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1. Single-cell stabilization method identifies gonadotrope transcriptional dynamics and pituitary cell type heterogeneity

Author

Ruf-Zamojski, Frederique, Ge, Yongchao, Nair, Venugopalan, Zamojski, Michel, Pincas, Hanna, Toufaily, Chirine, Tome-Garcia, Jessica, Stoeckius, Marlon, Stephenson, William, Smith, Gregory R, Bernard, Daniel J, Tsankova, Nadejda M, Hartmann, Boris M, Fribourg, Miguel, Smibert, Peter, Swerdlow, Harold, Turgeon, Judith L, and Sealfon, Stuart C

Subjects
Biotechnology, Genetics, Contraception/Reproduction, Underpinning research, 1.1 Normal biological development and functioning, Animals, Buffers, Cell Line, Tumor, Dose-Response Relationship, Drug, Early Growth Response Protein 1, Early Growth Response Protein 2, Genes, Immediate-Early, Genetic Heterogeneity, Gonadotrophs, Gonadotropin-Releasing Hormone, Mice, Proto-Oncogene Proteins c-fos, RNA Stability, RNA, Messenger, Sequence Analysis, RNA, Single-Cell Analysis, Transcriptional Activation, Transcriptome, Environmental Sciences, Biological Sciences, Information and Computing Sciences, Developmental Biology
Abstract

Immediate-early response genes (IEGs) are rapidly and transiently induced following an extracellular signal. Elucidating the IEG response patterns in single cells (SCs) requires assaying large numbers of timed samples at high accuracy while minimizing handling effects. To achieve this, we developed and validated RNA stabilization Buffer for Examination of Single-cell Transcriptomes (RNA-Best), a versatile single-step cell and tissue preservation protocol that stabilizes RNA in intact SCs without perturbing transcription patterns. We characterize for the first time SC heterogeneity in IEG responses to pulsatile gonadotropin-releasing hormone (GnRH) stimuli in pituitary gonadotrope cells. Our study identifies a gene-specific hierarchical pattern of all-or-none transcript induction elicited by increasing concentrations of GnRH. This quantal pattern of gene activation raises the possibility that IEG activation, when accurately resolved at the SC level, may be mediated by gene bits that behave as pure binary switches.

Published
2018

2. International network of cancer genome projects

Author

Hudson (Chairperson), Thomas J, Anderson, Warwick, Aretz, Axel, Barker, Anna D, Bell, Cindy, Bernabé, Rosa R, Bhan, MK, Calvo, Fabien, Eerola, Iiro, Gerhard, Daniela S, Guttmacher, Alan, Guyer, Mark, Hemsley, Fiona M, Jennings, Jennifer L, Kerr, David, Klatt, Peter, Kolar, Patrik, Kusuda, Jun, Lane, David P, Laplace, Frank, Lu, Youyong, Nettekoven, Gerd, Ozenberger, Brad, Peterson, Jane, Rao, TS, Remacle, Jacques, Schafer, Alan J, Shibata, Tatsuhiro, Stratton, Michael R, Vockley, Joseph G, Watanabe, Koichi, Yang, Huanming, Yuen, Matthew MF, Knoppers (Leader), Bartha M, Bobrow, Martin, Cambon-Thomsen, Anne, Dressler, Lynn G, Dyke, Stephanie OM, Joly, Yann, Kato, Kazuto, Kennedy, Karen L, Nicolás, Pilar, Parker, Michael J, Rial-Sebbag, Emmanuelle, Romeo-Casabona, Carlos M, Shaw, Kenna M, Wallace, Susan, Wiesner, Georgia L, Zeps, Nikolajs, Lichter (Leader), Peter, Biankin, Andrew V, Chabannon, Christian, Chin, Lynda, Clément, Bruno, de Alava, Enrique, Degos, Françoise, Ferguson, Martin L, Geary, Peter, Hayes, D Neil, Hudson, Thomas J, Johns, Amber L, Kasprzyk, Arek, Nakagawa, Hidewaki, Penny, Robert, Piris, Miguel A, Sarin, Rajiv, Scarpa, Aldo, van de Vijver, Marc, Futreal (Leader), P Andrew, Aburatani, Hiroyuki, Bayés, Mónica, Bowtell, David DL, Campbell, Peter J, Estivill, Xavier, Grimmond, Sean M, Gut, Ivo, Hirst, Martin, López-Otín, Carlos, Majumder, Partha, Marra, Marco, McPherson, John D, Ning, Zemin, Puente, Xose S, Ruan, Yijun, Stunnenberg, Hendrik G, Swerdlow, Harold, Velculescu, Victor E, Wilson, Richard K, Xue, Hong H, Yang, Liu, Spellman (Leader), Paul T, Bader, Gary D, Boutros, Paul C, and Flicek, Paul

Subjects
Cancer, Genetics, Human Genome, DNA Methylation, DNA Mutational Analysis, Databases, Genetic, Genes, Neoplasm, Genetics, Medical, Genome, Human, Genomics, Humans, Intellectual Property, International Cooperation, Mutation, Neoplasms, International Cancer Genome Consortium, General Science & Technology
Abstract

The International Cancer Genome Consortium (ICGC) was launched to coordinate large-scale cancer genome studies in tumours from 50 different cancer types and/or subtypes that are of clinical and societal importance across the globe. Systematic studies of more than 25,000 cancer genomes at the genomic, epigenomic and transcriptomic levels will reveal the repertoire of oncogenic mutations, uncover traces of the mutagenic influences, define clinically relevant subtypes for prognosis and therapeutic management, and enable the development of new cancer therapies.

