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1. Associations of Circulating Estrogens and Estrogen Metabolites with Fecal and Oral Microbiome in Postmenopausal Women in the Ghana Breast Health Study

Author

Wu, Zeni, Pfeiffer, Ruth M, Byrd, Doratha A, Wan, Yunhu, Ansong, Daniel, Clegg-Lamptey, Joe-Nat, Wiafe-Addai, Beatrice, Edusei, Lawrence, Adjei, Ernest, Titiloye, Nicholas, Dedey, Florence, Aitpillah, Francis, Oppong, Joseph, Vanderpuye, Verna, Osei-Bonsu, Ernest, Dagnall, Casey L, Jones, Kristine, Hutchinson, Amy, Hicks, Belynda D, Ahearn, Thomas U, Knight, Rob, Biritwum, Richard, Yarney, Joel, Wiafe, Seth, Awuah, Baffour, Nyarko, Kofi, Garcia-Closas, Montserrat, Sinha, Rashmi, Figueroa, Jonine D, Brinton, Louise A, Trabert, Britton, and Vogtmann, Emily

Abstract

The human fecal and oral microbiome may play a role in the etiology of breast cancer through modulation of endogenous estrogen metabolism. This study aimed to investigate associations of circulating estrogens and estrogen metabolites with the fecal and oral microbiome in postmenopausal African women. A total of 117 women with fecal (N = 110) and oral (N = 114) microbiome data measured by 16S rRNA gene sequencing, and estrogens and estrogen metabolites data measured by liquid chromatography tandem mass spectrometry were included. The outcomes were measures of the microbiome and the independent variables were the estrogens and estrogen metabolites. Estrogens and estrogen metabolites were associated with the fecal microbial Shannon index (global P

Published
2023

2. Additional file 5 of DNA methylation age in paired tumor and adjacent normal breast tissue in Chinese women with breast cancer

Author

Koka, Hela, Bodelon, Clara, Horvath, Steve, Lee, Priscilla Ming Yi, Wang, Difei, Song, Lei, Zhang, Tongwu, Hurson, Amber N., Guida, Jennifer Lyn, Zhu, Bin, Bailey-Whyte, Maeve, Wang, Feng, Wu, Cherry, Tsang, Koon Ho, Tsoi, Yee-Kei, Chan, W. C., Law, Sze Hong, Hung, Ray Ka Wai, Tse, Gary M., Yuen, Karen Ka-wan, Karlins, Eric, Jones, Kristine, Vogt, Aurelie, Hutchinson, Amy, Hicks, Belynda, Garcia-Closas, Montserrat, Chanock, Stephen, Barnholtz-Sloan, Jill, Tse, Lap Ah, and Yang, Xiaohong R.

Abstract

Additional file 5. Associations between DNAm age acceleration in tumor tissue and tumor features in Hong Kong breast cancer women.

Published
2023
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3. Additional file 7 of DNA methylation age in paired tumor and adjacent normal breast tissue in Chinese women with breast cancer

Author

Koka, Hela, Bodelon, Clara, Horvath, Steve, Lee, Priscilla Ming Yi, Wang, Difei, Song, Lei, Zhang, Tongwu, Hurson, Amber N., Guida, Jennifer Lyn, Zhu, Bin, Bailey-Whyte, Maeve, Wang, Feng, Wu, Cherry, Tsang, Koon Ho, Tsoi, Yee-Kei, Chan, W. C., Law, Sze Hong, Hung, Ray Ka Wai, Tse, Gary M., Yuen, Karen Ka-wan, Karlins, Eric, Jones, Kristine, Vogt, Aurelie, Hutchinson, Amy, Hicks, Belynda, Garcia-Closas, Montserrat, Chanock, Stephen, Barnholtz-Sloan, Jill, Tse, Lap Ah, and Yang, Xiaohong R.

Abstract

Additional file 7. Breast cancer risk factors in Hong Kong (HKBC) women by DNA methylation (DNAm) age and its acceleration (AA) in normal tissue.

Published
2023
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4. Additional file 6 of DNA methylation age in paired tumor and adjacent normal breast tissue in Chinese women with breast cancer

Author

Koka, Hela, Bodelon, Clara, Horvath, Steve, Lee, Priscilla Ming Yi, Wang, Difei, Song, Lei, Zhang, Tongwu, Hurson, Amber N., Guida, Jennifer Lyn, Zhu, Bin, Bailey-Whyte, Maeve, Wang, Feng, Wu, Cherry, Tsang, Koon Ho, Tsoi, Yee-Kei, Chan, W. C., Law, Sze Hong, Hung, Ray Ka Wai, Tse, Gary M., Yuen, Karen Ka-wan, Karlins, Eric, Jones, Kristine, Vogt, Aurelie, Hutchinson, Amy, Hicks, Belynda, Garcia-Closas, Montserrat, Chanock, Stephen, Barnholtz-Sloan, Jill, Tse, Lap Ah, and Yang, Xiaohong R.

Abstract

Additional file 6. Associations between DNAm age acceleration in tumor tissue and tumor features in The Cancer Genome Atlas breast cancer women.

Published
2023
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5. Additional file 4 of DNA methylation age in paired tumor and adjacent normal breast tissue in Chinese women with breast cancer

Author

Koka, Hela, Bodelon, Clara, Horvath, Steve, Lee, Priscilla Ming Yi, Wang, Difei, Song, Lei, Zhang, Tongwu, Hurson, Amber N., Guida, Jennifer Lyn, Zhu, Bin, Bailey-Whyte, Maeve, Wang, Feng, Wu, Cherry, Tsang, Koon Ho, Tsoi, Yee-Kei, Chan, W. C., Law, Sze Hong, Hung, Ray Ka Wai, Tse, Gary M., Yuen, Karen Ka-wan, Karlins, Eric, Jones, Kristine, Vogt, Aurelie, Hutchinson, Amy, Hicks, Belynda, Garcia-Closas, Montserrat, Chanock, Stephen, Barnholtz-Sloan, Jill, Tse, Lap Ah, and Yang, Xiaohong R.

Abstract

Additional file 4. Distributions of DNAm age acceleration by genomic features after the exclusion of tumors displaying extensive somatic copy number alterations in the Horvath clocks sites.

Published
2023
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6. Additional file 1 of DNA methylation age in paired tumor and adjacent normal breast tissue in Chinese women with breast cancer

Author

Koka, Hela, Bodelon, Clara, Horvath, Steve, Lee, Priscilla Ming Yi, Wang, Difei, Song, Lei, Zhang, Tongwu, Hurson, Amber N., Guida, Jennifer Lyn, Zhu, Bin, Bailey-Whyte, Maeve, Wang, Feng, Wu, Cherry, Tsang, Koon Ho, Tsoi, Yee-Kei, Chan, W. C., Law, Sze Hong, Hung, Ray Ka Wai, Tse, Gary M., Yuen, Karen Ka-wan, Karlins, Eric, Jones, Kristine, Vogt, Aurelie, Hutchinson, Amy, Hicks, Belynda, Garcia-Closas, Montserrat, Chanock, Stephen, Barnholtz-Sloan, Jill, Tse, Lap Ah, and Yang, Xiaohong R.

