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3. Hurt, tired and queasy: Specific variants in the ATPase domain of the TRAP1 mitochondrial chaperone are associated with common, chronic “functional” symptomatology including pain, fatigue and gastrointestinal dysmotility

Author

Boles, Richard G., Hornung, Holly A., Moody, Alastair E., Ortiz, Thomas B., Wong, Stacey A., Eggington, Julie M., Stanley, Christine M., Gao, Mu, Zhou, Hongyi, McLaughlin, Stephen, Zare, Amir S., Sheldon, Katherine M., Skolnick, Jeffrey, and McKernan, Kevin J.

Published
2015
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5. Mutation in The Nuclear-Encoded Mitochondrial Isoleucyl–tRNA Synthetase IARS2 in Patients with Cataracts, Growth Hormone Deficiency with Short Stature, Partial Sensorineural Deafness, and Peripheral Neuropathy or with Leigh Syndrome

Author

Schwartzentruber, Jeremy, Buhas, Daniela, Majewski, Jacek, Sasarman, Florin, Papillon-Cavanagh, Simon, Thiffaut, Isabelle, Sheldon, Katherine M., Massicotte, Christine, Patry, Lysanne, Simon, Mariella, Zare, Amir S., McKernan, Kevin J., Consortium, FORGE Canada, Michaud, Jacques, Boles, Richard G., Deal, Cheri L., Desilets, Valerie, Shoubridge, Eric A., and Samuels, Mark E.

Published
2014
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6. An integrated semiconductor device enabling non-optical genome sequencing

Author

Rothberg, Jonathan M., Hinz, Wolfgang, Rearick, Todd M., Schultz, Jonathan, Mileski, William, Davey, Mel, Leamon, John H., Johnson, Kim, Milgrew, Mark J., Edwards, Matthew, Hoon, Jeremy, Simons, Jan F., Marran, David, Myers, Jason W., Davidson, John F., Branting, Annika, Nobile, John R., Puc, Bernard P., Light, David, Clark, Travis A., Huber, Martin, Branciforte, Jeffrey T., Stoner, Isaac B., Cawley, Simon E., Lyons, Michael, Fu, Yutao, Homer, Nils, Sedova, Marina, Miao, Xin, Reed, Brian, Sabina, Jeffrey, Feierstein, Erika, Schorn, Michelle, Alanjary, Mohammad, Dimalanta, Eileen, Dressman, Devin, Kasinskas, Rachel, Sokolsky, Tanya, Fidanza, Jacqueline A., Namsaraev, Eugeni, McKernan, Kevin J., and Williams, Alan

Published
2011
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7. 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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8. A small-cell lung cancer genome with complex signatures of tobacco exposure

Author

Pleasance, Erin D., Stephens, Philip J., OʼMeara, Sarah, McBride, David J., Meynert, Alison, Jones, David, Lin, Meng-Lay, Beare, David, Lau, King Wai, Greenman, Chris, Varela, Ignacio, Nik-Zainal, Serena, Davies, Helen R., Ordoñez, Gonzalo R., Mudie, Laura J., Latimer, Calli, Edkins, Sarah, Stebbings, Lucy, Chen, Lina, Jia, Mingming, Leroy, Catherine, Marshall, John, Menzies, Andrew, Butler, Adam, Teague, Jon W., Mangion, Jonathon, Sun, Yongming A., McLaughlin, Stephen F., Peckham, Heather E., Tsung, Eric F., Costa, Gina L., Lee, Clarence C., Minna, John D., Gazdar, Adi, Birney, Ewan, Rhodes, Michael D., McKernan, Kevin J., Stratton, Michael R., Futreal, Andrew P., and Campbell, Peter J.

