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1. Functional annotation of the 2q35 breast cancer risk locus implicates a structural variant in influencing activity of a long-range enhancer element

Author

Baxter, J.S., Johnson, N., Tomczyk, K., Gillespie, A., Maguire, S., Brough, R., Fachal, L., Michailidou, K., Bolla, M.K., Wang, Q., Dennis, J., Ahearn, T.U., Andrulis, I.L., Anton-Culver, H., Antonenkova, N.N., Arndt, V., Aronson, K.J., Augustinsson, A., Becher, H., Beckmann, M.W., Behrens, S., Benitez, J., Bermisheva, M., Bogdanova, N.V., Bojesen, S.E., Brenner, H., Brucker, S.Y., Cai, Q.Y., Campa, D., Canzian, F., Castelao, J.E., Chan, T.L., Chang-Claude, J., Chanock, S.J., Chenevix-Trench, G., Choi, J.Y., Clarke, C.L., Collaborators, N., Colonna, S., Conroy, D.M., Couch, F.J., Cox, A., Cross, S.S., Czene, K., Daly, M.B., Devilee, P., Dork, T., Dossus, L., Dwek, M., Eccles, D.M., Ekici, A.B., Eliassen, A.H., Engel, C., Fasching, P.A., Figueroa, J., Flyger, H., Gago-Dominguez, M., Gao, C., Garcia-Closas, M., Garcia-Saenz, J.A., Ghoussaini, M., Giles, G.G., Goldberg, M.S., Gonzalez-Neira, A., Guenel, P., Gundert, M., Haeberle, L., Hahnen, E., Haiman, C.A., Hall, P., Hamann, U., Hartman, M., Hatse, S., Hauke, J., Hollestelle, A., Hoppe, R., Hopper, J.L., Hou, M.F., Ito, H., Iwasaki, M., Jager, A., Jakubowska, A., Janni, W., John, E.M., Joseph, V., Jung, A., Kaaks, R., Kang, D., Keeman, R., Khusnutdinova, E., Kim, S.W., Kosma, V.M., Kraft, P., Kristensen, V.N., Kubelka-Sabit, K., Kurian, A.W., Kwong, A., Lacey, J.V., Lambrechts, D., Larson, N.L., Larsson, S.C., Marchand, L. le, Lejbkowicz, F., Li, J.M., Long, J.R., Lophatananon, A., LubiNski, J., Mannermaa, A., Manoochehri, M., Manoukian, S., Margolin, S., Matsuo, K., Mavroudis, D., Mayes, R., Menon, U., Milne, R.L., Taib, N.A.M., Muir, K., Muranen, T.A., Murphy, R.A., Nevanlinna, H., O'Brien, K.M., Offit, K., Olson, J.E., Olsson, H., Park, S.K., Park-Simon, T.W., Patel, A.V., Peterlongo, P., Peto, J., Plaseska-Karanfilska, D., Presneau, N., Pylkas, K., Rack, B., Rennert, G., Romero, A., Ruebner, M., Rudiger, T., Saloustros, E., Sandler, D.P., Sawyer, E.J., Schmidt, M.K., Schmutzler, R.K., Schneeweiss, A., Schoemaker, M.J., Shah, M., Shen, C.Y., Shu, X.O., Simard, J., Southey, M.C., Stone, J., Surowy, H., Swerdlow, A.J., Tamimi, R.M., Tapper, W.J., Taylor, J.A., Teo, S.H., Teras, L.R., Terry, M.B., Toland, A.E., Tomlinson, I., Truong, T., Tseng, C.C., Untch, M., Vachon, C.M., Ouweland, A.M.W. van den, Wang, S.S., Weinberg, C.R., Wendt, C., Winham, S.J., Winqvist, R., Wolk, A., Wu, A.H., Yamaji, T., Zheng, W., Ziogas, A., Pharoah, P.D.P., Dunning, A.M., Easton, D.F., Pettitt, S.J., Lord, C.J., Haider, S., Orr, N., Fletcher, O., kConFab Investigators, ABCTB Investigators, Medical Oncology, Clinical Genetics, HUS Gynecology and Obstetrics, Department of Obstetrics and Gynecology, Biosciences, Dennis, Joe [0000-0003-4591-1214], Pharoah, Paul [0000-0001-8494-732X], Dunning, Alison [0000-0001-6651-7166], Easton, Douglas [0000-0003-2444-3247], and Apollo - University of Cambridge Repository

Subjects
Basic medicine, breast cancer risk, 0302 clinical medicine, Transcription (biology), Risk Factors, WIDE ASSOCIATION, TRANSCRIPTION, Promoter Regions, Genetic, Genetics (clinical), Sequence Deletion, Genetics, Genetics & Heredity, 0303 health sciences, Chromosome Mapping, 3. Good health, 030220 oncology & carcinogenesis, Chromosomes, Human, Pair 2, Pair 2, Female, Medical Genetics, Life Sciences & Biomedicine, Human, Tumor suppressor gene, SUSCEPTIBILITY LOCI, In silico, 3122 Cancers, Locus (genetics), Breast Neoplasms, Biology, Chromosomes, Article, Cell Line, RNAS, Promoter Regions, 03 medical and health sciences, functional annotation, risk locus, CRISPR-Cas Systems, Genetic Association Studies, Genetic Variation, Humans, Insulin-Like Growth Factor Binding Protein 5, Molecular Sequence Annotation, 11Q13, Genetic, SDG 3 - Good Health and Well-being, Enhancer, Transcription factor, 030304 developmental biology, Medicinsk genetik, Reporter gene, Science & Technology, IDENTIFICATION, Clinical medicine, Estrogen receptor alpha
Abstract