Abstract

Additional file 1 Distribution of DNAm age acceleration by RNA-based functional TP53 mutation status.

Published
2023
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7. Additional file 3 of DNA methylation age in paired tumor and adjacent normal breast tissue in Chinese women with breast cancer

Author

Koka, Hela, Bodelon, Clara, Horvath, Steve, Lee, Priscilla Ming Yi, Wang, Difei, Song, Lei, Zhang, Tongwu, Hurson, Amber N., Guida, Jennifer Lyn, Zhu, Bin, Bailey-Whyte, Maeve, Wang, Feng, Wu, Cherry, Tsang, Koon Ho, Tsoi, Yee-Kei, Chan, W. C., Law, Sze Hong, Hung, Ray Ka Wai, Tse, Gary M., Yuen, Karen Ka-wan, Karlins, Eric, Jones, Kristine, Vogt, Aurelie, Hutchinson, Amy, Hicks, Belynda, Garcia-Closas, Montserrat, Chanock, Stephen, Barnholtz-Sloan, Jill, Tse, Lap Ah, and Yang, Xiaohong R.

Abstract

Additional file 3. DNAm age acceleration in The Cancer Genome Atlas (TCGA) dataset.

Published
2023
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9. Low mutation burden and frequent loss of CDKN2A/B and SMARCA2, but not PRC2, define pre-malignant neurofobromatosis type1-associated atypical neurofibromas

Author

Pemov, Alexander, Hansen, Nancy F, Sindiri, Sivasish, Patidar, Rajesh, Higham, Christine S, Dombi, Eva, Miettinen, Markku M, Fetsch, Patricia, Brems, Hilde, Chandrasekharappa, Settara, Jones, Kristine, Zhu, Bin, Wei, Jun S, NISC Comparative Sequencing Program, NCI DCEG Cancer Genomics Research Laboratory, Mullikin, James C, Wallace, Margaret R, Khan, Javed, Legius, Eric, Widemann, Brigitte C, and Stewart, Douglas R

Subjects
0301 basic medicine, Cancer Research, Malignant peripheral nerve sheath tumor, NISC Comparative Sequencing Program, Biology, medicine.disease, NCI DCEG Cancer Genomics Research Laboratory, Malignant transformation, 03 medical and health sciences, 030104 developmental biology, 0302 clinical medicine, Germline mutation, Oncology, CDKN2A, 030220 oncology & carcinogenesis, medicine, Cancer research, otorhinolaryngologic diseases, Neurofibroma, Neurology (clinical), Neurofibromatosis, Exome sequencing, Nerve sheath neoplasm, hormones, hormone substitutes, and hormone antagonists
Abstract

Background Neurofibromatosis type 1 (NF1) is a tumor-predisposition disorder caused by germline mutations in NF1. NF1 patients have an 8–16% lifetime risk of developing a malignant peripheral nerve sheath tumor (MPNST), a highly aggressive soft-tissue sarcoma, often arising from preexisting benign plexiform neurofibromas (PNs) and atypical neurofibromas (ANFs). ANFs are distinct from both PN and MPNST, representing an intermediate step in malignant transformation. Methods In the first comprehensive genomic analysis of ANF originating from multiple patients, we performed tumor/normal whole-exome sequencing (WES) of 16 ANFs. In addition, we conducted WES of 3 MPNSTs, copy-number meta-analysis of 26 ANFs and 28 MPNSTs, and whole transcriptome sequencing analysis of 5 ANFs and 5 MPNSTs. Results We identified a low number of mutations (median 1, range 0–5) in the exomes of ANFs (only NF1 somatic mutations were recurrent), and frequent deletions of CDKN2A/B (69%) and SMARCA2 (42%). We determined that polycomb repressor complex 2 (PRC2) genes EED and SUZ12 were frequently mutated, deleted, or downregulated in MPNSTs but not in ANFs. Our pilot gene expression study revealed upregulated NRAS, MDM2, CCND1/2/3, and CDK4/6 in ANFs and MPNSTs, and overexpression of EZH2 in MPNSTs only. Conclusions The PN-ANF transition is primarily driven by the deletion of CDKN2A/B. Further progression from ANF to MPNST likely involves broad chromosomal rearrangements and frequent inactivation of the PRC2 genes, loss of the DNA repair genes, and copy-number increase of signal transduction and cell-cycle and pluripotency self-renewal genes.

Published
2019

10. Low mutation burden and frequent loss of CDKN2A/B and SMARCA2, but not PRC2, define premalignant neurofibromatosis type 1-associated atypical neurofibromas

Author

Pemov, Alexander, Hansen, Nancy F, Sindiri, Sivasish, Patidar, Rajesh, Higham, Christine S, Dombi, Eva, Miettinen, Markku M, Fetsch, Patricia, Brems, Hilde, Chandrasekharappa, Settara C, Jones, Kristine, Zhu, Bin, Wei, Jun S, National Intramural Sequencing Center (NISC) Comparative Sequencing Program, National Cancer Institute (NCI) Division of Cancer Epidemiology and Genetics (DCEG) Cancer Genomics Research Laboratory, Mullikin, James C, Wallace, Margaret R, Khan, Javed, Legius, Eric, Widemann, Brigitte C, and Stewart, Douglas R

Subjects
National Intramural Sequencing Center (NISC) Comparative Sequencing Program, Neurofibromatosis 1, Oncology and Carcinogenesis, neurofibromatosis type 1, Nerve Sheath Neoplasms, Neurofibromatosis, Rare Diseases, Genetics, Humans, malignant peripheral nerve sheath tumor, Oncology & Carcinogenesis, Cyclin-Dependent Kinase Inhibitor p16, Cyclin-Dependent Kinase Inhibitor p15, Cancer, Pediatric, Neurofibroma, atypical neurofibromas, benign-to-malignant transformation, Human Genome, Neurosciences, Plexiform, plexiform neurofibromas, Neurofibrosarcoma, Mutation, National Cancer Institute (NCI) Division of Cancer Epidemiology and Genetics (DCEG) Cancer Genomics Research Laboratory, Transcription Factors
Abstract

BackgroundNeurofibromatosis type 1 (NF1) is a tumor-predisposition disorder caused by germline mutations in NF1. NF1 patients have an 8-16% lifetime risk of developing a malignant peripheral nerve sheath tumor (MPNST), a highly aggressive soft-tissue sarcoma, often arising from preexisting benign plexiform neurofibromas (PNs) and atypical neurofibromas (ANFs). ANFs are distinct from both PN and MPNST, representing an intermediate step in malignant transformation.MethodsIn the first comprehensive genomic analysis of ANF originating from multiple patients, we performed tumor/normal whole-exome sequencing (WES) of 16 ANFs. In addition, we conducted WES of 3 MPNSTs, copy-number meta-analysis of 26 ANFs and 28 MPNSTs, and whole transcriptome sequencing analysis of 5 ANFs and 5 MPNSTs.ResultsWe identified a low number of mutations (median 1, range 0-5) in the exomes of ANFs (only NF1 somatic mutations were recurrent), and frequent deletions of CDKN2A/B (69%) and SMARCA2 (42%). We determined that polycomb repressor complex 2 (PRC2) genes EED and SUZ12 were frequently mutated, deleted, or downregulated in MPNSTs but not in ANFs. Our pilot gene expression study revealed upregulated NRAS, MDM2, CCND1/2/3, and CDK4/6 in ANFs and MPNSTs, and overexpression of EZH2 in MPNSTs only.ConclusionsThe PN-ANF transition is primarily driven by the deletion of CDKN2A/B. Further progression from ANF to MPNST likely involves broad chromosomal rearrangements and frequent inactivation of the PRC2 genes, loss of the DNA repair genes, and copy-number increase of signal transduction and cell-cycle and pluripotency self-renewal genes.

