Melbourne School of Population and Global Health - Research Publications

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    Gene and pathway level analyses of germline DNA-repair gene variants and prostate cancer susceptibility using the iCOGS-genotyping array.
    Saunders, EJ ; Dadaev, T ; Leongamornlert, DA ; Al Olama, AA ; Benlloch, S ; Giles, GG ; Wiklund, F ; Grönberg, H ; Haiman, CA ; Schleutker, J ; Nordestgaard, BG ; Travis, RC ; Neal, D ; Pasayan, N ; Khaw, K-T ; Stanford, JL ; Blot, WJ ; Thibodeau, SN ; Maier, C ; Kibel, AS ; Cybulski, C ; Cannon-Albright, L ; Brenner, H ; Park, JY ; Kaneva, R ; Batra, J ; Teixeira, MR ; Pandha, H ; Govindasami, K ; Muir, K ; UK Genetic Prostate Cancer Study Collaborators, ; UK ProtecT Study Collaborators, ; PRACTICAL Consortium, ; Easton, DF ; Eeles, RA ; Kote-Jarai, Z (Springer Science and Business Media LLC, 2018-03-20)
    This corrects the article DOI: 10.1038/bjc.2016.50.
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    Height, selected genetic markers and prostate cancer risk: results from the PRACTICAL consortium.
    Lophatananon, A ; Stewart-Brown, S ; Kote-Jarai, Z ; Al Olama, AA ; Garcia, SB ; Neal, DE ; Hamdy, FC ; Donovan, JL ; Giles, GG ; Fitzgerald, LM ; Southey, MC ; Pharoah, P ; Pashayan, N ; Gronberg, H ; Wiklund, F ; Aly, M ; Stanford, JL ; Brenner, H ; Dieffenbach, AK ; Arndt, V ; Park, JY ; Lin, H-Y ; Sellers, T ; Slavov, C ; Kaneva, R ; Mitev, V ; Batra, J ; Spurdle, A ; Clements, JA ; APCB BioResource, ; PRACTICAL consortium, ; Easton, D ; Eeles, RA ; Muir, K (Springer Science and Business Media LLC, 2018-03-20)
    This corrects the article DOI: 10.1038/bjc.2017.231.
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    Methylation alteration of SHANK1 as a predictive, diagnostic and prognostic biomarker for chronic lymphocytic leukemia.
    Loi, E ; Moi, L ; Fadda, A ; Satta, G ; Zucca, M ; Sanna, S ; Amini Nia, S ; Cabras, G ; Padoan, M ; Magnani, C ; Miligi, L ; Piro, S ; Gentilini, D ; Ennas, MG ; Southey, MC ; Giles, GG ; Wong Doo, N ; Cocco, P ; Zavattari, P (Impact Journals, LLC, 2019-08-13)
    Chronic lymphocytic leukemia (CLL) is a clinically heterogeneous disease characterized by the clonal expansion of malignant B cells. To predict the clinical course of the disease, the identification of diagnostic biomarkers is urgently needed. Aberrant methylation patterns may predict CLL development and its course, being very early changes during carcinogenesis. Our aim was to identify CLL specific methylation patterns and to evaluate whether methylation aberrations in selected genes are associated with changes in gene expression. Here, by performing a genome-wide methylation analysis, we identified several CLL-specific methylation alterations. We focused on the most altered one, at a CpG island located in the body of SHANK1 gene, in our CLL cases compared to healthy controls. This methylation alteration was successfully validated in a larger cohort including 139 CLL and 20 control in silico samples. We also found a positive correlation between SHANK1 methylation level and absolute lymphocyte count, in particular CD19+ B cells, in CLL patients. Moreover, we were able to detect gains of methylation at SHANK1 in blood samples collected years prior to diagnosis. Overall, our results suggest methylation alteration at this SHANK1 CpG island as a biomarker for risk and diagnosis of CLL, and also in the personalized quantification of tumor aggressiveness.