A combination of genetic and functional approaches has identified three independent breast cancer risk loci at 2q35. A recent fine-scale mapping analysis to refine these associations resulted in 1 (signal 1), 5 (signal 2), and 42 (signal 3) credible causal variants at these loci. We used publicly available in silico DNase I and ChIP-seq data with in vitro reporter gene and CRISPR assays to annotate signals 2 and 3. We identified putative regulatory elements that enhanced cell-type-specific transcription from the IGFBP5 promoter at both signals (30- to 40-fold increased expression by the putative regulatory element at signal 2, 2- to 3-fold by the putative regulatory element at signal 3). We further identified one of the five credible causal variants at signal 2, a 1.4 kb deletion (esv3594306), as the likely causal variant; the deletion allele of this variant was associated with an average additional increase in IGFBP5 expression of 1.3-fold (MCF-7) and 2.2-fold (T-47D). We propose a model in which the deletion allele of esv3594306 juxtaposes two transcription factor binding regions (annotated by estrogen receptor alpha ChIP-seq peaks) to generate a single extended regulatory element. This regulatory element increases cell-type-specific expression of the tumor suppressor gene IGFBP5 and, thereby, reduces risk of estrogen receptor-positive breast cancer (odds ratio = 0.77, 95% CI 0.74-0.81, p = 3.1 × 10-31). ispartof: AMERICAN JOURNAL OF HUMAN GENETICS vol:108 issue:7 pages:1190-1203 ispartof: location:United States status: published

Published
2021
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2. Disparities in Dolutegravir Uptake Affecting Females of Reproductive Age With HIV in Low- and Middle-Income Countries After Initial Concerns About Teratogenicity : An Observational Study

Author

Romo, M.L., Patel, R.C., Edwards, J.K., Humphrey, J.M., Musick, B.S., Bernard, C., Maina, M.W., Brazier, E., Castelnuovo, B., Penner, J., Wyka, K., Cardoso, S.W., Ly, P.S., Kunzekwenyika, C., Cortés, C.P., Panczak, R., Kelvin, E.A., Wools-Kaloustian, K.K., Nash, D., Khol, V., Zhang, F.J., Zhao, H.X., Han, N., Lee, M.P., Li, P.C.K., Lam, W., Wong, H.Y., Kumarasamy, N., Ezhilarasi, C., Pujari, S., Joshi, K., Gaikwad, S., Chitalikar, A., Merati, T.P., Wirawan, D.N., Yuliana, F., Yunihastuti, E., Imran, D., Widhani, A., Tanuma, J., Oka, S., Nishijima, T., Choi, J.Y., Na, S., Kim, J.M., Gani, Y.M., Rudi, N.B., Azwa, I., Kamarulzaman, A., Syed Omar, S.F., Ponnampalavanar, S., Ditangco, R., Pasayan, M.K., Mationg, M.L., Chan, Y.J., Ku, W.W., Ke, E., Wu, P.C., Ng, O.T., Lim, P.L., Lee, L.S., Yap, J.K., Avihingsanon, A., Gatechompol, S., Phanuphak, P., Phadungphon, C., Kiertiburanakul, S., Phuphuakrat, A., Chumla, L., Sanmeema, N., Chaiwarith, R., Sirisanthana, T., Praparattanapan, J., Nuket, K., Khuwuwan, S., Kantipong, P., Kambua, P., Nguyen, K.V., Bui, H.V., Nguyen, D.T.H., Nguyen, D.T., Do, C.D., Ngo, A.V., Nguyen, L.T., Sohn, A.H., Ross, J.L., Petersen, B., Law, M.G., Jiamsakul, A., Bijker, R., Rupasinghe, D., Cahn, P., Cesar, C., Fink, V., Sued, O., Dell'Isola, E., Perez, H., Valiente, J., Yamamoto, C., Grinsztejn, B., Veloso, V., Luz, P., de Boni, R., Wagner, S.C., Friedman, R., Moreira, R., Pinto, J., Ferreira, F., Maia, M., de Menezes Succi, R.C., Machado, D.M., de Fátima Barbosa Gouvêa, A., Wolff, M., Rodriguez, M.F., Allendes, G., Pape, J.W., Rouzier, V., Marcelin, A., Perodin, C., Luque, M.T., Padgett, D., Madero, J.S., Ramirez, B.C., Belaunzaran, P., Vega, Y.C., Gotuzzo Herencia, José Eduardo, Mejía Cordero, Fernando Alonso, Carriquiry, G., McGowan, C.C., Shepherd, B.E., Sterling, T., Jayathilake, K., Person, A.K., Rebeiro, P.F., Castilho, J., Duda, S.N., Maruri, F., Vansell, H., Jenkins, C., Kim, A., Lotspeich, S., Pélagie, N., Gateretse, P., Munezero, J., Nitereka, V., Niyongabo, T., Twizere, C., Bukuru, H., Nahimana, T., Baransaka, E., Barasukana, P., Kabanda, E., Manirakiza, M., Ndikumwenayo, F., Biziragusenyuka, J., Munezero, A.M.M., Nforniwe, D.N., Ajeh, R., Ngamani, M.L., Dzudie, A., Mbuh, A., Amadou, D., Yone, E.W.P., Kendowo, E., Akele, C., Clever, A., Kitetele, F., Lelo, P., Tabala, M., Ekembe, C., Kaba, D., Diafouka, M., Ekat, M.H., Nsonde, D.M., Mafoua, A., Christ, M.N., Igirimbabazi, J., Ayinkamiye, N., Uwineza, P., Ndamijimana, E., Habarurema, E., Nyiraneza, M.L., Nyiransabimana, M.L., Tuyisenge, L., Shyaka, C., Kankindi, C., Uwakijijwe, B., Ingabire, M.G., Ndumuhire, J., Nyirabahutu, M.G., Muyango, F., Bihibindi, J.C., Uwamahoro, O., Ndoli, Y., Nsanzimana, S., Mugwaneza, P., Remera, E., Umumararungu, E., Rwibasira, G.N., Habimana, D.S., Gasana, J., Kanyabwisha, F., Kubwimana, G., Muhoza, B., Munyaneza, A., Murenzi, G., Musabyimana, F., Umwiza, F., Ingabire, C., Tuyisenge, P., Butera, A.M., Kabahizi, J., Rurangwa, E., Feza, R., Mukashyaka, E., Benekigeri, C., Musaninyange, J., Adedimeji, A., Anastos, K., Dilorenzo, M., Murchison, L., Ross, J., Yotebieng, M., Addison, D., Jones, H., Kulkarni, S., Tymejczyk, O., Elul, B., Cai, X., Dong, A., Hoover, D., Kim, H.-Y., Li, C., Shi, Q., Lancaster, K., Kuniholm, M., Edmonds, A., Parcesepe, A., Edwards, J., Keiser, O., Kimmel, A., Diero, L., Ayaya, S., Sang, E., Bukusi, E., Mulwa, E., Nyanaro, G., Kasozi, C., Ssemakadde, M., Bwana, M.B., Muyindike, W., Byakwaga, H., Kanyesigye, M., Semeere, A., Matovu, J.M., Nalugoda, F., Wasswa, F.X., Kazyoba, P., Mayige, M., Lyamuya, R.E., Mayanga, F., Ngonyani, K., Lwali, J., Urassa, M., Nyaga, C., Machemba, R., Yiannoutsos, C., Vreeman, R., Syvertsen, J., Kantor, R., Martin, J., Wenger, M., Cohen, C., Kulzer, J., Maartens, G., Bolton, C., Wood, R., Sipambo, N., Tanser, F., Boulle, A., Fatti, G., Mbewe, S., Singh, E., Chimbetete, C., Technau, K., Eley, B., Muhairwe, J., Rafael, I., Fox, M.P., Prozesky, H., Anderegg, N., Ballif, M., Ostinelli, C.H.D., Egger, M., Fenner, L., Haas, A., Hossmann, S., Rohner, E., Riou, J., Skrivankova, V., Smith, L., Taghavi, K., von Groote, P., Wandeler, G., Zaniewski, E., Zürcher, K., Anderson, K., Cornell, M., Davies, M.-A., Iyun, V., Johnson, L., Kassanjee, R., Kehoe, K., Kubjane, M., Maxwell, N., Nyakato, P., Patten, G., Tlali, M., Tsondai, P., de Waal, R., and International epidemiology Databases to Evaluate AIDS (IeDEA)