Published
2019

11. MOESM1 of Immune gene expression profiling reveals heterogeneity in luminal breast tumors

Author

Zhu, Bin, Tse, Lap, Difei Wang, Koka, Hela, Tongwu Zhang, Abubakar, Mustapha, Lee, Priscilla, Wang, Feng, Wu, Cherry, Koon Tsang, Wing-Cheong Chan, Sze Law, Mengjie Li, Wentao Li, Suyang Wu, Zhiguang Liu, Bixia Huang, Zhang, Han, Tang, Eric, Zhengyan Kan, Soohyeon Lee, Park, Yeon, Nam, Seok, Mingyi Wang, Xuezheng Sun, Jones, Kristine, Hutchinson, Amy, Belynda Hicks, Prokunina-Olsson, Ludmila, Jianxin Shi, Garcia-Closas, Montserrat, Chanock, Stephen, and Xiaohong Yang

Subjects
bacteria, chemical and pharmacologic phenomena, biochemical phenomena, metabolism, and nutrition
Abstract

Additional file 1: Figure S1. Schematic representation of the strategy for the quantification of TILs in H&E stained images. Figure S2. Expression levels of immune-related genes in the three luminal immune subtypes and non-luminal (HER2-enriched and basal-like) tumors in HKBC. Figure S3. MCP-counter scores and CIBERSORT relative fractions of a subset of immune cell subpopulations in the three luminal immune subtypes and non-luminal (HER2-enriched and basal-like, separately) tumors in HKBC. Figure S4. MCP-counter scores of eight immune cell subpopulations in the three luminal immune subtypes and non-luminal (HER2-enriched and basal-like) tumors with the adjustment of tumor purity in HKBC. Figure S5. Replication of luminal immune subtypes in TCGA and KBC datasets: a) MCP-counter scores for eight immune cell subpopulations; b) Relative fractions of immune cell subpopulations by CIBERSORT (cell populations with extremely low fractions were not shown); c) High-TIL tumors showed upregulation of genes in immune activation and regulation activities than tumors in the other two luminal immune subtypes; d) High-ISG tumors expressed higher levels of ISG genes than tumors in the other two luminal immune subtypes. Figure S6. Genomic features associated with luminal immune subtypes in HKBC (HER2-enriched and basal-like, separately): a) ESR1/ESR2 ratios; b) number of mutations. Figure S7. Replication of genomic features associated with luminal immune subtypes in TCGA and KBC datasets: a) ESR1/ESR2 ratios; b) age at diagnosis; c) 10-year overall survival. Figure S8. Expression of APOBEC3B in normal and tumor tissue in relation to the polymorphic germline APOBEC3B deletion represented by rs12628403-C allele in HKBC. Figure S9. MCP-counter scores of eight immune cell subpopulations in adjacent normal breast tissue in the three luminal immune subgroups and non-luminal (HER2-enriched and basal-like) patients of HKBC.

Published
2019
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12. Multiple new susceptibility loci identified in genome-wide association study of Ewing sarcoma

Author

Machiela, Mitchell J., Grünewald, Thomas, Surdez, Didier, Reynaud, Stephanie, Mirabeau, Olivier, Karlins, Eric, Rubio, Rebeca Alba, Zaidi, Sakina, Grossetete-Lalami, Sandrine, Ballet, Stelly, Lapouble, Eve, Laurence, Valérie, Michon, Jean, Pierron, Gaelle, Kovar, Heinrich, Gaspar, Nathalie, Kontny, Udo, González-Neira, Anna, Picci, Piero, Alonso, Javier, Patino-Garcia, Ana, Corradini, Nadège, Freedman, Neal D., Rothman, Nathaniel, Dagnall, Casey L., Burdette, Laurie, Jones, Kristine, Manning, Michelle, Wyatt, Kathleen, Zhou, Weiyin, Yeager, Meredith, Cox, David G., Hoover, Robert N., Khan, Javed, Armstrong, Gregory T., Leisenring, Wendy M., Bhatia, Smita, Robison, Leslie L., Dirksen, Uta, Metzler, Markus, Hartmann, Wolfgang, Strauch, Konstantin, Kirchner, Thomas, Kulozik, Andreas E., Morton, Lindsay M., Mirabello, Lisa, Tucker, Margaret A., Tirode, Franck, Chanock, Stephen J., and Delattre, Olivier

Subjects
Medizin
Published
2018

13. Genome-wide association study identifies multiple new loci associated with Ewing sarcoma susceptibility

Author

Machiela, Mitchell J., Grünewald, Thomas G. P., Surdez, Didier, Reynaud, Stephanie, Mirabeau, Olivier, Karlins, Eric, Rubio, Rebeca Alba, Zaidi, Sakina, Grossetete-Lalami, Sandrine, Ballet, Stelly, Lapouble, Eve, Laurence, Valérie, Michon, Jean, Pierron, Gaelle, Kovar, Heinrich, Gaspar, Nathalie, Kontny, Udo, González-Neira, Anna, Picci, Piero, Alonso, Javier, Patino-Garcia, Ana, Corradini, Nadège, Bérard, Perrine Marec, Freedman, Neal D., Rothman, Nathaniel, Dagnall, Casey L., Burdett, Laurie, Jones, Kristine, Manning, Michelle, Wyatt, Kathleen, Zhou, Weiyin, Yeager, Meredith, Cox, David G., Hoover, Robert N., Khan, Javed, Armstrong, Gregory T., Leisenring, Wendy M., Bhatia, Smita, Robison, Leslie L., Kulozik, Andreas E., Kriebel, Jennifer, Meitinger, Thomas, Metzler, Markus, Hartmann, Wolfgang, Strauch, Konstantin, Kirchner, Thomas, Dirksen, Uta, Morton, Lindsay M., Mirabello, Lisa, Tucker, Margaret A., Tirode, Franck, Chanock, Stephen J., and Delattre, Olivier

Abstract

Nature Communications 9(1), 3184 (2018). doi:10.1038/s41467-018-05537-2

Published
2018
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14. Identification of ten variants associated with risk of estrogen-receptor-negative breast cancer

