Search

Your search keyword '"Kibriya, Muhammad G."' showing total 513 results
Start Over Author "Kibriya, Muhammad G."
513 results on '"Kibriya, Muhammad G."'

4. Genetic drivers of heterogeneity in type 2 diabetes pathophysiology

Author

Suzuki, Ken, Hatzikotoulas, Konstantinos, Southam, Lorraine, Taylor, Henry J., Yin, Xianyong, Lorenz, Kim M., Mandla, Ravi, Huerta-Chagoya, Alicia, Melloni, Giorgio E. M., Kanoni, Stavroula, Rayner, Nigel W., Bocher, Ozvan, Arruda, Ana Luiza, Sonehara, Kyuto, Namba, Shinichi, Lee, Simon S. K., Preuss, Michael H., Petty, Lauren E., Schroeder, Philip, Vanderwerff, Brett, Kals, Mart, Bragg, Fiona, Lin, Kuang, Guo, Xiuqing, Zhang, Weihua, Yao, Jie, Kim, Young Jin, Graff, Mariaelisa, Takeuchi, Fumihiko, Nano, Jana, Lamri, Amel, Nakatochi, Masahiro, Moon, Sanghoon, Scott, Robert A., Cook, James P., Lee, Jung-Jin, Pan, Ian, Taliun, Daniel, Parra, Esteban J., Chai, Jin-Fang, Bielak, Lawrence F., Tabara, Yasuharu, Hai, Yang, Thorleifsson, Gudmar, Grarup, Niels, Sofer, Tamar, Wuttke, Matthias, Sarnowski, Chloé, Gieger, Christian, Nousome, Darryl, Trompet, Stella, Kwak, Soo-Heon, Long, Jirong, Sun, Meng, Tong, Lin, Chen, Wei-Min, Nongmaithem, Suraj S., Noordam, Raymond, Lim, Victor J. Y., Tam, Claudia H. T., Joo, Yoonjung Yoonie, Chen, Chien-Hsiun, Raffield, Laura M., Prins, Bram Peter, Nicolas, Aude, Yanek, Lisa R., Chen, Guanjie, Brody, Jennifer A., Kabagambe, Edmond, An, Ping, Xiang, Anny H., Choi, Hyeok Sun, Cade, Brian E., Tan, Jingyi, Broadaway, K. Alaine, Williamson, Alice, Kamali, Zoha, Cui, Jinrui, Thangam, Manonanthini, Adair, Linda S., Adeyemo, Adebowale, Aguilar-Salinas, Carlos A., Ahluwalia, Tarunveer S., Anand, Sonia S., Bertoni, Alain, Bork-Jensen, Jette, Brandslund, Ivan, Buchanan, Thomas A., Burant, Charles F., Butterworth, Adam S., Canouil, Mickaël, Chan, Juliana C. N., Chang, Li-Ching, Chee, Miao-Li, Chen, Ji, Chen, Shyh-Huei, Chen, Yuan-Tsong, Chen, Zhengming, Chuang, Lee-Ming, Cushman, Mary, Danesh, John, Das, Swapan K., de Silva, H. Janaka, Dedoussis, George, Dimitrov, Latchezar, Doumatey, Ayo P., Du, Shufa, Duan, Qing, Eckardt, Kai-Uwe, Emery, Leslie S., Evans, Daniel S., Evans, Michele K., Fischer, Krista, Floyd, James S., Ford, Ian, Franco, Oscar H., Frayling, Timothy M., Freedman, Barry I., Genter, Pauline, Gerstein, Hertzel C., Giedraitis, Vilmantas, González-Villalpando, Clicerio, González-Villalpando, Maria Elena, Gordon-Larsen, Penny, Gross, Myron, Guare, Lindsay A., Hackinger, Sophie, Hakaste, Liisa, Han, Sohee, Hattersley, Andrew T., Herder, Christian, Horikoshi, Momoko, Howard, Annie-Green, Hsueh, Willa, Huang, Mengna, Huang, Wei, Hung, Yi-Jen, Hwang, Mi Yeong, Hwu, Chii-Min, Ichihara, Sahoko, Ikram, Mohammad Arfan, Ingelsson, Martin, Islam, Md. Tariqul, Isono, Masato, Jang, Hye-Mi, Jasmine, Farzana, Jiang, Guozhi, Jonas, Jost B., Jørgensen, Torben, Kamanu, Frederick K., Kandeel, Fouad R., Kasturiratne, Anuradhani, Katsuya, Tomohiro, Kaur, Varinderpal, Kawaguchi, Takahisa, Keaton, Jacob M., Kho, Abel N., Khor, Chiea-Chuen, Kibriya, Muhammad G., Kim, Duk-Hwan, Kronenberg, Florian, Kuusisto, Johanna, Läll, Kristi, Lange, Leslie A., Lee, Kyung Min, Lee, Myung-Shik, Lee, Nanette R., Leong, Aaron, Li, Liming, Li, Yun, Li-Gao, Ruifang, Ligthart, Symen, Lindgren, Cecilia M., Linneberg, Allan, Liu, Ching-Ti, Liu, Jianjun, Locke, Adam E., Louie, Tin, Luan, Jian’an, Luk, Andrea O., Luo, Xi, Lv, Jun, Lynch, Julie A., Lyssenko, Valeriya, Maeda, Shiro, Mamakou, Vasiliki, Mansuri, Sohail Rafik, Matsuda, Koichi, Meitinger, Thomas, Melander, Olle, Metspalu, Andres, Mo, Huan, Morris, Andrew D., Moura, Filipe A., Nadler, Jerry L., Nalls, Michael A., Nayak, Uma, Ntalla, Ioanna, Okada, Yukinori, Orozco, Lorena, Patel, Sanjay R., Patil, Snehal, Pei, Pei, Pereira, Mark A., Peters, Annette, Pirie, Fraser J., Polikowsky, Hannah G., Porneala, Bianca, Prasad, Gauri, Rasmussen-Torvik, Laura J., Reiner, Alexander P., Roden, Michael, Rohde, Rebecca, Roll, Katheryn, Sabanayagam, Charumathi, Sandow, Kevin, Sankareswaran, Alagu, Sattar, Naveed, Schönherr, Sebastian, Shahriar, Mohammad, Shen, Botong, Shi, Jinxiu, Shin, Dong Mun, Shojima, Nobuhiro, Smith, Jennifer A., So, Wing Yee, Stančáková, Alena, Steinthorsdottir, Valgerdur, Stilp, Adrienne M., Strauch, Konstantin, Taylor, Kent D., Thorand, Barbara, Thorsteinsdottir, Unnur, Tomlinson, Brian, Tran, Tam C., Tsai, Fuu-Jen, Tuomilehto, Jaakko, Tusie-Luna, Teresa, Udler, Miriam S., Valladares-Salgado, Adan, van Dam, Rob M., van Klinken, Jan B., Varma, Rohit, Wacher-Rodarte, Niels, Wheeler, Eleanor, Wickremasinghe, Ananda R., van Dijk, Ko Willems, Witte, Daniel R., Yajnik, Chittaranjan S., Yamamoto, Ken, Yamamoto, Kenichi, Yoon, Kyungheon, Yu, Canqing, Yuan, Jian-Min, Yusuf, Salim, Zawistowski, Matthew, Zhang, Liang, Zheng, Wei, Raffel, Leslie J., Igase, Michiya, Ipp, Eli, Redline, Susan, Cho, Yoon Shin, Lind, Lars, Province, Michael A., Fornage, Myriam, Hanis, Craig L., Ingelsson, Erik, Zonderman, Alan B., Psaty, Bruce M., Wang, Ya-Xing, Rotimi, Charles N., Becker, Diane M., Matsuda, Fumihiko, Liu, Yongmei, Yokota, Mitsuhiro, Kardia, Sharon L. R., Peyser, Patricia A., Pankow, James S., Engert, James C., Bonnefond, Amélie, Froguel, Philippe, Wilson, James G., Sheu, Wayne H. H., Wu, Jer-Yuarn, Hayes, M. Geoffrey, Ma, Ronald C. W., Wong, Tien-Yin, Mook-Kanamori, Dennis O., Tuomi, Tiinamaija, Chandak, Giriraj R., Collins, Francis S., Bharadwaj, Dwaipayan, Paré, Guillaume, Sale, Michèle M., Ahsan, Habibul, Motala, Ayesha A., Shu, Xiao-Ou, Park, Kyong-Soo, Jukema, J. Wouter, Cruz, Miguel, Chen, Yii-Der Ida, Rich, Stephen S., McKean-Cowdin, Roberta, Grallert, Harald, Cheng, Ching-Yu, Ghanbari, Mohsen, Tai, E-Shyong, Dupuis, Josee, Kato, Norihiro, Laakso, Markku, Köttgen, Anna, Koh, Woon-Puay, Bowden, Donald W., Palmer, Colin N. A., Kooner, Jaspal S., Kooperberg, Charles, Liu, Simin, North, Kari E., Saleheen, Danish, Hansen, Torben, Pedersen, Oluf, Wareham, Nicholas J., Lee, Juyoung, Kim, Bong-Jo, Millwood, Iona Y., Walters, Robin G., Stefansson, Kari, Ahlqvist, Emma, Goodarzi, Mark O., Mohlke, Karen L., Langenberg, Claudia, Haiman, Christopher A., Loos, Ruth J. F., Florez, Jose C., Rader, Daniel J., Ritchie, Marylyn D., Zöllner, Sebastian, Mägi, Reedik, Marston, Nicholas A., Ruff, Christian T., van Heel, David A., Finer, Sarah, Denny, Joshua C., Yamauchi, Toshimasa, Kadowaki, Takashi, Chambers, John C., Ng, Maggie C. Y., Sim, Xueling, Below, Jennifer E., Tsao, Philip S., Chang, Kyong-Mi, McCarthy, Mark I., Meigs, James B., Mahajan, Anubha, Spracklen, Cassandra N., Mercader, Josep M., Boehnke, Michael, Rotter, Jerome I., Vujkovic, Marijana, Voight, Benjamin F., Morris, Andrew P., and Zeggini, Eleftheria

Published
2024
Full Text
View/download PDF

7. An Overview of Cancer in the First 315,000 All of Us Participants

Author

Aschebrook-Kilfoy, Briseis, Zakin, Paul, Craver, Andrew, Shah, Sameep, Kibriya, Muhammad G, Stepniak, Elizabeth, Ramirez, Andrea, Clark, Cheryl, Cohn, Elizabeth, Ohno-Machado, Lucila, Cicek, Mine, Boerwinkle, Eric, Schully, Sheri D, Mockrin, Stephen, Gebo, Kelly, Mayo, Kelsey, Ratsimbazafy, Francis, Sanders, Alan, Shah, Raj C, Argos, Maria, Ho, Joyce, Kim, Karen, Daviglus, Martha, Greenland, Philip, and Ahsan, Habibul

Subjects
Cancer, Good Health and Well Being, Cohort Studies, Electronic Health Records, Humans, Neoplasms, Population Health, Surveys and Questionnaires, All of Us Research Program Investigators, General Science & Technology
Abstract

IntroductionThe NIH All of Us Research Program will have the scale and scope to enable research for a wide range of diseases, including cancer. The program's focus on diversity and inclusion promises a better understanding of the unequal burden of cancer. Preliminary cancer ascertainment in the All of Us cohort from two data sources (self-reported versus electronic health records (EHR)) is considered.Materials and methodsThis work was performed on data collected from the All of Us Research Program's 315,297 enrolled participants to date using the Researcher Workbench, where approved researchers can access and analyze All of Us data on cancer and other diseases. Cancer case ascertainment was performed using data from EHR and self-reported surveys across key factors. Distribution of cancer types and concordance of data sources by cancer site and demographics is analyzed.Results and discussionData collected from 315,297 participants resulted in 13,298 cancer cases detected in the survey (in 89,261 participants), 23,520 cancer cases detected in the EHR (in 203,813 participants), and 7,123 cancer cases detected across both sources (in 62,497 participants). Key differences in survey completion by race/ethnicity impacted the makeup of cohorts when compared to cancer in the EHR and national NCI SEER data.ConclusionsThis study provides key insight into cancer detection in the All of Us Research Program and points to the existing strengths and limitations of All of Us as a platform for cancer research now and in the future.

