Search

Your search keyword '"Adey, Andrew"' showing total 184 results
Start Over Author "Adey, Andrew" Search Limiters Available in Library Collection
184 results on '"Adey, Andrew"'

1. Systematic benchmarking of single-cell ATAC-sequencing protocols.

Author

De Rop, Florian, Hulselmans, Gert, Flerin, Chris, Soler-Vila, Paula, Rafels, Albert, Christiaens, Valerie, González-Blas, Carmen, Marchese, Domenica, Caratù, Ginevra, Poovathingal, Suresh, Rozenblatt-Rosen, Orit, Slyper, Michael, Luo, Wendy, Muus, Christoph, Duarte, Fabiana, Shrestha, Rojesh, Bagdatli, S, Corces, M, Mamanova, Lira, Knights, Andrew, Meyer, Kerstin, Mulqueen, Ryan, Taherinasab, Akram, Maschmeyer, Patrick, Pezoldt, Jörn, Lambert, Camille, Iglesias, Marta, Najle, Sebastián, Dossani, Zain, Martelotto, Luciano, Burkett, Zach, Lebofsky, Ronald, Martin-Subero, José, Pillai, Satish, Sebé-Pedrós, Arnau, Deplancke, Bart, Teichmann, Sarah, Ludwig, Leif, Braun, Theodore, Adey, Andrew, Greenleaf, William, Buenrostro, Jason, Regev, Aviv, Aerts, Stein, and Heyn, Holger

Subjects
Humans, Single-Cell Analysis, Benchmarking, Leukocytes, Mononuclear, Chromatin Immunoprecipitation Sequencing, Chromatin, Transposases, Sequence Analysis, DNA, High-Throughput Nucleotide Sequencing
Abstract

Single-cell assay for transposase-accessible chromatin by sequencing (scATAC-seq) has emerged as a powerful tool for dissecting regulatory landscapes and cellular heterogeneity. However, an exploration of systemic biases among scATAC-seq technologies has remained absent. In this study, we benchmark the performance of eight scATAC-seq methods across 47 experiments using human peripheral blood mononuclear cells (PBMCs) as a reference sample and develop PUMATAC, a universal preprocessing pipeline, to handle the various sequencing data formats. Our analyses reveal significant differences in sequencing library complexity and tagmentation specificity, which impact cell-type annotation, genotype demultiplexing, peak calling, differential region accessibility and transcription factor motif enrichment. Our findings underscore the importance of sample extraction, method selection, data processing and total cost of experiments, offering valuable guidance for future research. Finally, our data and analysis pipeline encompasses 169,000 PBMC scATAC-seq profiles and a best practices code repository for scATAC-seq data analysis, which are freely available to extend this benchmarking effort to future protocols.

Published
2024

2. Novel recruitment approaches and operational results for a statewide population Cohort for cancer research: The Healthy Oregon Project.

Author

Zhang, Zhenzhen, Shafer, Autumn, Johnson-Camacho, Katie, Adey, Andrew, Anur, Pavana, Brown, Kim, Conrad, Casey, Crist, Rachel, Farris, Paige, Harrington, Christina, Marriott, Lisa, Mitchell, Asia, ORoak, Brian, Serrato, Vanessa, Richards, C, Spellman, Paul, and Shannon, Jackilen

Subjects
Cohort, HOP, app, genetics, population
Abstract

BACKGROUND: Cancer health research relies on large-scale cohorts to derive generalizable results for different populations. While traditional epidemiological cohorts often use costly random sampling or self-motivated, preselected groups, a shift toward health system-based cohorts has emerged. However, such cohorts depend on participants remaining within a single system. Recent consumer engagement models using smartphone-based communication, driving projects, and social media have begun to upend these paradigms. METHODS: We initiated the Healthy Oregon Project (HOP) to support basic and clinical cancer research. HOP study employs a novel, cost-effective remote recruitment approach to effectively establish a large-scale cohort for population-based studies. The recruitment leverages the unique email account, the HOP website, and social media platforms to direct smartphone users to the study app, which facilitates saliva sample collection and survey administration. Monthly newsletters further facilitate engagement and outreach to broader communities. RESULTS: By the end of 2022, the HOP has enrolled approximately 35,000 participants aged 18-100 years (median = 44.2 years), comprising more than 1% of the Oregon adult population. Among those who have app access, ∼87% provided consent to genetic screening. The HOP monthly email newsletters have an average open rate of 38%. Efforts continue to be made to improve survey response rates. CONCLUSION: This study underscores the efficacy of remote recruitment approaches in establishing large-scale cohorts for population-based cancer studies. The implementation of the study facilitates the collection of extensive survey and biological data into a repository that can be broadly shared and supports collaborative clinical and translational research.

Published
2024

6. Population screening shows risk of inherited cancer and familial hypercholesterolemia in Oregon

Author

O’Brien, Timothy D., Potter, Amiee B., Driscoll, Catherine C., Goh, Gregory, Letaw, John H., McCabe, Sarah, Thanner, Jane, Kulkarni, Arpita, Wong, Rossana, Medica, Samuel, Week, Tiana, Buitrago, Jacob, Larson, Aaron, Camacho, Katie Johnson, Brown, Kim, Crist, Rachel, Conrad, Casey, Evans-Dutson, Sara, Lutz, Ryan, Mitchell, Asia, Anur, Pavana, Serrato, Vanessa, Shafer, Autumn, Marriott, Lisa K., Hamman, K.J., Mulford, Amelia, Wiszniewski, Wojciech, Sampson, Jone E., Adey, Andrew, O’Roak, Brian J., Harrington, Christina A., Shannon, Jackilen, Spellman, Paul T., and Richards, C. Sue