Author

Milne, Roger L., Kuchenbaecker, Karoline B., Michailidou, Kyriaki, Beesley, Jonathan, Kar, Siddhartha, Lindstrom, Sara, Hui, Shirley, Lemaçon, Audrey, Soucy, Penny, Dennis, Joe, Jiang, Xia, Rostamianfar, Asha, Finucane, Hilary, Bolla, Manjeet K., McGuffog, Lesley, Wang, Qin, Aalfs, Cora M., Abctctb, Investigators, Adams, Marcia, Adlard, Julian, Agata, Simona, Ahmed, Shahana, Ahsan, Habibul, Aittom, Kristiina Äki, Fares, Al Ejeh, Allen, Jamie, Ambrosone, Christine B., Amos, Christopher I., Andrulis, Irene L., Anton-Culver, Hoda, Antonenkova, Natalia N., Arndt, Volker, Arnold, Norbert, Aronson, Kristan J., Auber, Bernd, Auer, Paul L., Ausems, Margreet G.M., Azzollini, Jacopo, François, Bacot, Balma, Judith Nã, Barile, Monica, Barjhoux, Laure, Barkardottir, Rosa B., Barrdahl, Myrto, Barnes, Daniel, Barrowdale, Daniel, Baynes, Caroline, Beckmann, Matthias W., Benitez, Javier, Bermisheva, Marina, Bernstein, Leslie, Bignon, Yves Jean, Blazer, Kathleen R., Blok, Marinus J., Blomqvist, Carl, Blot, William, Bobolis, Kristie, Boeckx, Bram, Bogdanova, Natalia V., Bojesen, Anders, Bojesen, Stig E., Bonanni, Bernardo, Anne-Lise, Børresen Dale, Bozsik, Aniko, Bradbury, Angela R., Brand, Judith S., Brauch, Hiltrud, Brenner, Hermann, Brigitte, Bressac De Paillerets, Brewer, Carole, Brinton, Louise, Broberg, Per, Angela, Brooks Wilson, Brunet, Joan, Brüning, Thomas, Burwinkel, Barbara, Buys, Saundra S., Byun, Jinyoung, Cai, Qiuyin, Cald, Trinidad És, Caligo, Maria A., Campbell, Ian, Canzian, Federico, Caron, Olivier, Carracedo, Angel, Carter, Brian D., Esteban, Castelao, Castera, Laurent, Virginie, Caux Moncoutier, Chan, Salina B., Jenny, Chang Claude, Chanock, Stephen J., Chen, Xiaoqing, Cheng, Ting Yuan David, Chiquette, Jocelyne, Christiansen, Hans, Claes, Kathleen B., Clarke, Christine L., Conner, Thomas, Conroy, Don M., Cook, Jackie, Cordina-Duverger, Emilie, Cornelissen, Sten, Coupier, Isabelle, Cox, Angela, Cox, David G., Cross, Simon S., Cuk, Katarina, Cunningham, J. M., Czene, Kamila, Daly, Mary B., Damiola, Francesca, Darabi, Hatef, Davidson, Rosemarie, Leeneer, Kim De L., Devilee, Peter, Dicks, Ed, Diez, Orland, Ding, Yuan Chun, Ditsch, Nina, Doheny, Kimberly F., Domchek, Susan M., Dorfling, Cecilia M., Dörk, Thilo, Dos-Santos-Silva, Isabel, Dubois, Stéphane, Dugué, Pierre Antoine, Dumont, Martine, Dunning, Alison M., Durcan, Lorraine, Dwek, Miriam, Dworniczak, Bernd, Eccles, Diana, Eeles, Ros, Ehrencrona, Hans, Eilber, Ursula, Ejlertsen, Bent, Ekici, Arif B., Eliassen, A. Heather, Engel, Christoph, Eriksson, Mikael, Fachal, Laura, Faivre, Laurence, Fasching, Peter A., Faust, Ulrike, Figueroa, Jonine, Flesch-Janys, Dieter, Fletcher, Olivia, Flyger, Henrik, Foulkes, William D., Friedman, Eitan, Fritschi, Lin, Frost, Debra, Gabrielson, Marike, Gaddam, Pragna, Gammon, Marilie D., Ganz, Patricia A., Gapstur, Susan M., Garber, Judy, Garcia-Barberan, Vanesa, Garciá-Saénz, José A., Gaudet, Mia M., Gauthier-Villars, Marion, Gehrig, Andrea, Georgoulias, Vassilios, Gerdes, Anne Marie, Giles, Graham G., Glendon, Gord, Godwin, Andrew K., Goldberg, Mark S., Goldgar, David E., González-Neira, Anna, Goodfellow, Paul, Greene, Mark H., Grenaker, Grethe Alnæs I., Grip, Mervi, Gronwald, Jacek, Grundy, Anne, Gschwantler, Daphne Kaulich, Guénel, Pascal, Guo, Qi, Haeberle, Lothar, Hahnen, Eric, Haiman, Christopher A., Håkansson, Niclas, Hallberg, Emily, Hamann, Ute, Hamel, Nathalie, Hankinson, Susan, Hansen, Thomas V., Harrington, Patricia, Hart, Steven N., Hartikainen, Jaana M., Healey, Catherine S., Hein, Alexander, Helbig, Sonja, Henderson, Alex, Heyworth, Jane, Hicks, Belynda, Hillemanns, Peter, Hodgson, Shirley, Hogervorst, Frans B., Hollestelle, Antoinette, Hooning, Maartje J., Hoover, Bob, Hopper, John L., Hu, Chunling, Huang, Guanmengqian, Hulick, Peter J., Humphreys, Keith, Hunter, David J., Imyanitov, Evgeny N., Isaacs, Claudine, Iwasaki, Motoki, Izatt, Louise, Jakubowska, Anna, James, Paul, Janavicius, Ramunas, Janni, Wolfgang, Jensen, Uffe Birk, John, Esther M., Johnson, Nichola, Jones, Kristine, Jones, Michael, Jukkola-Vuorinen, Arja, Kaaks, Rudolf, Kabisch, Maria, Kaczmarek, Katarzyna, Kang, Daehee, Kast, Karin, Keeman, Renske, Kerin, Michael J., Kets, Carolien M., Keupers, Mac Hteld, Khan, Sofia, Khusnutdinova, Elza, Kiiski, Johanna I., Kim, Sung Won, Knight, Julia A., Konstantopoulou, Irene, Kosma, Veli Matti, Kristensen, Vessela N., Kruse, Torben A., Kwong, Ava, Lænkholm, Anne Vibeke, Laitman, Yael, Lalloo, Fiona, Lambrechts, Diether, Landsman, Keren, Lasset, Christine, Lazaro, Conxi, Marchand, Loic Le, Lindström, Sara, Al-Ejeh, Fares, Margreet, G. M.Ausems, Bacot, François, Børresen-Dale, Anne Lise, Bressac-De, Brigitte Paillerets, Brooks-Wilson, Angela, Castelao, J. Esteban, Caux-Moncoutier, Virginie, Chang-Claude, Jenny, McLaes, Kathleen B., Leeneer, Kim De, Dieter, Flesch Janys, Gschwantler-Kaulich, Daphne, Keupers, MacHteld, Lecarpentier, Julie, Lee, Andrew, Lee, Eunjung, Won, Jong Lee, Lee, Min Hyuk, Lejbkowicz, Flavio, Lesueur, Fabienne, Li, Jingmei, Lilyquist, Jenna, Lincoln, Anne, Lindblom, Annika, Lissowska, Jolanta, Lo, Wing Yee, Loibl, Sibylle, Long, Jirong, Loud, Jennifer T., Lubinski, Jan, Luccarini, Craig, Lush, Michael, MacInnis, Robert J., Maishman, Tom, Makalic, Enes, Kostovska, Ivana Maleva, Malone, Kathleen E., Siranoush, Manoukian, Manson, Joann E., Margolin, Sara, Martens, John W., Martinez, Maria Elena, Matsuo, Keitaro, Mavroudis, Dimitrios, Mazoyer, Sylvie, McLean, Catriona, Meijers-Heijboer, Hanne, Menéndez, Primitiva, Meyer, Jeffery, Miao, Hui, Miller, Austin, Miller, Nicola, Mitchell, Gillian, Montagna, Marco, Muir, Kenneth, Mulligan, Anna Marie, Mulot, Claire, Nadesan, Sue, Nathanson, Katherine L., Neuhausen, Susan L., Nevanlinna, Heli, Nevelsteen, Ines, Niederacher, Dieter, Nielsen, Sune F., Nordestgaard, Børge G., Norman, Aaron, Nussbaum, Robert L., Olah, Edith, Olopade, Olufunmilayo I., Olson, Janet E., Olswold, Curtis, Ong, Kai Ren, Oosterwijk, Jan C., Orr, Nick, Osorio, Ana, Pankratz, V. Shane, Papi, Laura, Park-Simon, Tjoung Won, Paulsson-Karlsson, Ylva, Lloyd, Rachel, Pedersen, Inge Søkilde, Peissel, Bernard, Peixoto, Ana, Perez, Jose I., Peterlongo, Paolo, Peto, Julian, Pfeiler, Georg, Phelan, Catherine M., Pinchev, Mila, Plaseska-Karanfilska, Dijana, Poppe, Bruce, Porteous, Mary E., Prentice, Ross, Presneau, Nadege, Prokofieva, Darya, Pugh, Elizabeth, Pujana, Miquel Angel, Pylkäs, Katri, Rack, Brigitte, Radice, Paolo, Rahman, Nazneen, Rantala, Johanna, Rappaport-Fuerhauser, Christine, Rennert, Gad, Rennert, Hedy S., Rhenius, Valerie, Rhiem, Kerstin, Richardson, Andrea, Rodriguez, Gustavo C., Romero, Atocha, Romm, Jane, Rookus, Matti A., Rudolph, Anja, Ruediger, Thomas, Saloustros, Emmanouil, Sanders, Joyce, Sandler, Dale P., Sangrajrang, Suleeporn, Sawyer, Elinor J., Schmidt, Daniel F., Schoemaker, Minouk J., Schumacher, Fredrick, Schürmann, Peter, Schwentner, Lukas, Scott, Christopher, Scott, Rodney J., Seal, Sheila, Senter, Leigha, Seynaeve, Caroline, Shah, Mitul, Sharma, Priyanka, Shen, Chen Yang, Sheng, Xin, Shimelis, Hermela, Shrubsole, Martha J., Shu, Xiao Ou, Side, Lucy E., Singer, Christian F., Sohn, Christof, Southey, Melissa C., Spinelli, John J., Spurdle, Amanda B., Stegmaier, Christa, Stoppa-Lyonnet, Dominique, Sukiennicki, Grzegorz, Surowy, Harald, Sutter, Christian, Swerdlow, Anthony, Szabo, Csilla I., Tamimi, Rulla M., Tan, Yen Y., Taylor, Jack A., Tejada, Maria Isabel, Tengström, Maria, Teo, Soo H., Terry, Mary B., Tessier, Daniel C., Teul, Alex E., Thöne, Kathrin, Thull, Darcy L., Tibiletti, Maria Grazia, Tihomirova, Laima, Tischkowitz, Marc, Toland, Amanda E., Tollenaar, Rob A.M., Tomlinson, Ian, Tong, Ling, Torres, Diana, Tranchant, Martine, Truong, Thérèse, Tucker, Kathy, Tung, Nadine, Tyrer, Jonathan, Ulmer, Hans Ulrich, Vachon, Celine, Christi, Van Asperen J., Den Berg, David Van, Ouweland, Ans M.Vanden, Rensburg, Elizabeth J., Varesco, Liliana, Varon-Mateeva, Raymonda, Vega, Ana, Viel, Alessandra, Vijai, Joseph, Vincent, Daniel, Vollenweider, Jason, Walker, Lisa, Wang, Zhaoming, Wang-Gohrke, Shan, Wappenschmidt, Barbara, Weinberg, Clarice R., Weitzel, Jeffrey N., Wendt, Camilla, Wesseling, Jelle, Whittemore, Alice S., Wijnen, Juul T., Willett, Walter, Winqvist, Robert, Wolk, Alicja, Wu, Anna H., Xia, Lucy, Yang, Xiaohong R., Yannoukakos, Drakoulis, Zaffaroni, Daniela, Zheng, Wei, Zhu, Bin, Ziogas, Argyrios, Ziv, Elad, Zorn, Kristin K., Gago-Dominguez, Manuela, Mannermaa, Arto, Olsson, Håkan, Teixeira, Manuel R., Stone, Jennifer, Offit, Kenneth, Ottini, Laura, Park, Sue K., Thomassen, Mads, Hall, Per, Meindl, Alfons, Schmutzler, Rita K., Droit, Arnaud, Bader, Gary D., Pharoah, Paul D., Couch, Fergus J., Easton, Douglas F., Kraft, Peter, Chenevix-Trench, Georgia, Garciá-Closas, Montserrat, Schmidt, Marjanka K., Antoniou, Antonis C., Simard, Jacques, Damage and Repair in Cancer Development and Cancer Treatment (DARE), Targeted Gynaecologic Oncology (TARGON), Human Genetics, CCA - Cancer biology and immunology, Epidemiology and Data Science, Amsterdam Neuroscience - Complex Trait Genetics, Human genetics, Amsterdam Reproduction & Development (AR&D), Clinical Genetics, Medical Oncology, Internal Medicine, Obstetrics & Gynecology, MUMC+: DA KG Lab Centraal Lab (9), and RS: GROW - R4 - Reproductive and Perinatal Medicine