Subjects
Adult, medicine.medical_specialty, Prevention, policy, and public health, Adolescent, Pyridones, Reproductive age, HIV Infections, Choice Behavior, Article, Piperazines, chemistry.chemical_compound, Acquired immunodeficiency syndrome (AIDS), Pregnancy, Epidemiology, Oxazines, Internal Medicine, Medicine, Humans, Maternal Health Services, Cumulative incidence, HIV Integrase Inhibitors, 610 Medicine & health, Developing Countries, Health equity, business.industry, HIV, Contraceptives, General Medicine, Middle Aged, medicine.disease, Antiretroviral therapy, Regimen, Pharmaceutical Preparations, chemistry, Dolutegravir, Observational study, Female, Age groups, Safety, business, Heterocyclic Compounds, 3-Ring, 360 Social problems & social services, Demography, Cohort study
Abstract

BACKGROUND The transition to dolutegravir-containing antiretroviral therapy (ART) in low- and middle-income countries (LMICs) was complicated by an initial safety signal in May 2018 suggesting that exposure to dolutegravir at conception was possibly associated with infant neural tube defects. On the basis of additional evidence, in July 2019, the World Health Organization recommended dolutegravir for all adults and adolescents living with HIV. OBJECTIVE To describe dolutegravir uptake and disparities by sex and age group in LMICs. DESIGN Observational cohort study. SETTING 87 sites that began using dolutegravir in 11 LMICs in the Asia-Pacific; Caribbean, Central and South America network for HIV epidemiology (CCASAnet); and sub-Saharan African regions of the International epidemiology Databases to Evaluate AIDS (IeDEA) consortium. PATIENTS 134��672 patients aged 16 years or older who received HIV care from January 2017 through March 2020. MEASUREMENTS Sex, age group, and dolutegravir uptake (that is, newly initiating ART with dolutegravir or switching to dolutegravir from another regimen). RESULTS Differences in dolutegravir uptake among females of reproductive age (16 to 49 years) emerged after the safety signal. By the end of follow-up, the cumulative incidence of dolutegravir uptake among females 16 to 49 years old was 29.4% (95% CI, 29.0% to 29.7%) compared with 57.7% (CI, 57.2% to 58.3%) among males 16 to 49 years old. This disparity was greater in countries that began implementing dolutegravir before the safety signal and initially had highly restrictive policies versus countries with a later rollout. Dolutegravir uptake was similar among females and males aged 50 years or older. LIMITATION Follow-up was limited to 6 to 8 months after international guidelines recommended expanding access to dolutegravir. CONCLUSION Substantial disparities in dolutegravir uptake affecting females of reproductive age through early 2020 are documented. Although this disparity was anticipated because of country-level restrictions on access, the results highlight its extent and initial persistence. PRIMARY FUNDING SOURCE National Institutes of Health.