Published
2010

3. International network of cancer genome projects.

Author

International Cancer Genome Consortium, Hudson, Thomas J, Anderson, Warwick, Artez, Axel, Barker, Anna D, Bell, Cindy, Bernabé, Rosa R, Bhan, MK, Calvo, Fabien, Eerola, Iiro, Gerhard, Daniela S, Guttmacher, Alan, Guyer, Mark, Hemsley, Fiona M, Jennings, Jennifer L, Kerr, David, Klatt, Peter, Kolar, Patrik, Kusada, Jun, Lane, David P, Laplace, Frank, Youyong, Lu, Nettekoven, Gerd, Ozenberger, Brad, Peterson, Jane, Rao, TS, Remacle, Jacques, Schafer, Alan J, Shibata, Tatsuhiro, Stratton, Michael R, Vockley, Joseph G, Watanabe, Koichi, Yang, Huanming, Yuen, Matthew MF, Knoppers, Bartha M, Bobrow, Martin, Cambon-Thomsen, Anne, Dressler, Lynn G, Dyke, Stephanie OM, Joly, Yann, Kato, Kazuto, Kennedy, Karen L, Nicolás, Pilar, Parker, Michael J, Rial-Sebbag, Emmanuelle, Romeo-Casabona, Carlos M, Shaw, Kenna M, Wallace, Susan, Wiesner, Georgia L, Zeps, Nikolajs, Lichter, Peter, Biankin, Andrew V, Chabannon, Christian, Chin, Lynda, Clément, Bruno, de Alava, Enrique, Degos, Françoise, Ferguson, Martin L, Geary, Peter, Hayes, D Neil, Johns, Amber L, Kasprzyk, Arek, Nakagawa, Hidewaki, Penny, Robert, Piris, Miguel A, Sarin, Rajiv, Scarpa, Aldo, van de Vijver, Marc, Futreal, P Andrew, Aburatani, Hiroyuki, Bayés, Mónica, Botwell, David DL, Campbell, Peter J, Estivill, Xavier, Grimmond, Sean M, Gut, Ivo, Hirst, Martin, López-Otín, Carlos, Majumder, Partha, Marra, Marco, McPherson, John D, Ning, Zemin, Puente, Xose S, Ruan, Yijun, Stunnenberg, Hendrik G, Swerdlow, Harold, Velculescu, Victor E, Wilson, Richard K, Xue, Hong H, Yang, Liu, Spellman, Paul T, Bader, Gary D, and Boutros, Paul C

Subjects
International Cancer Genome Consortium, Humans, Neoplasms, DNA Mutational Analysis, Genetics, Medical, Genomics, DNA Methylation, Mutation, Genome, Human, International Cooperation, Intellectual Property, Databases, Genetic, Genes, Neoplasm, Genetics, Medical, Genome, Human, Databases, Genetic, Genes, Neoplasm, General Science & Technology
Abstract

The International Cancer Genome Consortium (ICGC) was launched to coordinate large-scale cancer genome studies in tumours from 50 different cancer types and/or subtypes that are of clinical and societal importance across the globe. Systematic studies of more than 25,000 cancer genomes at the genomic, epigenomic and transcriptomic levels will reveal the repertoire of oncogenic mutations, uncover traces of the mutagenic influences, define clinically relevant subtypes for prognosis and therapeutic management, and enable the development of new cancer therapies.

Published
2010

4. Complex landscapes of somatic rearrangement in human breast cancer genomes

Author

Stephens, Philip J, McBride, David J, Lin, Meng-Lay, Varela, Ignacio, Pleasance, Erin D, Simpson, Jared T, Stebbings, Lucy A, Leroy, Catherine, Edkins, Sarah, Mudie, Laura J, Greenman, Chris D, Jia, Mingming, Latimer, Calli, Teague, Jon W, Lau, King Wai, Burton, John, Quail, Michael A, Swerdlow, Harold, Churcher, Carol, Natrajan, Rachael, Sieuwerts, Anieta M, Martens, John WM, Silver, Daniel P, Langerød, Anita, Russnes, Hege EG, Foekens, John A, Reis-Filho, Jorge S, van ’t Veer, Laura, Richardson, Andrea L, Børresen-Dale, Anne-Lise, Campbell, Peter J, Futreal, P Andrew, and Stratton, Michael R

Subjects
Cancer, Human Genome, Breast Cancer, Genetics, Aetiology, 2.1 Biological and endogenous factors, Breast Neoplasms, Cell Line, Tumor, Cells, Cultured, Chromosome Aberrations, DNA Breaks, Female, Gene Rearrangement, Genome, Human, Genomic Library, Humans, Sequence Analysis, DNA, General Science & Technology
Abstract

Multiple somatic rearrangements are often found in cancer genomes; however, the underlying processes of rearrangement and their contribution to cancer development are poorly characterized. Here we use a paired-end sequencing strategy to identify somatic rearrangements in breast cancer genomes. There are more rearrangements in some breast cancers than previously appreciated. Rearrangements are more frequent over gene footprints and most are intrachromosomal. Multiple rearrangement architectures are present, but tandem duplications are particularly common in some cancers, perhaps reflecting a specific defect in DNA maintenance. Short overlapping sequences at most rearrangement junctions indicate that these have been mediated by non-homologous end-joining DNA repair, although varying sequence patterns indicate that multiple processes of this type are operative. Several expressed in-frame fusion genes were identified but none was recurrent. The study provides a new perspective on cancer genomes, highlighting the diversity of somatic rearrangements and their potential contribution to cancer development.