Published
2022

12. Multi-ancestry genetic study of type 2 diabetes highlights the power of diverse populations for discovery and translation

Author

Mahajan, Anubha, Spracklen, Cassandra N., Zhang, Weihua, Ng, Maggie C. Y., Petty, Lauren E., Kitajima, Hidetoshi, Yu, Grace Z., Rüeger, Sina, Speidel, Leo, Kim, Young Jin, Horikoshi, Momoko, Mercader, Josep M., Taliun, Daniel, Moon, Sanghoon, Kwak, Soo-Heon, Robertson, Neil R., Rayner, Nigel W., Loh, Marie, Kim, Bong-Jo, Chiou, Joshua, Miguel-Escalada, Irene, della Briotta Parolo, Pietro, Lin, Kuang, Bragg, Fiona, Preuss, Michael H., Takeuchi, Fumihiko, Nano, Jana, Guo, Xiuqing, Lamri, Amel, Nakatochi, Masahiro, Scott, Robert A., Lee, Jung-Jin, Huerta-Chagoya, Alicia, Graff, Mariaelisa, Chai, Jin-Fang, Parra, Esteban J., Yao, Jie, Bielak, Lawrence F., Tabara, Yasuharu, Hai, Yang, Steinthorsdottir, Valgerdur, Cook, James P., Kals, Mart, Grarup, Niels, Schmidt, Ellen M., Pan, Ian, Sofer, Tamar, Wuttke, Matthias, Sarnowski, Chloe, Gieger, Christian, Nousome, Darryl, Trompet, Stella, Long, Jirong, Sun, Meng, Tong, Lin, Chen, Wei-Min, Ahmad, Meraj, Noordam, Raymond, Lim, Victor J. Y., Tam, Claudia H. T., Joo, Yoonjung Yoonie, Chen, Chien-Hsiun, Raffield, Laura M., Lecoeur, Cécile, Prins, Bram Peter, Nicolas, Aude, Yanek, Lisa R., Chen, Guanjie, Jensen, Richard A., Tajuddin, Salman, Kabagambe, Edmond K., An, Ping, Xiang, Anny H., Choi, Hyeok Sun, Cade, Brian E., Tan, Jingyi, Flanagan, Jack, Abaitua, Fernando, Adair, Linda S., Adeyemo, Adebowale, Aguilar-Salinas, Carlos A., Akiyama, Masato, Anand, Sonia S., Bertoni, Alain, Bian, Zheng, Bork-Jensen, Jette, Brandslund, Ivan, Brody, Jennifer A., Brummett, Chad M., Buchanan, Thomas A., Canouil, Mickaël, Chan, Juliana C. N., Chang, Li-Ching, Chee, Miao-Li, Chen, Ji, Chen, Shyh-Huei, Chen, Yuan-Tsong, Chen, Zhengming, Chuang, Lee-Ming, Cushman, Mary, Das, Swapan K., de Silva, H. Janaka, Dedoussis, George, Dimitrov, Latchezar, Doumatey, Ayo P., Du, Shufa, Duan, Qing, Eckardt, Kai-Uwe, Emery, Leslie S., Evans, Daniel S., Evans, Michele K., Fischer, Krista, Floyd, James S., Ford, Ian, Fornage, Myriam, Franco, Oscar H., Frayling, Timothy M., Freedman, Barry I., Fuchsberger, Christian, Genter, Pauline, Gerstein, Hertzel C., Giedraitis, Vilmantas, González-Villalpando, Clicerio, González-Villalpando, Maria Elena, Goodarzi, Mark O., Gordon-Larsen, Penny, Gorkin, David, Gross, Myron, Guo, Yu, Hackinger, Sophie, Han, Sohee, Hattersley, Andrew T., Herder, Christian, Howard, Annie-Green, Hsueh, Willa, Huang, Mengna, Huang, Wei, Hung, Yi-Jen, Hwang, Mi Yeong, Hwu, Chii-Min, Ichihara, Sahoko, Ikram, Mohammad Arfan, Ingelsson, Martin, Islam, Md Tariqul, Isono, Masato, Jang, Hye-Mi, Jasmine, Farzana, Jiang, Guozhi, Jonas, Jost B., Jørgensen, Marit E., Jørgensen, Torben, Kamatani, Yoichiro, Kandeel, Fouad R., Kasturiratne, Anuradhani, Katsuya, Tomohiro, Kaur, Varinderpal, Kawaguchi, Takahisa, Keaton, Jacob M., Kho, Abel N., Khor, Chiea-Chuen, Kibriya, Muhammad G., Kim, Duk-Hwan, Kohara, Katsuhiko, Kriebel, Jennifer, Kronenberg, Florian, Kuusisto, Johanna, Läll, Kristi, Lange, Leslie A., Lee, Myung-Shik, Lee, Nanette R., Leong, Aaron, Li, Liming, Li, Yun, Li-Gao, Ruifang, Ligthart, Symen, Lindgren, Cecilia M., Linneberg, Allan, Liu, Ching-Ti, Liu, Jianjun, Locke, Adam E., Louie, Tin, Luan, Jian’an, Luk, Andrea O., Luo, Xi, Lv, Jun, Lyssenko, Valeriya, Mamakou, Vasiliki, Mani, K. Radha, Meitinger, Thomas, Metspalu, Andres, Morris, Andrew D., Nadkarni, Girish N., Nadler, Jerry L., Nalls, Michael A., Nayak, Uma, Nongmaithem, Suraj S., Ntalla, Ioanna, Okada, Yukinori, Orozco, Lorena, Patel, Sanjay R., Pereira, Mark A., Peters, Annette, Pirie, Fraser J., Porneala, Bianca, Prasad, Gauri, Preissl, Sebastian, Rasmussen-Torvik, Laura J., Reiner, Alexander P., Roden, Michael, Rohde, Rebecca, Roll, Kathryn, Sabanayagam, Charumathi, Sander, Maike, Sandow, Kevin, Sattar, Naveed, Schönherr, Sebastian, Schurmann, Claudia, Shahriar, Mohammad, Shi, Jinxiu, Shin, Dong Mun, Shriner, Daniel, Smith, Jennifer A., So, Wing Yee, Stančáková, Alena, Stilp, Adrienne M., Strauch, Konstantin, Suzuki, Ken, Takahashi, Atsushi, Taylor, Kent D., Thorand, Barbara, Thorleifsson, Gudmar, Thorsteinsdottir, Unnur, Tomlinson, Brian, Torres, Jason M., Tsai, Fuu-Jen, Tuomilehto, Jaakko, Tusie-Luna, Teresa, Udler, Miriam S., Valladares-Salgado, Adan, van Dam, Rob M., van Klinken, Jan B., Varma, Rohit, Vujkovic, Marijana, Wacher-Rodarte, Niels, Wheeler, Eleanor, Whitsel, Eric A., Wickremasinghe, Ananda R., van Dijk, Ko Willems, Witte, Daniel R., Yajnik, Chittaranjan S., Yamamoto, Ken, Yamauchi, Toshimasa, Yengo, Loïc, Yoon, Kyungheon, Yu, Canqing, Yuan, Jian-Min, Yusuf, Salim, Zhang, Liang, Zheng, Wei, Raffel, Leslie J., Igase, Michiya, Ipp, Eli, Redline, Susan, Cho, Yoon Shin, Lind, Lars, Province, Michael A., Hanis, Craig L., Peyser, Patricia A., Ingelsson, Erik, Zonderman, Alan B., Psaty, Bruce M., Wang, Ya-Xing, Rotimi, Charles N., Becker, Diane M., Matsuda, Fumihiko, Liu, Yongmei, Zeggini, Eleftheria, Yokota, Mitsuhiro, Rich, Stephen S., Kooperberg, Charles, Pankow, James S., Engert, James C., Chen, Yii-Der Ida, Froguel, Philippe, Wilson, James G., Sheu, Wayne H. H., Kardia, Sharon L. R., Wu, Jer-Yuarn, Hayes, M. Geoffrey, Ma, Ronald C. W., Wong, Tien-Yin, Groop, Leif, Mook-Kanamori, Dennis O., Chandak, Giriraj R., Collins, Francis S., Bharadwaj, Dwaipayan, Paré, Guillaume, Sale, Michèle M., Ahsan, Habibul, Motala, Ayesha A., Shu, Xiao-Ou, Park, Kyong-Soo, Jukema, J. Wouter, Cruz, Miguel, McKean-Cowdin, Roberta, Grallert, Harald, Cheng, Ching-Yu, Bottinger, Erwin P., Dehghan, Abbas, Tai, E-Shyong, Dupuis, Josée, Kato, Norihiro, Laakso, Markku, Köttgen, Anna, Koh, Woon-Puay, Palmer, Colin N. A., Liu, Simin, Abecasis, Goncalo, Kooner, Jaspal S., Loos, Ruth J. F., North, Kari E., Haiman, Christopher A., Florez, Jose C., Saleheen, Danish, Hansen, Torben, Pedersen, Oluf, Mägi, Reedik, Langenberg, Claudia, Wareham, Nicholas J., Maeda, Shiro, Kadowaki, Takashi, Lee, Juyoung, Millwood, Iona Y., Walters, Robin G., Stefansson, Kari, Myers, Simon R., Ferrer, Jorge, Gaulton, Kyle J., Meigs, James B., Mohlke, Karen L., Gloyn, Anna L., Bowden, Donald W., Below, Jennifer E., Chambers, John C., Sim, Xueling, Boehnke, Michael, Rotter, Jerome I., McCarthy, Mark I., and Morris, Andrew P.

Published
2022
Full Text
View/download PDF

13. Comparison of oral collection methods for studies of microbiota

Author

Vogtmann, Emily, Chen, Jun, Kibriya, Muhammad G, Amir, Amnon, Shi, Jianxin, Chen, Yu, Islam, Tariqul, Eunes, Mahbubul, Ahmed, Alauddin, Naher, Jabun, Rahman, Anisur, Barmon, Bhaswati, Knight, Rob, Chia, Nicholas, Ahsan, Habibul, Abnet, Christian C, and Sinha, Rashmi

Subjects
Biomedical and Clinical Sciences, Health Sciences, Clinical Research, Bacteria, Bangladesh, Cetylpyridinium, DNA Barcoding, Taxonomic, DNA, Bacterial, Drug Combinations, Healthy Volunteers, Humans, Microbiota, Quaternary Ammonium Compounds, RNA, Ribosomal, 16S, Saliva, Specimen Handling, United States, Medical and Health Sciences, Epidemiology, Biomedical and clinical sciences, Health sciences
Abstract

BackgroundA number of cohort studies have collected Scope mouthwash samples by mail, which are being used for microbiota measurements. We evaluated the stability of Scope mouthwash samples at ambient temperature and determined the comparability of Scope mouthwash with saliva collection using the OMNIgene ORAL Kit.MethodsFifty-three healthy volunteers from Mayo Clinic and 50 cohort members from Bangladesh provided oral samples. One aliquot of the OMNIgene ORAL and Scope mouthwash were frozen immediately and one aliquot of the Scope mouthwash remained at ambient temperature for 4 days and was then frozen. DNA was extracted and the V4 region of the 16S rRNA gene was PCR amplified and sequenced using the HiSeq. Intraclass correlation coefficients (ICC) were calculated.ResultsThe overall stability of the Scope mouthwash samples was relatively high for alpha and beta diversity. For example, the meta-analyzed ICC for the Shannon index was 0.86 (95% confidence interval, 0.76-0.96). Similarly, the ICCs for the relative abundance of the top 25 genera were generally high. The comparability of the two sample types was relatively low when measured using ICCs, but were increased by using a Spearman correlation coefficient (SCC) to compare the rank order of individuals.ConclusionsOverall, the Scope mouthwash samples appear to be stable at ambient temperature, which suggests that oral rinse samples received by the mail can be used for microbial analyses. However, Scope mouthwash samples were distinct compared with OMNIgene ORAL samples.ImpactStudies should try to compare oral microbial metrics within one sample collection type.

Published
2019

14. Reproducibility, stability, and accuracy of microbial profiles by fecal sample collection method in three distinct populations.