Published
2021
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3. Two truncating variants in FANCC and breast cancer risk

Author

Dork, T., Peterlongo, P., Mannermaa, A., Bolla, M.K., Wang, Q., Dennis, J., Ahearn, T., Andrulis, I.L., Anton-Culver, H., Arndt, V., Aronson, K.J., Augustinsson, A., Freeman, L.E.B., Beckmann, M.W., Beeghly-Fadiel, A., Behrens, S., Bermisheva, M., Blomqvist, C., Bogdanova, N., Bojesen, S.E., Brauch, H., Brenner, H., Burwinkel, B., Canzian, F., Chan, T.L., Chang-Claude, J., Chanock, S.J., Choi, J.Y., Christiansen, H., Clarke, C.L., Couch, F.J., Czene, K., Daly, M.B., dos-Santos-Silva, I., Dwek, M., Eccles, D.M., Ekici, A.B., Eriksson, M., Evans, D.G., Fasching, P.A., Figueroa, J., Flyger, H., Fritschisl, L., Gabrielson, M., Gago-Dominguez, M., Gao, C., Gapstur, S.M., Garcia-Closas, M., Garcia-Saenz, J.A., Gaudet, M.M., Giles, G.G., Goldberg, M.S., Goldgar, D.E., Guenel, P., Haeberle, L., Haiman, C.A., Hakansson, N., Hall, P., Hamann, U., Hartman, M., Hauke, J., Hein, A., Hillemanns, P., Hogervorst, F.B.L., Hooning, M.J., Hopper, J.L., Howell, T., Huo, D.Z., Ito, H., Iwasaki, M., Jakubowska, A., Janni, W., John, E.M., Jung, A., Kaaks, R., Kang, D., Kapoor, P.M., Khusnutdinova, E., Kim, S.W., Kitahara, C.M., Koutros, S., Kraft, P., Kristensen, V.N., Kwon, A., Lambrechts, D., Marchand, L. le, Li, J.M., Lindstrom, S., Linet, M., W.Y. lo, Long, J.R., Lophatananon, A., Lubinski, J., Manoochehri, M., Manoukian, S., Margolin, S., Martinez, E., Matsuo, K., Mavroudis, D., Meindl, A., Menon, U., Milne, R.L., Taib, N.A.M., Muir, K., Mulligan, A.M., Neuhausen, S.L., Nevanlinna, H., Neven, P., Newman, W.G., Offit, K., Olopade, O.I., Olshan, A.F., Olson, J.E., Olsson, H., Park, S.K., Park-Simon, T.W., Peto, J., Plaseska-Karanfilska, D., Pohl-Rescigno, E., Presneau, N., Rack, B., Radice, P., Rashid, M.U., Rennert, G., Rennert, H.S., Romero, A., Ruebner, M., Saloustros, E., Schmidt, M.K., Schmutzler, R.K., Schneider, M.O., Schoemaker, M.J., Scott, C., Shen, C.Y., Shu, X.O., Simard, J., Slager, S., Smichkoska, S., Southey, M.C., Spinelli, J.J., Stone, J., Surowy, H., Swerdlow, A.J., Tamimi, R.M., Tapper, W.J., Teo, S.H., Terry, M.B., Toland, A.E., Tollenaar, R.A.E.M., Torres, D., Torres-Mejia, G., Troester, M.A., Truong, T., Tsugane, S., Untch, M., Vachon, C.M., Ouweland, A.M.W. van den, Veen, E.M. van, Vijai, J., Wendt, C., Wolk, A., Yu, J.C., Zheng, W., Ziogas, A., Ziv, E., Dunning, A.M., Pharoah, P.D.P., Schindler, D., Devilee, P., Easton, D.F., Balleine, R., Baxter, R., Braye, S., Carpenter, J., Dahlstrom, J., Forbes, J., Lee, C.S., Marsh, D., Morey, A., Pathmanathan, N., Scott, R., Simpson, P., Spigelman, A., Wilcken, N., Yip, D., Zeps, N., Borresen-Dale, A.L., Alnaes, G.I.G., Sahlberg, K.K., Ottestad, L., Karesen, R., Schlichting, E., Holmen, M.M., Sauer, T., Haakensen, V., Engebraten, O., Naume, B., Fossa, A., Kiserud, C.E., Reinertsen, K.V., Helland, A., Riis, M., Geisler, J., ABCTB Investigators, NBCS Collaborators, Andrulis, Irene L [0000-0002-4226-6435], Arndt, Volker [0000-0001-9320-8684], Brauch, Hiltrud [0000-0001-7531-2736], Dwek, Miriam [0000-0001-7184-2932], Ekici, Arif B [0000-0001-6099-7066], Fasching, Peter A [0000-0003-4885-8471], Figueroa, Jonine [0000-0002-5100-623X], Hein, Alexander [0000-0003-2601-3398], Ito, Hidemi [0000-0002-8023-4581], Matsuo, Keitaro [0000-0003-1761-6314], Menon, Usha [0000-0003-3708-1732], Milne, Roger L [0000-0001-5764-7268], Muir, Kenneth [0000-0001-6429-988X], Nevanlinna, Heli [0000-0002-0916-2976], Newman, William G [0000-0002-6382-4678], Peto, Julian [0000-0002-1685-8912], Rennert, Gad [0000-0002-8512-068X], Romero, Atocha [0000-0002-1634-7397], Schmidt, Marjanka K [0000-0002-2228-429X], Scott, Christopher [0000-0003-1340-0647], Stone, Jennifer [0000-0001-5077-0124], Truong, Thérèse [0000-0002-2943-6786], Tsugane, Shoichiro [0000-0003-4105-2774], Ziogas, Argyrios [0000-0003-4529-3727], Dunning, Alison M [0000-0001-6651-7166], Pharoah, Paul DP [0000-0001-8494-732X], Devilee, Peter [0000-0002-8023-2009], Easton, Douglas F [0000-0003-2444-3247], Apollo - University of Cambridge Repository, Andrulis, Irene L. [0000-0002-4226-6435], Ekici, Arif B. [0000-0001-6099-7066], Fasching, Peter A. [0000-0003-4885-8471], Milne, Roger L. [0000-0001-5764-7268], Newman, William G. [0000-0002-6382-4678], Schmidt, Marjanka K. [0000-0002-2228-429X], Dunning, Alison M. [0000-0001-6651-7166], Pharoah, Paul D. P. [0000-0001-8494-732X], Easton, Douglas F. [0000-0003-2444-3247], HUS Comprehensive Cancer Center, Clinicum, University Management, Department of Oncology, University of Helsinki, Department of Obstetrics and Gynecology, HUS Gynecology and Obstetrics, Medical Oncology, and Clinical Genetics