Published
2023
Full Text
View/download PDF

8. Differentiation-state plasticity is a targetable resistance mechanism in basal-like breast cancer.

Author

Risom, Tyler, Langer, Ellen M, Chapman, Margaret P, Rantala, Juha, Fields, Andrew J, Boniface, Christopher, Alvarez, Mariano J, Kendsersky, Nicholas D, Pelz, Carl R, Johnson-Camacho, Katherine, Dobrolecki, Lacey E, Chin, Koei, Aswani, Anil J, Wang, Nicholas J, Califano, Andrea, Lewis, Michael T, Tomlin, Claire J, Spellman, Paul T, Adey, Andrew, Gray, Joe W, and Sears, Rosalie C

Subjects
Cell Line, Tumor, Chromatin, Animals, Mice, Inbred NOD, Humans, Mice, SCID, Breast Neoplasms, Azepines, Triazoles, Antineoplastic Agents, Cell Differentiation, Drug Resistance, Neoplasm, Female, Molecular Targeted Therapy, Triple Negative Breast Neoplasms, Cell Plasticity, Breast Cancer, Human Genome, Genetics, Orphan Drug, Rare Diseases, Cancer, 5.1 Pharmaceuticals
Abstract

Intratumoral heterogeneity in cancers arises from genomic instability and epigenomic plasticity and is associated with resistance to cytotoxic and targeted therapies. We show here that cell-state heterogeneity, defined by differentiation-state marker expression, is high in triple-negative and basal-like breast cancer subtypes, and that drug tolerant persister (DTP) cell populations with altered marker expression emerge during treatment with a wide range of pathway-targeted therapeutic compounds. We show that MEK and PI3K/mTOR inhibitor-driven DTP states arise through distinct cell-state transitions rather than by Darwinian selection of preexisting subpopulations, and that these transitions involve dynamic remodeling of open chromatin architecture. Increased activity of many chromatin modifier enzymes, including BRD4, is observed in DTP cells. Co-treatment with the PI3K/mTOR inhibitor BEZ235 and the BET inhibitor JQ1 prevents changes to the open chromatin architecture, inhibits the acquisition of a DTP state, and results in robust cell death in vitro and xenograft regression in vivo.