Author

Byrd, Doratha A, Chen, Jun, Vogtmann, Emily, Hullings, Autumn, Song, Se Jin, Amir, Amnon, Kibriya, Muhammad G, Ahsan, Habibul, Chen, Yu, Nelson, Heidi, Knight, Rob, Shi, Jianxin, Chia, Nicholas, and Sinha, Rashmi

Subjects
Feces, Humans, DNA, Bacterial, RNA, Ribosomal, 16S, Specimen Handling, Immunochemistry, Feasibility Studies, Reproducibility of Results, Healthy Volunteers, Gastrointestinal Microbiome, General Science & Technology
Abstract

The gut microbiome likely plays a role in the etiology of multiple health conditions, especially those affecting the gastrointestinal tract. Little consensus exists as to the best, standard methods to collect fecal samples for future microbiome analysis. We evaluated three distinct populations (N = 132 participants) using 16S rRNA gene amplicon sequencing data to investigate the reproducibility, stability, and accuracy of microbial profiles in fecal samples collected and stored via fecal occult blood test (FOBT) or Flinders Technology Associates (FTA) cards, fecal immunochemical tests (FIT) tubes, 70% and 95% ethanol, RNAlater, or with no solution. For each collection method, based on relative abundance of select phyla and genera, two alpha diversity metrics, and four beta diversity metrics, we calculated intraclass correlation coefficients (ICCs) to estimate reproducibility and stability, and Spearman correlation coefficients (SCCs) to estimate accuracy of the fecal microbial profile. Comparing duplicate samples, reproducibility ICCs for all collection methods were excellent (ICCs ≥75%). After 4-7 days at ambient temperature, ICCs for microbial profile stability were excellent (≥75%) for most collection methods, except those collected via no-solution and 70% ethanol. SCCs comparing each collection method to immediately-frozen no-solution samples ranged from fair to excellent for most methods; however, accuracy of genus-level relative abundances differed by collection method. Our findings, taken together with previous studies and feasibility considerations, indicated that FOBT/FTA cards, FIT tubes, 95% ethanol, and RNAlater are excellent choices for fecal sample collection methods in future microbiome studies. Furthermore, establishing standard collection methods across studies is highly desirable.

Published
2019

15. Association of KRAS Mutation and Gene Pathways in Colorectal Carcinoma: A Transcriptome- and Methylome-Wide Study and Potential Implications for Therapy.

Author

Jasmine, Farzana, Almazan, Armando, Khamkevych, Yuliia, Bissonnette, Marc, Ahsan, Habibul, and Kibriya, Muhammad G.

Subjects
GENE expression, RAS oncogenes, COLORECTAL cancer, DNA methylation, PROTEASOME inhibitors, P16 gene
Abstract

Kirsten Rat Sarcoma (KRAS) is the most commonly mutated oncogene in colorectal carcinoma (CRC). We have previously reported the interactions between microsatellite instability (MSI), DNA promoter methylation, and gene expression. In this study, we looked for associations between KRAS mutation, gene expression, and methylation that may help with precision medicine. Genome-wide gene expression and DNA methylation were done in paired CRC tumor and surrounding healthy tissues. The results suggested that (a) the magnitude of dysregulation of many major gene pathways in CRC was significantly greater in patients with the KRAS mutation, (b) the up- and down-regulation of these dysregulated gene pathways could be correlated with the corresponding hypo- and hyper-methylation, and (c) the up-regulation of CDKN2A was more pronounced in tumors with the KRAS mutation. A recent cell line study showed that there were higher CDKN2A levels in 5-FU-resistant CRC cells and that these could be down-regulated by Villosol. Our findings suggest the possibility of a better response to anti-CDKN2A therapy with Villosol in KRAS-mutant CRC. Also, the more marked up-regulation of genes in the proteasome pathway in CRC tissue, especially with the KRAS mutation and MSI, may suggest a potential role of a proteasome inhibitor (bortezomib, carfilzomib, or ixazomib) in selected CRC patients if necessary. [ABSTRACT FROM AUTHOR]

Published
2024
Full Text
View/download PDF

18. Comparison of Fecal Collection Methods for Microbiota Studies in Bangladesh

Author

Vogtmann, Emily, Chen, Jun, Kibriya, Muhammad G, Chen, Yu, Islam, Tariqul, Eunes, Mahbubul, Ahmed, Alauddin, Naher, Jabun, Rahman, Anisur, Amir, Amnon, Shi, Jianxin, Abnet, Christian C, Nelson, Heidi, Knight, Rob, Chia, Nicholas, Ahsan, Habibul, and Sinha, Rashmi

Subjects
Medical Microbiology, Biomedical and Clinical Sciences, Aging, Clinical Trials and Supportive Activities, Clinical Research, Adult, Bacteria, Bangladesh, Feces, Female, Freezing, Humans, Male, Microbiota, Middle Aged, Specimen Handling, feces, low/middle-income countries, microbiota, sampling methods, stability, Microbiology, Medical microbiology
Abstract

To our knowledge, fecal microbiota collection methods have not been evaluated in low- and middle-income countries. Therefore, we evaluated five different fecal sample collection methods for technical reproducibility, stability, and accuracy within the Health Effects of Arsenic Longitudinal Study (HEALS) in Bangladesh. Fifty participants from the HEALS provided fecal samples in the clinic which were aliquoted into no solution, 95% ethanol, RNAlater, postdevelopment fecal occult blood test (FOBT) cards, and fecal immunochemical test (FIT) tubes. Half of the aliquots were frozen immediately at -80°C (day 0) and the remaining samples were left at ambient temperature for 96 h and then frozen (day 4). Intraclass correlation coefficients (ICC) were calculated for the relative abundances of the top three phyla, for two alpha diversity measures, and for four beta diversity measures. The duplicate samples had relatively high ICCs for technical reproducibility at day 0 and day 4 (range, 0.79 to 0.99). The FOBT card and samples preserved in RNAlater and 95% ethanol had the highest ICCs for stability over 4 days. The FIT tube had lower stability measures overall. In comparison to the "gold standard" method using immediately frozen fecal samples with no solution, the ICCs for many of the microbial metrics were low, but the rank order appeared to be preserved as seen by the Spearman correlation. The FOBT cards, 95% ethanol, and RNAlater were effective fecal preservatives. These fecal collection methods are optimal for future cohort studies, particularly in low- and middle-income countries.IMPORTANCE The collection of fecal samples in prospective cohort studies is essential to provide the opportunity to study the effect of the human microbiota on numerous health conditions. However, these collection methods have not been adequately tested in low- and middle-income countries. We present estimates of technical reproducibility, stability at ambient temperature for 4 days, and accuracy comparing a "gold standard" for fecal samples in no solution, 95% ethanol, RNAlater, postdevelopment fecal occult blood test cards, and fecal immunochemical test tubes in a study conducted in Bangladesh. Fecal occult blood test cards and fecal samples stored in 95% ethanol or RNAlater adequately preserve fecal samples in this setting. Therefore, new studies in low- and middle-income countries should include collection of fecal samples using fecal occult blood test cards, 95% ethanol, or RNAlater for prospective cohort studies.

Published
2017

19. Molecular Profiling and the Interaction of Somatic Mutations with Transcriptomic Profiles in Non-Melanoma Skin Cancer (NMSC) in a Population Exposed to Arsenic.

Author

Jasmine, Farzana, Argos, Maria, Khamkevych, Yuliia, Islam, Tariqul, Rakibuz-Zaman, Muhammad, Shahriar, Mohammad, Shea, Christopher R., Ahsan, Habibul, and Kibriya, Muhammad G.

Subjects
SOMATIC mutation, SKIN cancer, BASAL cell carcinoma, HEDGEHOG signaling proteins, MOLECULAR interactions, ARSENIC compounds
Abstract

Exposure to inorganic arsenic (As) is recognized as a risk factor for non-melanoma skin cancer (NMSC). We followed up with 7000 adults for 6 years who were exposed to As. During follow-up, 2.2% of the males and 1.3% of the females developed basal cell carcinoma (BCC), while 0.4% of the male and 0.2% of the female participants developed squamous cell carcinoma (SCC). Using a panel of more than 400 cancer-related genes, we detected somatic mutations (SMs) in the first 32 NMSC samples (BCC = 26 and SCC = 6) by comparing paired (tissue–blood) samples from the same individual and then comparing them to the SM in healthy skin tissue from 16 participants. We identified (a) a list of NMSC-associated SMs, (b) SMs present in both NMSC and healthy skin, and (c) SMs found only in healthy skin. We also demonstrate that the presence of non-synonymous SMs in the top mutated genes (like PTCH1, NOTCH1, SYNE1, PKHD1 in BCC and TP53 in SCC) significantly affects the magnitude of differential expressions of major genes and gene pathways (basal cell carcinoma pathways, NOTCH signaling, IL-17 signaling, p53 signaling, Wnt signaling pathway). These findings may help select groups of patients for targeted therapy, like hedgehog signaling inhibitors, IL17 inhibitors, etc., in the future. [ABSTRACT FROM AUTHOR]

Published
2024
Full Text
View/download PDF

20. Air quality and cancer risk in the All of Us Research Program

Author

Craver, Andrew, primary, Luo, Jiajun, additional, Kibriya, Muhammad G., additional, Randorf, Nina, additional, Bahl, Kendall, additional, Connellan, Elizabeth, additional, Powell, Johnny, additional, Zakin, Paul, additional, Jones, Rena R., additional, Argos, Maria, additional, Ho, Joyce, additional, Kim, Karen, additional, Daviglus, Martha L., additional, Greenland, Philip, additional, Ahsan, Habibul, additional, and Aschebrook-Kilfoy, Briseis, additional

Published
2023
Full Text
View/download PDF

21. Duration-sensitive association between air pollution exposure and changes in cardiometabolic biomarkers: Evidence from a predominantly African American cohort

Author

Luo, Jiajun, primary, Kibriya, Muhammad G., additional, Jasmine, Farzana, additional, Shaikh, Afzal, additional, Jin, Zhihao, additional, Sargis, Robert, additional, Kim, Karen, additional, Olopade, Christopher O., additional, Pinto, Jayant, additional, Ahsan, Habibul, additional, and Aschebrook-Kilfoy, Briseis, additional

Published
2023
Full Text
View/download PDF

26. The contribution of parent-to-offspring transmission of telomeres to the heritability of telomere length in humans

Author

Delgado, Dayana A., Zhang, Chenan, Gleason, Kevin, Demanelis, Kathryn, Chen, Lin S., Gao, Jianjun, Roy, Shantanu, Shinkle, Justin, Sabarinathan, Mekala, Argos, Maria, Tong, Lin, Ahmed, Alauddin, Islam, Tariqul, Rakibuz-Zaman, Muhammad, Sarwar, Golam, Shahriar, Hasan, Rahman, Mahfuzar, Yunus, Muhammad, Doherty, Jennifer A., Jasmine, Farzana, Kibriya, Muhammad G., Ahsan, Habibul, and Pierce, Brandon L.

Published
2019
Full Text
View/download PDF

28. The Role of Health Insurance Type and Clinic Visit on Hypertension Status Among Multiethnic Chicago Residents

Author

Luo, Jiajun, Krakowka, William I., Craver, Andrew, Connellan, Elizabeth, King, Jaime, Kibriya, Muhammad G., Pinto, Jayant, Polonsky, Tamar, Kim, Karen, Ahsan, Habibul, and Aschebrook-Kilfoy, Briseis

Abstract

Purpose To investigate the joint relationship of health insurance and clinic visit with hypertension among underserved populations.Design Population-based cohort study.Subjects Data from 1092 participants from the Chicago Multiethnic Prevention and Surveillance Study (COMPASS) between 2013 and 2020 were analyzed.Measures Five health insurance types were included: uninsured, Medicaid, Medicare, private, and other. Clinic visit over past 12 months were retrieved from medical records and categorized into 4 groups: no clinic visit, 1-3 visits, 4-7 visits, >7 visits.Analysis Inverse-probability weighted logistic regression was used to estimate odds ratios (OR) and 95% confidence interval (CI) for hypertension status according to health insurance and clinic visit. Models were adjusted for individual socio-demographic variables and medical history.Results The study population was predominantly Black (>85%) of low socioeconomic status. Health insurance was not associated with more clinic visit. Measured hypertension was more frequently found in private insurance (OR = 6.48, 95% CI: 1.92-21.85) compared to the uninsured group, while 1-3 clinic visits were associated with less prevalence (OR = .59, 95% CI: .35-1.00) compared to no clinic visit. These associations remained unchanged when health insurance and clinic visit were adjusted for each other.Conclusion In this study population, private insurance was associated with higher measured hypertension prevalence compared to no insurance. The associations of health insurance and clinic visit were independent of each other.