Subjects
0301 basic medicine, Oncology, PROTEIN, lcsh:Medicine, 45/47, 0302 clinical medicine, Fanconi anemia, Genotype, lcsh:Science, Sequence Deletion, Multidisciplinary, BRCA1 Protein, Fanconi Anemia Complementation Group C Protein, 1184 Genetics, developmental biology, physiology, BRCA2 Protein, 3. Good health, BIALLELIC MUTATIONS, DNA-REPAIR, Female, 692/499, Medical Genetics, medicine.medical_specialty, PALB2, 3122 Cancers, ABCTB Investigators, Breast Neoplasms, FANCONIS ANEMIA, Article, 692/4028, NBCS Collaborators, 03 medical and health sciences, Breast cancer, SDG 3 - Good Health and Well-being, Internal medicine, medicine, Humans, NONSENSE MUTATION, Genetic Predisposition to Disease, Medicinsk genetik, 45, business.industry, Genetic heterogeneity, lcsh:R, Case-control study, Genetic Variation, Odds ratio, medicine.disease, GENE, Fanconi Anemia, 030104 developmental biology, Risk factors, Case-Control Studies, lcsh:Q, 3111 Biomedicine, business, 030217 neurology & neurosurgery
Abstract

Fanconi anemia (FA) is a genetically heterogeneous disorder with 22 disease-causing genes reported to date. In some FA genes, monoallelic mutations have been found to be associated with breast cancer risk, while the risk associations of others remain unknown. The gene for FA type C, FANCC, has been proposed as a breast cancer susceptibility gene based on epidemiological and sequencing studies. We used the Oncoarray project to genotype two truncating FANCC variants (p.R185X and p.R548X) in 64,760 breast cancer cases and 49,793 controls of European descent. FANCC mutations were observed in 25 cases (14 with p.R185X, 11 with p.R548X) and 26 controls (18 with p.R185X, 8 with p.R548X). There was no evidence of an association with the risk of breast cancer, neither overall (odds ratio 0.77, 95%CI 0.44–1.33, p = 0.4) nor by histology, hormone receptor status, age or family history. We conclude that the breast cancer risk association of these two FANCC variants, if any, is much smaller than for BRCA1, BRCA2 or PALB2 mutations. If this applies to all truncating variants in FANCC it would suggest there are differences between FA genes in their roles on breast cancer risk and demonstrates the merit of large consortia for clarifying risk associations of rare variants.

Published
2019
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4. Evidence that the 5p12 Variant rs10941679 Confers Susceptibility to Estrogen-Receptor-Positive Breast Cancer through FGF10 and MRPS30 Regulation

Author

Ghoussaini, M., French, J.D., Michailidou, K., Nord, S., Beesley, J., Canisus, S., Hillman, K.M., Kaufmann, S., Sivakumaran, H., Marjaneh, M.M., Lee, J.S., Dennis, J., Bolla, M.K., Wang, Q., Dicks, E., Milne, R.L., Hopper, J.L., Southey, M.C., Schmidt, M.K., Broeks, A., Muir, K., Lophatananon, A., Fasching, P.A., Beckmann, M.W., Fletcher, O., Johnson, N., Sawyer, E.J., Tomlinson, I., Burwinkel, B., Marme, F., Guenel, P., Truong, T., Bojesen, S.E., Flyger, H., Benitez, J., Gonzalez-Neira, A., Alonso, R., Pita, G., Neuhausen, S.L., Anton-Culver, H., Brenner, H., Arndt, V., Meindl, A., Schmutzler, R.K., Brauch, H., Hamann, U., Tessier, D.C., Vincent, D., Nevanlinna, H., Khan, S., Matsuo, K., Ito, H., Dork, T., Bogdanova, N.V., Lindblom, A., Margolin, S., Mannermaa, A., Kosma, V.M., Wu, A.H., Berg, D. van den, Lambrechts, D., Floris, G., Chang-Claude, J., Rudolph, A., Radice, P., Barile, M., Couch, F.J., Hallberg, E., Giles, G.G., Haiman, C.A., Marchand, L. le, Goldberg, M.S., Teo, S.H., Yip, C.H., Borresen-Dale, A.L., Zheng, W., Cai, Q.Y., Winqvist, R., Pylkas, K., Andrulis, I.L., Devilee, P., Tollenaar, R.A.E.M., Garcia-Closas, M., Figueroa, J., Hall, P., Czene, K., Brand, J.S., Darabi, H., Eriksson, M., Hooning, M.J., Koppert, L.B., Li, J.M., Shu, X.O., Zheng, Y., Cox, A., Cross, S.S., Shah, M., Rhenius, V., Choi, J.Y., Kang, D., Hartman, M., Chia, K.S., Kabisch, M., Torres, D., Luccarini, C., Conroy, D.M., Jakubowska, A., Lubinski, J., Sangrajrang, S., Brennan, P., Olswold, C., Slager, S., Shen, C.Y., Hou, M.F., Swerdlow, A., Schoemaker, M.J., Simard, J., Pharoah, P.D.P., Kristensen, V., Chenevix-Trench, G., Easton, D.F., Dunning, A.M., Edwards, S.L., kConFab AOCS, NBCS Collaborators, Dennis, Joe [0000-0003-4591-1214], Wang, Jean [0000-0002-9139-0627], Dicks, Ed [0000-0002-0617-0401], Rhenius, Valerie [0000-0003-4215-3235], Pharoah, Paul [0000-0001-8494-732X], Easton, Douglas [0000-0003-2444-3247], Dunning, Alison [0000-0001-6651-7166], and Apollo - University of Cambridge Repository

