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1. Genomic profiles and clinical presentation of chordoma.

Author

Koka, Hela, Zhou, Weiyin, McMaster, Mary, Bai, Jiwei, Luo, Wen, Klein, Alyssa, Zhang, Tongwu, Hua, Xing, Li, Xin, Wang, Difei, Xiong, Yujia, Jones, Kristine, Vogt, Aurelie, Hicks, Belynda, Parry, Dilys, Goldstein, Allen, and Yang, Xiaohong

Subjects
Chordoma, Chordoma sites, Clinical outcome, Genomic landscape, Treatment, Humans, Chordoma, Male, Female, Middle Aged, Aged, Adult, Adolescent, Young Adult, Child, Child, Preschool, DNA-Binding Proteins, Mutation, Class I Phosphatidylinositol 3-Kinases, T-Box Domain Proteins, Transcription Factors, Nuclear Proteins, Skull Base Neoplasms, Spinal Neoplasms, Canada, Polymorphism, Single Nucleotide, Fetal Proteins, Histone-Lysine N-Methyltransferase
Abstract

Chordoma is a rare bone cancer with variable clinical outcomes. Here, we recruited 184 sporadic chordoma patients from the US and Canada and collected their clinical and treatment data. The average age at diagnosis was 45.5 years (Range 5-78) and the chordoma site distribution was 49.2% clivus, 26.2% spinal, and 24.0% sacral. Most patients (97.5%) received surgery as the primary treatment, among whom 85.3% also received additional treatment. Except for the most prevalent cancers like prostate, lung, breast, and skin cancer, there was no discernible enrichment for any specific cancer type among patients or their family members. Among a subset of patients (N = 70) with tumor materials, we conducted omics analyses and obtained targeted panel sequencing and SNP array genotyping data for 51 and 49 patients, respectively. The most recurrent somatic driver mutations included PIK3CA (12%), followed by chromatin remodeling genes PBRM1 and SETD2. Amplification of the 6q27 region, containing the chordoma susceptibility gene TBXT, was detected in eight patients (16.3%). Clival patients appeared to be less likely to carry driver gene mutations, chromosome arm level deletion events (e.g., 5p, 5p, and 9p), or 6q27 amplification compared to sacral patients. After adjusting for age, sex, tumor site, and additional treatment, patients with somatic deletions of 14q (OR = 13.73, 95% CI 1.96-96.02, P = 0.008) and 18p (OR = 13.68, 95% CI 1.77-105.89, P = 0.012) were more likely to have persistent chordoma. The study highlights genomic heterogeneity in chordoma, potentially linked to location and clinical progression.

Published
2024

2. Genomic characterization of cervical lymph node metastases in papillary thyroid carcinoma following the Chornobyl accident

Author

Morton, Lindsay M., Lee, Olivia W., Karyadi, Danielle M., Bogdanova, Tetiana I., Stewart, Chip, Hartley, Stephen W., Breeze, Charles E., Schonfeld, Sara J., Cahoon, Elizabeth K., Drozdovitch, Vladimir, Masiuk, Sergii, Chepurny, Mykola, Zurnadzhy, Liudmyla Yu, Dai, Jieqiong, Krznaric, Marko, Yeager, Meredith, Hutchinson, Amy, Hicks, Belynda D., Dagnall, Casey L., Steinberg, Mia K., Jones, Kristine, Jain, Komal, Jordan, Ben, Machiela, Mitchell J., Dawson, Eric T., Vij, Vibha, Gastier-Foster, Julie M., Bowen, Jay, Mabuchi, Kiyohiko, Hatch, Maureen, Berrington de Gonzalez, Amy, Getz, Gad, Tronko, Mykola D., Thomas, Gerry A., and Chanock, Stephen J.