Published
2010
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9. Mapping and sequencing of structural variation from eight human genomes

Author

Kidd, Jeffrey M., Cooper, Gregory M., Donahue, William F., Hayden, Hillary S., Sampas, Nick, Graves, Tina, Hansen, Nancy, Teague, Brian, Alkan, Can, Antonacci, Francesca, Haugen, Eric, Zerr, Troy, Yamada, N. Alice, Tsang, Peter, Newman, Tera L., Tüzün, Eray, Cheng, Ze, Ebling, Heather M., Tusneem, Nadeem, David, Robert, Gillett, Will, Phelps, Karen A., Weaver, Molly, Saranga, David, Brand, Adrianne, Tao, Wei, Gustafson, Erik, McKernan, Kevin, Chen, Lin, Malig, Maika, Smith, Joshua D., Korn, Joshua M., McCarroll, Steven A., Altshuler, David A., Peiffer, Daniel A., Dorschner, Michael, Stamatoyannopoulos, John, Schwartz, David, Nickerson, Deborah A., Mullikin, James C., Wilson, Richard K., Bruhn, Laurakay, Olson, Maynard V., Kaul, Rajinder, Smith, Douglas R., and Eichler, Evan E.

Published
2008
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10. Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype

Author

Jaillon, Olivier, Aury, Jean-Marc, Brunet, Frédéric, Petit, Jean-Louis, Stange-Thomann, Nicole, Mauceli, Evan, Bouneau, Laurence, Fischer, Cécile, Ozouf-Costaz, Catherine, Bernot, Alain, Nicaud, Sophie, Jaffe, David, Fisher, Sheila, Lutfalla, Georges, Dossat, Carole, Segurens, Béatrice, Dasilva, Corinne, Salanoubat, Marcel, Levy, Michael, Boudet, Nathalie, Castellano, Sergi, Anthouard, Véronique, Jubin, Claire, Castelli, Vanina, Katinka, Michael, Vacherie, Benoît, Biémont, Christian, Skalli, Zineb, Cattolico, Laurence, Poulain, Julie, de Berardinis, Véronique, Cruaud, Corinne, Duprat, Simone, Brottier, Philippe, Coutanceau, Jean-Pierre, Gouzy, Jérôme, Parra, Genis, Lardier, Guillaume, Chapple, Charles, McKernan, Kevin J., McEwan, Paul, Bosak, Stephanie, Kellis, Manolis, Volff, Jean-Nicolas, Guigó, Roderic, Zody, Michael C., Mesirov, Jill, Lindblad-Toh, Kerstin, Birren, Bruce, Nusbaum, Chad, Kahn, Daniel, Robinson-Rechavi, Marc, Laudet, Vincent, Schachter, Vincent, Quétier, Francis, Saurin, William, Scarpelli, Claude, Wincker, Patrick, Lander, Eric S., Weissenbach, Jean, and Roest Crollius, Hugues

Published
2004

12. Genomic characterization of the complete terpene synthase gene family from Cannabis sativa.

Author

Allen, Keith D., McKernan, Kevin, Pauli, Christopher, Roe, Jim, Torres, Anthony, and Gaudino, Reggie

Subjects
*GENE families, *CANNABIS (Genus), *MONOTERPENES, *COMPUTATIONAL biology, *PLANT cells & tissues, *ORGANIC chemistry
Abstract

Terpenes are responsible for most or all of the odor and flavor properties of Cannabis sativa, and may also impact effects users experience either directly or indirectly. We report the diversity of terpene profiles across samples bound for the Washington dispensary market. The remarkable degree of variation in terpene profiles ultimately results from action of a family of terpene synthase genes, only some of which have been described. Using a recently available genome assembly we describe 55 terpene synthases with genomic context, and tissue specific expression. The family is quite diverse from a protein similarity perspective, and subsets of the family are expressed in all tissues in the plant, including a set of root specific monoterpene synthases that could well have agronomic importance. Ultimately understanding and breeding for specific terpene profiles will require a good understanding of the gene family that underlies it. We intend for this work to serve as a foundation for that. [ABSTRACT FROM AUTHOR]

Published
2019
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13. Rare genetic variants in the endocannabinoid system genes CNR1 and DAGLA are associated with neurological phenotypes in humans.