Subjects
Quantitative Trait Loci, Breast Neoplasms, Polymorphism, Single Nucleotide, Enhancer Elements, Genetic, Haplotypes, Receptors, Estrogen, Case-Control Studies, Cell Line, Tumor, Chromosomes, Human, Pair 5, Humans, Genetic Predisposition to Disease, Receptor, Fibroblast Growth Factor, Type 2, Promoter Regions, Genetic, Fibroblast Growth Factor 10, Alleles
Abstract

Genome-wide association studies (GWASs) have revealed increased breast cancer risk associated with multiple genetic variants at 5p12. Here, we report the fine mapping of this locus using data from 104,660 subjects from 50 case-control studies in the Breast Cancer Association Consortium (BCAC). With data for 3,365 genotyped and imputed SNPs across a 1 Mb region (positions 44,394,495-45,364,167; NCBI build 37), we found evidence for at least three independent signals: the strongest signal, consisting of a single SNP rs10941679, was associated with risk of estrogen-receptor-positive (ER+) breast cancer (per-g allele OR ER+ = 1.15; 95% CI 1.13-1.18; p = 8.35 × 10-30). After adjustment for rs10941679, we detected signal 2, consisting of 38 SNPs more strongly associated with ER-negative (ER-) breast cancer (lead SNP rs6864776: per-a allele OR ER- = 1.10; 95% CI 1.05-1.14; p conditional = 1.44 × 10-12), and a single signal 3 SNP (rs200229088: per-t allele OR ER+ = 1.12; 95% CI 1.09-1.15; p conditional = 1.12 × 10-05). Expression quantitative trait locus analysis in normal breast tissues and breast tumors showed that the g (risk) allele of rs10941679 was associated with increased expression of FGF10 and MRPS30. Functional assays demonstrated that SNP rs10941679 maps to an enhancer element that physically interacts with the FGF10 and MRPS30 promoter regions in breast cancer cell lines. FGF10 is an oncogene that binds to FGFR2 and is overexpressed in ∼10% of human breast cancers, whereas MRPS30 plays a key role in apoptosis. These data suggest that the strongest signal of association at 5p12 is mediated through coordinated activation of FGF10 and MRPS30, two candidate genes for breast cancer pathogenesis.

Published
2016

5. No evidence that protein truncating variants in BRIP1 are associated with breast cancer risk: implications for gene panel testing

Author

Easton, D.F., Lesueur, F., Decker, B., Michailidou, K., Li, J., Allen, J., Luccarini, C., Pooley, K.A., Shah, M., Bolla, M.K., Wang, Q., Dennis, J., Ahmad, J., Thompson, E.R., Damiola, F., Pertesi, M., Voegele, C., Mebirouk, N., Robinot, N., Durand, G., Forey, N., Luben, R.N., Ahmed, S., Aittomaki, K., Anton-Culver, H., Arndt, V., Baynes, C., Beckman, M.W., Benitez, J., Berg, D. van den, Blot, W.J., Bogdanova, N.V., Bojesen, S.E., Brenner, H., Chang-Claude, J., Chia, K.S., Choi, J.Y., Conroy, D.M., Cox, A., Cross, S.S., Czene, K., Darabi, H., Devilee, P., Eriksson, M., Fasching, P.A., Figueroa, J., Flyger, H., Fostira, F., Garcia-Closas, M., Giles, G.G., Glendon, G., Gonzalez-Neira, A., Guenel, P., Haiman, C.A., Hall, P., Hart, S.N., Hartman, M., Hooning, M.J., Hsiung, C.N., Ito, H., Jakubowska, A., James, P.A., John, E.M., Johnson, N., Jones, M., Kabisch, M., Kang, D., Kosma, V.M., Kristensen, V., Lambrechts, D., Li, N., Lindblom, A., Long, J., Lophatananon, A., Lubinski, J., Mannermaa, A., Manoukian, S., Margolin, S., Matsuo, K., Meindl, A., Mitchell, G., Muir, K., Nevelsteen, I., Ouweland, A. van den, Peterlongo, P., Phuah, S.Y., Pylkas, K., Rowley, S.M., Sangrajrang, S., Schmutzler, R.K., Shen, C.Y., Shu, X.O., Southey, M.C., Surowy, H., Swerdlow, A., Teo, S.H., Tollenaar, R.A.E.M., Tomlinson, I., Torres, D., Truong, T., Vachon, C., Verhoef, S., Wong-Brown, M., Zheng, W., Zheng, Y., Nevanlinna, H., Scott, R.J., Andrulis, I.L., Wu, A.H., Hopper, J.L., Couch, F.J., Winqvist, R., Burwinkel, B., Sawyer, E.J., Schmidt, M.K., Rudolph, A., Dork, T., Brauch, H., Hamann, U., Neuhausen, S.L., Milne, R.L., Fletcher, O., Pharoah, P.D.P., Campbell, I.G., Dunning, A.M., Calvez-Kelm, F. le, Goldgar, D.E., Tavtigian, S.V., Chenevix-Trench, G., Australian Ovarian Canc Study Grp, kConFab Investigators, Lifepool Investigators, NBCS Investigators, Luben, Robert N [0000-0002-5088-6343], Apollo - University of Cambridge Repository, Clinical Genetics, Medical Oncology, and Molecular Genetics