Published
2024
Full Text
View/download PDF

30. Erratum: 'Rare, protein-altering variants in AS3MT and arsenic metabolism efficiency: a multi-population association study'

Author

Delgado, Dayana A., Chernoff, Meytal, Huang, Lei, Tong, Lin, Chen, Lin, Jasmine, Farzana, Shinkle, Justin, Cole, Shelley A., Haack, Karin, Kent, Jack, Umans, Jason, Best, Lyle G., Nelson, Heather, Griend, Donald Vander, Graziano, Joseph, Kibriya, Muhammad G., Navas-Acien, Ana, Karagas, Margaret R., Ahsan, Habibul, and Pierce, Brandon L.

Subjects
Environmental issues, Health
Abstract

EnvironHealthPerspect129(4):047007,2021. https://doi.org/10.1289/EHP8152 The 'Acknowledgments' section was missing several funding sources relevant to this work. The 'Acknowledgments' section should read as follows: 'The authors thank all the men and women who [...]

Published
2021
Full Text
View/download PDF

31. Screening for gene–environment (G×E) interaction using omics data from exposed individuals: an application to gene-arsenic interaction

Author

Argos, Maria, Tong, Lin, Roy, Shantanu, Sabarinathan, Mekala, Ahmed, Alauddin, Islam, Md. Tariqul, Islam, Tariqul, Rakibuz-Zaman, Muhammad, Sarwar, Golam, Shahriar, Hasan, Rahman, Mahfuzar, Yunus, Md., Graziano, Joseph H., Jasmine, Farzana, Kibriya, Muhammad G., Zhou, Xiang, Ahsan, Habibul, and Pierce, Brandon L.

Published
2018
Full Text
View/download PDF

32. The impact of rare variation on gene expression across tissues

Author

Li, Xin, Kim, Yungil, Tsang, Emily K., Davis, Joe R., Damani, Farhan N., Chiang, Colby, Hess, Gaelen T., Zappala, Zachary, Strober, Benjamin J., Scott, Alexandra J., Li, Amy, Ganna, Andrea, Bassik, Michael C., Merker, Jason D., Aguet, Franois, Ardlie, Kristin G., Cummings, Beryl B., Gelfand, Ellen T., Getz, Gad, Hadley, Kane, Handsaker, Robert E., Huang, Katherine H., Kashin, Seva, Karczewski, Konrad J., Lek, Monkol, Li, Xiao, MacArthur, Daniel G., Nedzel, Jared L., Nguyen, Duyen T., Noble, Michael S., Segr, Ayellet V., Trowbridge, Casandra A., Tukiainen, Taru, Abell, Nathan S., Balliu, Brunilda, Barshir, Ruth, Basha, Omer, Battle, Alexis, Bogu, Gireesh K., Brown, Andrew, Brown, Christopher D., Castel, Stephane E., Chen, Lin S., Conrad, Donald F., Cox, Nancy J., Delaneau, Olivier, Dermitzakis, Emmanouil T., Engelhardt, Barbara E., Eskin, Eleazar, Ferreira, Pedro G., Frsard, Laure, Gamazon, Eric R., Garrido-Martn, Diego, Gewirtz, Ariel D.H., Gliner, Genna, Gloudemans, Michael J., Guigo, Roderic, Hall, Ira M., Han, Buhm, He, Yuan, Hormozdiari, Farhad, Howald, Cedric, Kyung Im, Hae, Jo, Brian, Yong Kang, Eun, Kim-Hellmuth, Sarah, Lappalainen, Tuuli, Li, Gen, Liu, Boxiang, Mangul, Serghei, McCarthy, Mark I., McDowell, Ian C., Mohammadi, Pejman, Monlong, Jean, Montgomery, Stephen B., Muoz-Aguirre, Manuel, Ndungu, Anne W., Nicolae, Dan L., Nobel, Andrew B., Oliva, Meritxell, Ongen, Halit, Palowitch, John J., Panousis, Nikolaos, Papasaikas, Panagiotis, Park, YoSon, Parsana, Princy, Payne, Anthony J., Peterson, Christine B., Quan, Jie, Reverter, Ferran, Sabatti, Chiara, Saha, Ashis, Sammeth, Michael, Shabalin, Andrey A., Sodaei, Reza, Stephens, Matthew, Stranger, Barbara E., Sul, Jae Hoon, Urbut, Sarah, van de Bunt, Martijn, Wang, Gao, Wen, Xiaoquan, Wright, Fred A., Xi, Hualin S., Yeger-Lotem, Esti, Zaugg, Judith B., Zhou, Yi-Hui, Akey, Joshua M., Bates, Daniel, Chan, Joanne, Claussnitzer, Melina, Demanelis, Kathryn, Diegel, Morgan, Doherty, Jennifer A., Feinberg, Andrew P., Fernando, Marian S., Halow, Jessica, Hansen, Kasper D., Haugen, Eric, Hickey, Peter F., Hou, Lei, Jasmine, Farzana, Jian, Ruiqi, Jiang, Lihua, Johnson, Audra, Kaul, Rajinder, Kellis, Manolis, Kibriya, Muhammad G., Lee, Kristen, Billy Li, Jin, Li, Qin, Lin, Jessica, Lin, Shin, Linder, Sandra, Linke, Caroline, Liu, Yaping, Maurano, Matthew T., Molinie, Benoit, Nelson, Jemma, Neri, Fidencio J., Park, Yongjin, Pierce, Brandon L., Rinaldi, Nicola J., Rizzardi, Lindsay F., Sandstrom, Richard, Skol, Andrew, Smith, Kevin S., Snyder, Michael P., Stamatoyannopoulos, John, Tang, Hua, Wang, Li, Wang, Meng, Van Wittenberghe, Nicholas, Wu, Fan, Zhang, Rui, Nierras, Concepcion R., Branton, Philip A., Carithers, Latarsha J., Guan, Ping, Moore, Helen M., Rao, Abhi, Vaught, Jimmie B., Gould, Sarah E., Lockart, Nicole C., Martin, Casey, Struewing, Jeffery P., Volpi, Simona, Addington, Anjene M., Koester, Susan E., Little, A. Roger, Brigham, Lori E., Hasz, Richard, Hunter, Marcus, Johns, Christopher, Johnson, Mark, Kopen, Gene, Leinweber, William F., Lonsdale, John T., McDonald, Alisa, Mestichelli, Bernadette, Myer, Kevin, Roe, Brian, Salvatore, Michael, Shad, Saboor, Thomas, Jeffrey A., Walters, Gary, Washington, Michael, Wheeler, Joseph, Bridge, Jason, Foster, Barbara A., Gillard, Bryan M., Karasik, Ellen, Kumar, Rachna, Miklos, Mark, Moser, Michael T., Jewell, Scott D., Montroy, Robert G., Rohrer, Daniel C., Valley, Dana R., Davis, David A., Mash, Deborah C., Undale, Anita H., Smith, Anna M., Tabor, David E., Roche, Nancy V., McLean, Jeffrey A., Vatanian, Negin, Robinson, Karna L., Sobin, Leslie, Barcus, Mary E., Valentino, Kimberly M., Qi, Liqun, Hunter, Steven, Hariharan, Pushpa, Singh, Shilpi, Um, Ki Sung, Matose, Takunda, Tomaszewski, Maria M., Barker, Laura K., Mosavel, Maghboeba, Siminoff, Laura A., Traino, Heather M., Flicek, Paul, Juettemann, Thomas, Ruffier, Magali, Sheppard, Dan, Taylor, Kieron, Trevanion, Stephen J., Zerbino, Daniel R., Craft, Brian, Goldman, Mary, Haeussler, Maximilian, Kent, W. James, Lee, Christopher M., Paten, Benedict, Rosenbloom, Kate R., Vivian, John, and Zhu, Jingchun

Subjects
Disease susceptibility -- Genetic aspects, Genetic variation -- Observations, Gene expression -- Observations, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): Xin Li [1]; Yungil Kim [2]; Emily K. Tsang [1, 3]; Joe R. Davis [1, 4]; Farhan N. Damani [2]; Colby Chiang [5]; Gaelen T. Hess [4]; Zachary Zappala [...]

Published
2017
Full Text
View/download PDF

33. Dynamic landscape and regulation of RNA editing in mammals

Author

Tan, Meng How, Li, Qin, Shanmugam, Raghuvaran, Piskol, Robert, Kohler, Jennefer, Young, Amy N., Liu, Kaiwen Ivy, Zhang, Rui, Ramaswami, Gokul, Ariyoshi, Kentaro, Gupte, Ankita, Keegan, Liam P., George, Cyril X., Ramu, Avinash, Huang, Ni, Pollina, Elizabeth A., Leeman, Dena S., Rustighi, Alessandra, Goh, Y. P. Sharon, Aguet, Franois, Ardlie, Kristin G., Cummings, Beryl B., Gelfand, Ellen T., Getz, Gad, Hadley, Kane, Handsaker, Robert E., Huang, Katherine H., Kashin, Seva, Karczewski, Konrad J., Lek, Monkol, Li, Xiao, MacArthur, Daniel G., Nedzel, Jared L., Nguyen, Duyen T., Noble, Michael S., Segr, Ayellet V., Trowbridge, Casandra A., Tukiainen, Taru, Abell, Nathan S., Balliu, Brunilda, Barshir, Ruth, Basha, Omer, Battle, Alexis, Bogu, Gireesh K., Brown, Andrew, Brown, Christopher D., Castel, Stephane E., Chen, Lin S., Chiang, Colby, Conrad, Donald F., Cox, Nancy J., Damani, Farhan N., Davis, Joe R., Delaneau, Olivier, Dermitzakis, Emmanouil T., Engelhardt, Barbara E., Eskin, Eleazar, Ferreira, Pedro G., Frsard, Laure, Gamazon, Eric R., Garrido-Martn, Diego, Gewirtz, Ariel D. H., Gliner, Genna, Gloudemans, Michael J., Guigo, Roderic, Hall, Ira M., Han, Buhm, He, Yuan, Hormozdiari, Farhad, Howald, Cedric, Kyung Im, Hae, Jo, Brian, Yong Kang, Eun, Kim, Yungil, Kim-Hellmuth, Sarah, Lappalainen, Tuuli, Li, Gen, Li, Xin, Liu, Boxiang, Mangul, Serghei, McCarthy, Mark I., McDowell, Ian C., Mohammadi, Pejman, Monlong, Jean, Montgomery, Stephen B., Muoz-Aguirre, Manuel, Ndungu, Anne W., Nicolae, Dan L., Nobel, Andrew B., Oliva, Meritxell, Ongen, Halit, Palowitch, John J., Panousis, Nikolaos, Papasaikas, Panagiotis, Park, YoSon, Parsana, Princy, Payne, Anthony J., Peterson, Christine B., Quan, Jie, Reverter, Ferran, Sabatti, Chiara, Saha, Ashis, Sammeth, Michael, Scott, Alexandra J., Shabalin, Andrey A., Sodaei, Reza, Stephens, Matthew, Stranger, Barbara E., Strober, Benjamin J., Sul, Jae Hoon, Tsang, Emily K., Urbut, Sarah, van de Bunt, Martijn, Wang, Gao, Wen, Xiaoquan, Wright, Fred A., Xi, Hualin S., Yeger-Lotem, Esti, Zappala, Zachary, Zaugg, Judith B., Zhou, Yi-Hui, Akey, Joshua M., Bates, Daniel, Chan, Joanne, Claussnitzer, Melina, Demanelis, Kathryn, Diegel, Morgan, Doherty, Jennifer A., Feinberg, Andrew P., Fernando, Marian S., Halow, Jessica, Hansen, Kasper D., Haugen, Eric, Hickey, Peter F., Hou, Lei, Jasmine, Farzana, Jian, Ruiqi, Jiang, Lihua, Johnson, Audra, Kaul, Rajinder, Kellis, Manolis, Kibriya, Muhammad G., Lee, Kristen, Li, Jin Billy, Lin, Jessica, Lin, Shin, Linder, Sandra, Linke, Caroline, Liu, Yaping, Maurano, Matthew T., Molinie, Benoit, Nelson, Jemma, Neri, Fidencio J., Park, Yongjin, Pierce, Brandon L., Rinaldi, Nicola J., Rizzardi, Lindsay F., Sandstrom, Richard, Skol, Andrew, Smith, Kevin S., Snyder, Michael P., Stamatoyannopoulos, John, Tang, Hua, Wang, Li, Wang, Meng, Van Wittenberghe, Nicholas, Wu, Fan, Nierras, Concepcion R., Branton, Philip A., Carithers, Latarsha J., Guan, Ping, Moore, Helen M., Rao, Abhi, Vaught, Jimmie B., Gould, Sarah E., Lockart, Nicole C., Martin, Casey, Struewing, Jeffery P., Volpi, Simona, Addington, Anjene M., Koester, Susan E., Little, A. Roger, Brigham, Lori E., Hasz, Richard, Hunter, Marcus, Johns, Christopher, Johnson, Mark, Kopen, Gene, Leinweber, William F., Lonsdale, John T., McDonald, Alisa, Mestichelli, Bernadette, Myer, Kevin, Roe, Brian, Salvatore, Michael, Shad, Saboor, Thomas, Jeffrey A., Walters, Gary, Washington, Michael, Wheeler, Joseph, Bridge, Jason, Foster, Barbara A., Gillard, Bryan M., Karasik, Ellen, Kumar, Rachna, Miklos, Mark, Moser, Michael T., Jewell, Scott D., Montroy, Robert G., Rohrer, Daniel C., Valley, Dana R., Davis, David A., Mash, Deborah C., Undale, Anita H., Smith, Anna M., Tabor, David E., Roche, Nancy V., McLean, Jeffrey A., Vatanian, Negin, Robinson, Karna L., Sobin, Leslie, Barcus, Mary E., Valentino, Kimberly M., Qi, Liqun, Hunter, Steven, Hariharan, Pushpa, Singh, Shilpi, Um, Ki Sung, Matose, Takunda, Tomaszewski, Maria M., Barker, Laura K., Mosavel, Maghboeba, Siminoff, Laura A., Traino, Heather M., Flicek, Paul, Juettemann, Thomas, Ruffier, Magali, Sheppard, Dan, Taylor, Kieron, Trevanion, Stephen J., Zerbino, Daniel R., Craft, Brian, Goldman, Mary, Haeussler, Maximilian, Kent, W. James, Lee, Christopher M., Paten, Benedict, Rosenbloom, Kate R., Vivian, John, Zhu, Jingchun, Chawla, Ajay, Del Sal, Giannino, Peltz, Gary, Brunet, Anne, Samuel, Charles E., OConnell, Mary A., Walkley, Carl R., and Nishikura, Kazuko