Author

Smith, Douglas R., Stanley, Christine M., Foss, Theodore, Boles, Richard G., and McKernan, Kevin

Subjects
NEUROLOGICAL disorders, CANNABINOID receptors, SLEEP disorders, MEMORY disorders, DIGLYCERIDES, LIPASES, GENETICS, PATIENTS
Abstract

Rare genetic variants in the core endocannabinoid system genes CNR1, CNR2, DAGLA, MGLL and FAAH were identified in molecular testing data from 6,032 patients with a broad spectrum of neurological disorders. The variants were evaluated for association with phenotypes similar to those observed in the orthologous gene knockouts in mice. Heterozygous rare coding variants in CNR1, which encodes the type 1 cannabinoid receptor (CB1), were found to be significantly associated with pain sensitivity (especially migraine), sleep and memory disorders—alone or in combination with anxiety—compared to a set of controls without such CNR1 variants. Similarly, heterozygous rare variants in DAGLA, which encodes diacylglycerol lipase alpha, were found to be significantly associated with seizures and neurodevelopmental disorders, including autism and abnormalities of brain morphology, compared to controls. Rare variants in MGLL, FAAH and CNR2 were not associated with any neurological phenotypes in the patients tested. Diacylglycerol lipase alpha synthesizes the endocannabinoid 2-AG in the brain, which interacts with CB1 receptors. The phenotypes associated with rare CNR1 variants are reminiscent of those implicated in the theory of clinical endocannabinoid deficiency syndrome. The severe phenotypes associated with rare DAGLA variants underscore the critical role of rapid 2-AG synthesis and the endocannabinoid system in regulating neurological function and development. Mapping of the variants to the 3D structure of the type 1 cannabinoid receptor, or primary structure of diacylglycerol lipase alpha, reveals clustering of variants in certain structural regions and is consistent with impacts to function. [ABSTRACT FROM AUTHOR]

Published
2017
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14. Mutation in The Nuclear-Encoded Mitochondrial Isoleucyl-t RNA Synthetase IARS2 in Patients with Cataracts, Growth Hormone Deficiency with Short Stature, Partial Sensorineural Deafness, and Peripheral Neuropathy or with Leigh Syndrome.

Author

Schwartzentruber, Jeremy, Buhas, Daniela, Majewski, Jacek, Sasarman, Florin, Papillon‐Cavanagh, Simon, Thiffaut, Isabelle, Sheldon, Katherine M., Massicotte, Christine, Patry, Lysanne, Simon, Mariella, Zare, Amir S., McKernan, Kevin J., Michaud, Jacques, Boles, Richard G., Deal, Cheri L., Desilets, Valerie, Shoubridge, Eric A., and Samuels, Mark E.

Abstract

ABSTRACT Mutations in the nuclear-encoded mitochondrial aminoacyl-t RNA synthetases are associated with a range of clinical phenotypes. Here, we report a novel disorder in three adult patients with a phenotype including cataracts, short-stature secondary to growth hormone deficiency, sensorineural hearing deficit, peripheral sensory neuropathy, and skeletal dysplasia. Using SNP genotyping and whole-exome sequencing, we identified a single likely causal variant, a missense mutation in a conserved residue of the nuclear gene IARS2, encoding mitochondrial isoleucyl-t RNA synthetase. The mutation is homozygous in the affected patients, heterozygous in carriers, and absent in control chromosomes. IARS2 protein level was reduced in skin cells cultured from one of the patients, consistent with a pathogenic effect of the mutation. Compound heterozygous mutations in IARS2 were independently identified in a previously unreported patient with a more severe mitochondrial phenotype diagnosed as Leigh syndrome. This is the first report of clinical findings associated with IARS2 mutations. [ABSTRACT FROM AUTHOR]

Published
2014
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15. Expanded Genetic Codes in Next Generation Sequencing Enable Decontamination and Mitochondrial Enrichment.

Author

McKernan, Kevin J., Spangler, Jessica, Zhang, Lei, Tadigotla, Vasisht, McLaughlin, Stephen, Warner, Jason, Zare, Amir, and Boles, Richard G.