Published
2018

11. The Human Tumor Atlas Network: Charting Tumor Transitions across Space and Time at Single-Cell Resolution

Author

Aberle, Denise, Achilefu, Samuel I., Ademuyiwa, Foluso O., Adey, Andrew C., Aft, Rebecca L., Agarwal, Rachana, Aguilar, Ruben A., Alikarami, Fatemeh, Allaj, Viola, Amos, Christopher, Anders, Robert A., Angelo, Michael R., Anton, Kristen, Ashenberg, Orr, Aster, Jon C., Babur, Ozgun, Bahmani, Amir, Balsubramani, Akshay, Barrett, David, Beane, Jennifer, Bender, Diane E., Bernt, Kathrin, Berry, Lynne, Betts, Courtney B., Bletz, Julie, Blise, Katie, Boire, Adrienne, Boland, Genevieve, Borowsky, Alexander, Bosse, Kristopher, Bott, Matthew, Boyden, Ed, Brooks, James, Bueno, Raphael, Burlingame, Erik A., Cai, Qiuyin, Campbell, Joshua, Caravan, Wagma, Cerami, Ethan, Chaib, Hassan, Chan, Joseph M., Chang, Young Hwan, Chatterjee, Deyali, Chaudhary, Ojasvi, Chen, Alyce A., Chen, Bob, Chen, Changya, Chen, Chia-hui, Chen, Feng, Chen, Yu-An, Chheda, Milan G., Chin, Koei, Chiu, Roxanne, Chu, Shih-Kai, Chuaqui, Rodrigo, Chun, Jaeyoung, Cisneros, Luis, Coffey, Robert J., Colditz, Graham A., Cole, Kristina, Collins, Natalie, Contrepois, Kevin, Coussens, Lisa M., Creason, Allison L., Crichton, Daniel, Curtis, Christina, Davidsen, Tanja, Davies, Sherri R., de Bruijn, Ino, Dellostritto, Laura, De Marzo, Angelo, Demir, Emek, DeNardo, David G., Diep, Dinh, Ding, Li, Diskin, Sharon, Doan, Xengie, Drewes, Julia, Dubinett, Stephen, Dyer, Michael, Egger, Jacklynn, Eng, Jennifer, Engelhardt, Barbara, Erwin, Graham, Esplin, Edward D., Esserman, Laura, Felmeister, Alex, Feiler, Heidi S., Fields, Ryan C., Fisher, Stephen, Flaherty, Keith, Flournoy, Jennifer, Ford, James M., Fortunato, Angelo, Frangieh, Allison, Frye, Jennifer L., Fulton, Robert S., Galipeau, Danielle, Gan, Siting, Gao, Jianjiong, Gao, Long, Gao, Peng, Gao, Vianne R., Geiger, Tim, George, Ajit, Getz, Gad, Ghosh, Sharmistha, Giannakis, Marios, Gibbs, David L., Gillanders, William E., Goecks, Jeremy, Goedegebuure, Simon P., Gould, Alanna, Gowers, Kate, Gray, Joe W., Greenleaf, William, Gresham, Jeremy, Guerriero, Jennifer L., Guha, Tuhin K., Guimaraes, Alexander R., Guinney, Justin, Gutman, David, Hacohen, Nir, Hanlon, Sean, Hansen, Casey R., Harismendy, Olivier, Harris, Kathleen A., Hata, Aaron, Hayashi, Akimasa, Heiser, Cody, Helvie, Karla, Herndon, John M., Hirst, Gilliam, Hodi, Frank, Hollmann, Travis, Horning, Aaron, Hsieh, James J., Hughes, Shannon, Huh, Won Jae, Hunger, Stephen, Hwang, Shelley E., Iacobuzio-Donahue, Christine A., Ijaz, Heba, Izar, Benjamin, Jacobson, Connor A., Janes, Samuel, Jané-Valbuena, Judit, Jayasinghe, Reyka G., Jiang, Lihua, Johnson, Brett E., Johnson, Bruce, Ju, Tao, Kadara, Humam, Kaestner, Klaus, Kagan, Jacob, Kalinke, Lukas, Keith, Robert, Khan, Aziz, Kibbe, Warren, Kim, Albert H., Kim, Erika, Kim, Junhyong, Kolodzie, Annette, Kopytra, Mateusz, Kotler, Eran, Krueger, Robert, Krysan, Kostyantyn, Kundaje, Anshul, Ladabaum, Uri, Lake, Blue B., Lam, Huy, Laquindanum, Rozelle, Lau, Ken S., Laughney, Ashley M., Lee, Hayan, Lenburg, Marc, Leonard, Carina, Leshchiner, Ignaty, Levy, Rochelle, Li, Jerry, Lian, Christine G., Lim, Kian-Huat, Lin, Jia-Ren, Lin, Yiyun, Liu, Qi, Liu, Ruiyang, Lively, Tracy, Longabaugh, William J.R., Longacre, Teri, Ma, Cynthia X., Macedonia, Mary Catherine, Madison, Tyler, Maher, Christopher A., Maitra, Anirban, Makinen, Netta, Makowski, Danika, Maley, Carlo, Maliga, Zoltan, Mallo, Diego, Maris, John, Markham, Nick, Marks, Jeffrey, Martinez, Daniel, Mashl, Robert J., Masilionais, Ignas, Mason, Jennifer, Massagué, Joan, Massion, Pierre, Mattar, Marissa, Mazurchuk, Richard, Mazutis, Linas, Mazzilli, Sarah A., McKinley, Eliot T., McMichael, Joshua F., Merrick, Daniel, Meyerson, Matthew, Miessner, Julia R., Mills, Gordon B., Mills, Meredith, Mondal, Suman B., Mori, Motomi, Mori, Yuriko, Moses, Elizabeth, Mosse, Yael, Muhlich, Jeremy L., Murphy, George F., Navin, Nicholas E., Nawy, Tal, Nederlof, Michel, Ness, Reid, Nevins, Stephanie, Nikolov, Milen, Nirmal, Ajit Johnson, Nolan, Garry, Novikov, Edward, Oberdoerffer, Philipp, O’Connell, Brendan, Offin, Michael, Oh, Stephen T., Olson, Anastasiya, Ooms, Alex, Ossandon, Miguel, Owzar, Kouros, Parmar, Swapnil, Patel, Tasleema, Patti, Gary J., Pe’er, Dana, Pe'er, Itsik, Peng, Tao, Persson, Daniel, Petty, Marvin, Pfister, Hanspeter, Polyak, Kornelia, Pourfarhangi, Kamyar, Puram, Sidharth V., Qiu, Qi, Quintanal-Villalonga, Álvaro, Raj, Arjun, Ramirez-Solano, Marisol, Rashid, Rumana, Reeb, Ashley N., Regev, Aviv, Reid, Mary, Resnick, Adam, Reynolds, Sheila M., Riesterer, Jessica L., Rodig, Scott, Roland, Joseph T., Rosenfield, Sonia, Rotem, Asaf, Roy, Sudipta, Rozenblatt-Rosen, Orit, Rudin, Charles M., Ryser, Marc D., Santagata, Sandro, Santi-Vicini, Maria, Sato, Kazuhito, Schapiro, Denis, Schrag, Deborah, Schultz, Nikolaus, Sears, Cynthia L., Sears, Rosalie C., Sen, Subrata, Sen, Triparna, Shalek, Alex, Sheng, Jeff, Sheng, Quanhu, Shoghi, Kooresh I., Shrubsole, Martha J., Shyr, Yu, Sibley, Alexander B., Siex, Kiara, Simmons, Alan J., Singer, Dinah S., Sivagnanam, Shamilene, Slyper, Michal, Snyder, Michael P., Sokolov, Artem, Song, Sheng-Kwei, Sorger, Peter K., Southard-Smith, Austin, Spira, Avrum, Srivastava, Sudhir, Stein, Janet, Storm, Phillip, Stover, Elizabeth, Strand, Siri H., Su, Timothy, Sudar, Damir, Sullivan, Ryan, Surrey, Lea, Suvà, Mario, Tan, Kai, Terekhanova, Nadezhda V., Ternes, Luke, Thammavong, Lisa, Thibault, Guillaume, Thomas, George V., Thorsson, Vésteinn, Todres, Ellen, Tran, Linh, Tyler, Madison, Uzun, Yasin, Vachani, Anil, Van Allen, Eliezer, Vandekar, Simon, Veis, Deborah J., Vigneau, Sébastien, Vossough, Arastoo, Waanders, Angela, Wagle, Nikhil, Wang, Liang-Bo, Wendl, Michael C., West, Robert, Williams, Elizabeth H., Wu, Chi-yun, Wu, Hao, Wu, Hung-Yi, Wyczalkowski, Matthew A., Xie, Yubin, Yang, Xiaolu, Yapp, Clarence, Yu, Wenbao, Yuan, Yinyin, Zhang, Dadong, Zhang, Kun, Zhang, Mianlei, Zhang, Nancy, Zhang, Yantian, Zhao, Yanyan, Zhou, Daniel Cui, Zhou, Zilu, Zhu, Houxiang, Zhu, Qin, Zhu, Xiangzhu, Zhu, Yuankun, Zhuang, Xiaowei, Hupalowska, Anna, Rood, Jennifer E., Hanlon, Sean E., Hughes, Shannon K., Hwang, E. Shelley, Johnson, Bruce E., Shalek, Alex K., Spira, Avrum E., and West, Robert B.