Subjects
0301 basic medicine, Oncology, Estrogen receptor, Genome-wide association study, consortium, Gene mutation, DISEASE, Breast cancer, Risk Factors, Receptors, common variants, BRCA2 MUTATION CARRIERS, Medicine and Health Sciences, CONFER SUSCEPTIBILITY, skin and connective tissue diseases, ovarian cancers, BRCA1 Protein, COMMON VARIANTS, Single Nucleotide, OVARIAN CANCERS, 3. Good health, Women's cancers Radboud Institute for Health Sciences [Radboudumc 17], Receptors, Estrogen, functional variants, Female, estrogen receptor, SNPs, EXPRESSION, medicine.medical_specialty, Heterozygote, SUSCEPTIBILITY LOCI, European Continental Ancestry Group, Breast cancer, estrogen receptor, SNPs, Single-nucleotide polymorphism, Breast Neoplasms, Biology, Polymorphism, Single Nucleotide, White People, Article, Càncer de mama, 03 medical and health sciences, SDG 3 - Good Health and Well-being, Internal medicine, expression, medicine, Genetic predisposition, Genetics, Journal Article, Humans, Genetic Predisposition to Disease, ddc:610, Risk factor, Polymorphism, GENOME-WIDE ASSOCIATION, FUNCTIONAL VARIANTS, disease, CONSORTIUM, Case-control study, Biology and Life Sciences, medicine.disease, confer susceptibility, Estrogen, susceptibility loci, 030104 developmental biology, Mutation, genome-wide association, brca2 mutation carriers, Genome-Wide Association Study
Abstract