Published
2024
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3. Differential long-term bivalent HPV vaccine cross-protection by variants in the Costa Rica HPV vaccine trial

Author

Shing, Jaimie Z., Porras, Carolina, Pinheiro, Maísa, Herrero, Rolando, Hildesheim, Allan, Liu, Danping, Gail, Mitchell H., Romero, Byron, Schiller, John T., Zúñiga, Michael, Mishra, Sambit, Burdette, Laurie, Jones, Kristine, Schussler, John, Ocampo, Rebeca, Fang, Jianwen, Liu, Zhiwei, Lowy, Douglas R., Tsang, Sabrina H., Rodríguez, Ana Cecilia, Schiffman, Mark, Haas, Cameron B., Carvajal, Loretto J., Brown, Jalen R., Kreimer, Aimée R., and Mirabello, Lisa

Published
2024
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4. 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, Byrd, Doratha, 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, Jones, Kristine, Hutchinson, Amy, Hicks, Belynda, Ahearn, Thomas, Biritwum, Richard, Yarney, Joel, Wiafe, Seth, Awuah, Baffour, Nyarko, Kofi, Garcia-Closas, Montserrat, Sinha, Rashmi, Figueroa, Jonine, Brinton, Louise, Trabert, Britton, Vogtmann, Emily, and Knight, Robin

Subjects
estrogens, fecal microbiome, oral microbiome, postmenopausal African women, Female, Humans, Estrogens, Postmenopause, RNA, Ribosomal, 16S, Ghana, Breast Neoplasms, Microbiota, Lactobacillales
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

5. Impact of Transcript (p16/p14ARF) Alteration on Cancer Risk in CDKN2A Germline Pathogenic Variant Carriers.

Author

Sargen, Michael R, Helgadottir, Hildur, Yang, Xiaohong R, Harland, Mark, Hatton, Jessica N, Jones, Kristine, Hicks, Belynda D, Hutchinson, Amy, Curry, Michael, Tucker, Margaret A, Goldstein, Alisa M, and Pfeiffer, Ruth M

Subjects
Biomedical and Clinical Sciences, Oncology and Carcinogenesis, Rare Diseases, Digestive Diseases, Lung, Cancer, Prevention, Clinical Research, Humans, United States, Aged, Tumor Suppressor Protein p14ARF, Squamous Cell Carcinoma of Head and Neck, Cyclin-Dependent Kinase Inhibitor p16, Melanoma, Risk Factors, Head and Neck Neoplasms, Oncology and carcinogenesis
Abstract

Few studies have evaluated the relationship between CDKN2A germline pathogenic variants (GPV), transcript (p16/p14ARF) alteration, and cancer risk. Standardized incidence ratios (SIRs) comparing cancer risk with the general population were calculated for 385 CDKN2A GPV carriers from 2 large cohorts (259 United States and 126 Swedish individuals) using Poisson regression; statistical significance was defined as P less than .002 (Bonferroni correction). Cumulative incidence is reported for melanoma and nonmelanoma cancer. Incidence was increased for melanoma (SIR = 159.8, 95% confidence interval [CI] = 132.1 to 193.2), pancreatic cancer (SIR = 24.1, 95% CI = 14.7 to 39.4), head and neck squamous cell carcinoma (SIR = 16.2, 95% CI = 9.5 to 27.6), and lung cancer (SIR = 5.6, 95% CI = 3.4 to 9.1) in GPV carriers. Similar associations were observed with p16 alteration. Combined p16 and p14ARF alteration was associated with increased incidence of esophageal cancer (SIR = 16.7, 95% CI = 5.7 to 48.9) and malignant peripheral nerve sheath tumor (SIR = 113.0, 95% CI = 16.4 to 780.9), although cancer events were limited (n

Published
2022

6. The oral microbiome and breast cancer and nonmalignant breast disease, and its relationship with the fecal microbiome in the Ghana Breast Health Study.

Author

Wu, Zeni, Byrd, Doratha, 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, Jones, Kristine, Hutchinson, Amy, Hicks, Belynda, Ahearn, Thomas, Shi, Jianxin, Biritwum, Richard, Yarney, Joel, Wiafe, Seth, Awuah, Baffour, Nyarko, Kofi, Figueroa, Jonine, Sinha, Rashmi, Garcia-Closas, Montserrat, Brinton, Louise, Vogtmann, Emily, and Knight, Robin