Published
2020
Full Text
View/download PDF

12. Nanopore Sequencing of the phi X 174 genome

Author

Laszlo, Andrew H., Derrington, Ian M., Ross, Brian C., Brinkerhoff, Henry, Adey, Andrew, Nova, Ian C., Craig, Jonathan M., Langford, Kyle W., Samson, Jenny Mae, Daza, Riza, Doering, Kenji, Shendure, Jay, and Gundlach, Jens H.

Subjects
Quantitative Biology - Genomics, Physics - Biological Physics
Abstract

Nanopore sequencing of DNA is a single-molecule technique that may achieve long reads, low cost, and high speed with minimal sample preparation and instrumentation. Here, we build on recent progress with respect to nanopore resolution and DNA control to interpret the procession of ion current levels observed during the translocation of DNA through the pore MspA. As approximately four nucleotides affect the ion current of each level, we measured the ion current corresponding to all 256 four-nucleotide combinations (quadromers). This quadromer map is highly predictive of ion current levels of previously unmeasured sequences derived from the bacteriophage phi X 174 genome. Furthermore, we show nanopore sequencing reads of phi X 174 up to 4,500 bases in length that can be unambiguously aligned to the phi X 174 reference genome, and demonstrate proof-of-concept utility with respect to hybrid genome assembly and polymorphism detection. All methods and data are made fully available., Comment: 11 pages, 4 figures, 27 page supplement with 15 figures and 6 tables

Published
2014

14. Spatially mapped single-cell chromatin accessibility

Author

Thornton, Casey A., Mulqueen, Ryan M., Torkenczy, Kristof A., Nishida, Andrew, Lowenstein, Eve G., Fields, Andrew J., Steemers, Frank J., Zhang, Wenri, McConnell, Heather L., Woltjer, Randy L., Mishra, Anusha, Wright, Kevin M., and Adey, Andrew C.

Published
2021
Full Text
View/download PDF

22. Systematic benchmarking of single-cell ATAC-sequencing protocols

Author

De Rop, Florian V., primary, Hulselmans, Gert, additional, Flerin, Chris, additional, Soler-Vila, Paula, additional, Rafels, Albert, additional, Christiaens, Valerie, additional, González-Blas, Carmen Bravo, additional, Marchese, Domenica, additional, Caratù, Ginevra, additional, Poovathingal, Suresh, additional, Rozenblatt-Rosen, Orit, additional, Slyper, Michael, additional, Luo, Wendy, additional, Muus, Christoph, additional, Duarte, Fabiana, additional, Shrestha, Rojesh, additional, Bagdatli, S. Tansu, additional, Corces, M. Ryan, additional, Mamanova, Lira, additional, Knights, Andrew, additional, Meyer, Kerstin B., additional, Mulqueen, Ryan, additional, Taherinasab, Akram, additional, Maschmeyer, Patrick, additional, Pezoldt, Jörn, additional, Lambert, Camille Lucie Germaine, additional, Iglesias, Marta, additional, Najle, Sebastián R., additional, Dossani, Zain Y., additional, Martelotto, Luciano G., additional, Burkett, Zach, additional, Lebofsky, Ronald, additional, Martin-Subero, José Ignacio, additional, Pillai, Satish, additional, Sebé-Pedrós, Arnau, additional, Deplancke, Bart, additional, Teichmann, Sarah A., additional, Ludwig, Leif S., additional, Braun, Theodore P., additional, Adey, Andrew C., additional, Greenleaf, William J., additional, Buenrostro, Jason D., additional, Regev, Aviv, additional, Aerts, Stein, additional, and Heyn, Holger, additional

Published
2023
Full Text
View/download PDF

23. Novel recruitment approaches and operational results for a statewide population Cohort for cancer research: The Healthy Oregon Project.

Author

Zhenzhen Zhang, Shafer, Autumn, Johnson-Camacho, Katie, Adey, Andrew, Anur, Pavana, Brown, Kim A., Conrad, Casey, Crist, Rachel, Farris, Paige E., Harrington, Christina A., Marriott, Lisa K., Mitchell, Asia, O'Roak, Brian, Serrato, Vanessa, Richards, C. Sue, Spellman, Paul T., and Shannon, Jackilen

Abstract

The Healthy Oregon Project (HOP) is a research study focused on cancer research. It has successfully recruited over 35,000 participants, representing over 1% of the adult population in Oregon, using smartphone-based communication and social media. The study emphasizes the importance of collecting comprehensive survey and biological data for collaborative research. HOP also offers genetic health screening for cancer risk and aims to improve early detection strategies. Efforts have been made to engage participants through various methods, including in-person events and social media campaigns. The study population is diverse, but there are challenges in terms of long-term engagement and demographic limitations. The authors suggest integrating HOP with other similar projects across the US to diversify the population base and provide equal access to research cohorts. The study provides a cost-effective approach for establishing large-scale cohorts for cancer research. [Extracted from the article]