Subjects
Genetic research, Mammals -- Genetic aspects, RNA processing -- Research, Genetic regulation, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): Meng How Tan (corresponding author) [1, 2, 3]; Qin Li [1]; Raghuvaran Shanmugam [2, 3]; Robert Piskol [1]; Jennefer Kohler [1]; Amy N. Young [1]; Kaiwen Ivy Liu [3]; [...]

Published
2017
Full Text
View/download PDF

34. Landscape of X chromosome inactivation across human tissues

Author

Tukiainen, Taru, Villani, Alexandra-Chlo, Yen, Angela, Rivas, Manuel A., Marshall, Jamie L., Satija, Rahul, Aguirre, Matt, Gauthier, Laura, Fleharty, Mark, Kirby, Andrew, Cummings, Beryl B., Castel, Stephane E., Karczewski, Konrad J., Aguet, Franois, Byrnes, Andrea, Ardlie, Kristin G., Gelfand, Ellen T., Getz, Gad, Hadley, Kane, Handsaker, Robert E., Huang, Katherine H., Kashin, Seva, Lek, Monkol, Li, Xiao, MacArthur, Daniel G., Nedzel, Jared L., Nguyen, Duyen T., Noble, Michael S., Segr, Ayellet V., Trowbridge, Casandra A., Abell, Nathan S., Balliu, Brunilda, Barshir, Ruth, Basha, Omer, Battle, Alexis, Bogu, Gireesh K., Brown, Andrew, Brown, Christopher D., Chen, Lin S., Chiang, Colby, Conrad, Donald F., Cox, Nancy J., Damani, Farhan N., Davis, Joe R., Delaneau, Olivier, Dermitzakis, Emmanouil T., Engelhardt, Barbara E., Eskin, Eleazar, Ferreira, Pedro G., Frsard, Laure, Gamazon, Eric R., Garrido-Martn, Diego, Gewirtz, Ariel D. H., Gliner, Genna, Gloudemans, Michael J., Guigo, Roderic, Hall, Ira M., Han, Buhm, He, Yuan, Hormozdiari, Farhad, Howald, Cedric, Kyung Im, Hae, Jo, Brian, Yong Kang, Eun, Kim, Yungil, Kim-Hellmuth, Sarah, Lappalainen, Tuuli, Li, Gen, Li, Xin, Liu, Boxiang, Mangul, Serghei, McCarthy, Mark I., McDowell, Ian C., Mohammadi, Pejman, Monlong, Jean, Montgomery, Stephen B., Muoz-Aguirre, Manuel, Ndungu, Anne W., Nicolae, Dan L., Nobel, Andrew B., Oliva, Meritxell, Ongen, Halit, Palowitch, John J., Panousis, Nikolaos, Papasaikas, Panagiotis, Park, YoSon, Parsana, Princy, Payne, Anthony J., Peterson, Christine B., Quan, Jie, Reverter, Ferran, Sabatti, Chiara, Saha, Ashis, Sammeth, Michael, Scott, Alexandra J., Shabalin, Andrey A., Sodaei, Reza, Stephens, Matthew, Stranger, Barbara E., Strober, Benjamin J., Sul, Jae Hoon, Tsang, Emily K., Urbut, Sarah, van de Bunt, Martijn, Wang, Gao, Wen, Xiaoquan, Wright, Fred A., Xi, Hualin S., Yeger-Lotem, Esti, Zappala, Zachary, Zaugg, Judith B., Zhou, Yi-Hui, Akey, Joshua M., Bates, Daniel, Chan, Joanne, Claussnitzer, Melina, Demanelis, Kathryn, Diegel, Morgan, Doherty, Jennifer A., Feinberg, Andrew P., Fernando, Marian S., Halow, Jessica, Hansen, Kasper D., Haugen, Eric, Hickey, Peter F., Hou, Lei, Jasmine, Farzana, Jian, Ruiqi, Jiang, Lihua, Johnson, Audra, Kaul, Rajinder, Kellis, Manolis, Kibriya, Muhammad G., Lee, Kristen, Li, Jin Billy, Li, Qin, Lin, Jessica, Lin, Shin, Linder, Sandra, Linke, Caroline, Liu, Yaping, Maurano, Matthew T., Molinie, Benoit, Nelson, Jemma, Neri, Fidencio J., Park, Yongjin, Pierce, Brandon L., Rinaldi, Nicola J., Rizzardi, Lindsay F., Sandstrom, Richard, Skol, Andrew, Smith, Kevin S., Snyder, Michael P., Stamatoyannopoulos, John, Tang, Hua, Wang, Li, Wang, Meng, Van Wittenberghe, Nicholas, Wu, Fan, Zhang, Rui, Nierras, Concepcion R., Branton, Philip A., Carithers, Latarsha J., Guan, Ping, Moore, Helen M., Rao, Abhi, Vaught, Jimmie B., Gould, Sarah E., Lockart, Nicole C., Martin, Casey, Struewing, Jeffery P., Volpi, Simona, Addington, Anjene M., Koester, Susan E., Little, A. Roger, Brigham, Lori E., Hasz, Richard, Hunter, Marcus, Johns, Christopher, Johnson, Mark, Kopen, Gene, Leinweber, William F., Lonsdale, John T., McDonald, Alisa, Mestichelli, Bernadette, Myer, Kevin, Roe, Brian, Salvatore, Michael, Shad, Saboor, Thomas, Jeffrey A., Walters, Gary, Washington, Michael, Wheeler, Joseph, Bridge, Jason, Foster, Barbara A., Gillard, Bryan M., Karasik, Ellen, Kumar, Rachna, Miklos, Mark, Moser, Michael T., Jewell, Scott D., Montroy, Robert G., Rohrer, Daniel C., Valley, Dana R., Davis, David A., Mash, Deborah C., Undale, Anita H., Smith, Anna M., Tabor, David E., Roche, Nancy V., McLean, Jeffrey A., Vatanian, Negin, Robinson, Karna L., Sobin, Leslie, Barcus, Mary E., Valentino, Kimberly M., Qi, Liqun, Hunter, Steven, Hariharan, Pushpa, Singh, Shilpi, Um, Ki Sung, Matose, Takunda, Tomaszewski, Maria M., Barker, Laura K., Mosavel, Maghboeba, Siminoff, Laura A., Traino, Heather M., Flicek, Paul, Juettemann, Thomas, Ruffier, Magali, Sheppard, Dan, Taylor, Kieron, Trevanion, Stephen J., Zerbino, Daniel R., Craft, Brian, Goldman, Mary, Haeussler, Maximilian, Kent, W. James, Lee, Christopher M., Paten, Benedict, Rosenbloom, Kate R., Vivian, John, Zhu, Jingchun, Regev, Aviv, and Hacohen, Nir

Subjects
Chromosomes -- Physiological aspects, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): Taru Tukiainen (corresponding author) [1, 2]; Alexandra-Chlo Villani [2, 3]; Angela Yen [2, 4]; Manuel A. Rivas [1, 2, 5]; Jamie L. Marshall [1, 2]; Rahul Satija [2, 6, [...]

Published
2017
Full Text
View/download PDF

35. Supplementary Table 1 from Cross-Cancer Genome-Wide Analysis of Lung, Ovary, Breast, Prostate, and Colorectal Cancer Reveals Novel Pleiotropic Associations

Author

Fehringer, Gordon, primary, Kraft, Peter, primary, Pharoah, Paul D., primary, Eeles, Rosalind A., primary, Chatterjee, Nilanjan, primary, Schumacher, Fredrick R., primary, Schildkraut, Joellen M., primary, Lindström, Sara, primary, Brennan, Paul, primary, Bickeböller, Heike, primary, Houlston, Richard S., primary, Landi, Maria Teresa, primary, Caporaso, Neil, primary, Risch, Angela, primary, Amin Al Olama, Ali, primary, Berndt, Sonja I., primary, Giovannucci, Edward L., primary, Grönberg, Henrik, primary, Kote-Jarai, Zsofia, primary, Ma, Jing, primary, Muir, Kenneth, primary, Stampfer, Meir J., primary, Stevens, Victoria L., primary, Wiklund, Fredrik, primary, Willett, Walter C., primary, Goode, Ellen L., primary, Permuth, Jennifer B., primary, Risch, Harvey A., primary, Reid, Brett M., primary, Bezieau, Stephane, primary, Brenner, Hermann, primary, Chan, Andrew T., primary, Chang-Claude, Jenny, primary, Hudson, Thomas J., primary, Kocarnik, Jonathan K., primary, Newcomb, Polly A., primary, Schoen, Robert E., primary, Slattery, Martha L., primary, White, Emily, primary, Adank, Muriel A., primary, Ahsan, Habibul, primary, Aittomäki, Kristiina, primary, Baglietto, Laura, primary, Blomquist, Carl, primary, Canzian, Federico, primary, Czene, Kamila, primary, dos-Santos-Silva, Isabel, primary, Eliassen, A. Heather, primary, Figueroa, Jonine D., primary, Flesch-Janys, Dieter, primary, Fletcher, Olivia, primary, Garcia-Closas, Montserrat, primary, Gaudet, Mia M., primary, Johnson, Nichola, primary, Hall, Per, primary, Hazra, Aditi, primary, Hein, Rebecca, primary, Hofman, Albert, primary, Hopper, John L., primary, Irwanto, Astrid, primary, Johansson, Mattias, primary, Kaaks, Rudolf, primary, Kibriya, Muhammad G., primary, Lichtner, Peter, primary, Liu, Jianjun, primary, Lund, Eiliv, primary, Makalic, Enes, primary, Meindl, Alfons, primary, Müller-Myhsok, Bertram, primary, Muranen, Taru A., primary, Nevanlinna, Heli, primary, Peeters, Petra H., primary, Peto, Julian, primary, Prentice, Ross L., primary, Rahman, Nazneen, primary, Sanchez, Maria Jose, primary, Schmidt, Daniel F., primary, Schmutzler, Rita K., primary, Southey, Melissa C., primary, Tamimi, Rulla, primary, Travis, Ruth C., primary, Turnbull, Clare, primary, Uitterlinden, Andre G., primary, Wang, Zhaoming, primary, Whittemore, Alice S., primary, Yang, Xiaohong R., primary, Zheng, Wei, primary, Buchanan, Daniel D., primary, Casey, Graham, primary, Conti, David V., primary, Edlund, Christopher K., primary, Gallinger, Steven, primary, Haile, Robert W., primary, Jenkins, Mark, primary, Le Marchand, Loïc, primary, Li, Li, primary, Lindor, Noralene M., primary, Schmit, Stephanie L., primary, Thibodeau, Stephen N., primary, Woods, Michael O., primary, Rafnar, Thorunn, primary, Gudmundsson, Julius, primary, Stacey, Simon N., primary, Stefansson, Kari, primary, Sulem, Patrick, primary, Chen, Y. Ann, primary, Tyrer, Jonathan P., primary, Christiani, David C., primary, Wei, Yongyue, primary, Shen, Hongbing, primary, Hu, Zhibin, primary, Shu, Xiao-Ou, primary, Shiraishi, Kouya, primary, Takahashi, Atsushi, primary, Bossé, Yohan, primary, Obeidat, Ma'en, primary, Nickle, David, primary, Timens, Wim, primary, Freedman, Matthew L., primary, Li, Qiyuan, primary, Seminara, Daniela, primary, Chanock, Stephen J., primary, Gong, Jian, primary, Peters, Ulrike, primary, Gruber, Stephen B., primary, Amos, Christopher I., primary, Sellers, Thomas A., primary, Easton, Douglas F., primary, Hunter, David J., primary, Haiman, Christopher A., primary, Henderson, Brian E., primary, and Hung, Rayjean J., primary