Subjects
0301 basic medicine, Bioinformatics, Medical and Health Sciences, Cohort Studies, Breast cancer screening, 0302 clinical medicine, Medizinische Fakultät, Missense mutation, Genetics (clinical), Genetics & Heredity, education.field_of_study, medicine.diagnostic_test, Biological Sciences, Middle Aged, Fanconi Anemia Complementation Group Proteins, 3. Good health, ddc, DNA-Binding Proteins, 030220 oncology & carcinogenesis, kConFab Investigators, Female, RNA Helicases, Australian Ovarian Cancer Study Group, Adult, Risk, medicine.medical_specialty, PALB2, Population, European Continental Ancestry Group, Breast Neoplasms, NBCS Investigators, Biology, Article, White People, 03 medical and health sciences, Breast cancer, SDG 3 - Good Health and Well-being, Molecular genetics, Genetics, medicine, breast [Cancer], Humans, Genetic Predisposition to Disease, Genetic Testing, ddc:610, Allele, education, Genetic Association Studies, Aged, Cancer: breast, BRIP1, medicine.disease, 030104 developmental biology, Lifepool Investigators, Mutation
Abstract

Background: BRCA1 interacting protein C-terminal helicase 1 (BRIP1) is one of the Fanconi Anaemia Complementation (FANC) group family of DNA repair proteins. Biallelic mutations in BRIP1 are responsible for FANC group J, and previous studies have also suggested that rare protein truncating variants in BRIP1 are associated with an increased risk of breast cancer. These studies have led to inclusion of BRIP1 on targeted sequencing panels for breast cancer risk prediction. Methods: We evaluated a truncating variant, p.Arg798Ter (rs137852986), and 10 missense variants of BRIP1, in 48 144 cases and 43 607 controls of European origin, drawn from 41 studies participating in the Breast Cancer Association Consortium (BCAC). Additionally, we sequenced the coding regions of BRIP1 in 13 213 cases and 5242 controls from the UK, 1313 cases and 1123 controls from three population-based studies as part of the Breast Cancer Family Registry, and 1853 familial cases and 2001 controls from Australia. Results: The rare truncating allele of rs137852986 was observed in 23 cases and 18 controls in Europeans in BCAC (OR 1.09, 95% CI 0.58 to 2.03, p=0.79). Truncating variants were found in the sequencing studies in 34 cases (0.21%) and 19 controls (0.23%) (combined OR 0.90, 95% CI 0.48 to 1.70, p=0.75). Conclusions: These results suggest that truncating variants in BRIP1, and in particular p.Arg798Ter, are not associated with a substantial increase in breast cancer risk. Such observations have important implications for the reporting of results from breast cancer screening panels.

Published
2015
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6. Common non-synonymous SNPs associated with breast cancer susceptibility: findings from the Breast Cancer Association Consortium

Author

Milne, R.L., Burwinkel, B., Michailidou, K., Arias-Perez, J.I., Zamora, M.P., Menendez-Rodriguez, P., Hardisson, D., Mendiola, M., Gonzalez-Neira, A., Pita, G., Alonso, M.R., Dennis, J., Wang, Q., Bolla, M.K., Swerdlow, A., Ashworth, A., Orr, N., Schoemaker, M., Ko, Y.D., Brauch, H., Hamann, U., Andrulis, I.L., Knight, J.A., Glendon, G., Tchatchou, S., Matsuo, K., Ito, H., Iwata, H., Tajima, K., Li, J.M., Brand, J.S., Brenner, H., Dieffenbach, A.K., Arndt, V., Stegmaier, C., Lambrechts, D., Peuteman, G., Christiaens, M.R., Smeets, A., Jakubowska, A., Lubinski, J., Jaworska-Bieniek, K., Durda, K., Hartman, M., Hui, M., Lim, W.Y., Chan, C.W., Marme, F., Yang, R.X., Bugert, P., Lindblom, A., Margolin, S., Garcia-Closas, M., Chanock, S.J., Lissowska, J., Figueroa, J.D., Bojesen, S.E., Nordestgaard, B.G., Flyger, H., Hooning, M.J., Kriege, M., Ouweland, A.M.W. van den, Koppert, L.B., Fletcher, O., Johnson, N., Dos-Santos-Silva, I., Peto, J., Zheng, W., Deming-Halverson, S., Shrubsole, M.J., Long, J.R., Chang-Claude, J., Rudolph, A., Seibold, P., Flesch-Janys, D., Winqvist, R., Pylkas, K., Jukkola-Vuorinen, A., Grip, M., Cox, A., Cross, S.S., Reed, M.W.R., Schmidt, M.K., Broeks, A., Cornelissen, S., Braaf, L., Kang, D., Choi, J.Y., Park, S.K., Noh, D.Y., Simard, J., Dumont, M., Goldberg, M.S., Labreche, F., Fasching, P.A., Hein, A., Ekici, A.B., Beckmann, M.W., Radice, P., Peterlongo, P., Azzollini, J., Barile, M., Sawyer, E., Tomlinson, I., Kerin, M., Miller, N., Hopper, J.L., Schmidt, D.F., Makalic, E., Southey, M.C., Teo, S.H., Yip, C.H., Sivanandan, K., Tay, W.T., Shen, C.Y., Hsiung, C.N., Yu, J.C., Hou, M.F., Guenel, P., Truong, T., Sanchez, M., Mulot, C., Blot, W., Cai, Q.Y., Nevanlinna, H., Muranen, T.A., Aittomaki, K., Blomqvist, C., Wu, A.H., Tseng, C.C., Berg, D. van den, Stram, D.O., Bogdanova, N., Dork, T., Muir, K., Lophatananon, A., Stewart-Brown, S., Siriwanarangsan, P., Mannermaa, A., Kataja, V., Kosma, V.M., Hartikainen, J.M., Shu, X.O., Lu, W., Gao, Y.T., Zhang, B., Couch, F.J., Toland, A.E., Yannoukakos, D., Sangrajrang, S., McKay, J., Wang, X.S., Olson, J.E., Vachon, C., Purrington, K., Severi, G., Baglietto, L., Haiman, C.A., Henderson, B.E., Schumacher, F., Marchand, L. le, Devilee, P., Tollenaar, R.A.E.M., Seynaeve, C., Czene, K., Eriksson, M., Humphreys, K., Darabi, H., Ahmed, S., Shah, M., Pharoah, P.D.P., Hall, P., Giles, G.G., Benitez, J., Dunning, A.M., Chenevix-Trench, G., Easton, D.F., GENICA Network, kConFab Investigators, Australian Ovarian Canc Study Grp, TNBCC, Dennis, Joe [0000-0003-4591-1214], Wang, Jean [0000-0002-9139-0627], Pharoah, Paul [0000-0001-8494-732X], Dunning, Alison [0000-0001-6651-7166], Easton, Douglas [0000-0003-2444-3247], and Apollo - University of Cambridge Repository