Subjects
*GENETIC code, *NUCLEOTIDE sequence, *BIOLOGICAL decontamination, *MITOCHONDRIAL membranes, *POLYMERASE chain reaction, *NUCLEOTIDE analysis
Abstract

We have developed a PCR method, coined Déjà vu PCR, that utilizes six nucleotides in PCR with two methyl specific restriction enzymes that respectively digest these additional nucleotides. Use of this enzyme-and-nucleotide combination enables what we term a “DNA diode”, where DNA can advance in a laboratory in only one direction and cannot feedback into upstream assays. Here we describe aspects of this method that enable consecutive amplification with the introduction of a 5th and 6th base while simultaneously providing methylation dependent mitochondrial DNA enrichment. These additional nucleotides enable a novel DNA decontamination technique that generates ephemeral and easy to decontaminate DNA. [ABSTRACT FROM AUTHOR]

Published
2014
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16. DREAMing of a patent-free human genome for clinical sequencing.

Author

McKernan, Kevin J, Spangler, Jessica, Helbert, Yvonne, Zhang, Lei, and Tadigotla, Vasisht

Subjects
*HUMAN genome, *SEQUENCE alignment, *POLYMERASE chain reaction, *GENE patents
Abstract

In this article, authors discuss a study related to the dreaming of patent free human genome for clinical sequencing. They state that a Myriad Genetics Inc. Myriad cDNA-based patent is not the only gene patent to make short sequences. In this study a simple PCR (Polymerase chain reaction) method has been demonstrated that utilizes additional methylated nucleotides. The study shows an alternative economic perspective on profit motivation and its impact on the ethics of gene patents.

Published
2013
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19. Whole Methylome Analysis by Ultra-Deep Sequencing Using Two-Base Encoding.

Author

Chung, Christina A. Bormann, Boyd, Victoria L., McKernan, Kevin J., Yutao Fu, Monighetti, Cinna, Peckham, Heather E., and Barker, Melissa

Subjects
METHYLATION, ALKYLATION, THYMINE, URACIL, DNA, DEOXYRIBOSE, NUCLEIC acids, GENE expression, GENOMES, GENOMICS
Abstract

Methylation, the addition of methyl groups to cytosine (C), plays an important role in the regulation of gene expression in both normal and dysfunctional cells. During bisulfite conversion and subsequent PCR amplification, unmethylated Cs are converted into thymine (T), while methylated Cs will not be converted. Sequencing of this bisulfite-treated DNA permits the detection of methylation at specific sites. Through the introduction of next-generation sequencing technologies (NGS) simultaneous analysis of methylation motifs in multiple regions provides the opportunity for hypothesis-free study of the entire methylome. Here we present a whole methylome sequencing study that compares two different bisulfite conversion methods (in solution versus in gel), utilizing the high throughput of the SOLiD™ System. Advantages and disadvantages of the two different bisulfite conversion methods for constructing sequencing libraries are discussed. Furthermore, the application of the SOLiD™ bisulfite sequencing to larger and more complex genomes is shown with preliminary in silico created bisulfite converted reads. [ABSTRACT FROM AUTHOR]

Published
2010
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20. Stem cell transcriptome profiling via massive-scale mRNA sequencing.

Author

Cloonan, Nicole, Forrest, Alistair R. R., Kolle, Gabriel, Gardiner, Brooke B. A., Faulkner, Geoffrey J., Brown, Mellissa K., Taylor, Darrin F., Steptoe, Anita L., Wani, Shivangi, Bethel, Graeme, Robertson, Alan J., Perkins, Andrew C., Bruce, Stephen J., Lee, Clarence C., Ranade, Swati S., Peckham, Heather E., Manning, Jonathan M., McKernan, Kevin J., and Grimmond, Sean M.