Published
2009

6. A map of human genome variation from population-scale sequencing

Author

Durbin, Richard M., Altshuler, David L., Durbin, Richard M., Abecasis, Gonçalo R., Bentley, David R., Chakravarti, Aravinda, Clark, Andrew G., Collins, Francis S., De La Vega, Francisco M., Donnelly, Peter, Egholm, Michael, Flicek, Paul, Gabriel, Stacey B., Gibbs, Richard A., Knoppers, Bartha M., Lander, Eric S., Lehrach, Hans, Mardis, Elaine R., McVean, Gil A., Nickerson, Debbie A., Peltonen, Leena, Schafer, Alan J., Sherry, Stephen T., Wang, Jun, Wilson, Richard K., Gibbs, Richard A., Deiros, David, Metzker, Mike, Muzny, Donna, Reid, Jeff, Wheeler, David, Wang, Jun, Li, Jingxiang, Jian, Min, Li, Guoqing, Li, Ruiqiang, Liang, Huiqing, Tian, Geng, Wang, Bo, Wang, Jian, Wang, Wei, Yang, Huanming, Zhang, Xiuqing, Zheng, Huisong, Lander, Eric S., Altshuler, David L., Ambrogio, Lauren, Bloom, Toby, Cibulskis, Kristian, Fennell, Tim J., Gabriel, Stacey B., Jaffe, David B., Shefler, Erica, Sougnez, Carrie L., Bentley, David R., Gormley, Niall, Humphray, Sean, Kingsbury, Zoya, Koko-Gonzales, Paula, Stone, Jennifer, McKernan, Kevin J., Costa, Gina L., Ichikawa, Jeffry K., Lee, Clarence C., Sudbrak, Ralf, Lehrach, Hans, Borodina, Tatiana A., Dahl, Andreas, Davydov, Alexey N., Marquardt, Peter, Mertes, Florian, Nietfeld, Wilfiried, Rosenstiel, Philip, Schreiber, Stefan, Soldatov, Aleksey V., Timmermann, Bernd, Tolzmann, Marius, Egholm, Michael, Affourtit, Jason, Ashworth, Dana, Attiya, Said, Bachorski, Melissa, Buglione, Eli, Burke, Adam, Caprio, Amanda, Celone, Christopher, Clark, Shauna, Conners, David, Desany, Brian, Gu, Lisa, Guccione, Lorri, Kao, Kalvin, Kebbel, Andrew, Knowlton, Jennifer, Labrecque, Matthew, McDade, Louise, Mealmaker, Craig, Minderman, Melissa, Nawrocki, Anne, Niazi, Faheem, Pareja, Kristen, Ramenani, Ravi, Riches, David, Song, Wanmin, Turcotte, Cynthia, Wang, Shally, Mardis, Elaine R., Wilson, Richard K., Dooling, David, Fulton, Lucinda, Fulton, Robert, Weinstock, George, Durbin, Richard M., Burton, John, Carter, David M., Churcher, Carol, Coffey, Alison, Cox, Anthony, Palotie, Aarno, Quail, Michael, Skelly, Tom, Stalker, James, Swerdlow, Harold P., Turner, Daniel, De Witte, Anniek, Giles, Shane, Bainbridge, Matthew, Challis, Danny, Sabo, Aniko, Yu, Fuli, Yu, Jin, Fang, Xiaodong, Guo, Xiaosen, Li, Yingrui, Luo, Ruibang, Tai, Shuaishuai, Wu, Honglong, Zheng, Hancheng, Zheng, Xiaole, Zhou, Yan, Marth, Gabor T., Garrison, Erik P., Huang, Weichun, Indap, Amit, Kural, Deniz, Lee, Wan-Ping, Fung Leong, Wen, Quinlan, Aaron R., Stewart, Chip, Stromberg, Michael P., Ward, Alistair N., Wu, Jiantao, Lee, Charles, Mills, Ryan E., Shi, Xinghua, Daly, Mark J., DePristo, Mark A., Ball, Aaron D., Banks, Eric, Browning, Brian L., Garimella, Kiran V., Grossman, Sharon R., Handsaker, Robert E., Hanna, Matt, Hartl, Chris, Kernytsky, Andrew M., Korn, Joshua M., Li, Heng, Maguire, Jared R., McCarroll, Steven A., McKenna, Aaron, Nemesh, James C., Philippakis, Anthony A., Poplin, Ryan E., Price, Alkes, Rivas, Manuel A., Sabeti, Pardis C., Schaffner, Stephen F., Shlyakhter, Ilya A., Cooper, David N., Ball, Edward V., Mort, Matthew, Phillips, Andrew D., Stenson, Peter D., Sebat, Jonathan, Makarov, Vladimir, Ye, Kenny, Yoon, Seungtai C., Bustamante, Carlos D., Clark, Andrew G., Boyko, Adam, Degenhardt, Jeremiah, Gravel, Simon, Gutenkunst, Ryan N., Kaganovich, Mark, Keinan, Alon, Lacroute, Phil, Ma, Xin, Reynolds, Andy, Clarke, Laura, Flicek, Paul, Cunningham, Fiona, Herrero, Javier, Keenen, Stephen, Kulesha, Eugene, Leinonen, Rasko, McLaren, William