Most common breast cancer susceptibility variants have been identified through genome-wide association studies (GWAS) of predominantly estrogen receptor (ER)-positive disease1. We conducted a GWAS using 21,468 ER-negative cases and 100,594 controls combined with 18,908 BRCA1 mutation carriers (9,414 with breast cancer), all of European origin. We identified independent associations at P < 5 × 10−8 with ten variants at nine new loci. At P < 0.05, we replicated associations with 10 of 11 variants previously reported in ER-negative disease or BRCA1mutation carrier GWAS and observed consistent associations with ER-negative disease for 105 susceptibility variants identified by other studies. These 125 variants explain approximately 16% of the familial risk of this breast cancer subtype. There was high genetic correlation (0.72) between risk of ER-negative breast cancer and breast cancer risk for BRCA1 mutation carriers. These findings may lead to improved risk prediction and inform further fine-mapping and functional work to better understand the biological basis of ER-negative breast cancer.

Published
2017

15. Subsequent neoplasm risk associated with rare variants in DNA repair and clinical radiation sensitivity syndrome genes: A report from the Childhood Cancer Survivor Study

Author

Lindsay M. Morton, Megan N. Frone, Wendy M. Leisenring, Joseph Philip Neglia, Bin Zhu, Yutaka Yasui, Gregory T. Armstrong, Margaret A. Tucker, Danielle M. Karyadi, Stephen J. Chanock, Joshua N. Sampson, Michael Arnold, Rebecca M. Howell, Belynda Hicks, Casey L. Dagnall, Steven Hartley, Leslie L. Robison, Smita Bhatia, and Jones Kristine

Subjects
Oncology, Cancer Research, medicine.medical_specialty, business.industry, DNA repair, medicine.medical_treatment, Childhood cancer, Childhood Cancer Survivor Study, medicine.disease, Radiation therapy, 03 medical and health sciences, 0302 clinical medicine, Radiation sensitivity, 030220 oncology & carcinogenesis, Internal medicine, Medicine, Neoplasm, business, Gene, 030215 immunology
Abstract

10028 Background: Radiotherapy for childhood cancer is associated with strikingly elevated risk for developing subsequent neoplasms (SNs). Whether mutations in DNA repair and radiation sensitivity genes modulate SN risks is largely unknown. Methods: We conducted whole-exome sequencing in 5105 long-term childhood cancer survivors of European descent (mean follow-up = 32.7 years). SnpEff and ClinVar identified potentially damaging rare variants in 476 DNA repair or radiation sensitivity genes. Conditional logistic regression assessed SN risk associated with these variants aggregated by gene or pathway (N = 155 with ≥5 carriers). Controls were matched on sex, childhood cancer type and diagnosis age, radiation dose to the SN site, and survival. Exact p-values were calculated by permutation. Analyses used all survivors or subsets stratified on radiation dose. Results: A total of 1108 (21.7%) survivors developed at least one SN type known to be related to ionizing radiation exposure (e.g., breast cancer, basal cell carcinoma, meningioma, thyroid cancer, sarcoma). Radiation-related SN risk was associated with homologous recombination (HR) gene variants for SN sites that received > 0- < 10 Gy (20.9% cases, 11.0% controls; odds ratio [OR] = 2.20, 95% confidence interval [CI] 1.52-3.18; P = 1.41x10-4), most notably for FANCM (3.1% cases, 0.5% controls; OR = 9.91, 95%CI 3.73-26.4; P = 2.85x10-4). For radiation-related SNs at sites with higher doses (≥10 Gy), associations were not observed for the HR pathway (14.4% cases, 12.4% controls, P = 0.17) but were observed for two individual genes implicated in double-strand DNA break repair, EXO1 (1.8% cases, 0.4% controls; OR = 6.50, 95%CI 3.49-12.1; P = 7.43x10-4) and NEIL3 (0% cases, 1.0% controls; P = 3.23x10-4). Conclusions: In this discovery study, we identified dose-specific novel associations between SN risk after radiotherapy for childhood cancer and potentially damaging rare variants in genes involved in double-strand DNA break repair, particularly HR. If replicated, these results could impact long-term screening of childhood cancer survivors and risk-benefit assessments of treatment approaches.

Published
2019

16. Additional file 2: Table S2. of Distinguishing highly similar gene isoforms with a clustering-based bioinformatics analysis of PacBio single-molecule long reads

Author

Liang, Ma, Castle Raley, Zheng, Xin, Kutty, Geetha, Gogineni, Emile, Sherman, Brad, Sun, Qiang, Xiongfong Chen, Skelly, Thomas, Jones, Kristine, Stephens, Robert, Zhou, Bin, Lau, William, Johnson, Calvin, Tomozumi Imamichi, Minkang Jiang, Dewar, Robin, Lempicki, Richard, Tran, Bao, Kovacs, Joseph, and Huang, Da

Abstract

Explanation of the Uclust-based analysis pipeline in details. (DOC 27Â kb)

Published
2016
Full Text
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17. Additional file 2: Table S2. of Distinguishing highly similar gene isoforms with a clustering-based bioinformatics analysis of PacBio single-molecule long reads

Author

Liang, Ma, Castle Raley, Zheng, Xin, Kutty, Geetha, Gogineni, Emile, Sherman, Brad, Sun, Qiang, Xiongfong Chen, Skelly, Thomas, Jones, Kristine, Stephens, Robert, Zhou, Bin, Lau, William, Johnson, Calvin, Tomozumi Imamichi, Minkang Jiang, Dewar, Robin, Lempicki, Richard, Tran, Bao, Kovacs, Joseph, and Huang, Da

Abstract

Explanation of the Uclust-based analysis pipeline in details. (DOC 27Â kb)

Published
2016
Full Text
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18. Additional file 1: Table S1. of Distinguishing highly similar gene isoforms with a clustering-based bioinformatics analysis of PacBio single-molecule long reads

Author

Liang, Ma, Castle Raley, Zheng, Xin, Kutty, Geetha, Gogineni, Emile, Sherman, Brad, Sun, Qiang, Xiongfong Chen, Skelly, Thomas, Jones, Kristine, Stephens, Robert, Zhou, Bin, Lau, William, Johnson, Calvin, Tomozumi Imamichi, Minkang Jiang, Dewar, Robin, Lempicki, Richard, Tran, Bao, Kovacs, Joseph, and Huang, Da

Abstract

Representative results of failure of de novo assembly of 454 reads for an ~1.5Â kb segment of 10 known msg isoforms of P. jirovecii. (DOCX 18Â kb)

Published
2016
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19. Draft genome sequence of the ricin-producing oilseed castor bean

Author

Chan, Agnes P., Crabtree, Jonathan, Zhao, Qi, Lorenzi, Hernan, Orvis, Joshua, Puiu, Daniela, Melake-Berhan, Admasu, Jones, Kristine M., Redman, Julia, Chen, Grace, Cahoon, Edgar B., Gedil, Melaku, Stanke, Mario, Haas, Brian J., Wortman, Jennifer R., Fraser-Liggett, Claire M., Ravel, Jacques, and Rabinowicz, Pablo D.