Published
2023
Full Text
View/download PDF

36. Data from Cross-Cancer Genome-Wide Analysis of Lung, Ovary, Breast, Prostate, and Colorectal Cancer Reveals Novel Pleiotropic Associations

Author

Fehringer, Gordon, primary, Kraft, Peter, primary, Pharoah, Paul D., primary, Eeles, Rosalind A., primary, Chatterjee, Nilanjan, primary, Schumacher, Fredrick R., primary, Schildkraut, Joellen M., primary, Lindström, Sara, primary, Brennan, Paul, primary, Bickeböller, Heike, primary, Houlston, Richard S., primary, Landi, Maria Teresa, primary, Caporaso, Neil, primary, Risch, Angela, primary, Amin Al Olama, Ali, primary, Berndt, Sonja I., primary, Giovannucci, Edward L., primary, Grönberg, Henrik, primary, Kote-Jarai, Zsofia, primary, Ma, Jing, primary, Muir, Kenneth, primary, Stampfer, Meir J., primary, Stevens, Victoria L., primary, Wiklund, Fredrik, primary, Willett, Walter C., primary, Goode, Ellen L., primary, Permuth, Jennifer B., primary, Risch, Harvey A., primary, Reid, Brett M., primary, Bezieau, Stephane, primary, Brenner, Hermann, primary, Chan, Andrew T., primary, Chang-Claude, Jenny, primary, Hudson, Thomas J., primary, Kocarnik, Jonathan K., primary, Newcomb, Polly A., primary, Schoen, Robert E., primary, Slattery, Martha L., primary, White, Emily, primary, Adank, Muriel A., primary, Ahsan, Habibul, primary, Aittomäki, Kristiina, primary, Baglietto, Laura, primary, Blomquist, Carl, primary, Canzian, Federico, primary, Czene, Kamila, primary, dos-Santos-Silva, Isabel, primary, Eliassen, A. Heather, primary, Figueroa, Jonine D., primary, Flesch-Janys, Dieter, primary, Fletcher, Olivia, primary, Garcia-Closas, Montserrat, primary, Gaudet, Mia M., primary, Johnson, Nichola, primary, Hall, Per, primary, Hazra, Aditi, primary, Hein, Rebecca, primary, Hofman, Albert, primary, Hopper, John L., primary, Irwanto, Astrid, primary, Johansson, Mattias, primary, Kaaks, Rudolf, primary, Kibriya, Muhammad G., primary, Lichtner, Peter, primary, Liu, Jianjun, primary, Lund, Eiliv, primary, Makalic, Enes, primary, Meindl, Alfons, primary, Müller-Myhsok, Bertram, primary, Muranen, Taru A., primary, Nevanlinna, Heli, primary, Peeters, Petra H., primary, Peto, Julian, primary, Prentice, Ross L., primary, Rahman, Nazneen, primary, Sanchez, Maria Jose, primary, Schmidt, Daniel F., primary, Schmutzler, Rita K., primary, Southey, Melissa C., primary, Tamimi, Rulla, primary, Travis, Ruth C., primary, Turnbull, Clare, primary, Uitterlinden, Andre G., primary, Wang, Zhaoming, primary, Whittemore, Alice S., primary, Yang, Xiaohong R., primary, Zheng, Wei, primary, Buchanan, Daniel D., primary, Casey, Graham, primary, Conti, David V., primary, Edlund, Christopher K., primary, Gallinger, Steven, primary, Haile, Robert W., primary, Jenkins, Mark, primary, Le Marchand, Loïc, primary, Li, Li, primary, Lindor, Noralene M., primary, Schmit, Stephanie L., primary, Thibodeau, Stephen N., primary, Woods, Michael O., primary, Rafnar, Thorunn, primary, Gudmundsson, Julius, primary, Stacey, Simon N., primary, Stefansson, Kari, primary, Sulem, Patrick, primary, Chen, Y. Ann, primary, Tyrer, Jonathan P., primary, Christiani, David C., primary, Wei, Yongyue, primary, Shen, Hongbing, primary, Hu, Zhibin, primary, Shu, Xiao-Ou, primary, Shiraishi, Kouya, primary, Takahashi, Atsushi, primary, Bossé, Yohan, primary, Obeidat, Ma'en, primary, Nickle, David, primary, Timens, Wim, primary, Freedman, Matthew L., primary, Li, Qiyuan, primary, Seminara, Daniela, primary, Chanock, Stephen J., primary, Gong, Jian, primary, Peters, Ulrike, primary, Gruber, Stephen B., primary, Amos, Christopher I., primary, Sellers, Thomas A., primary, Easton, Douglas F., primary, Hunter, David J., primary, Haiman, Christopher A., primary, Henderson, Brian E., primary, and Hung, Rayjean J., primary

Published
2023
Full Text
View/download PDF

37. Supplementary Methods, Tables 1 - 6 from A Genome-wide Association Study of Early-Onset Breast Cancer Identifies PFKM as a Novel Breast Cancer Gene and Supports a Common Genetic Spectrum for Breast Cancer at Any Age

Author

Ahsan, Habibul, primary, Halpern, Jerry, primary, Kibriya, Muhammad G., primary, Pierce, Brandon L., primary, Tong, Lin, primary, Gamazon, Eric, primary, McGuire, Valerie, primary, Felberg, Anna, primary, Shi, Jianxin, primary, Jasmine, Farzana, primary, Roy, Shantanu, primary, Brutus, Rachelle, primary, Argos, Maria, primary, Melkonian, Stephanie, primary, Chang-Claude, Jenny, primary, Andrulis, Irene, primary, Hopper, John L., primary, John, Esther M., primary, Malone, Kathi, primary, Ursin, Giske, primary, Gammon, Marilie D., primary, Thomas, Duncan C., primary, Seminara, Daniela, primary, Casey, Graham, primary, Knight, Julia A., primary, Southey, Melissa C., primary, Giles, Graham G., primary, Santella, Regina M., primary, Lee, Eunjung, primary, Conti, David, primary, Duggan, David, primary, Gallinger, Steve, primary, Haile, Robert, primary, Jenkins, Mark, primary, Lindor, Noralane M., primary, Newcomb, Polly, primary, Michailidou, Kyriaki, primary, Apicella, Carmel, primary, Park, Daniel J., primary, Peto, Julian, primary, Fletcher, Olivia, primary, dos Santos Silva, Isabel, primary, Lathrop, Mark, primary, Hunter, David J., primary, Chanock, Stephen J., primary, Meindl, Alfons, primary, Schmutzler, Rita K., primary, Müller-Myhsok, Bertram, primary, Lochmann, Magdalena, primary, Beckmann, Lars, primary, Hein, Rebecca, primary, Makalic, Enes, primary, Schmidt, Daniel F., primary, Bui, Quang Minh, primary, Stone, Jennifer, primary, Flesch-Janys, Dieter, primary, Dahmen, Norbert, primary, Nevanlinna, Heli, primary, Aittomäki, Kristiina, primary, Blomqvist, Carl, primary, Hall, Per, primary, Czene, Kamila, primary, Irwanto, Astrid, primary, Liu, Jianjun, primary, Rahman, Nazneen, primary, Turnbull, Clare, primary, Dunning, Alison M., primary, Pharoah, Paul, primary, Waisfisz, Quinten, primary, Meijers-Heijboer, Hanne, primary, Uitterlinden, Andre G., primary, Rivadeneira, Fernando, primary, Nicolae, Dan, primary, Easton, Douglas F., primary, Cox, Nancy J., primary, and Whittemore, Alice S., primary

Published
2023
Full Text
View/download PDF

38. Supplementary Table 2 and Supplemental Figures from Cross-Cancer Genome-Wide Analysis of Lung, Ovary, Breast, Prostate, and Colorectal Cancer Reveals Novel Pleiotropic Associations

Author

Fehringer, Gordon, primary, Kraft, Peter, primary, Pharoah, Paul D., primary, Eeles, Rosalind A., primary, Chatterjee, Nilanjan, primary, Schumacher, Fredrick R., primary, Schildkraut, Joellen M., primary, Lindström, Sara, primary, Brennan, Paul, primary, Bickeböller, Heike, primary, Houlston, Richard S., primary, Landi, Maria Teresa, primary, Caporaso, Neil, primary, Risch, Angela, primary, Amin Al Olama, Ali, primary, Berndt, Sonja I., primary, Giovannucci, Edward L., primary, Grönberg, Henrik, primary, Kote-Jarai, Zsofia, primary, Ma, Jing, primary, Muir, Kenneth, primary, Stampfer, Meir J., primary, Stevens, Victoria L., primary, Wiklund, Fredrik, primary, Willett, Walter C., primary, Goode, Ellen L., primary, Permuth, Jennifer B., primary, Risch, Harvey A., primary, Reid, Brett M., primary, Bezieau, Stephane, primary, Brenner, Hermann, primary, Chan, Andrew T., primary, Chang-Claude, Jenny, primary, Hudson, Thomas J., primary, Kocarnik, Jonathan K., primary, Newcomb, Polly A., primary, Schoen, Robert E., primary, Slattery, Martha L., primary, White, Emily, primary, Adank, Muriel A., primary, Ahsan, Habibul, primary, Aittomäki, Kristiina, primary, Baglietto, Laura, primary, Blomquist, Carl, primary, Canzian, Federico, primary, Czene, Kamila, primary, dos-Santos-Silva, Isabel, primary, Eliassen, A. Heather, primary, Figueroa, Jonine D., primary, Flesch-Janys, Dieter, primary, Fletcher, Olivia, primary, Garcia-Closas, Montserrat, primary, Gaudet, Mia M., primary, Johnson, Nichola, primary, Hall, Per, primary, Hazra, Aditi, primary, Hein, Rebecca, primary, Hofman, Albert, primary, Hopper, John L., primary, Irwanto, Astrid, primary, Johansson, Mattias, primary, Kaaks, Rudolf, primary, Kibriya, Muhammad G., primary, Lichtner, Peter, primary, Liu, Jianjun, primary, Lund, Eiliv, primary, Makalic, Enes, primary, Meindl, Alfons, primary, Müller-Myhsok, Bertram, primary, Muranen, Taru A., primary, Nevanlinna, Heli, primary, Peeters, Petra H., primary, Peto, Julian, primary, Prentice, Ross L., primary, Rahman, Nazneen, primary, Sanchez, Maria Jose, primary, Schmidt, Daniel F., primary, Schmutzler, Rita K., primary, Southey, Melissa C., primary, Tamimi, Rulla, primary, Travis, Ruth C., primary, Turnbull, Clare, primary, Uitterlinden, Andre G., primary, Wang, Zhaoming, primary, Whittemore, Alice S., primary, Yang, Xiaohong R., primary, Zheng, Wei, primary, Buchanan, Daniel D., primary, Casey, Graham, primary, Conti, David V., primary, Edlund, Christopher K., primary, Gallinger, Steven, primary, Haile, Robert W., primary, Jenkins, Mark, primary, Le Marchand, Loïc, primary, Li, Li, primary, Lindor, Noralene M., primary, Schmit, Stephanie L., primary, Thibodeau, Stephen N., primary, Woods, Michael O., primary, Rafnar, Thorunn, primary, Gudmundsson, Julius, primary, Stacey, Simon N., primary, Stefansson, Kari, primary, Sulem, Patrick, primary, Chen, Y. Ann, primary, Tyrer, Jonathan P., primary, Christiani, David C., primary, Wei, Yongyue, primary, Shen, Hongbing, primary, Hu, Zhibin, primary, Shu, Xiao-Ou, primary, Shiraishi, Kouya, primary, Takahashi, Atsushi, primary, Bossé, Yohan, primary, Obeidat, Ma'en, primary, Nickle, David, primary, Timens, Wim, primary, Freedman, Matthew L., primary, Li, Qiyuan, primary, Seminara, Daniela, primary, Chanock, Stephen J., primary, Gong, Jian, primary, Peters, Ulrike, primary, Gruber, Stephen B., primary, Amos, Christopher I., primary, Sellers, Thomas A., primary, Easton, Douglas F., primary, Hunter, David J., primary, Haiman, Christopher A., primary, Henderson, Brian E., primary, and Hung, Rayjean J., primary