Subjects
Ghana, breast cancer, fecal microbiome, nonmalignant breast diseases, oral microbiome, Breast Neoplasms, Case-Control Studies, Feces, Female, Gastrointestinal Microbiome, Ghana, Humans, Logistic Models, Microbiota, Phylogeny, RNA, Ribosomal, 16S
Abstract

The oral microbiome, like the fecal microbiome, may be related to breast cancer risk. Therefore, we investigated whether the oral microbiome was associated with breast cancer and nonmalignant breast disease, and its relationship with the fecal microbiome in a case-control study in Ghana. A total of 881 women were included (369 breast cancers, 93 nonmalignant cases and 419 population-based controls). The V4 region of the 16S rRNA gene was sequenced from oral and fecal samples. Alpha-diversity (observed amplicon sequence variants [ASVs], Shannon index and Faiths Phylogenetic Diversity) and beta-diversity (Bray-Curtis, Jaccard and weighted and unweighted UniFrac) metrics were computed. MiRKAT and logistic regression models were used to investigate the case-control associations. Oral sample alpha-diversity was inversely associated with breast cancer and nonmalignant breast disease with odds ratios (95% CIs) per every 10 observed ASVs of 0.86 (0.83-0.89) and 0.79 (0.73-0.85), respectively, compared to controls. Beta-diversity was also associated with breast cancer and nonmalignant breast disease compared to controls (P ≤ .001). The relative abundances of Porphyromonas and Fusobacterium were lower for breast cancer cases compared to controls. Alpha-diversity and presence/relative abundance of specific genera from the oral and fecal microbiome were strongly correlated among breast cancer cases, but weakly correlated among controls. Particularly, the relative abundance of oral Porphyromonas was strongly, inversely correlated with fecal Bacteroides among breast cancer cases (r = -.37, P ≤ .001). Many oral microbial metrics were strongly associated with breast cancer and nonmalignant breast disease, and strongly correlated with fecal microbiome among breast cancer cases, but not controls.

Published
2022

8. Mosaic chromosomal alterations in peripheral blood leukocytes of children in sub-Saharan Africa

Author

Zhou, Weiyin, Fischer, Anja, Ogwang, Martin D., Luo, Wen, Kerchan, Patrick, Reynolds, Steven J., Tenge, Constance N., Were, Pamela A., Kuremu, Robert T., Wekesa, Walter N., Masalu, Nestory, Kawira, Esther, Kinyera, Tobias, Otim, Isaac, Legason, Ismail D., Nabalende, Hadijah, Ayers, Leona W., Bhatia, Kishor, Goedert, James J., Gouveia, Mateus H., Cole, Nathan, Hicks, Belynda, Jones, Kristine, Hummel, Michael, Schlesner, Mathias, Chagaluka, George, Mutalima, Nora, Borgstein, Eric, Liomba, George N., Kamiza, Steve, Mkandawire, Nyengo, Mitambo, Collins, Molyneux, Elizabeth M., Newton, Robert, Glaser, Selina, Kretzmer, Helene, Manning, Michelle, Hutchinson, Amy, Hsing, Ann W., Tettey, Yao, Adjei, Andrew A., Chanock, Stephen J., Siebert, Reiner, Yeager, Meredith, Prokunina-Olsson, Ludmila, Machiela, Mitchell J., and Mbulaiteye, Sam M.

Published
2023
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9. 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, Zhu, Bin, Hutchinson, Amy, Hicks, Belynda, Garcia-Closas, Montserrat, Chanock, Stephen, Barnholtz-Sloan, Jill, Tse, Lap Ah, and Yang, Xiaohong R.

Published
2023
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11. GWAS Explorer: an open-source tool to explore, visualize, and access GWAS summary statistics in the PLCO Atlas

Author

Machiela, Mitchell J., Huang, Wen-Yi, Wong, Wendy, Berndt, Sonja I., Sampson, Joshua, De Almeida, Jonas, Abubakar, Mustapha, Hislop, Jada, Chen, Kai-Ling, Dagnall, Casey, Diaz-Mayoral, Norma, Ferrell, Mary, Furr, Michael, Gonzalez, Alex, Hicks, Belynda, Hubbard, Aubrey K., Hutchinson, Amy, Jiang, Kevin, Jones, Kristine, Liu, Jia, Loftfield, Erikka, Loukissas, Jennifer, Mabie, Jerome, Merkle, Shannon, Miller, Eric, Minasian, Lori M., Nordgren, Ellen, Park, Brian, Pinsky, Paul, Riley, Thomas, Sandoval, Lorena, Saxena, Neeraj, Vogt, Aurelie, Wang, Jiahui, Williams, Craig, Wright, Patrick, Yeager, Meredith, Zhu, Bin, Zhu, Claire, Chanock, Stephen J., Garcia-Closas, Montserrat, and Freedman, Neal D.