Published
2024
Full Text
View/download PDF

24. Abstract 4164: Relieving immune suppressive pathways in breast cancer to improve outcomes

Author

Poissonnier, Amanda, primary, Egeland, Eivind Valen, additional, Erbe, Rossin, additional, Horton, Wesley, additional, Howells-Ferreira, Ana, additional, Sivagnanam, Shamilene, additional, Kirchberger, Nell, additional, Murugan, Dhaarini, additional, Fields, Andrew, additional, Ordentlich, Peter, additional, Adey, Andrew C., additional, Fertig, Elana J., additional, and Coussens, Lisa M., additional

Published
2023
Full Text
View/download PDF

26. Validation and Implementation of Targeted Capture and Sequencing for the Detection of Actionable Mutation, Copy Number Variation, and Gene Rearrangement in Clinical Cancer Specimens

Author

Pritchard, Colin C., Salipante, Stephen J., Koehler, Karen, Smith, Christina, Scroggins, Sheena, Wood, Brent, Wu, David, Lee, Ming K., Dintzis, Suzanne, Adey, Andrew, Liu, Yajuan, Eaton, Keith D., Martins, Renato, Stricker, Kari, Margolin, Kim A., Hoffman, Noah, Churpek, Jane E., Tait, Jonathan F., King, Mary-Claire, and Walsh, Tom

Published
2014
Full Text
View/download PDF

34. The haplotype-resolved genome and epigenome of the aneuploid HeLa cancer cell line

Author

Adey, Andrew, Burton, Joshua N., Kitzman, Jacob O., Hiatt, Joseph B., Lewis, Alexandra P., Martin, Beth K., Qiu, Ruolan, Lee, Choli, and Shendure, Jay

Subjects
Oncology, Experimental -- Equipment and supplies, Haplotypes -- Research, Cancer -- Research, HeLa cells -- Testing, Genomic libraries -- Identification and classification, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

The HeLa cell line was established in 1951 from cervical cancer cells taken from a patient, Henrietta Lacks. This was the first successful attempt to immortalize human-derived cells in vitro (1). The robust growth and unrestricted distribution of HeLa cells resulted in its broad adoption--both intentionally and through widespread cross-contamination (2) --and for the past 60 years it has served a role analogous to that of a model organism (3). The cumulative impact of the HeLa cell line on research is demonstrated by its occurrence in more than 74,000 PubMed abstracts (approximately 0.3%).The genomic architecture of HeLa remains largely unexplored beyond its karyotype (4), partly because like many cancers, its extensive aneuploidy renders such analyses challenging. We carried out haplotype-resolved whole-genome sequencing (5) of the HeLa CCL-2 strain, examined point-and indel-mutation variations, mapped copy-number variations and loss of heterozygosity regions, and phased variants across full chromosome arms. We also investigated variation and copy-number profiles for HeLa S3 and eight additional strains. We find that HeLa is relatively stable in terms of point variation, with few new mutations accumulating after early passaging. Haplotype resolution facilitated reconstruction of an amplified, highly rearranged region of chromosome 8q24.21 at which integration of the human papilloma virus type 18 (HPV-18) genome occurred and that is likely to be the event that initiated tumorigenesis. We combined these maps with RNA-seq AA (6) and ENCODE Project (7) data sets to phase the HeLa epigenome. This revealed strong, haplotype-specific activation of the proto-oncogene MYC by the integrated HPV-18 genome approximately 500 kilobases upstream, and enabled global analyses of the relationship between gene dosage and expression. These data provide an extensively phased, high-quality reference genome for past and future experiments relying on HeLa, and demonstrate the value of haplotype resolution for characterizing cancer genomes and epigenomes., We generated a haplotype-resolved genome sequence of HeLa CCL-2 using a multifaceted approach that included shotgun, mate-pair and long-read sequencing, as well as sequencing of pools of fosmid clones5 (Supplementary [...]