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    Identification of multiple risk loci and regulatory mechanisms influencing susceptibility to multiple myeloma (vol 9, 3707, 2018)
    Went, M ; Sud, A ; Foersti, A ; Halvarsson, B-M ; Weinhold, N ; Kimber, S ; van Duin, M ; Thorleifsson, G ; Holroyd, A ; Johnson, DC ; Li, N ; Orlando, G ; Law, PJ ; Ali, M ; Chen, B ; Mitchell, JS ; Gudbjartsson, DF ; Kuiper, R ; Stephens, OW ; Bertsch, U ; Broderick, P ; Campo, C ; Bandapalli, OR ; Einsele, H ; Gregory, WA ; Gullberg, U ; Hillengass, J ; Hoffmann, P ; Jackson, GH ; Joeckel, K-H ; Johnsson, E ; Kristinsson, SY ; Mellqvist, U-H ; Nahi, H ; Easton, D ; Pharoah, P ; Dunning, A ; 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 ; Grindedal, EM ; Neal, DE ; Hamdy, FC ; Donovan, JL ; 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 ; Khaw, K-T ; Cannon-Albright, L ; Pandha, H ; Thibodeau, SN ; Nickel, J ; Noethen, MM ; Rafnar, T ; Ross, FM ; Filho, MIDS ; Thomsen, H ; Turesson, I ; Vangsted, A ; Andersen, NF ; Waage, A ; Walker, BA ; Wihlborg, A-K ; Broyl, A ; Davies, FE ; Thorsteinsdottir, U ; Langer, C ; Hansson, M ; Goldschmidt, H ; Kaiser, M ; Sonneveld, P ; Stefansson, K ; Morgan, GJ ; Hemminki, K ; Nilsson, B ; Houlston, RS (NATURE PUBLISHING GROUP, 2019-01-10)
    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.
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    Genome-wide association study identifies susceptibility loci for B-cell childhood acute lymphoblastic leukemia (vol 9, 1340, 2018)
    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 (NATURE PUBLISHING GROUP, 2019-01-21)
    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.
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    Genome-wide association study of classical Hodgkin lymphoma identifies key regulators of disease susceptibility (vol 8, 1892, 2017)
    Sud, A ; Thomsen, H ; Law, PJ ; Foersti, A ; Filho, MIDS ; Holroyd, A ; Broderick, P ; Orlando, G ; Lenive, O ; Wright, L ; Cooke, R ; Easton, D ; Pharoah, P ; Dunning, A ; Peto, J ; Canzian, F ; Eeles, R ; Kote-Jarai, Z ; Muir, K ; Pashayan, N ; Hoffmann, P ; Noethen, MM ; Joeckel, K-H ; von Strandmann, EP ; Lightfoot, T ; Kane, E ; Roman, E ; Lake, A ; Montgomery, D ; Jarrett, RF ; Swerdlow, AJ ; Engert, A ; Orr, N ; Hemminki, K ; Houlston, RS ; 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 (NATURE PUBLISHING GROUP, 2019-01-08)
    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.
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    Large-scale transcriptome-wide association study identifies new prostate cancer risk regions (vol 9, 4079, 2018)
    Mancuso, N ; Gayther, S ; Gusev, A ; Zheng, W ; Penney, KL ; Kote-Jarai, Z ; Eeles, R ; Freedman, M ; Haiman, C ; Pasaniuc, B ; Henderson, BE ; Benlloch, S ; Schumacher, FR ; Al Olama, AA ; Muir, K ; Berndt, SI ; Conti, DV ; Wiklund, F ; Chanock, S ; Stevens, VL ; Tangen, CM ; Batra, J ; Clements, J ; Gronberg, H ; Pashayan, N ; Schleutker, J ; Albanes, D ; Weinstein, S ; Wolk, A ; West, C ; Mucci, L ; Cancel-Tassin, G ; Koutros, S ; Sorensen, KD ; Maehle, L ; Neal, DE ; Hamdy, FC ; Donovan, JL ; Travis, RC ; Hamilton, RJ ; Ingles, SA ; Rosenstein, B ; Lu, Y-J ; Giles, GG ; Kibel, AS ; Vega, A ; Kogevinas, M ; 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 ; Khaw, K-T ; Cannon-Albright, L ; Pandha, H ; Thibodeau, SN ; Hunter, DJ ; Kraft, P (NATURE PUBLISHING GROUP, 2019-01-08)
    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 consortium PRACTICAL consortium was incorrectly listed after Bogdan Pasaniuc and should have been listed after Kathryn L. Penney. This error has been corrected in the HTML version of the Article; the PDF version was correct at the time of publication.