Published
2023
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16. Targeted long-read sequencing of the Ewing sarcoma 6p25.1 susceptibility locus identifies germline-somatic interactions with EWSR1-FLI1 binding

Author

Lee, Olivia W., Rodrigues, Calvin, Lin, Shu-Hong, Luo, Wen, Jones, Kristine, Brown, Derek W., Zhou, Weiyin, Karlins, Eric, Khan, Sairah M., Baulande, Sylvain, Raynal, Virginie, Surdez, Didier, Reynaud, Stephanie, Rubio, Rebeca Alba, Zaidi, Sakina, Grossetête, Sandrine, Ballet, Stelly, Lapouble, Eve, Laurence, Valérie, Pierron, Gaelle, Gaspar, Nathalie, Corradini, Nadège, Marec-Bérard, Perrine, Rothman, Nathaniel, Dagnall, Casey L., Burdett, Laurie, Manning, Michelle, Wyatt, Kathleen, Yeager, Meredith, Chari, Raj, Leisenring, Wendy M., Kulozik, Andreas E., Kriebel, Jennifer, Meitinger, Thomas, Strauch, Konstantin, Kirchner, Thomas, Dirksen, Uta, Mirabello, Lisa, Tucker, Margaret A., Tirode, Franck, Armstrong, Gregory T., Bhatia, Smita, Robison, Leslie L., Yasui, Yutaka, Romero-Pérez, Laura, Hartmann, Wolfgang, Metzler, Markus, Diver, W. Ryan, Lori, Adriana, Freedman, Neal D., Hoover, Robert N., Morton, Lindsay M., Chanock, Stephen J., Grünewald, Thomas G.P., Delattre, Olivier, and Machiela, Mitchell J.

Published
2023
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17. Low mutation burden and frequent loss of CDKN2A/B and SMARCA2, but not PRC2, define pre-malignant 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, Jones, Kristine, Zhu, Bin, Wei, Jun S, Mullikin, James C, Wallace, Margaret R, Khan, Javed, Legius, Eric, Widemann, Brigitte C, and Stewart, Douglas R

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

20. Genetic testing in severe aplastic anemia is required for optimal hematopoietic cell transplant outcomes

Author

McReynolds, Lisa J., Rafati, Maryam, Wang, Youjin, Ballew, Bari J., Kim, Jung, Williams, Valencia V., Zhou, Weiyin, Hendricks, Rachel M., Dagnall, Casey, Freedman, Neal D., Carter, Brian, Strollo, Sara, Hicks, Belynda, Zhu, Bin, Jones, Kristine, Paczesny, Sophie, Marsh, Steven G.E., Spellman, Stephen R., He, Meilun, Wang, Tao, Lee, Stephanie J., Savage, Sharon A., and Gadalla, Shahinaz M.

Published
2022
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21. Germline-somatic JAK2 interactions are associated with clonal expansion in myelofibrosis

Author

Brown, Derek W., Zhou, Weiyin, Wang, Youjin, Jones, Kristine, Luo, Wen, Dagnall, Casey, Teshome, Kedest, Klein, Alyssa, Zhang, Tongwu, Lin, Shu-Hong, Lee, Olivia W., Khan, Sairah, Vo, Jacqueline B., Hutchinson, Amy, Liu, Jia, Wang, Jiahui, Zhu, Bin, Hicks, Belynda, Martin, Andrew St., Spellman, Stephen R., Wang, Tao, Deeg, H. Joachim, Gupta, Vikas, Lee, Stephanie J., Freedman, Neal D., Yeager, Meredith, Chanock, Stephen J., Savage, Sharon A., Saber, Wael, Gadalla, Shahinaz M., and Machiela, Mitchell J.