Published
2023
Full Text
View/download PDF

39. Supplementary Material: Funding, Acknowledgements, Consortia, and Bioinformatics Tools Funding sources from Cross-Cancer Genome-Wide Analysis of Lung, Ovary, Breast, Prostate, and Colorectal Cancer Reveals Novel Pleiotropic Associations

Author

Fehringer, Gordon, primary, Kraft, Peter, primary, Pharoah, Paul D., primary, Eeles, Rosalind A., primary, Chatterjee, Nilanjan, primary, Schumacher, Fredrick R., primary, Schildkraut, Joellen M., primary, Lindström, Sara, primary, Brennan, Paul, primary, Bickeböller, Heike, primary, Houlston, Richard S., primary, Landi, Maria Teresa, primary, Caporaso, Neil, primary, Risch, Angela, primary, Amin Al Olama, Ali, primary, Berndt, Sonja I., primary, Giovannucci, Edward L., primary, Grönberg, Henrik, primary, Kote-Jarai, Zsofia, primary, Ma, Jing, primary, Muir, Kenneth, primary, Stampfer, Meir J., primary, Stevens, Victoria L., primary, Wiklund, Fredrik, primary, Willett, Walter C., primary, Goode, Ellen L., primary, Permuth, Jennifer B., primary, Risch, Harvey A., primary, Reid, Brett M., primary, Bezieau, Stephane, primary, Brenner, Hermann, primary, Chan, Andrew T., primary, Chang-Claude, Jenny, primary, Hudson, Thomas J., primary, Kocarnik, Jonathan K., primary, Newcomb, Polly A., primary, Schoen, Robert E., primary, Slattery, Martha L., primary, White, Emily, primary, Adank, Muriel A., primary, Ahsan, Habibul, primary, Aittomäki, Kristiina, primary, Baglietto, Laura, primary, Blomquist, Carl, primary, Canzian, Federico, primary, Czene, Kamila, primary, dos-Santos-Silva, Isabel, primary, Eliassen, A. Heather, primary, Figueroa, Jonine D., primary, Flesch-Janys, Dieter, primary, Fletcher, Olivia, primary, Garcia-Closas, Montserrat, primary, Gaudet, Mia M., primary, Johnson, Nichola, primary, Hall, Per, primary, Hazra, Aditi, primary, Hein, Rebecca, primary, Hofman, Albert, primary, Hopper, John L., primary, Irwanto, Astrid, primary, Johansson, Mattias, primary, Kaaks, Rudolf, primary, Kibriya, Muhammad G., primary, Lichtner, Peter, primary, Liu, Jianjun, primary, Lund, Eiliv, primary, Makalic, Enes, primary, Meindl, Alfons, primary, Müller-Myhsok, Bertram, primary, Muranen, Taru A., primary, Nevanlinna, Heli, primary, Peeters, Petra H., primary, Peto, Julian, primary, Prentice, Ross L., primary, Rahman, Nazneen, primary, Sanchez, Maria Jose, primary, Schmidt, Daniel F., primary, Schmutzler, Rita K., primary, Southey, Melissa C., primary, Tamimi, Rulla, primary, Travis, Ruth C., primary, Turnbull, Clare, primary, Uitterlinden, Andre G., primary, Wang, Zhaoming, primary, Whittemore, Alice S., primary, Yang, Xiaohong R., primary, Zheng, Wei, primary, Buchanan, Daniel D., primary, Casey, Graham, primary, Conti, David V., primary, Edlund, Christopher K., primary, Gallinger, Steven, primary, Haile, Robert W., primary, Jenkins, Mark, primary, Le Marchand, Loïc, primary, Li, Li, primary, Lindor, Noralene M., primary, Schmit, Stephanie L., primary, Thibodeau, Stephen N., primary, Woods, Michael O., primary, Rafnar, Thorunn, primary, Gudmundsson, Julius, primary, Stacey, Simon N., primary, Stefansson, Kari, primary, Sulem, Patrick, primary, Chen, Y. Ann, primary, Tyrer, Jonathan P., primary, Christiani, David C., primary, Wei, Yongyue, primary, Shen, Hongbing, primary, Hu, Zhibin, primary, Shu, Xiao-Ou, primary, Shiraishi, Kouya, primary, Takahashi, Atsushi, primary, Bossé, Yohan, primary, Obeidat, Ma'en, primary, Nickle, David, primary, Timens, Wim, primary, Freedman, Matthew L., primary, Li, Qiyuan, primary, Seminara, Daniela, primary, Chanock, Stephen J., primary, Gong, Jian, primary, Peters, Ulrike, primary, Gruber, Stephen B., primary, Amos, Christopher I., primary, Sellers, Thomas A., primary, Easton, Douglas F., primary, Hunter, David J., primary, Haiman, Christopher A., primary, Henderson, Brian E., primary, and Hung, Rayjean J., primary

Published
2023
Full Text
View/download PDF

40. Data from A Genome-wide Association Study of Early-Onset Breast Cancer Identifies PFKM as a Novel Breast Cancer Gene and Supports a Common Genetic Spectrum for Breast Cancer at Any Age

Author

Ahsan, Habibul, primary, Halpern, Jerry, primary, Kibriya, Muhammad G., primary, Pierce, Brandon L., primary, Tong, Lin, primary, Gamazon, Eric, primary, McGuire, Valerie, primary, Felberg, Anna, primary, Shi, Jianxin, primary, Jasmine, Farzana, primary, Roy, Shantanu, primary, Brutus, Rachelle, primary, Argos, Maria, primary, Melkonian, Stephanie, primary, Chang-Claude, Jenny, primary, Andrulis, Irene, primary, Hopper, John L., primary, John, Esther M., primary, Malone, Kathi, primary, Ursin, Giske, primary, Gammon, Marilie D., primary, Thomas, Duncan C., primary, Seminara, Daniela, primary, Casey, Graham, primary, Knight, Julia A., primary, Southey, Melissa C., primary, Giles, Graham G., primary, Santella, Regina M., primary, Lee, Eunjung, primary, Conti, David, primary, Duggan, David, primary, Gallinger, Steve, primary, Haile, Robert, primary, Jenkins, Mark, primary, Lindor, Noralane M., primary, Newcomb, Polly, primary, Michailidou, Kyriaki, primary, Apicella, Carmel, primary, Park, Daniel J., primary, Peto, Julian, primary, Fletcher, Olivia, primary, dos Santos Silva, Isabel, primary, Lathrop, Mark, primary, Hunter, David J., primary, Chanock, Stephen J., primary, Meindl, Alfons, primary, Schmutzler, Rita K., primary, Müller-Myhsok, Bertram, primary, Lochmann, Magdalena, primary, Beckmann, Lars, primary, Hein, Rebecca, primary, Makalic, Enes, primary, Schmidt, Daniel F., primary, Bui, Quang Minh, primary, Stone, Jennifer, primary, Flesch-Janys, Dieter, primary, Dahmen, Norbert, primary, Nevanlinna, Heli, primary, Aittomäki, Kristiina, primary, Blomqvist, Carl, primary, Hall, Per, primary, Czene, Kamila, primary, Irwanto, Astrid, primary, Liu, Jianjun, primary, Rahman, Nazneen, primary, Turnbull, Clare, primary, Dunning, Alison M., primary, Pharoah, Paul, primary, Waisfisz, Quinten, primary, Meijers-Heijboer, Hanne, primary, Uitterlinden, Andre G., primary, Rivadeneira, Fernando, primary, Nicolae, Dan, primary, Easton, Douglas F., primary, Cox, Nancy J., primary, and Whittemore, Alice S., primary

Published
2023
Full Text
View/download PDF

43. Sequencing-based fine-mapping and in silico functional characterization of the 10q24.32 arsenic metabolism efficiency locus across multiple arsenic-exposed populations

Author

Chernoff, Meytal Batya, primary, Delgado, Dayana, additional, Tong, Lin, additional, Chen, Lin, additional, Oliva, Meritxell, additional, Tamayo, Lizeth I., additional, Best, Lyle G., additional, Cole, Shelley, additional, Jasmine, Farzana, additional, Kibriya, Muhammad G., additional, Nelson, Heather, additional, Huang, Lei, additional, Haack, Karin, additional, Kent, Jack, additional, Umans, Jason G., additional, Graziano, Joseph, additional, Navas-Acien, Ana, additional, Karagas, Margaret R., additional, Ahsan, Habib, additional, and Pierce, Brandon L., additional

Published
2023
Full Text
View/download PDF

44. Multi-ancestry genome-wide study in >2.5 million individuals reveals heterogeneity in mechanistic pathways of type 2 diabetes and complications