Published
2013

42. The Human Tumor Atlas Network: Charting Tumor Transitions across Space and Time at Single-Cell Resolution

Author

Rozenblatt-Rosen, Orit, primary, Regev, Aviv, additional, Oberdoerffer, Philipp, additional, Nawy, Tal, additional, Hupalowska, Anna, additional, Rood, Jennifer E., additional, Ashenberg, Orr, additional, Cerami, Ethan, additional, Coffey, Robert J., additional, Demir, Emek, additional, Ding, Li, additional, Esplin, Edward D., additional, Ford, James M., additional, Goecks, Jeremy, additional, Ghosh, Sharmistha, additional, Gray, Joe W., additional, Guinney, Justin, additional, Hanlon, Sean E., additional, Hughes, Shannon K., additional, Hwang, E. Shelley, additional, Iacobuzio-Donahue, Christine A., additional, Jané-Valbuena, Judit, additional, Johnson, Bruce E., additional, Lau, Ken S., additional, Lively, Tracy, additional, Mazzilli, Sarah A., additional, Pe’er, Dana, additional, Santagata, Sandro, additional, Shalek, Alex K., additional, Schapiro, Denis, additional, Snyder, Michael P., additional, Sorger, Peter K., additional, Spira, Avrum E., additional, Srivastava, Sudhir, additional, Tan, Kai, additional, West, Robert B., additional, Williams, Elizabeth H., additional, Aberle, Denise, additional, Achilefu, Samuel I., additional, Ademuyiwa, Foluso O., additional, Adey, Andrew C., additional, Aft, Rebecca L., additional, Agarwal, Rachana, additional, Aguilar, Ruben A., additional, Alikarami, Fatemeh, additional, Allaj, Viola, additional, Amos, Christopher, additional, Anders, Robert A., additional, Angelo, Michael R., additional, Anton, Kristen, additional, Aster, Jon C., additional, Babur, Ozgun, additional, Bahmani, Amir, additional, Balsubramani, Akshay, additional, Barrett, David, additional, Beane, Jennifer, additional, Bender, Diane E., additional, Bernt, Kathrin, additional, Berry, Lynne, additional, Betts, Courtney B., additional, Bletz, Julie, additional, Blise, Katie, additional, Boire, Adrienne, additional, Boland, Genevieve, additional, Borowsky, Alexander, additional, Bosse, Kristopher, additional, Bott, Matthew, additional, Boyden, Ed, additional, Brooks, James, additional, Bueno, Raphael, additional, Burlingame, Erik A., additional, Cai, Qiuyin, additional, Campbell, Joshua, additional, Caravan, Wagma, additional, Chaib, Hassan, additional, Chan, Joseph M., additional, Chang, Young Hwan, additional, Chatterjee, Deyali, additional, Chaudhary, Ojasvi, additional, Chen, Alyce A., additional, Chen, Bob, additional, Chen, Changya, additional, Chen, Chia-hui, additional, Chen, Feng, additional, Chen, Yu-An, additional, Chheda, Milan G., additional, Chin, Koei, additional, Chiu, Roxanne, additional, Chu, Shih-Kai, additional, Chuaqui, Rodrigo, additional, Chun, Jaeyoung, additional, Cisneros, Luis, additional, Colditz, Graham A., additional, Cole, Kristina, additional, Collins, Natalie, additional, Contrepois, Kevin, additional, Coussens, Lisa M., additional, Creason, Allison L., additional, Crichton, Daniel, additional, Curtis, Christina, additional, Davidsen, Tanja, additional, Davies, Sherri R., additional, de Bruijn, Ino, additional, Dellostritto, Laura, additional, De Marzo, Angelo, additional, DeNardo, David G., additional, Diep, Dinh, additional, Diskin, Sharon, additional, Doan, Xengie, additional, Drewes, Julia, additional, Dubinett, Stephen, additional, Dyer, Michael, additional, Egger, Jacklynn, additional, Eng, Jennifer, additional, Engelhardt, Barbara, additional, Erwin, Graham, additional, Esserman, Laura, additional, Felmeister, Alex, additional, Feiler, Heidi S., additional, Fields, Ryan C., additional, Fisher, Stephen, additional, Flaherty, Keith, additional, Flournoy, Jennifer, additional, Fortunato, Angelo, additional, Frangieh, Allison, additional, Frye, Jennifer L., additional, Fulton, Robert S., additional, Galipeau, Danielle, additional, Gan, Siting, additional, Gao, Jianjiong, additional, Gao, Long, additional, Gao, Peng, additional, Gao, Vianne R., additional, Geiger, Tim, additional, George, Ajit, additional, Getz, Gad, additional, Giannakis, Marios, additional, Gibbs, David L., additional, Gillanders, William E., additional, Goedegebuure, Simon P., additional, Gould, Alanna, additional, Gowers, Kate, additional, Greenleaf, William, additional, Gresham, Jeremy, additional, Guerriero, Jennifer L., additional, Guha, Tuhin K., additional, Guimaraes, Alexander R., additional, Gutman, David, additional, Hacohen, Nir, additional, Hanlon, Sean, additional, Hansen, Casey R., additional, Harismendy, Olivier, additional, Harris, Kathleen A., additional, Hata, Aaron, additional, Hayashi, Akimasa, additional, Heiser, Cody, additional, Helvie, Karla, additional, Herndon, John M., additional, Hirst, Gilliam, additional, Hodi, Frank, additional, Hollmann, Travis, additional, Horning, Aaron, additional, Hsieh, James J., additional, Hughes, Shannon, additional, Huh, Won Jae, additional, Hunger, Stephen, additional, Hwang, Shelley E., additional, Ijaz, Heba, additional, Izar, Benjamin, additional, Jacobson, Connor A., additional, Janes, Samuel, additional, Jayasinghe, Reyka G., additional, Jiang, Lihua, additional, Johnson, Brett E., additional, Johnson, Bruce, additional, Ju, Tao, additional, Kadara, Humam, additional, Kaestner, Klaus, additional, Kagan, Jacob, additional, Kalinke, Lukas, additional, Keith, Robert, additional, Khan, Aziz, additional, Kibbe, Warren, additional, Kim, Albert