Published
2022
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23. Monoallelic Germline Pathogenic Variants in DNA Damage Repair Genes and Their Impact on Post-Hematopoietic Cell Transplantation Outcomes in Severe Aplastic Anemia

Author

Rafati, Maryam, primary, Wang, Youjin, additional, McReynolds, Lisa J., additional, Jones, Kristine, additional, Hicks, Belynda, additional, Spellman, Stephen R., additional, He, Meilun, additional, Bolon, Yung-Tsi, additional, Lee, Stephanie J., additional, Savage, Sharon A., additional, and Gadalla, Shahinaz M., additional

Published
2024
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25. Increased frequency of germline BRCA2 mutations associates with prostate cancer metastasis in a racially diverse patient population

Author

Petrovics, Gyorgy, Price, Douglas K., Lou, Hong, Chen, Yongmei, Garland, Lisa, Bass, Sara, Jones, Kristine, Kohaar, Indu, Ali, Amina, Ravindranath, Lakshmi, Young, Denise, Cullen, Jennifer, Dorsey, Tiffany H., Sesterhenn, Isabell A., Brassell, Stephen A., Rosner, Inger L., Ross, Doug, Dahut, William, Ambs, Stefan, Figg, William Douglas, Srivastava, Shiv, and Dean, Michael

Published
2019
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29. The Genome of the African Trypanosome Trypanosoma brucei

Author

Berriman, Matthew, Ghedin, Elodie, Hertz-Fowler, Christiane, Blandin, Gaëlle, Renauld, Hubert, Bartholomeu, Daniella C., Lennard, Nicola J., Caler, Elisabet, Hamlin, Nancy E., Haas, Brian, Böhme, Ulrike, Hannick, Linda, Aslett, Martin A., Shallom, Joshua, Marcello, Lucio, Hou, Lihua, Wickstead, Bill, Arrowsmith, Claire, Atkin, Rebecca J., Barron, Andrew J., Bringaud, Frederic, Brooks, Karen, Carrington, Mark, Cherevach, Inna, Chillingworth, Tracey-Jane, Churcher, Carol, Clark, Louise N., Corton, Craig H., Cronin, Ann, Davies, Rob M., Doggett, Jonathon, Djikeng, Appolinaire, Feldblyum, Tamara, Field, Mark C., Fraser, Audrey, Goodhead, Ian, Hance, Zahra, Harper, David, Harris, Barbara R., Hauser, Heidi, Hostetler, Jessica, Ivens, Al, Jagels, Kay, Johnson, David, Johnson, Justin, Jones, Kristine, Kerhornou, Arnaud X., Koo, Hean, Larke, Natasha, Landfear, Scott, Larkin, Christopher, Leech, Vanessa, Line, Alexandra, Lord, Angela, MacLeod, Annette, Mooney, Paul J., Moule, Sharon, Morgan, Gareth W., Mungall, Karen, Norbertczak, Halina, Ormond, Doug, Pai, Grace, Peacock, Chris S., Peterson, Jeremy, Quail, Michael A., Rabbinowitsch, Ester, Rajandream, Marie-Adele, Reitter, Chris, Salzberg, Steven L., Sanders, Mandy, Schobel, Seth, Sharp, Sarah, Simmonds, Mark, Simpson, Anjana J., Tallon, Luke, Tait, Andrew, Tivey, Adrian R., Van Aken, Susan, Walker, Danielle, Wanless, David, Wang, Shiliang, White, Brian, White, Owen, Whitehead, Sally, Woodward, John, Wortman, Jennifer, Adams, Mark D., Embley, T. Martin, Gull, Keith, Ullu, Elisabetta, Barry, J. David, Fairlamb, Alan H., Opperdoes, Fred, Barrell, Barclay G., Donelson, John E., Hall, Neil, Fraser, Claire M., Melville, Sara E., and El-Sayed, Najib M.