Subjects
Adult, Ataxin-7, A Kinase Anchor Proteins, Breast Neoplasms, Nerve Tissue Proteins, Middle Aged, Protein Serine-Threonine Kinases, Polymorphism, Single Nucleotide, Cytoskeletal Proteins, Case-Control Studies, Humans, NIMA-Related Kinases, Female, Genetic Predisposition to Disease, health care economics and organizations, Alleles, Genome-Wide Association Study
Abstract

Candidate variant association studies have been largely unsuccessful in identifying common breast cancer susceptibility\ud variants, although most studies have been underpowered to detect associations of a realistic magnitude.\ud We assessed 41 common non-synonymous single-nucleotide polymorphisms (nsSNPs) for which\ud evidence of association with breast cancer risk had been previously reported. Case-control data were combined\ud from 38 studies of white European women (46 450 cases and 42 600 controls) and analyzed using unconditional\ud logistic regression. Strong evidence of association was observed for three nsSNPs: ATXN7-K264R at 3p21\ud [rs1053338, per allele OR 5 1.07, 95% confidence interval (CI) 5 1.04–1.10, P 5 2.9 3 1026\ud ], AKAP9-M463I at\ud 7q21 (rs6964587, OR 5 1.05, 95% CI 5 1.03–1.07, P 5 1.7 3 1026\ud ) and NEK10-L513S at 3p24 (rs10510592,\ud OR 5 1.10, 95% CI 5 1.07 –1.12, P 5 5.1 3 10217). The first two associations reached genome-wide statistical\ud significance in a combined analysis of available data, including independent data from nine genome-wide association\ud studies (GWASs): for ATXN7-K264R, OR 5 1.07 (95% CI 5 1.05–1.10, P 5 1.0 3 1028\ud ); for AKAP9-M463I,\ud OR 5 1.05 (95% CI 5 1.04–1.07, P 5 2.0 3 10210). Further analysis of other common variants in these two\ud regions suggested that intronic SNPs nearby are more strongly associated with disease risk. We have thus identified\ud a novel susceptibility locus at 3p21, and confirmed previous suggestive evidence that rs6964587 at 7q21 is\ud associated with risk. The third locus, rs10510592, is located in an established breast cancer susceptibility\ud region; the association was substantially attenuated after adjustment for the known GWAS hit. Thus, each of\ud the associated nsSNPs is likely to be a marker for another, non-coding, variant causally related to breast\ud cancer risk. Further fine-mapping and functional studies are required to identify the underlying risk-modifying\ud variants and the genes through which they act.

Published
2014

7. Neurothekeoma of the Tongue: CT, MR, and FDG PET Imaging Findings

Author

Kim, H.-J., Baek, C.H., Ko, Y.H., and Choi, J.Y.

Subjects
Blood Glucose, Adolescent, Tongue, Fluorodeoxyglucose F18, Positron-Emission Tomography, Biomarkers, Tumor, Humans, Female, Tomography, X-Ray Computed, Head & Neck, Magnetic Resonance Imaging, Neurothekeoma, Tongue Neoplasms
Abstract

SUMMARY: We report CT, MR, and fluorodeoxyglucose–positron-emission tomography (FDG-PET) imaging findings of a case of cellular neurothekeoma of the tongue, a rare benign soft-tissue tumor with neural differentiation, occurring in a 15-year-old girl. CT and MR imaging showed a well-defined, well-enhancing submucosal soft-tissue mass in the midline dorsal tongue. There was high FDG uptake on PET scans. Although imaging findings are rather nonspecific, neurothekeoma may be one of diagnostic inclusions of soft-tissue masses of the tongue in a young female patient.

Published
2006

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