M., Radhakrishnan, Rajesh, Smith, Richard E., Zalunin, Vadim, Zheng-Bradley, Xiangqun, Korbel, Jan O., Stütz, Adrian M., Humphray, Sean, Bauer, Markus, Cheetham, Keira R., Cox, Tony, Eberle, Michael, James, Terena, Kahn, Scott, Murray, Lisa, Ye, Kai, De La Vega, Francisco M., Fu, Yutao, Hyland, Fiona C. L., Manning, Jonathan M., McLaughlin, Stephen F., Peckham, Heather E., Sakarya, Onur, Sun, Yongming A., Tsung, Eric F., Batzer, Mark A., Konkel, Miriam K., Walker, Jerilyn A., Albrecht, Marcus W., Amstislavskiy, Vyacheslav S., Herwig, Ralf, Parkhomchuk, Dimitri V., Sherry, Stephen T., Agarwala, Richa, Khouri, Hoda M., Morgulis, Aleksandr O., Paschall, Justin E., Phan, Lon D., Rotmistrovsky, Kirill E., Sanders, Robert D., Shumway, Martin F., Xiao, Chunlin, McVean, Gil A., Auton, Adam, Iqbal, Zamin, Lunter, Gerton, Marchini, Jonathan L., Moutsianas, Loukas, Myers, Simon, Tumian, Afidalina, Desany, Brian, Knight, James, Winer, Roger, Craig, David W., Beckstrom-Sternberg, Steve M., Christoforides, Alexis, Kurdoglu, Ahmet A., Pearson, John V., Sinari, Shripad A., Tembe, Waibhav D., Haussler, David, Hinrichs, Angie S., Katzman, Sol J., Kern, Andrew, Kuhn, Robert M., Przeworski, Molly, Hernandez, Ryan D., Howie, Bryan, Kelley, Joanna L., Cord Melton, S., Abecasis, Gonçalo R., Li, Yun, Anderson, Paul, Blackwell, Tom, Chen, Wei, Cookson, William O., Ding, Jun, Min Kang, Hyun, Lathrop, Mark, Liang, Liming, Moffatt, Miriam F., Scheet, Paul, Sidore, Carlo, Snyder, Matthew, Zhan, Xiaowei, Zöllner, Sebastian, Awadalla, Philip, Casals, Ferran, Idaghdour, Youssef, Keebler, John, Stone, Eric A., Zilversmit, Martine, Jorde, Lynn, Xing, Jinchuan, Eichler, Evan E., Aksay, Gozde, Alkan, Can, Hajirasouliha, Iman, Hormozdiari, Fereydoun, Sahinalp, Cenk S., Sudmant, Peter H., Mardis, Elaine R., Chen, Ken, Chinwalla, Asif, Ding, Li, Koboldt, Daniel C., McLellan, Mike D., Wallis, John W., Wendl, Michael C., Zhang, Qunyuan, Albers, Cornelis A., Ayub, Qasim, Balasubramaniam, Senduran, Barrett, Jeffrey C., Chen, Yuan, Conrad, Donald F., Danecek, Petr, Dermitzakis, Emmanouil T., Hu, Min, Huang, Ni, Hurles, Matt E., Jin, Hanjun, Jostins, Luke, Keane, Thomas M., Quang Le, Si, Lindsay, Sarah, Long, Quan, MacArthur, Daniel G., Montgomery, Stephen B., Parts, Leopold, Tyler-Smith, Chris, Walter, Klaudia, Zhang, Yujun, Gerstein, Mark B., Snyder, Michael, Abyzov, Alexej, Balasubramanian, Suganthi, Bjornson, Robert, Du, Jiang, Grubert, Fabian, Habegger, Lukas, Haraksingh, Rajini, Jee, Justin, Khurana, Ekta, Lam, Hugo Y. K., Leng, Jing, Jasmine Mu, Xinmeng, Urban, Alexander E., Zhang, Zhengdong, Lee, Charles, McCarroll, Steven A., DePristo, Mark A., Korbel, Jan O., De La Vega, Francisco M., Blackwell, Tom, Eichler, Evan E., Kidd, Jeffrey M., Hurles, Matt E., Gibbs, Richard A., Coafra, Cristian, Dinh, Huyen, Kovar, Christie, Lee, Sandy, Nazareth, Lynne, Marth, Gabor T., Wilkinson, Jane, Flicek, Paul, Sherry, Stephen T., Abecasis, Gonçalo R., Mardis, Elaine R., Coffey, Allison, Scott, Carol, Gerstein, Mark B., Chakravarti, Aravinda, Knoppers, Bartha M., Bustamante, Carlos D., Gharani, Neda, Jorde, Lynn, Kaye, Jane S., Kent, Alastair, Li, Taosha, McGuire, Amy L., Ossorio, Pilar N., Rotimi, Charles N., Su, Yeyang, Toji, Lorraine H., Brooks, Lisa D., Felsenfeld, Adam L., McEwen, Jean E., Abdallah, Assya, Juenger, Christopher R., Clemm, Nicholas C., Duncanson, Audrey, Green, Eric D., Guyer, Mark S., and Peterson, Jane L.