Published
2005

32. The genomic and epigenomic evolutionary history of papillary renal cell carcinomas

Author

Zhu, Bin, Poeta, Maria Luana, Costantini, Manuela, Zhang, Tongwu, Shi, Jianxin, Sentinelli, Steno, Zhao, Wei, Pompeo, Vincenzo, Cardelli, Maurizio, Alexandrov, Boian S., Otlu, Burcak, Hua, Xing, Jones, Kristine, Brodie, Seth, Dabrowska, Malgorzata Ewa, Toro, Jorge R., Yeager, Meredith, Wang, Mingyi, Hicks, Belynda, Alexandrov, Ludmil B., Brown, Kevin M., Wedge, David C., Chanock, Stephen, Fazio, Vito Michele, Gallucci, Michele, and Landi, Maria Teresa

Published
2020
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34. Immune gene expression profiling reveals heterogeneity in luminal breast tumors

Author

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

Published
2019
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35. Life in hot carbon monoxide: the complete genome sequence of Carboxydothermus hydrogenoformans Z-2901.

Author

Wu, Martin, Ren, Qinghu, Durkin, A Scott, Daugherty, Sean C, Brinkac, Lauren M, Dodson, Robert J, Madupu, Ramana, Sullivan, Steven A, Kolonay, James F, Haft, Daniel H, Nelson, William C, Tallon, Luke J, Jones, Kristine M, Ulrich, Luke E, Gonzalez, Juan M, Zhulin, Igor B, Robb, Frank T, and Eisen, Jonathan A

Subjects
Peptococcaceae, Carbon Monoxide, Sequence Analysis, DNA, Genomics, Base Sequence, Oxidative Stress, Genes, Bacterial, Genome, Bacterial, Models, Biological, Molecular Sequence Data, Hot Temperature, Genes, Bacterial, Genome, Models, Biological, Sequence Analysis, DNA, Genetics, Developmental Biology
Abstract

We report here the sequencing and analysis of the genome of the thermophilic bacterium Carboxydothermus hydrogenoformans Z-2901. This species is a model for studies of hydrogenogens, which are diverse bacteria and archaea that grow anaerobically utilizing carbon monoxide (CO) as their sole carbon source and water as an electron acceptor, producing carbon dioxide and hydrogen as waste products. Organisms that make use of CO do so through carbon monoxide dehydrogenase complexes. Remarkably, analysis of the genome of C. hydrogenoformans reveals the presence of at least five highly differentiated anaerobic carbon monoxide dehydrogenase complexes, which may in part explain how this species is able to grow so much more rapidly on CO than many other species. Analysis of the genome also has provided many general insights into the metabolism of this organism which should make it easier to use it as a source of biologically produced hydrogen gas. One surprising finding is the presence of many genes previously found only in sporulating species in the Firmicutes Phylum. Although this species is also a Firmicutes, it was not known to sporulate previously. Here we show that it does sporulate and because it is missing many of the genes involved in sporulation in other species, this organism may serve as a "minimal" model for sporulation studies. In addition, using phylogenetic profile analysis, we have identified many uncharacterized gene families found in all known sporulating Firmicutes, but not in any non-sporulating bacteria, including a sigma factor not known to be involved in sporulation previously.

Published
2005

37. Evaluation of alcohol-free mouthwash for studies of the oral microbiome

Author

Yano, Yukiko, primary, Vogtmann, Emily, additional, Shreves, Alaina H., additional, Weinstein, Stephanie J., additional, Black, Amanda, additional, Diaz-Mayoral, Norma, additional, Wan, Yunhu, additional, Zhou, Weiyin, additional, Hua, Xing, additional, Dagnall, Casey L., additional, Hutchinson, Amy, additional, Jones, Kristine, additional, Hicks, Belynda D., additional, Wyatt, Kathleen, additional, Brotzman, Michelle, additional, Gerlanc, Nicole, additional, Huang, Wen-Yi, additional, Albert, Paul S., additional, Wentzensen, Nicolas, additional, and Abnet, Christian C., additional

Published
2023
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38. Abstract 3055: Associations of the mucosal microbiome and circulating bile acids with colorectal adenoma among average-risk women