H., additional, Kim, Erika, additional, Kim, Junhyong, additional, Kolodzie, Annette, additional, Kopytra, Mateusz, additional, Kotler, Eran, additional, Krueger, Robert, additional, Krysan, Kostyantyn, additional, Kundaje, Anshul, additional, Ladabaum, Uri, additional, Lake, Blue B., additional, Lam, Huy, additional, Laquindanum, Rozelle, additional, Laughney, Ashley M., additional, Lee, Hayan, additional, Lenburg, Marc, additional, Leonard, Carina, additional, Leshchiner, Ignaty, additional, Levy, Rochelle, additional, Li, Jerry, additional, Lian, Christine G., additional, Lim, Kian-Huat, additional, Lin, Jia-Ren, additional, Lin, Yiyun, additional, Liu, Qi, additional, Liu, Ruiyang, additional, Longabaugh, William J.R., additional, Longacre, Teri, additional, Ma, Cynthia X., additional, Macedonia, Mary Catherine, additional, Madison, Tyler, additional, Maher, Christopher A., additional, Maitra, Anirban, additional, Makinen, Netta, additional, Makowski, Danika, additional, Maley, Carlo, additional, Maliga, Zoltan, additional, Mallo, Diego, additional, Maris, John, additional, Markham, Nick, additional, Marks, Jeffrey, additional, Martinez, Daniel, additional, Mashl, Robert J., additional, Masilionais, Ignas, additional, Mason, Jennifer, additional, Massagué, Joan, additional, Massion, Pierre, additional, Mattar, Marissa, additional, Mazurchuk, Richard, additional, Mazutis, Linas, additional, McKinley, Eliot T., additional, McMichael, Joshua F., additional, Merrick, Daniel, additional, Meyerson, Matthew, additional, Miessner, Julia R., additional, Mills, Gordon B., additional, Mills, Meredith, additional, Mondal, Suman B., additional, Mori, Motomi, additional, Mori, Yuriko, additional, Moses, Elizabeth, additional, Mosse, Yael, additional, Muhlich, Jeremy L., additional, Murphy, George F., additional, Navin, Nicholas E., additional, Nederlof, Michel, additional, Ness, Reid, additional, Nevins, Stephanie, additional, Nikolov, Milen, additional, Nirmal, Ajit Johnson, additional, Nolan, Garry, additional, Novikov, Edward, additional, O’Connell, Brendan, additional, Offin, Michael, additional, Oh, Stephen T., additional, Olson, Anastasiya, additional, Ooms, Alex, additional, Ossandon, Miguel, additional, Owzar, Kouros, additional, Parmar, Swapnil, additional, Patel, Tasleema, additional, Patti, Gary J., additional, Pe'er, Itsik, additional, Peng, Tao, additional, Persson, Daniel, additional, Petty, Marvin, additional, Pfister, Hanspeter, additional, Polyak, Kornelia, additional, Pourfarhangi, Kamyar, additional, Puram, Sidharth V., additional, Qiu, Qi, additional, Quintanal-Villalonga, Álvaro, additional, Raj, Arjun, additional, Ramirez-Solano, Marisol, additional, Rashid, Rumana, additional, Reeb, Ashley N., additional, Reid, Mary, additional, Resnick, Adam, additional, Reynolds, Sheila M., additional, Riesterer, Jessica L., additional, Rodig, Scott, additional, Roland, Joseph T., additional, Rosenfield, Sonia, additional, Rotem, Asaf, additional, Roy, Sudipta, additional, Rozenblatt-Rosen, Orit, additional, Rudin, Charles M., additional, Ryser, Marc D., additional, Santi-Vicini, Maria, additional, Sato, Kazuhito, additional, Schrag, Deborah, additional, Schultz, Nikolaus, additional, Sears, Cynthia L., additional, Sears, Rosalie C., additional, Sen, Subrata, additional, Sen, Triparna, additional, Shalek, Alex, additional, Sheng, Jeff, additional, Sheng, Quanhu, additional, Shoghi, Kooresh I., additional, Shrubsole, Martha J., additional, Shyr, Yu, additional, Sibley, Alexander B., additional, Siex, Kiara, additional, Simmons, Alan J., additional, Singer, Dinah S., additional, Sivagnanam, Shamilene, additional, Slyper, Michal, additional, Sokolov, Artem, additional, Song, Sheng-Kwei, additional, Southard-Smith, Austin, additional, Spira, Avrum, additional, Stein, Janet, additional, Storm, Phillip, additional, Stover, Elizabeth, additional, Strand, Siri H., additional, Su, Timothy, additional, Sudar, Damir, additional, Sullivan, Ryan, additional, Surrey, Lea, additional, Suvà, Mario, additional, Terekhanova, Nadezhda V., additional, Ternes, Luke, additional, Thammavong, Lisa, additional, Thibault, Guillaume, additional, Thomas, George V., additional, Thorsson, Vésteinn, additional, Todres, Ellen, additional, Tran, Linh, additional, Tyler, Madison, additional, Uzun, Yasin, additional, Vachani, Anil, additional, Van Allen, Eliezer, additional, Vandekar, Simon, additional, Veis, Deborah J., additional, Vigneau, Sébastien, additional, Vossough, Arastoo, additional, Waanders, Angela, additional, Wagle, Nikhil, additional, Wang, Liang-Bo, additional, Wendl, Michael C., additional, West, Robert, additional, Wu, Chi-yun, additional, Wu, Hao, additional, Wu, Hung-Yi, additional, Wyczalkowski, Matthew A., additional, Xie, Yubin, additional, Yang, Xiaolu, additional, Yapp, Clarence, additional, Yu, Wenbao, additional, Yuan, Yinyin, additional, Zhang, Dadong, additional, Zhang, Kun, additional, Zhang, Mianlei, additional, Zhang, Nancy, additional, Zhang, Yantian, additional, Zhao, Yanyan, additional, Zhou, Daniel Cui, additional, Zhou, Zilu, additional, Zhu, Houxiang, additional, Zhu, Qin, additional, Zhu, Xiangzhu, additional, Zhu, Yuankun, additional, and Zhuang, Xiaowei, additional