Subjects
Base Sequence, food and beverages, Molecular Sequence Annotation, Ricin, Sequence Analysis, DNA, Castor Bean, Genes, Plant, Article, Immunity, Innate, Protein Structure, Tertiary, Polyploidy, Multigene Family, Seeds, Plant Oils, Genome, Plant, Repetitive Sequences, Nucleic Acid
Abstract

Castor bean (Ricinus communis) is an oilseed crop that belongs to the spurge (Euphorbiaceae) family, which comprises approximately 6,300 species that include cassava (Manihot esculenta), rubber tree (Hevea brasiliensis) and physic nut (Jatropha curcas). It is primarily of economic interest as a source of castor oil, used for the production of high-quality lubricants because of its high proportion of the unusual fatty acid ricinoleic acid. However, castor bean genomics is also relevant to biosecurity as the seeds contain high levels of ricin, a highly toxic, ribosome-inactivating protein. Here we report the draft genome sequence of castor bean (4.6-fold coverage), the first for a member of the Euphorbiaceae. Whereas most of the key genes involved in oil synthesis and turnover are single copy, the number of members of the ricin gene family is larger than previously thought. Comparative genomics analysis suggests the presence of an ancient hexaploidization event that is conserved across the dicotyledonous lineage.

Published
2010

20. A transcriptome-wide association study of 229,000 women identifies new candidate susceptibility genes for breast cancer

Author

Wu, Lang, Shi, Wei, Long, Jirong, Guo, Xingyi, Michailidou, Kyriaki, Beesley, Jonathan, Bolla, Manjeet K, Shu, Xiao-Ou, Lu, Yingchang, Cai, Qiuyin, Al-Ejeh, Fares, Rozali, Esdy, Wang, Qin, Dennis, Joe, Li, Bingshan, Zeng, Chenjie, Feng, Helian, Gusev, Alexander, Barfield, Richard T, Andrulis, Irene L, Anton-Culver, Hoda, Arndt, Volker, Aronson, Kristan J, Auer, Paul L, Barrdahl, Myrto, Baynes, Caroline, Beckmann, Matthias W, Benitez, Javier, Bermisheva, Marina, Blomqvist, Carl, Bogdanova, Natalia V, Bojesen, Stig E, Brauch, Hiltrud, Brenner, Hermann, Brinton, Louise, Broberg, Per, Brucker, Sara Y, Burwinkel, Barbara, Caldés, Trinidad, Canzian, Federico, Carter, Brian D, Castelao, J Esteban, Chang-Claude, Jenny, Chen, Xiaoqing, Cheng, Ting-Yuan David, Christiansen, Hans, Clarke, Christine L, NBCS Collaborators, Collée, Margriet, Cornelissen, Sten, Couch, Fergus J, Cox, David, Cox, Angela, Cross, Simon S, Cunningham, Julie M, Czene, Kamila, Daly, Mary B, Devilee, Peter, Doheny, Kimberly F, Dörk, Thilo, Dos-Santos-Silva, Isabel, Dumont, Martine, Dwek, Miriam, Eccles, Diana M, Eilber, Ursula, Eliassen, A Heather, Engel, Christoph, Eriksson, Mikael, Fachal, Laura, Fasching, Peter A, Figueroa, Jonine, Flesch-Janys, Dieter, Fletcher, Olivia, Flyger, Henrik, Fritschi, Lin, Gabrielson, Marike, Gago-Dominguez, Manuela, Gapstur, Susan M, García-Closas, Montserrat, Gaudet, Mia M, Ghoussaini, Maya, Giles, Graham G, Goldberg, Mark S, Goldgar, David E, González-Neira, Anna, Guénel, Pascal, Hahnen, Eric, Haiman, Christopher A, Håkansson, Niclas, Hall, Per, Hallberg, Emily, Hamann, Ute, Harrington, Patricia, Hein, Alexander, Hicks, Belynda, Hillemanns, Peter, Hollestelle, Antoinette, Hoover, Robert N, Hopper, John L, Huang, Guanmengqian, Humphreys, Keith, Hunter, David J, Jakubowska, Anna, Janni, Wolfgang, John, Esther M, Johnson, Nichola, Jones, Kristine, Jones, Michael E, Jung, Audrey, Kaaks, Rudolf, Kerin, Michael J, Khusnutdinova, Elza, Kosma, Veli-Matti, Kristensen, Vessela N, Lambrechts, Diether, Le Marchand, Loic, Li, Jingmei, Lindström, Sara, Lissowska, Jolanta, Lo, Wing-Yee, Loibl, Sibylle, Lubinski, Jan, Luccarini, Craig, Lux, Michael P, MacInnis, Robert J, Maishman, Tom, Kostovska, Ivana Maleva, Mannermaa, Arto, Manson, JoAnn E, Margolin, Sara, Mavroudis, Dimitrios, Meijers-Heijboer, Hanne, Meindl, Alfons, Menon, Usha, Meyer, Jeffery, Mulligan, Anna Marie, Neuhausen, Susan L, Nevanlinna, Heli, Neven, Patrick, Nielsen, Sune F, Nordestgaard, Børge G, Olopade, Olufunmilayo I, Olson, Janet E, Olsson, Håkan, Peterlongo, Paolo, Peto, Julian, Plaseska-Karanfilska, Dijana, Prentice, Ross, Presneau, Nadege, Pylkäs, Katri, Rack, Brigitte, Radice, Paolo, Rahman, Nazneen, Rennert, Gad, Rennert, Hedy S, Rhenius, Valerie, Romero, Atocha, Romm, Jane, Rudolph, Anja, Saloustros, Emmanouil, Sandler, Dale P, Sawyer, Elinor J, Schmidt, Marjanka K, Schmutzler, Rita K, Schneeweiss, Andreas, Scott, Rodney J, Scott, Christopher G, Seal, Sheila, Shah, Mitul, Shrubsole, Martha J, Smeets, Ann, Southey, Melissa C, Spinelli, John J, Stone, Jennifer, Surowy, Harald, Swerdlow, Anthony J, Tamimi, Rulla M, Tapper, William, Taylor, Jack A, Terry, Mary Beth, Tessier, Daniel C, Thomas, Abigail, Thöne, Kathrin, Tollenaar, Rob AEM, Torres, Diana, Truong, Thérèse, Untch, Michael, Vachon, Celine, Van Den Berg, David, Vincent, Daniel, Waisfisz, Quinten, Weinberg, Clarice R, Wendt, Camilla, Whittemore, Alice S, Wildiers, Hans, Willett, Walter C, Winqvist, Robert, Wolk, Alicja, Xia, Lucy, Yang, Xiaohong R, Ziogas, Argyrios, Ziv, Elad, KConFab/AOCS Investigators, Dunning, Alison M, Pharoah, Paul DP, Simard, Jacques, Milne, Roger L, Edwards, Stacey L, Kraft, Peter, Easton, Douglas F, Chenevix-Trench, Georgia, and Zheng, Wei