Author

Gomez, Maria F., primary, Byrd, Doratha A., additional, Hogue, Stephanie R., additional, Burns, Jessica R., additional, Smith, Nathan, additional, Sampson, Joshua, additional, Loftfield, Erikka, additional, Warner, Andrew, additional, Dagnall, Casey, additional, Jones, Kristine, additional, Hicks, Belynda, additional, Wan, Yunhu, additional, Kim, Youngchul, additional, Xu, Jin, additional, Sinha, Rashmi, additional, and Vogtmann, Emily, additional

Published
2023
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39. Targeted long-read sequencing of the Ewing sarcoma 6p25.1 susceptibility locus identifies germline-somatic interactions with EWSR1-FLI1 binding

Author

Lee, Olivia W, Rodrigues, Calvin, Lin, Shu-Hong, Luo, Wen, Jones, Kristine, Brown, Derek W, Zhou, Weiyin, Karlins, Eric, Khan, Sairah M, Baulande, Sylvain, Raynal, Virginie, Surdez, Didier; https://orcid.org/0000-0002-7118-7859, Reynaud, Stephanie, Rubio, Rebeca Alba, Zaidi, Sakina, Grossetête, Sandrine, Ballet, Stelly, Lapouble, Eve, Laurence, Valérie, Pierron, Gaelle, Gaspar, Nathalie, Corradini, Nadège, Marec-Bérard, Perrine, Rothman, Nathaniel, Dagnall, Casey L, Burdett, Laurie, Manning, Michelle, Wyatt, Kathleen, Yeager, Meredith, Chari, Raj, et al, Lee, Olivia W, Rodrigues, Calvin, Lin, Shu-Hong, Luo, Wen, Jones, Kristine, Brown, Derek W, Zhou, Weiyin, Karlins, Eric, Khan, Sairah M, Baulande, Sylvain, Raynal, Virginie, Surdez, Didier; https://orcid.org/0000-0002-7118-7859, Reynaud, Stephanie, Rubio, Rebeca Alba, Zaidi, Sakina, Grossetête, Sandrine, Ballet, Stelly, Lapouble, Eve, Laurence, Valérie, Pierron, Gaelle, Gaspar, Nathalie, Corradini, Nadège, Marec-Bérard, Perrine, Rothman, Nathaniel, Dagnall, Casey L, Burdett, Laurie, Manning, Michelle, Wyatt, Kathleen, Yeager, Meredith, Chari, Raj, and et al

Abstract

Ewing sarcoma (EwS) is a rare bone and soft tissue malignancy driven by chromosomal translocations encoding chimeric transcription factors, such as EWSR1-FLI1, that bind GGAA motifs forming novel enhancers that alter nearby expression. We propose that germline microsatellite variation at the 6p25.1 EwS susceptibility locus could impact downstream gene expression and EwS biology. We performed targeted long-read sequencing of EwS blood DNA to characterize variation and genomic features important for EWSR1-FLI1 binding. We identified 50 microsatellite alleles at 6p25.1 and observed that EwS-affected individuals had longer alleles (>135 bp) with more GGAA repeats. The 6p25.1 GGAA microsatellite showed chromatin features of an EWSR1-FLI1 enhancer and regulated expression of RREB1, a transcription factor associated with RAS/MAPK signaling. RREB1 knockdown reduced proliferation and clonogenic potential and reduced expression of cell cycle and DNA replication genes. Our integrative analysis at 6p25.1 details increased binding of longer GGAA microsatellite alleles with acquired EWSR-FLI1 to promote Ewing sarcomagenesis by RREB1-mediated proliferation.

Published
2023

40. JAK2V617Fmutation and associated chromosomal alterations in primary and secondary myelofibrosis and post-HCT outcomes

Author

Rafati, Maryam, Brown, Derek W., Zhou, Weiyin, Jones, Kristine, Luo, Wen, St. Martin, Andrew, Wang, Youjin, He, Meilun, Spellman, Stephen R., Wang, Tao, Deeg, H. Joachim, Gupta, Vikas, Lee, Stephanie J., Bolon, Yung-Tsi, Chanock, Stephen J., Machiela, Mitchell J., Saber, Wael, and Gadalla, Shahinaz M.