Published
2010
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7. Accurate whole human genome sequencing using reversible terminator chemistry

Author

Bentley, David R., Balasubramanian, Shankar, Swerdlow, Harold P., Smith, Geoffrey P., Milton, John, Brown, Clive G., Hall, Kevin P., Evers, Dirk J., Barnes, Colin L., Bignell, Helen R., Boutell, Jonathan M., Bryant, Jason, Carter, Richard J., Cheetham, R. Keira, Cox, Anthony J., Ellis, Darren J., Flatbush, Michael R., Gormley, Niall A., Humphray, Sean J., Irving, Leslie J., Karbelashvili, Mirian S., Kirk, Scott M., Li, Heng, Liu, Xiaohai, Maisinger, Klaus S., Murray, Lisa J., Obradovic, Bojan, Ost, Tobias, Parkinson, Michael L., Pratt, Mark R., Rasolonjatovo, Isabelle M. J., Reed, Mark T., Rigatti, Roberto, Rodighiero, Chiara, Ross, Mark T., Sabot, Andrea, Sankar, Subramanian V., Scally, Aylwyn, Schroth, Gary P., Smith, Mark E., Smith, Vincent P., Spiridou, Anastassia, Torrance, Peta E., Tzonev, Svilen S., Vermaas, Eric H., Walter, Klaudia, Wu, Xiaolin, Zhang, Lu, Alam, Mohammed D., Anastasi, Carole, Aniebo, Ify C., Bailey, David M. D., Bancarz, Iain R., Banerjee, Saibal, Barbour, Selena G., Baybayan, Primo A., Benoit, Vincent A., Benson, Kevin F., Bevis, Claire, Black, Phillip J., Boodhun, Asha, Brennan, Joe S., Bridgham, John A., Brown, Rob C., Brown, Andrew A., Buermann, Dale H., Bundu, Abass A., Burrows, James C., Carter, Nigel P., Castillo, Nestor, Catenazzi, Maria Chiara E., Chang, Simon, Cooley, R. Neil, Crake, Natasha R., Dada, Olubunmi O., Diakoumakos, Konstantinos D., Dominguez-Fernandez, Belen, Earnshaw, David J., Egbujor, Ugonna C., Elmore, David W., Etchin, Sergey S, Ewan, Mark R., Fedurco, Milan, Fraser, Louise J., Fuentes Fajardo, Karin V., Furey, W. Scott, George, David, Gietzen, Kimberley J., Goddard, Colin P., Golda, George S., Granieri, Philip A., Green, David E., Gustafson, David L., Hansen, Nancy F., Harnish, Kevin, Haudenschild, Christian D., Heyer, Narinder I, Hims, Matthew M., Ho, Johnny T., Horgan, Adrian M., Hoschler, Katya, Hurwitz, Steve, Ivanov, Denis V., Johnson, Maria Q., James, Terena, Huw Jones, T. A., Kang, Gyoung-Dong, Kerelska, Tzvetana H., Kersey, Alan D., Khrebtukova, Irina, Kindwall, Alex P., Kingsbury, Zoya, Kokko-Gonzales, Paula I., Kumar, Anil, Laurent, Marc A., Lawley, Cynthia T., Lee, Sarah E., Lee, Xavier, Liao, Arnold K., Loch, Jennifer A., Lok, Mitch, Luo, Shujun, Mammen, Radhika M., Martin, John W., McCauley, Patrick G., McNitt, Paul, Mehta, Parul, Moon, Keith W., Mullens, Joe W., Newington, Taksina, Ning, Zemin, Ling Ng, Bee, Novo, Sonia M., O'Neill, Michael J., Osborne, Mark A., Osnowski, Andrew, Ostadan, Omead, Paraschos, Lambros L., Pickering, Lea, Pike, Andrew C., Pike, Alger C., Pinkard, D. Chris, Pliskin, Daniel P., Podhasky, Joe, Quijano, Victor J., Raczy, Come, Rae, Vicki H., Rawlings, Stephen R., Rodriguez, Ana Chiva, Roe, Phyllida M., Rogers, John, Rogert Bacigalupo, Maria C., Romanov, Nikolai, Romieu, Anthony, Roth, Rithy K., Rourke, Natalie J., Ruediger, Silke T., Rusman, Eli, Sanches-Kuiper, Raquel M., Schenker, Martin R., Seoane, Josefina M., Shaw, Richard J., Shiver, Mitch K., Short, Steven W., Sizto, Ning L., Sluis, Johannes P., Smith, Melanie A., Sohna Sohna, Jean Ernest, Spence, Eric J., Stevens, Kim, Sutton, Neil, Szajkowski, Lukasz, Tregidgo, Carolyn L., Turcatti, Gerardo, vandeVondele, Stephanie, Verhovsky, Yuli, Virk, Selene M., Wakelin, Suzanne, Walcott, Gregory C., Wang, Jingwen, Worsley, Graham J., Yan, Juying, Yau, Ling, Zuerlein, Mike, Rogers, Jane, Mullikin, James C., Hurles, Matthew E., McCooke, Nick J., West, John S., Oaks, Frank L., Lundberg, Peter L., Klenerman, David, Durbin, Richard, and Smith, Anthony J.

Published
2008
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8. A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers

Author

Quail Michael A, Smith Miriam, Coupland Paul, Otto Thomas D, Harris Simon R, Connor Thomas R, Bertoni Anna, Swerdlow Harold P, and Gu Yong

Subjects
Next-generation sequencing, Ion torrent, Illumina, Pacific biosciences, MiSeq, PGM, SMRT, Bias, Genome coverage, GC-rich, AT-rich, Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background Next generation sequencing (NGS) technology has revolutionized genomic and genetic research. The pace of change in this area is rapid with three major new sequencing platforms having been released in 2011: Ion Torrent’s PGM, Pacific Biosciences’ RS and the Illumina MiSeq. Here we compare the results obtained with those platforms to the performance of the Illumina HiSeq, the current market leader. In order to compare these platforms, and get sufficient coverage depth to allow meaningful analysis, we have sequenced a set of 4 microbial genomes with mean GC content ranging from 19.3 to 67.7%. Together, these represent a comprehensive range of genome content. Here we report our analysis of that sequence data in terms of coverage distribution, bias, GC distribution, variant detection and accuracy. Results Sequence generated by Ion Torrent, MiSeq and Pacific Biosciences technologies displays near perfect coverage behaviour on GC-rich, neutral and moderately AT-rich genomes, but a profound bias was observed upon sequencing the extremely AT-rich genome of Plasmodium falciparum on the PGM, resulting in no coverage for approximately 30% of the genome. We analysed the ability to call variants from each platform and found that we could call slightly more variants from Ion Torrent data compared to MiSeq data, but at the expense of a higher false positive rate. Variant calling from Pacific Biosciences data was possible but higher coverage depth was required. Context specific errors were observed in both PGM and MiSeq data, but not in that from the Pacific Biosciences platform. Conclusions All three fast turnaround sequencers evaluated here were able to generate usable sequence. However there are key differences between the quality of that data and the applications it will support.