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    Steroid hormone measurements from different types of assays in relation to body mass index and breast cancer risk in postmenopausal women: Reanalysis of eighteen prospective studies
    Key, TJ ; Appleby, PN ; Reeves, GK ; Travis, RC ; Brinton, LA ; Dallal, CM ; Helzlsouer, KJ ; Hoffman-Bolton, J ; Visvanathan, K ; Dorgan, JF ; Falk, RT ; Gapstur, SM ; Gaudet, MM ; Kaaks, R ; Riboli, E ; Rinaldi, S ; Key, T ; Manjer, J ; Hallmans, G ; Giles, GG ; Le Marchand, L ; Kolonel, LN ; Henderson, BE ; Tworoger, SS ; Hankinson, SE ; Zeleniuch-Jacquotte, A ; Koenig, K ; Krogh, V ; Sieri, S ; Muti, P ; Ziegler, RG ; Schairer, C ; Fuhrman, BJ ; Barrett-Connor, E ; Laughlin, GA ; Grant, EJ ; Cologne, J ; Ohishi, W ; Hida, A ; Cauley, JA ; Fourkala, E-O ; Rohan, TE ; Strickler, HD ; Gunter, MJ (ELSEVIER SCIENCE INC, 2015-07-01)
    Epidemiological studies have examined breast cancer risk in relation to sex hormone concentrations measured by different methods: "extraction" immunoassays (with prior purification by organic solvent extraction, with or without column chromatography), "direct" immunoassays (no prior extraction or column chromatography), and more recently with mass spectrometry-based assays. We describe the associations of estradiol, estrone and testosterone with both body mass index and breast cancer risk in postmenopausal women according to assay method, using data from a collaborative pooled analysis of 18 prospective studies. In general, hormone concentrations were highest in studies that used direct assays and lowest in studies that used mass spectrometry-based assays. Estradiol and estrone were strongly positively associated with body mass index, regardless of the assay method; testosterone was positively associated with body mass index for direct assays, but less clearly for extraction assays, and there were few data for mass spectrometry assays. The correlations of estradiol with body mass index, estrone and testosterone were lower for direct assays than for extraction and mass spectrometry assays, suggesting that the estimates from the direct assays were less precise. For breast cancer risk, all three hormones were strongly positively associated with risk regardless of assay method (except for testosterone by mass spectrometry where there were few data), with no statistically significant differences in the trends, but differences may emerge as new data accumulate. Future epidemiological and clinical research studies should continue to use the most accurate assays that are feasible within the design characteristics of each study.
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    Identification of new breast cancer predisposition genes via whole exome sequencing
    Southey, MC ; Park, DJ ; Lesueur, F ; Odefrey, F ; Nguyen-Dumont, T ; Hammet, F ; Neuhausen, SL ; John, EM ; Andrulis, IL ; Chenevix-Trench, G ; Baglietto, L ; Le Calvez-Kelm, F ; Pertesi, M ; Lonie, A ; Pope, B ; Sinilnikova, O ; Tsimiklis, H ; Giles, GG ; Hopper, JL ; Tavtigian, SV ; Goldgar, DE (Springer Science and Business Media LLC, 2012-01)
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    DNA methylation-based biological aging and cancer risk and survival: Pooled analysis of seven prospective studies
    Dugue, P-A ; Bassett, JK ; Joo, JE ; Jung, C-H ; Wong, EM ; Moreno-Betancur, M ; Schmidt, D ; Makalic, E ; Li, S ; Severi, G ; Hodge, AM ; Buchanan, DD ; English, DR ; Hopper, JL ; Southey, MC ; Giles, GG ; Milne, RL (WILEY, 2018-04-15)
    The association between aging and cancer is complex. Recent studies have developed measures of biological aging based on DNA methylation and called them "age acceleration." We aimed to assess the associations of age acceleration with risk of and survival from seven common cancers. Seven case-control studies of DNA methylation and colorectal, gastric, kidney, lung, prostate and urothelial cancer and B-cell lymphoma nested in the Melbourne Collaborative Cohort Study were conducted. Cancer cases, vital status and cause of death were ascertained through linkage with cancer and death registries. Conditional logistic regression and Cox models were used to estimate odds ratios (OR) and hazard ratios (HR) and 95% confidence intervals (CI) for associations of five age acceleration measures derived from the Human Methylation 450 K Beadchip assay with cancer risk (N = 3,216 cases) and survival (N = 1,726 deaths), respectively. Epigenetic aging was associated with increased cancer risk, ranging from 4% to 9% per five-year age acceleration for the 5 measures considered. Heterogeneity by study was observed, with stronger associations for risk of kidney cancer and B-cell lymphoma. An associated increased risk of death following cancer diagnosis ranged from 2% to 6% per five-year age acceleration, with no evidence of heterogeneity by cancer site. Cancer risk and mortality were increased by 15-30% for the fourth versus first quartile of age acceleration. DNA methylation-based measures of biological aging are associated with increased cancer risk and shorter cancer survival, independently of major health risk factors.