Abstract

•HCT can mitigate the possible negative effect of JAK2V617Fmutation in patients with PMF and PPV-MF.•High allele burden in patients with PET-MF is associated with excess risk of NRM in the era of JAK inhibitors.

Published
2023
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41. Prospective and Cross-sectional Associations of the Rectal Tissue Microbiome with Colorectal Adenoma Recurrence

Author

Byrd, Doratha A., primary, Vogtmann, Emily, additional, Ortega-Villa, Ana M., additional, Wan, Yunhu, additional, Gomez, Maria, additional, Hogue, Stephanie, additional, Warner, Andrew, additional, Zhu, Bin, additional, Dagnall, Casey, additional, Jones, Kristine, additional, Hicks, Belynda, additional, Albert, Paul S., additional, Murphy, Gwen, additional, and Sinha, Rashmi, additional

Published
2022
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42. Massively parallel reporter assays and variant scoring identified functional variants and target genes for melanoma loci and highlighted cell-type specificity

Author

Long, Erping, primary, Yin, Jinhu, additional, Funderburk, Karen M., additional, Xu, Mai, additional, Feng, James, additional, Kane, Alexander, additional, Zhang, Tongwu, additional, Myers, Timothy, additional, Golden, Alyxandra, additional, Thakur, Rohit, additional, Kong, Hyunkyung, additional, Jessop, Lea, additional, Kim, Eun Young, additional, Jones, Kristine, additional, Chari, Raj, additional, Machiela, Mitchell J., additional, Yu, Kai, additional, Iles, Mark M., additional, Landi, Maria Teresa, additional, Law, Matthew H., additional, Chanock, Stephen J., additional, Brown, Kevin M., additional, and Choi, Jiyeon, additional

Published
2022
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43. 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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44. 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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45. 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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46. 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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47. 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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48. 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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49. Increased Frequency of Mosaic Chromosomal Alterations in Peripheral Blood Samples of Sub-Saharan African Children with Endemic Burkitt Lymphoma

Author

Zhou, Weiyin, primary, Pfaus, Anja, additional, Ogwang, Martin, additional, Luo, Wen, additional, Kerchan, Patrick, additional, Reynolds, Steven, additional, Tenge, Constance N, additional, Were, Pamela A, additional, Kuremu, Robert T, additional, Wekesa, Walter N, additional, Masalu, Nestory, additional, Kawira, Esther, additional, Kinyera, Tobias, additional, Otim, Isaac, additional, Legason, Ismail D, additional, Nabalende, Hadijah, additional, Ayers, Leona W, additional, Bhatia, Kishor, additional, Goedert, James J, additional, Cole, Nathan, additional, Hicks, Belynda, additional, Jones, Kristine, additional, Hummel, Michael, additional, Schlesner, Matthias, additional, Chagaluka, George, additional, Mutalima, Nora, additional, Borgstein, Eric, additional, Liomba, George N, additional, Kamiza, Steve, additional, Mkandawire, Nyengo, additional, Mitambo, Collins, additional, Molyneux, Elizabeth, additional, Newton, Robert, additional, Glaser, Selina, additional, Manning, Michelle, additional, Hutchinson, Amy, additional, Hsing, Ann W, additional, Tettey, Yao, additional, Adjei, Andrew Anthony, additional, Chanock, Stephen J., additional, Siebert, Reiner, additional, Yeager, Meredith, additional, Machiela, Mitchell, additional, and Mbulaiteye, Sam M., additional

Published
2022
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50. JAK2 V617F Mutation and Associated Chromosomal Alterations Involving JAK2 in Pre-HCT Blood Samples and Transplant Outcomes in Myelofibrosis Subtypes

Author

Rafati, Maryam, primary, Brown, Derek W, additional, Zhou, Weiyin, additional, Jones, Kristine, additional, Luo, Wen, additional, St. Martin, Andrew, additional, Wang, Youjin, additional, Spellman, Stephen R., additional, Wang, Tao, additional, Deeg, H. Joachim, additional, Gupta, Vikas, additional, Lee, Stephanie J., additional, Chanock, Stephen J., additional, Machiela, Mitchell, additional, Saber, Wael, additional, and Gadalla, Shahinaz M., additional

Published
2022
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