Published
2012
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9. Optimizing illumina next-generation sequencing library preparation for extremely at-biased genomes

Author

Oyola Samuel O, Otto Thomas D, Gu Yong, Maslen Gareth, Manske Magnus, Campino Susana, Turner Daniel J, MacInnis Bronwyn, Kwiatkowski Dominic P, Swerdlow Harold P, and Quail Michael A

Subjects
Next-Generation Sequencing, Illumina, Library, Plasmodium falciparum, AT-rich, Malaria, Clinical isolate, PCR, Tetramethyammonium chloride, PCR-free, Isothermal, Linear, Exponential, Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background Massively parallel sequencing technology is revolutionizing approaches to genomic and genetic research. Since its advent, the scale and efficiency of Next-Generation Sequencing (NGS) has rapidly improved. In spite of this success, sequencing genomes or genomic regions with extremely biased base composition is still a great challenge to the currently available NGS platforms. The genomes of some important pathogenic organisms like Plasmodium falciparum (high AT content) and Mycobacterium tuberculosis (high GC content) display extremes of base composition. The standard library preparation procedures that employ PCR amplification have been shown to cause uneven read coverage particularly across AT and GC rich regions, leading to problems in genome assembly and variation analyses. Alternative library-preparation approaches that omit PCR amplification require large quantities of starting material and hence are not suitable for small amounts of DNA/RNA such as those from clinical isolates. We have developed and optimized library-preparation procedures suitable for low quantity starting material and tolerant to extremely high AT content sequences. Results We have used our optimized conditions in parallel with standard methods to prepare Illumina sequencing libraries from a non-clinical and a clinical isolate (containing ~53% host contamination). By analyzing and comparing the quality of sequence data generated, we show that our optimized conditions that involve a PCR additive (TMAC), produces amplified libraries with improved coverage of extremely AT-rich regions and reduced bias toward GC neutral templates. Conclusion We have developed a robust and optimized Next-Generation Sequencing library amplification method suitable for extremely AT-rich genomes. The new amplification conditions significantly reduce bias and retain the complexity of either extremes of base composition. This development will greatly benefit sequencing clinical samples that often require amplification due to low mass of DNA starting material.

Published
2012
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10. Single-cell RNA-seq of rheumatoid arthritis synovial tissue using low-cost microfluidic instrumentation

Author

Stephenson, William, primary, Donlin, Laura T., additional, Butler, Andrew, additional, Rozo, Cristina, additional, Bracken, Bernadette, additional, Rashidfarrokhi, Ali, additional, Goodman, Susan M., additional, Ivashkiv, Lionel B., additional, Bykerk, Vivian P., additional, Orange, Dana E., additional, Darnell, Robert B., additional, Swerdlow, Harold P., additional, and Satija, Rahul, additional

Published
2018
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12. Single-cell RNA-seq of rheumatoid arthritis synovial tissue using low cost microfluidic instrumentation

Author

Stephenson, William, primary, Donlin, Laura T., additional, Butler, Andrew, additional, Rozo, Cristina, additional, Rashidfarrokhi, Ali, additional, Goodman, Susan M., additional, Ivashkiv, Lionel B., additional, Bykerk, Vivian P., additional, Orange, DE, additional, Darnell, Robert B., additional, Swerdlow, Harold P., additional, and Satija, Rahul, additional

Published
2017
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13. G&T-seq: parallel sequencing of single-cell genomes and transcriptomes

Author

Macaulay, Iain C., Haerty, Wilfried, Kumar, Parveen, Li, Yang I., Hu, Tim Xiaoming, Teng, Mabel J., Goolam, Mubeen, Saurat, Nathalie, Coupland, Paul, Shirley, Lesley M., Smith, Miriam, Van der Aa, Niels, Banerjee, Ruby, Ellis, Peter D., Quail, Michael A., Swerdlow, Harold P., Zernicka-Goetz, Magdalena, Livesey, Frederick J., Ponting, Chris P., and Voet, Thierry

Abstract

The ability to simultaneously sequence the genome and transcriptome of the same single cell offers a powerful means to dissect functional genetic heterogeneity at the cellular level. Here we describe G&T-seq, a method for separating and sequencing genomic DNA and full-length mRNA from single cells. By applying G&T-seq to over 220 single cells we reveal cellular properties that cannot be inferred from DNA or RNA sequencing alone, including associations between DNA copy number variation and gene expression dosage. We further demonstrate the detection of coding interchromosomal fusions and single nucleotide variants in both the genomes and transcriptomes of individual cells. G&T-seq enables the study of genotype-phenotype associations in single cells, and the investigation of DNA cell lineage trees of healthy and diseased tissues with transcriptome inferred cell types and states.