Subjects
Risk, Case-Control Studies, Gene Expression, Humans, Breast Neoplasms, Female, Genetic Predisposition to Disease, Transcriptome, Polymorphism, Single Nucleotide, 3. Good health, Genome-Wide Association Study
Abstract

The breast cancer risk variants identified in genome-wide association studies explain only a small fraction of the familial relative risk, and the genes responsible for these associations remain largely unknown. To identify novel risk loci and likely causal genes, we performed a transcriptome-wide association study evaluating associations of genetically predicted gene expression with breast cancer risk in 122,977 cases and 105,974 controls of European ancestry. We used data from the Genotype-Tissue Expression Project to establish genetic models to predict gene expression in breast tissue and evaluated model performance using data from The Cancer Genome Atlas. Of the 8,597 genes evaluated, significant associations were identified for 48 at a Bonferroni-corrected threshold of P < 5.82 × 10-6, including 14 genes at loci not yet reported for breast cancer. We silenced 13 genes and showed an effect for 11 on cell proliferation and/or colony-forming efficiency. Our study provides new insights into breast cancer genetics and biology.

21. Oral microbial community composition is associated with pancreatic cancer: A case-control study in Iran

Author

Vogtmann, Emily, Han, Yongli, Caporaso, J. Gregory, Bokulich, Nicholas, Mohamadkhani, Ashraf, Moayyedkazemi, Alireza, Hua, Xing, Kamangar, Farin, Wan, Yunhu, Suman, Shalabh, Zhu, Bin, Hutchinson, Amy, Dagnall, Casey, Jones, Kristine, Hicks, Belynda, Shi, Jianxin, Malekzadeh, Reza, Abnet, Christian C., and Pourshams, Akram

Subjects
2. Zero hunger, Case‐control study, Microbiota, Pancreatic cancer, 3. Good health
Abstract

Background Oral microbiota may be related to pancreatic cancer risk because periodontal disease, a condition linked to multiple specific microbes, has been associated with increased risk of pancreatic cancer. We evaluated the association between oral microbiota and pancreatic cancer in Iran. Methods A total of 273 pancreatic adenocarcinoma cases and 285 controls recruited from tertiary hospitals and a specialty clinic in Tehran, Iran provided saliva samples and filled out a questionnaire regarding demographics and lifestyle characteristics. DNA was extracted from saliva and the V4 region of the 16S rRNA gene was PCR amplified and sequenced on the MiSeq. The sequencing data were processed using the DADA2 plugin in QIIME 2 and taxonomy was assigned against the Human Oral Microbiome Database. Logistic regression and MiRKAT models were calculated with adjustment for potential confounders. Results No association was observed for alpha diversity with an average of 91.11 (standard deviation [SD] 2.59) sequence variants for cases and 89.42 (SD 2.58) for controls. However, there was evidence for an association between beta diversity and case status. The association between the Bray‐Curtis dissimilarity and pancreatic cancer was particularly strong with a MiRKAT P‐value of .000142 and specific principal coordinate vectors had strong associations with cancer risk. Several specific taxa were also associated with case status after adjustment for multiple comparisons. Conclusion The overall microbial community appeared to differ between pancreatic cancer cases and controls. Whether these reflect differences evident before development of pancreatic cancer will need to be evaluated in prospective studies., Cancer Medicine, 9 (2), ISSN:2045-7634

22. MOESM2 of Immune gene expression profiling reveals heterogeneity in luminal breast tumors

Author

Zhu, Bin, Tse, Lap, Difei Wang, Koka, Hela, Tongwu Zhang, Abubakar, Mustapha, Lee, Priscilla, Wang, Feng, Wu, Cherry, Koon Tsang, Wing-Cheong Chan, Sze Law, Mengjie Li, Wentao Li, Suyang Wu, Zhiguang Liu, Bixia Huang, Zhang, Han, Tang, Eric, Zhengyan Kan, Soohyeon Lee, Park, Yeon, Nam, Seok, Mingyi Wang, Xuezheng Sun, Jones, Kristine, Hutchinson, Amy, Belynda Hicks, Prokunina-Olsson, Ludmila, Jianxin Shi, Garcia-Closas, Montserrat, Chanock, Stephen, and Xiaohong Yang

Subjects
skin and connective tissue diseases, 3. Good health
Abstract

Additional file 2: Table S1. The distribution of clinical characteristics and key breast cancer risk factors in the Hong Kong breast cancer study (HKBC). Table S2. 130 immune-related genes used for the classification of luminal tumors. Table S3. The three luminal immune subtypes in relation to the luminal A/B classification in the Hong Kong breast cancer study (HKBC). Table S4. P values for comparisons of tumor MCP-counter abundance scores by immune subtype in the Hong Kong breast cancer study (HKBC). Table S5. P values for comparisons of tumor CIBERSORT fraction scores by immune subtype in the Hong Kong breast cancer study (HKBC). Table S6. The distribution of clinical characteristics and key breast cancer risk factors by luminal immune subtypes in the Hong Kong breast cancer study (HKBC). Table S7. P values for comparisons of the MCP-counter abundance scores between paired tumor and normal tissue (N = 80) by immune subtype in the Hong Kong breast cancer study (HKBC).

23. MOESM2 of Immune gene expression profiling reveals heterogeneity in luminal breast tumors

Author

Zhu, Bin, Tse, Lap, Difei Wang, Koka, Hela, Tongwu Zhang, Abubakar, Mustapha, Lee, Priscilla, Wang, Feng, Wu, Cherry, Koon Tsang, Wing-Cheong Chan, Sze Law, Mengjie Li, Wentao Li, Suyang Wu, Zhiguang Liu, Bixia Huang, Zhang, Han, Tang, Eric, Zhengyan Kan, Soohyeon Lee, Park, Yeon, Nam, Seok, Mingyi Wang, Xuezheng Sun, Jones, Kristine, Hutchinson, Amy, Belynda Hicks, Prokunina-Olsson, Ludmila, Jianxin Shi, Garcia-Closas, Montserrat, Chanock, Stephen, and Xiaohong Yang

Subjects
skin and connective tissue diseases, 3. Good health
Abstract

Additional file 2: Table S1. The distribution of clinical characteristics and key breast cancer risk factors in the Hong Kong breast cancer study (HKBC). Table S2. 130 immune-related genes used for the classification of luminal tumors. Table S3. The three luminal immune subtypes in relation to the luminal A/B classification in the Hong Kong breast cancer study (HKBC). Table S4. P values for comparisons of tumor MCP-counter abundance scores by immune subtype in the Hong Kong breast cancer study (HKBC). Table S5. P values for comparisons of tumor CIBERSORT fraction scores by immune subtype in the Hong Kong breast cancer study (HKBC). Table S6. The distribution of clinical characteristics and key breast cancer risk factors by luminal immune subtypes in the Hong Kong breast cancer study (HKBC). Table S7. P values for comparisons of the MCP-counter abundance scores between paired tumor and normal tissue (N = 80) by immune subtype in the Hong Kong breast cancer study (HKBC).

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