Subjects
NUCLEOTIDE sequence, EMBRYONIC stem cells, GENETIC polymorphisms, CELL differentiation, RNA splicing
Abstract

We developed a massive-scale RNA sequencing protocol, short quantitative random RNA libraries or SQRL, to survey the complexity, dynamics and sequence content of transcriptomes in a near-complete fashion. This method generates directional, random-primed, linear cDNA libraries that are optimized for next-generation short-tag sequencing. We surveyed the poly(A)+ transcriptomes of undifferentiated mouse embryonic stem cells (ESCs) and embryoid bodies (EBs) at an unprecedented depth (10 Gb), using the Applied Biosystems SOLiD technology. These libraries capture the genomic landscape of expression, state-specific expression, single-nucleotide polymorphisms (SNPs), the transcriptional activity of repeat elements, and both known and new alternative splicing events. We investigated the impact of transcriptional complexity on current models of key signaling pathways controlling ESC pluripotency and differentiation, highlighting how SQRL can be used to characterize transcriptome content and dynamics in a quantitative and reproducible manner, and suggesting that our understanding of transcriptional complexity is far from complete. [ABSTRACT FROM AUTHOR]

Published
2008
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21. Initial sequencing and analysis of the human genome.

Author

Lander, Eric S., Linton, Lauren M., Birren, Bruce, Nusbaum, Chad, Zody, Michael C., Baldwin, Jennifer, Devon, Keri, Dewar, Ken, Doyle, Michael, FitzHugh, William, Funke, Roel, Gage, Diane, Harris, Katrina, Heaford, Andrew, Howland, John, Kann, Lisa, Lehoczky, Jessica, LeVine, Rosie, McEwan, Paul, and McKernan, Kevin

Subjects
HUMAN genome, GENETIC research, HUMAN gene mapping, INTERNATIONAL cooperation
Abstract

Reports the results of international collaboration to produce and make freely available a draft sequence of the human genome. Background on the Human Genome Project; Presentation of an initial analysis of the data; Insights that can be gleaned from the sequence.

Published
2001

22. The chloroplast genome hidden in plain sight, open access publishing and anti-fragile distributed data sources.

Author

McKernan, Kevin Judd

Subjects
*CANNABIS (Genus), *CHLOROPLAST DNA, *MITOCHONDRIAL DNA, *OPEN access publishing, *DATA analysis, *PLANTS
Abstract

We sequenced several cannabis genomes in 2011 of June and the first and the longest contigs to emerge were the chloroplast and mitochondrial genomes. Having been a contributor to the Human Genome Project and an eye-witness to the real benefits of immediate data release, I have first hand experience with the potential mal-investment of millions of dollars of tax payer money narrowly averted due to the adopted global rapid data release policy. The policy was vital in reducing duplication of effort and economic waste. As a result, we felt obligated to publish the Cannabis genome data in a similar spirit and placed them immediately on a cloud based Amazon server in August of 2011. While these rapid data release practices were heralded by many in the media, we still find some authors fail to find or reference said work and hope to compel the readership that this omission has more pervasive repercussions than bruised egos and is a regression for our community. [ABSTRACT FROM AUTHOR]

Published
2016
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23. Mutation in The Nuclear-Encoded Mitochondrial Isoleucyl-tRNA Synthetase IARS2 in Patients with Cataracts, Growth Hormone Deficiency with Short Stature, Partial Sensorineural Deafness, and Peripheral Neuropathy or with Leigh Syndrome.

Author

Schwartzentruber, Jeremy, Buhas, Daniela, Majewski, Jacek, Sasarman, Florin, Papillon‐Cavanagh, Simon, Thiffault, Isabelle, Sheldon, Katherine M., Massicotte, Christine, Patry, Lysanne, Simon, Mariella, Zare, Amir S., McKernan, Kevin J., Consortium, FORGE Canada, Michaud, Jacques, Boles, Richard G., Deal, Cheri L., Desilets, Valerie, Shoubridge, Eric A., and Samuels, Mark E.

Published
2015
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25. Chronic pain, fatigue, GI dysmotility and the mitochondrial chaperone TRAP1.

