T, Linneberg A, Jess T, Cooper J, Humphries SE, Brilliant M, Kitchner T, Hakonarson H, Carrell DS, McCarty CA, Lester KH, Larson EB, Crosslin DR, de Andrade M, Roden DM, Denny JC, Carty C, Hancock S, Attia J, Holliday E, Scott R, Schofield P, O'Donnell M, Yusuf S, Chong M, Pare G, van der Harst P, Said MA, Eppinga RN, Verweij N, Snieder H, Christen T, Mook-Kanamori DO, Gustafsson S, Lind L, Ingelsson E, Pazoki R, Franco O, Hofman A, Uitterlinden A, Dehghan A, Teumer A, Baumeister S, Dörr M, Lerch MM, Völker U, Völzke H, Ward J, Pell JP, Meade T, Christophersen IE, Maitland-van der Zee AH, Baranova EV, Young R, Ford I, Campbell A, Padmanabhan S, Bots ML, Grobbee DE, Froguel P, Thuillier D, Roussel R, Bonnefond A, Cariou B, Smart M, Bao Y, Kumari M, Mahajan A, Hopewell JC, Seshadri S, Dale C, Costa RPE, Ridker PM, Chasman DI, Reiner AP, Ritchie MD, Lange LA, Cornish AJ, Dobbins SE, Hemminki K, Kinnersley B, Sanson M, Labreche K, Simon M, Bondy M, Law P, Speedy H, Allan J, Li N, Went M, Weinhold N, Morgan G, Sonneveld P, Nilsson B, Goldschmidt H, Sud A, Engert A, Hansson M, Hemingway H, Asselbergs FW, Patel RS, Keating BJ, Sattar N, Houlston R, Casas JP, and Hingorani AD
Subjects: Anticholesteremic Agents adverse effects, Biomarkers blood, Brain Ischemia epidemiology, Brain Ischemia prevention & control, Down-Regulation, Dyslipidemias blood, Dyslipidemias epidemiology, Genome-Wide Association Study, Humans, Myocardial Infarction epidemiology, Myocardial Infarction prevention & control, Randomized Controlled Trials as Topic, Risk Assessment, Risk Factors, Serine Proteinase Inhibitors adverse effects, Stroke epidemiology, Stroke prevention & control, Treatment Outcome, Anticholesteremic Agents therapeutic use, Cholesterol, LDL blood, Dyslipidemias drug therapy, Dyslipidemias genetics, PCSK9 Inhibitors, Polymorphism, Single Nucleotide, Proprotein Convertase 9 genetics, Serine Proteinase Inhibitors therapeutic use
Abstract: Background: We characterised the phenotypic consequence of genetic variation at the PCSK9 locus and compared findings with recent trials of pharmacological inhibitors of PCSK9., Methods: Published and individual participant level data (300,000+ participants) were combined to construct a weighted PCSK9 gene-centric score (GS). Seventeen randomized placebo controlled PCSK9 inhibitor trials were included, providing data on 79,578 participants. Results were scaled to a one mmol/L lower LDL-C concentration., Results: The PCSK9 GS (comprising 4 SNPs) associations with plasma lipid and apolipoprotein levels were consistent in direction with treatment effects. The GS odds ratio (OR) for myocardial infarction (MI) was 0.53 (95% CI 0.42; 0.68), compared to a PCSK9 inhibitor effect of 0.90 (95% CI 0.86; 0.93). For ischemic stroke ORs were 0.84 (95% CI 0.57; 1.22) for the GS, compared to 0.85 (95% CI 0.78; 0.93) in the drug trials. ORs with type 2 diabetes mellitus (T2DM) were 1.29 (95% CI 1.11; 1.50) for the GS, as compared to 1.00 (95% CI 0.96; 1.04) for incident T2DM in PCSK9 inhibitor trials. No genetic associations were observed for cancer, heart failure, atrial fibrillation, chronic obstructive pulmonary disease, or Alzheimer's disease - outcomes for which large-scale trial data were unavailable., Conclusions: Genetic variation at the PCSK9 locus recapitulates the effects of therapeutic inhibition of PCSK9 on major blood lipid fractions and MI. While indicating an increased risk of T2DM, no other possible safety concerns were shown; although precision was moderate.
Published: 2019
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50. Transcriptome-wide association study of multiple myeloma identifies candidate susceptibility genes.

Author: Went M, Kinnersley B, Sud A, Johnson DC, Weinhold N, Försti A, van Duin M, Orlando G, Mitchell JS, Kuiper R, Walker BA, Gregory WM, Hoffmann P, Jackson GH, Nöthen MM, da Silva Filho MI, Thomsen H, Broyl A, Davies FE, Thorsteinsdottir U, Hansson M, Kaiser M, Sonneveld P, Goldschmidt H, Stefansson K, Hemminki K, Nilsson B, Morgan GJ, and Houlston RS
Subjects: APOBEC-3G Deaminase genetics, Aminohydrolases genetics, Cytidine Deaminase genetics, Cytosine Deaminase genetics, Gene Expression Profiling, Genotype, Humans, Multiple Myeloma pathology, Polymorphism, Single Nucleotide genetics, Quantitative Trait Loci genetics, Genetic Predisposition to Disease, Genome-Wide Association Study, Multiple Myeloma genetics, Transcriptome genetics
Abstract: Background: While genome-wide association studies (GWAS) of multiple myeloma (MM) have identified variants at 23 regions influencing risk, the genes underlying these associations are largely unknown. To identify candidate causal genes at these regions and search for novel risk regions, we performed a multi-tissue transcriptome-wide association study (TWAS)., Results: GWAS data on 7319 MM cases and 234,385 controls was integrated with Genotype-Tissue Expression Project (GTEx) data assayed in 48 tissues (sample sizes, N = 80-491), including lymphocyte cell lines and whole blood, to predict gene expression. We identified 108 genes at 13 independent regions associated with MM risk, all of which were in 1 Mb of known MM GWAS risk variants. Of these, 94 genes, located in eight regions, had not previously been considered as a candidate gene for that locus., Conclusions: Our findings highlight the value of leveraging expression data from multiple tissues to identify candidate genes responsible for GWAS associations which provide insight into MM tumorigenesis. Among the genes identified, a number have plausible roles in MM biology, notably APOBEC3C, APOBEC3H, APOBEC3D, APOBEC3F, APOBEC3G, or have been previously implicated in other malignancies. The genes identified in this TWAS can be explored for follow-up and validation to further understand their role in MM biology.
Published: 2019
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