Published
2020
Full Text
View/download PDF

43. The Rhododendron Genome and Chromosomal Organization Provide Insight into Shared Whole-Genome Duplications across the Heath Family (Ericaceae)

Author

Soza, Valerie L, primary, Lindsley, Dale, additional, Waalkes, Adam, additional, Ramage, Elizabeth, additional, Patwardhan, Rupali P, additional, Burton, Joshua N, additional, Adey, Andrew, additional, Kumar, Akash, additional, Qiu, Ruolan, additional, Shendure, Jay, additional, and Hall, Benjamin, additional

Published
2019
Full Text
View/download PDF

45. Single-cell sequencing of primate preimplantation embryos reveals chromosome elimination via cellular fragmentation and blastomere exclusion

Author

Daughtry, Brittany L., primary, Rosenkrantz, Jimi L., additional, Lazar, Nathan H., additional, Fei, Suzanne S., additional, Redmayne, Nash, additional, Torkenczy, Kristof A., additional, Adey, Andrew, additional, Yan, Melissa, additional, Gao, Lina, additional, Park, Byung, additional, Nevonen, Kimberly A., additional, Carbone, Lucia, additional, and Chavez, Shawn L., additional

Published
2019
Full Text
View/download PDF

46. Post-translational modification localizes MYC to the nuclear pore basket to regulate a subset of target genes involved in cellular responses to environmental signals

Author

Su, Yulong, primary, Pelz, Carl, additional, Huang, Tao, additional, Torkenczy, Kristof, additional, Wang, Xiaoyan, additional, Cherry, Allison, additional, Daniel, Colin J., additional, Liang, Juan, additional, Nan, Xiaolin, additional, Dai, Mu-Shui, additional, Adey, Andrew, additional, Impey, Soren, additional, and Sears, Rosalie C., additional

Published
2018
Full Text
View/download PDF

47. Highly scalable generation of DNA methylation profiles in single cells

Author

Mulqueen, Ryan M, primary, Pokholok, Dmitry, additional, Norberg, Steven J, additional, Torkenczy, Kristof A, additional, Fields, Andrew J, additional, Sun, Duanchen, additional, Sinnamon, John R, additional, Shendure, Jay, additional, Trapnell, Cole, additional, O'Roak, Brian J, additional, Xia, Zheng, additional, Steemers, Frank J, additional, and Adey, Andrew C, additional

Published
2018
Full Text
View/download PDF

48. Recurrent Somatic Loss of TNFRSF14 in Classical Hodgkin Lymphoma

Author

Salipante, Stephen J., Adey, Andrew, Thomas, Anju, Lee, Choli, Liu, Yajuan J., Kumar, Akash, Lewis, Alexandra P., Wu, David, Fromm, Jonathan R., and Shendure, Jay

Subjects
Cell Line, Tumor, Humans, Cell Separation, Reed-Sternberg Cells, Flow Cytometry, Hodgkin Disease, Receptors, Tumor Necrosis Factor, Member 14, Article, Oligonucleotide Array Sequence Analysis
Abstract

Investigation of the genetic lesions underlying classical Hodgkin lymphoma (CHL) has been challenging due to the rarity of Hodgkin and Reed-Sternberg (HRS) cells, the pathognomonic neoplastic cells of CHL. In an effort to catalog more comprehensively recurrent copy number alterations occurring during oncogenesis, we investigated somatic alterations involved in CHL using whole-genome sequencing-mediated copy number analysis of purified HRS cells. We performed low-coverage sequencing of small numbers of intact HRS cells and paired non-neoplastic B lymphocytes isolated by flow cytometric cell sorting from 19 primary cases, as well as two commonly used HRS-derived cell lines (KM-H2 and L1236). We found that HRS cells contain strikingly fewer copy number abnormalities than CHL cell lines. A subset of cases displayed non-integral chromosomal copy number states, suggesting internal heterogeneity within the HRS cell population. Recurrent somatic copy number alterations involving known factors in CHL pathogenesis were identified (REL, the PD-1 pathway, and TNFAIP3). In eight cases (42%) we observed recurrent copy number loss of chr1:2,352,236-4,574,271, a region containing the candidate tumor suppressor TNFRSF14. Using flow cytometry, we demonstrated reduced TNFRSF14 expression in HRS cells from five of 22 additional cases (23%) and in two of three CHL cell lines. These studies suggest that TNFRSF14 dysregulation may contribute to the pathobiology of CHL in a subset of cases.

Published
2015

49. Increased Sensitivity in Whole-Genome Bisulfite Sequencing (Wgbs): A Novel 'Post-bisulfite Conversion' Library Construction Method from Sub-nanogram DNA Inputs

Author

Hitchen, John, Gabel, Dixie, Caruccio, Nick, Adey, Andrew, and Sooknanan, Roy

Subjects
Poster Session Abstracts
Abstract

Genome-wide analysis of 5-methylcytosines is possible with whole-genome bisulfite sequencing (WGBS), where unmethylated cytosine residues are converted to uracil. However, a major challenge in WGBS is the degradation of DNA that occurs during bisulfite conversion under conditions required for complete conversion. Typically, ∼90% of input DNA is degraded and thus, is especially problematic with limited starting amounts of DNA. Additionally, regions that are rich in unmethylated cytosines are more sensitive to strand breaks. As a consequence, a majority of DNA fragments contained in di-tagged NGS DNA libraries treated with bisulfite “post-library construction” can be rendered inactive due to strand breaks in the DNA sequence flanked by the adapter sequences. These mono-tagged templates are then excluded during library enrichment resulting in incomplete coverage and bias when performing whole genome bisulfite sequencing.

Published
2013

50. Decoding Long Nanopore Reads of Bacteriophage Phi X 174

Author

Laszlo, Andrew H., primary, Derrington, Ian M., additional, Ross, Brian C., additional, Brinkerhoff, Henry, additional, Adey, Andrew C., additional, Nova, Ian C., additional, Craig, Jon M., additional, Langford, Kyle W., additional, Samson, Jenny Mae, additional, Daza, Riza, additional, Doering, Kenji, additional, Shendure, Jay, additional, and Gundlach, Jens H., additional

Published
2015
Full Text
View/download PDF

Catalog

Books, media, physical & digital resources
See catalog results