Published
2015

14. G&T-seq: parallel sequencing of single-cell genomes and transcriptomes

Author

Macaulay, Iain C, primary, Haerty, Wilfried, additional, Kumar, Parveen, additional, Li, Yang I, additional, Hu, Tim Xiaoming, additional, Teng, Mabel J, additional, Goolam, Mubeen, additional, Saurat, Nathalie, additional, Coupland, Paul, additional, Shirley, Lesley M, additional, Smith, Miriam, additional, Van der Aa, Niels, additional, Banerjee, Ruby, additional, Ellis, Peter D, additional, Quail, Michael A, additional, Swerdlow, Harold P, additional, Zernicka-Goetz, Magdalena, additional, Livesey, Frederick J, additional, Ponting, Chris P, additional, and Voet, Thierry, additional

Published
2015
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16. Efficient Depletion of Host DNA Contamination in Malaria Clinical Sequencing

Author

Oyola, Samuel O., primary, Gu, Yong, additional, Manske, Magnus, additional, Otto, Thomas D., additional, O'Brien, John, additional, Alcock, Daniel, additional, MacInnis, Bronwyn, additional, Berriman, Matthew, additional, Newbold, Chris I., additional, Kwiatkowski, Dominic P., additional, Swerdlow, Harold P., additional, and Quail, Michael A., additional

Published
2013
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17. Simultaneous epitope and transcriptome measurement in single cells

Author

Stoeckius, Marlon, Hafemeister, Christoph, Stephenson, William, Houck-Loomis, Brian, Chattopadhyay, Pratip K, Swerdlow, Harold, Satija, Rahul, and Smibert, Peter

Abstract

High-throughput single-cell RNA sequencing has transformed our understanding of complex cell populations, but it does not provide phenotypic information such as cell-surface protein levels. Here, we describe cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq), a method in which oligonucleotide-labeled antibodies are used to integrate cellular protein and transcriptome measurements into an efficient, single-cell readout. CITE-seq is compatible with existing single-cell sequencing approaches and scales readily with throughput increases.

Published
2017
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18. Optimal enzymes for amplifying sequencing libraries

Author

Quail, Michael A, primary, Otto, Thomas D, additional, Gu, Yong, additional, Harris, Simon R, additional, Skelly, Thomas F, additional, McQuillan, Jacqueline A, additional, Swerdlow, Harold P, additional, and Oyola, Samuel O, additional

Published
2011
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19. High-Throughput Array Instrument for DNA-Based Breast Cancer Diagnostics

Author

KAROLINSKA INST STOCKHOLM (SWEDEN), Swerdlow, Harold P., KAROLINSKA INST STOCKHOLM (SWEDEN), and Swerdlow, Harold P.

Abstract

The aim of this project is to develop improved methods for the production, processing, and analysis of microarrays (gene-chips) for breast-cancer diagnostics. These methods are based upon large numbers of discrete DNA spots placed on glass microscope slides typically, and hybridized to a probe derived from a tIssue or blood sample. %or breast- cancer diagnostics, there are two likely predominant modes of use. TIssue samples from suspect lesions, e.g., can be assessed for patterns of gene expression on cDNA arrays, indicative of a specific disease type or state. Additionally, analysis of known mutations can be performed on oligonucleotide-based arrays. We are optimizing cDNA microarray methods, and have achieved excellent limits of detection, although not good enough to detect the rarest transcripts. To improve this situation, we are redesigning our novel imaging (non-scanning) fluorescence microarray reader that currently performs four times better (with respect to limit of detection) than a commercial scanner, and does so about 300 times faster. Our next goal is to implement oligonucleotide arrays by various methods including both padlock probe-based ligation assays and allele-specific hybridization tests for specific known mutations. We are also actively improving direct covalent attachment of oligonucleotides to glass, and methods for printing oligonucleotide arrays much faster and cheaper.

Published
2000

20. A Capillary Instrument for High Speed DNA-Based Tumor Diagnosis

Author

KAROLINSKA INST STOCKHOLM (SWEDEN), Swerdlow, Harold P., KAROLINSKA INST STOCKHOLM (SWEDEN), and Swerdlow, Harold P.

Abstract

This project addresses the design and prototyping of a multiple-capillary (ultimately 96- channel) electrophoresis system that will be ideally suited for the rapid and inexpensive analysis of allele-specific and DNA-sequence-based breast-cancer diagnostic tests with high throughput. A fully- automated capillary electrophoresis system (as opposed to an electrophoresis instrument) will perform the following steps without human intervention: 1) prepare and purify DNA, ideally from blood or tissue samples, 2) mix DNA samples with PCR reagents, 3) thermally cycle and purify PCR products, 4) mix PCR samples with DNA sequencing reagents, 5) perform sequencing reactions (thermal cycling typically) and purify the fragments, 6) pre-run the capillaries and load the samples, 7) perform the electrophoresis and detect the DNA bands, 8) record and analyze the data, and 9) flush the capillaries after the previous run and fill the capillaries with fresh polymer solution. The present study will automate steps 6-9 of this process.

Published
1999

21. A Capillary Instrument for High Speed DNA-Based Tumor Diagnosis.

Author

UTAH UNIV SALT LAKE CITY, Swerdlow, Harold P., UTAH UNIV SALT LAKE CITY, and Swerdlow, Harold P.

Abstract

In order to test individuals for familial breast-cancer susceptibility, a fluidic 96-channel capillary DNA sequencing and analysis instrument is under development. The major subsystems of this instrument have been designed and tested. A novel manifold system will allow automated unattended loading to be performed. Ostensibly minor technical issues stand in the way of application of the prototype system to real samples on a large scale. User-friendly software is close to fully functional. The instrument will have major benefits over other commercial instruments that have been announced. Foremost is the ability to perform preparation, processing, loading, separation, detection, and analysis of DNA sequencing reactions in a coupled in-line fashion in a single instrument. Simultaneously, techniques for the practice of capillary DNA sequencing are being refined. New matrices for separating DNA have been developed and optimized. Sample purity can be assessed using a novel miniature conductivity probe. A new technique for loading samples without purification has also been developed.