Author

Boles, Richard G., Hornung, Holly A., Moody, Alastair, Ortiz, Thomas, Wong, Stacey A., Eggington, Julie M., Stanley, Christine M., Gao, Mu, Zhou, Hongyi, Zare, Amir S., Skolnick, Jeffrey, and McKernan, Kevin J.

Subjects
*CHRONIC pain, *FATIGUE (Physiology), *MITOCHONDRIAL proteins, *MOLECULAR chaperones, *SYMPTOMS, *OXIDATIVE stress
Published
2015
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27. Deep-transcriptome and ribonome sequencing redefines the molecular networks of pluripotency and the extracellular space in human embryonic stem cells.

Author

Kolle, Gabriel, Shepherd, Jill L., Gardiner, Brooke, Kassahn, Karin S., Cloonan, Nicole, Wood, David L. A., Nourbakhsh, Ehsan, Wani, Shivangi, Chy, Hun S., Zhou, Qi, McKernan, Kevin, Kuersten, Scott, Laslett, Andrew L., Grimmond, Sean M., and Taylor, Darrin F.

Subjects
*NUCLEOTIDE sequence, *NUCLEIC acid analysis, *EMBRYONIC stem cells, *PROTEOMICS, *PLURIPOTENT stem cells
Abstract

Recent RNA-sequencing studies have shown remarkable complexity in the mammalian transcriptome. The ultimate impact of this complexity on the predicted proteomic output is less well defined. We have undertaken strand-specific RNA sequencing of multiple cellular RNA fractions (>20 Gb) to uncover the transcriptional complexity of human embryonic stem cells (hESCs). We have shown that human embryonic stem (ES) cells display a high degree of transcriptional diversity, with more than half of active genes generating RNAs that differ from conventional gene models. We found evidence that more than 1000 genes express long 5' and/or extended 3'UTRs, which was confirmed by "virtual Northern" analysis. Exhaustive sequencing of the membrane-polysome and cytosolic/untranslated fractions of hESCs was used to identify RNAs encoding peptides destined for secretion and the extracellular space and to demonstrate preferential selection of transcription complexity for translation in vitro. The impact of this newly defined complexity on known gene-centric network models such as the Plurinet and the cell surface signaling machinery in human ES cells revealed a significant expansion of known transcript isoforms at play, many predicting possible alternative functions based on sequence alterations within key functional domains. [ABSTRACT FROM AUTHOR]

Published
2011
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28. A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning.

Author

Valouev, Anton, Ichikawa, Jeffrey, Tonthat, Thaisan, Stuart, Jeremy, Ranade, Swati, Peckham, Heather, Zeng, Kathy, Malek, Joel A., Costa, Gina, McKernan, Kevin, Sidow, Arend, Fire, Andrew, and Johnson, Steven M.

Subjects
*GENE mapping, *CAENORHABDITIS elegans, *CHROMATIN, *OLIGONUCLEOTIDES, *GENOMES
Abstract

Using the massively parallel technique of sequencing by oligonucleotide ligation and detection (SOLiD; Applied Biosystems), we have assessed the in vivo positions of more than 44 million putative nucleosome cores in the multicellular genetic model organism Caenorhabditis elegans. These analyses provide a global view of the chromatin architecture of a multicellular animal at extremely high density and resolution. While we observe some degree of reproducible positioning throughout the genome in our mixed stage population of animals, we note that the major chromatin feature in the worm is a diversity of allowed nucleosome positions at the vast majority of individual loci. While absolute positioning of nucleosomes can vary substantially, relative positioning of nucleosomes (in a repeated array structure likely to be maintained at least in part by steric constraints) appears to be a significant property of chromatin structure. The high density of nucleosomal reads enabled a substantial extension of previous analysis describing the usage of individual oligonucleotide sequences along the span of the nucleosome core and linker. We release this data set, via the UCSC Genome Browser, as a resource for the high-resolution analysis of chromatin conformation and DNA accessibility at individual loci within the C. elegans genome. [ABSTRACT FROM AUTHOR]

Published
2008
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