Author

Suzuki, Ken, Hatzikotoulas, Konstantinos, Southam, Lorraine, Taylor, Henry J., Yin, Xianyong, Lorenz, Kim M., Mandla, Ravi, Huerta-Chagoya, Alicia, Rayner, Nigel W., Bocher, Ozvan, Ana Luiza de, S. V. Arruda, Sonehara, Kyuto, Namba, Shinichi, Lee, Simon S. K., Preuss, Michael H., Petty, Lauren E., Schroeder, Philip, Vanderwerff, Brett, Kals, Mart, Bragg, Fiona, Lin, Kuang, Guo, Xiuqing, Zhang, Weihua, Yao, Jie, Kim, Young Jin, Graff, Mariaelisa, Takeuchi, Fumihiko, Nano, Jana, Lamri, Amel, Nakatochi, Masahiro, Moon, Sanghoon, Scott, Robert A., Cook, James P., Lee, Jung-Jin, Pan, Ian, Taliun, Daniel, Parra, Esteban J., Chai, Jin-Fang, Bielak, Lawrence F., Tabara, Yasuharu, Hai, Yang, Thorleifsson, Gudmar, Grarup, Niels, Sofer, Tamar, Wuttke, Matthias, Sarnowski, Chloé, Gieger, Christian, Nousome, Darryl, Trompet, Stella, Kwak, Soo-Heon, Long, Jirong, Sun, Meng, Tong, Lin, Chen, Wei-Min, Nongmaithem, Suraj S., Noordam, Raymond, Lim, Victor J. Y., Tam, Claudia H. T., Joo, Yoonjung Yoonie, Chen, Chien-Hsiun, Raffield, Laura M., Prins, Bram Peter, Nicolas, Aude, Yanek, Lisa R., Chen, Guanjie, Brody, Jennifer A., Kabagambe, Edmond, An, Ping, Xiang, Anny H., Choi, Hyeok Sun, Cade, Brian E., Tan, Jingyi, Alaine Broadaway, K., Williamson, Alice, Kamali, Zoha, Cui, Jinrui, Adair, Linda S., Adeyemo, Adebowale, Aguilar-Salinas, Carlos A., Ahluwalia, Tarunveer S., Anand, Sonia S., Bertoni, Alain, Bork-Jensen, Jette, Brandslund, Ivan, Buchanan, Thomas A., Burant, Charles F., Butterworth, Adam S., Canouil, Mickaël, Chan, Juliana C. N., Chang, Li-Ching, Chee, Miao-Li, Chen, Ji, Chen, Shyh-Huei, Chen, Yuan-Tsong, Chen, Zhengming, Chuang, Lee-Ming, Cushman, Mary, Danesh, John, Das, Swapan K., Janaka de Silva, H., Dedoussis, George, Dimitrov, Latchezar, Doumatey, Ayo P., Du, Shufa, Duan, Qing, Eckardt, Kai-Uwe, Emery, Leslie S., Evans, Daniel S., Evans, Michele K., Fischer, Krista, Floyd, James S., Ford, Ian, Franco, Oscar H., Frayling, Timothy M., Freedman, Barry I., Genter, Pauline, Gerstein, Hertzel C., Giedraitis, Vilmantas, González-Villalpando, Clicerio, González-Villalpando, Maria Elena, Gordon-Larsen, Penny, Gross, Myron, Guare, Lindsay A., Hackinger, Sophie, Han, Sohee, Hattersley, Andrew T., Herder, Christian, Horikoshi, Momoko, Howard, Annie-Green, Hsueh, Willa, Huang, Mengna, Huang, Wei, Hung, Yi-Jen, Hwang, Mi Yeong, Hwu, Chii-Min, Ichihara, Sahoko, Ikram, Mohammad Arfan, Ingelsson, Martin, Islam, Md. Tariqul, Isono, Masato, Jang, Hye-Mi, Jasmine, Farzana, Jiang, Guozhi, Jonas, Jost B., Jørgensen, Torben, Kandeel, Fouad R., Kasturiratne, Anuradhani, Katsuya, Tomohiro, Kaur, Varinderpal, Kawaguchi, Takahisa, Keaton, Jacob M., Kho, Abel N., Khor, Chiea-Chuen, Kibriya, Muhammad G., Kim, Duk-Hwan, Kronenberg, Florian, Kuusisto, Johanna, Läll, Kristi, Lange, Leslie A., Lee, Kyung Min, Lee, Myung-Shik, Lee, Nanette R., Leong, Aaron, Li, Liming, Li, Yun, Li-Gao, Ruifang, Lithgart, Symen, Lindgren, Cecilia M., Linneberg, Allan, Liu, Ching-Ti, Liu, Jianjun, Locke, Adam E., Louie, Tin, Luan, Jian’an, Luk, Andrea O., Luo, Xi, Lv, Jun, Lynch, Julie A., Lyssenko, Valeriya, Maeda, Shiro, Mamakou, Vasiliki, Mansuri, Sohail Rafik, Matsuda, Koichi, Meitinger, Thomas, Metspalu, Andres, Mo, Huan, Morris, Andrew D., Nadler, Jerry L., Nalls, Michael A., Nayak, Uma, Ntalla, Ioanna, Okada, Yukinori, Orozco, Lorena, Patel, Sanjay R., Patil, Snehal, Pei, Pei, Pereira, Mark A, Peters, Annette, Pirie, Fraser J., Polikowsky, Hannah G., Porneala, Bianca, Prasad, Gauri, Rasmussen-Torvik, Laura J., Reiner, Alexander P., Roden, Michael, Rohde, Rebecca, Roll, Katheryn, Sabanayagam, Charumathi, Sandow, Kevin, Sankareswaran, Alagu, Sattar, Naveed, Schönherr, Sebastian, Shahriar, Mohammad, Shen, Botong, Shi, Jinxiu, Shin, Dong Mun, Shojima, Nobuhiro, Smith, Jennifer A., So, Wing Yee, Stančáková, Alena, Steinthorsdottir, Valgerdur, Stilp, Adrienne M., Strauch, Konstantin, Taylor, Kent D., Thorand, Barbara, Thorsteinsdottir, Unnur, Tomlinson, Brian, Tran, Tam C., Tsai, Fuu-Jen, Tuomilehto, Jaakko, Tusie-Luna, Teresa, Udler, Miriam S., Valladares-Salgado, Adan, van Dam, Rob M., van Klinken, Jan B., Varma, Rohit, Wacher-Rodarte, Niels, Wheeler, Eleanor, Wickremasinghe, Ananda R., van Dijk, Ko Willems, Witte, Daniel R., Yajnik, Chittaranjan S., Yamamoto, Ken, Yamamoto, Kenichi, Yoon, Kyungheon, Yu, Canqing, Yuan, Jian-Min, Yusuf, Salim, Zawistowski, Matthew, Zhang, Liang, Zheng, Wei, Project, Biobank Japan, BioBank, Penn Medicine, Center, Regeneron Genetics, Consortium, eMERGE, Raffel, Leslie J, Igase, Michiya, Ipp, Eli, Redline, Susan, Cho, Yoon Shin, Lind, Lars, Province, Michael A., Fornage, Myriam, Hanis, Craig L., Ingelsson, Erik, Zonderman, Alan B., Psaty, Bruce M., Wang, Ya-Xing, Rotimi, Charles N., Becker, Diane M., Matsuda, Fumihiko, Liu, Yongmei, Yokota, Mitsuhiro, Kardia, Sharon L. R., Peyser, Patricia A., Pankow, James S., Engert, James C., Bonnefond, Amélie, Froguel, Philippe, Wilson, James G., Sheu, Wayne H. H., Wu, Jer-Yuarn, Geoffrey Hayes, M., Ma, Ronald C. W., Wong, Tien-Yin, Mook-Kanamori, Dennis O., Tuomi, Tiinamaija, Chandak, Giriraj R., Collins, Francis S., Bharadwaj, Dwaipayan, Paré, Guillaume, Sale, Michèle M., Ahsan, Habibul, Motala, Ayesha A., Shu, Xiao-Ou, Park, Kyong-Soo, Jukema, J Wouter, Cruz, Miguel, Chen, Yii-Der Ida, Rich, Stephen S., McKean-Cowdin, Roberta, Grallert, Harald, Cheng, Ching-Yu, Ghanbari, Mohsen, Tai, E-Shyong, Dupuis, Josee, Kato, Norihiro, Laakso, Markku, Köttgen, Anna, Koh, Woon-Puay, Bowden, Donald W., Palmer, Colin N. A., Kooner, Jaspal S., Kooperberg, Charles, Liu, Simin, North, Kari E., Saleheen, Danish, Hansen, Torben, Pedersen, Oluf, Wareham, Nicholas J., Lee, Juyoung, Kim, Bong-Jo, Millwood, Iona Y., Walters, Robin G., Stefansson, Kari, Goodarzi, Mark O., Mohlke, Karen L., Langenberg, Claudia, Haiman, Christopher A., Loos, Ruth J. F., Florez, Jose C., Rader, Daniel J., Ritchie, Marylyn D., Zöllner, Sebastian, Mägi, Reedik, Denny, Joshua C., Yamauchi, Toshimasa, Kadowaki, Takashi, Chambers, John C., Ng, Maggie C. Y., Sim, Xueling, Below, Jennifer E., Tsao, Philip S., Chang, Kyong-Mi, McCarthy, Mark I., Meigs, James B., Mahajan, Anubha, Spracklen, Cassandra N., Mercader, Josep M., Boehnke, Michael, Rotter, Jerome I., Vujkovic, Marijana, Voight, Benjamin F., Morris, Andrew P., and Zeggini, Eleftheria

Subjects
Article
Abstract

Type 2 diabetes (T2D) is a heterogeneous disease that develops through diverse pathophysiological processes. To characterise the genetic contribution to these processes across ancestry groups, we aggregate genome-wide association study (GWAS) data from 2,535,601 individuals (39.7% non-European ancestry), including 428,452 T2D cases. We identify 1,289 independent association signals at genome-wide significance (P

Published
2023

45. Developing an algorithm across integrated healthcare systems to identify a history of cancer using electronic medical records

Author

Gander, Jennifer C, Maiyani, Mahesh, White, Larissa L, Sterrett, Andrew T, Güney, Brianna, Pawloski, Pamala A, DeFor, Teri, Olsen, YuanYuan, Rybicki, Benjamin A, Neslund-Dudas, Christine, Sheth, Darsheen, Krajenta, Richard, Purushothaman, Devaki, Honda, Stacey, Yonehara, Cyndee, Goddard, Katrina A B, Prado, Yolanda K, Ahsan, Habibul, Kibriya, Muhammad G, Aschebrook-Kilfoy, Briseis, Chan, Chun-Hung, Hague, Sarah, Clarke, Christina L, Thompson, Brooke, Sawyer, Jennifer, Gaudet, Mia M, and Feigelson, Heather Spencer

Subjects
Adult, Delivery of Health Care, Integrated, Data Collection, Neoplasms, Electronic Health Records, Humans, Health Informatics, Research and Applications, Algorithms
Abstract

ObjectiveTumor registries in integrated healthcare systems (IHCS) have high precision for identifying incident cancer but often miss recently diagnosed cancers or those diagnosed outside of the IHCS. We developed an algorithm using the electronic medical record (EMR) to identify people with a history of cancer not captured in the tumor registry to identify adults, aged 40–65 years, with no history of cancer.Materials and MethodsThe algorithm was developed at Kaiser Permanente Colorado, and then applied to 7 other IHCS. We included tumor registry data, diagnosis and procedure codes, chemotherapy files, oncology encounters, and revenue data to develop the algorithm. Each IHCS adapted the algorithm to their EMR data and calculated sensitivity and specificity to evaluate the algorithm’s performance after iterative chart review.ResultsWe included data from over 1.26 million eligible people across 8 IHCS; 55 601 (4.4%) were in a tumor registry, and 44848 (3.5%) had a reported cancer not captured in a registry. The common attributes of the final algorithm at each site were diagnosis and procedure codes. The sensitivity of the algorithm at each IHCS was 90.65%–100%, and the specificity was 87.91%–100%.DiscussionRelying only on tumor registry data would miss nearly half of the identified cancers. Our algorithm was robust and required only minor modifications to adapt to other EMR systems.ConclusionThis algorithm can identify cancer cases regardless of when the diagnosis occurred and may be useful for a variety of research applications or quality improvement projects around cancer care.

Published
2022

47. Somatic loss of the Y chromosome is associated with arsenic exposure among Bangladeshi men.

Author

Demanelis, Kathryn, Delgado, Dayana A, Tong, Lin, Jasmine, Farzana, Ahmed, Alauddin, Islam, Tariqul, Parvez, Faruque, Kibriya, Muhammad G, Graziano, Joseph H, Ahsan, Habibul, and Pierce, Brandon L

Subjects
Y chromosome, ARSENIC, ARSENIC in water, DRINKING water, LOGISTIC regression analysis, DISEASE risk factors
Abstract

Background Arsenic exposure increases the risk of several cancers in humans and contributes to genomic instability. Somatic loss of the Y chromosome (LoY) is a potential biomarker of genomic instability and cancer risk. Smoking is associated with LoY, but few other carcinogens have been investigated. We tested the cross-sectional association between arsenic exposure and LoY in leukocytes among genotyped Bangladeshi men (age 20–70 years) from the Health Effects of Arsenic Longitudinal Study. Methods We extracted the median of logR-ratios from probes on the Y chromosome (mLRR-chrY) from genotyping arrays (n  =   1364) and estimated the percentage of cells with LoY (% LoY) from mLRR-chrY. We evaluated the association between arsenic exposure (measured in drinking water and urine) and LoY using multivariable linear and logistic regression models. The association between LoY and incident arsenic-induced skin lesions was also examined. Results Ten percent of genotyped men had LoY in at least 5% of cells and % LoY increased with age. Among men randomly selected for genotyping (n  =   778), higher arsenic in drinking water, arsenic consumed and urinary arsenic were associated with increased % LoY (P  =   0.006, P  =   0.06 and P  =   0.13, respectively). LoY was associated with increased risk of incident skin lesions (P  =   0.008). Conclusion Arsenic exposure was associated with increased LoY, providing additional evidence that arsenic contributes to genomic instability. LoY was associated with developing skin lesions, a risk factor for cancer, suggesting that LoY may be a biomarker of susceptibility in arsenic-exposed populations. The effect of arsenic on somatic events should be further explored in cancer-prone tissue types. [ABSTRACT FROM AUTHOR]

Published
2023
Full Text
View/download PDF

50. Interaction of Arsenic Exposure and Transcriptomic Profile in Basal Cell Carcinoma

Author

Kibriya, Muhammad G., primary, Jasmine, Farzana, additional, Munoz, Aaron, additional, Islam, Tariqul, additional, Ahmed, Alauddin, additional, Tong, Lin, additional, Rakibuz-Zaman, Muhammad, additional, Shahriar, Mohammad, additional, Kamal, Mohammed, additional, Shea, Christopher R., additional, Graziano, Joseph H., additional, Argos, Maria, additional, and Ahsan, Habibul, additional

Published
2022
Full Text
View/download PDF

Catalog

Books, media, physical & digital resources
See catalog results