Published
1998

22. DNA Immobilization: Silanized Nucleic Acids and Nanoprinting.

Author

Wittmann, Christine, Du, Quan, Larsson, Ola, Swerdlow, Harold, and Liang, Zicai

Abstract

Over the last decade, the development of DNA microarray technology has allowed the simultaneous analysis of many thousands of different genes in histological or cytological specimens. Although DNA microarrays can also be fabricated by photolithographic synthesis, the current paper focuses mainly on methods of DNA attachment by spotting on solid surfaces. Chemical modifications on solid surfaces (such as glass) and the DNA molecules have been presented with special focus on the approach of silanized nucleic acids, a method of DNA modification that can rid the need of glass surface modifications, and nanoprinting method, a way of producing high-density DNA arrays by a stamping mechanism. Different glass and DNA modifications have been applied to a different extent in the DNA microarray industry, but it is anticipated that, with the application of the DNA chip shifting gradually from large-scale expression profiling to more focused genotyping or diagnostics, the utilization of these methods may also shift according to the needs. [ABSTRACT FROM AUTHOR]

Published
2006
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24. Direct Sequencing of Small Genomes on the Pacific Biosciences RS Without Library Preparation

Author

Coupland, Paul, Chandra, Tamir, Quail, Mike, Reik, Wolf, and Swerdlow, Harold

Abstract

We have developed a sequencing method on the Pacific Biosciences RS sequencer (the PacBio) for small DNA molecules that avoids the need for a standard library preparation. To date this approach has been applied toward sequencing single-stranded and double-stranded viral genomes, bacterial plasmids, plasmid vector models for DNA-modification analysis, and linear DNA fragments covering an entire bacterial genome. Using direct sequencing it is possible to generate sequence data from as little as 1 ng of DNA, offering a significant advantage over current protocols which typically require 400–500 ng of sheared DNA for the library preparation.

Published
2012
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25. A Miniature Electrolytic Conductivity Probe with a Wide Linear Range

Author

Park, Sang‐Ryoul and Swerdlow, Harold

Abstract

A novel miniature electrolytic conductivity probe and its successful operation with modified bipolar pulse conductometry are presented. The probe based on a concentric ring‐disk electrode configuration of less than 1 mm in diameter featured extremely small detection volume, and conductivity was measured with a 1 μL solution. Rapid response, easy and quick washing, and virtually no consumption of samples by measurements were additional advantages of the suggested probe design. Poor linearity was observed with conventional AC conductometry due to a large cell constant and a small double layer capacitance of the probe. Measurement circuits for modified bipolar pulse conductometry were designed, and optimization of the various pulse parameters led to a wide linear dynamic range of 0.05–10 mS cm−1, thus achieving high accuracy with a single‐point calibration. The suggested conductometric device could be conveniently applied to biological reagents and samples that are usually too little to be measured with conventional conductometers.

Published
2007
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26. Optimal enzymes for amplifying sequencing libraries.

Author

Quail, Michael A, Otto, Thomas D, Gu, Yong, Harris, Simon R, Skelly, Thomas F, McQuillan, Jacqueline A, Swerdlow, Harold P, and Oyola, Samuel O

Subjects
LETTERS to the editor, ENZYME analysis, GENE amplification
Abstract

A letter to the editor is presented which discusses the identification of optimal enzymes for amplifying high complexity mixtures of DNA fragments.

Published
2012
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27. Improved Protocols for Illumina Sequencing

Author

Bronner, Iraad F., Quail, Michael A., Turner, Daniel J., and Swerdlow, Harold

Abstract

In this unit, we describe a set of improvements that have been made to the standard Illumina protocols to make the sequencing process more reliable in a high‐throughput environment, reduce amplification bias, narrow the distribution of insert sizes, and reliably obtain high yields of data. Curr. Protoc. Hum. Genet. 79:18.2.1‐18.2.42. © 2013 by John Wiley & Sons, Inc.

Published
2013
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28. Improved Protocols for the Illumina Genome Analyzer Sequencing System

Author

Quail, Michael A., Swerdlow, Harold, and Turner, Daniel J.

Abstract

In this unit, we describe a set of improvements we have made to the standard Illumina Genome Analyzer protocols to make the sequencing process more reliable in a high‐throughput environment, reduce amplification bias, narrow the distribution of insert sizes, and reliably obtain high yields of data. Curr. Protoc. Hum. Genet. 62:18.2.1‐18.2.27. © 2009 by John Wiley & Sons, Inc.

Published
2009
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29. Capillary gel electrophoresis for rapid, high resolution DNA sequencing

Author

Swerdlow, Harold and Gesteland, Raymond

Abstract

Capillary gel electrophoresis has been demonstrated for the separation and detection of DNA sequencing samples. Enzymatic dideoxy nucleotide chain termination was employed, using fluorescently tagged oligonucleotide primers and laser based on-column detection (limit of detection is 6,000 molecules per peak). Capillary gel separations were shown to be three times faster, with better resolution (2.4 ×), and higher separation efficiency (5.4 ×) than a conventional automated slab gel DNA sequencing instrument. Agreement of measured values for velocity, resolution and separation efficiency with theory, predicts further improvements will result from increased electric field strengths (higher voltages and shorter capillaries). Advantages of capillary gel electrophoresis for automatic DNA sequencing instruments and for genomic sequencing are discussed.

Published
1990
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