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143 results on '"Emde, Anne-Katrin"'

1. Mid-pass whole-genome sequencing in a Malagasy cohort uncovers body composition associations

Author

Hamid, Iman, Raveloson, Séverine Nantenaina Stéphie, Spiral, Germain Jules, Ravelonjanahary, Soanorolalao, Raharivololona, Brigitte Marie, Randria, José Mahenina, Zafimaro, Mosa, Randriambola, Tsiorimanitra Aimée, Andriantsoa, Rota Mamimbahiny, Andriamahefa, Tojo Julio, Rafidison, Bodonomena Fitahiana Laza, Mughal, Mehreen, Emde, Anne-Katrin, Hendershott, Melissa, LeBaron von Baeyer, Sarah, Wasik, Kaja A., Ranaivoarisoa, Jean Freddy, Yerges-Armstrong, Laura, Castel, Stephane E., and Rakotoarivony, Rindra

Published
2024
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2. The gout epidemic in French Polynesia: a modelling study of data from the Ma’i u’u epidemiological survey

Author

Pascart, Tristan, Wasik, Kaja A, Preda, Cristian, Chune, Valérie, Torterat, Jérémie, Prud’homme, Nicolas, Nassih, Maryline, Martin, Agathe, Le Masson, Julien, Rodière, Vahinetua, Frogier, Sylvain, Canova, Georges, Pescheux, Jean-Paul, Shan Sei Fan, Charles, Jauffret, Charlotte, Claeys, Patrick, von Baeyer, Sarah LeBaron, Castel, Stephane E, Emde, Anne-Katrin, Yerges-Armstrong, Laura, Fox, Keolu, Leask, Megan, Vitagliano, Jean-Jacques, Graf, Sahara, Norberciak, Laurène, Raynal, Jacques, Dalbeth, Nicola, Merriman, Tony, Bardin, Thomas, and Oehler, Erwan

Published
2024
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3. Sequencing of 53,831 diverse genomes from the NHLBI TOPMed Program

Author

Taliun, Daniel, Harris, Daniel N, Kessler, Michael D, Carlson, Jedidiah, Szpiech, Zachary A, Torres, Raul, Taliun, Sarah A Gagliano, Corvelo, André, Gogarten, Stephanie M, Kang, Hyun Min, Pitsillides, Achilleas N, LeFaive, Jonathon, Lee, Seung-been, Tian, Xiaowen, Browning, Brian L, Das, Sayantan, Emde, Anne-Katrin, Clarke, Wayne E, Loesch, Douglas P, Shetty, Amol C, Blackwell, Thomas W, Smith, Albert V, Wong, Quenna, Liu, Xiaoming, Conomos, Matthew P, Bobo, Dean M, Aguet, François, Albert, Christine, Alonso, Alvaro, Ardlie, Kristin G, Arking, Dan E, Aslibekyan, Stella, Auer, Paul L, Barnard, John, Barr, R Graham, Barwick, Lucas, Becker, Lewis C, Beer, Rebecca L, Benjamin, Emelia J, Bielak, Lawrence F, Blangero, John, Boehnke, Michael, Bowden, Donald W, Brody, Jennifer A, Burchard, Esteban G, Cade, Brian E, Casella, James F, Chalazan, Brandon, Chasman, Daniel I, Chen, Yii-Der Ida, Cho, Michael H, Choi, Seung Hoan, Chung, Mina K, Clish, Clary B, Correa, Adolfo, Curran, Joanne E, Custer, Brian, Darbar, Dawood, Daya, Michelle, de Andrade, Mariza, DeMeo, Dawn L, Dutcher, Susan K, Ellinor, Patrick T, Emery, Leslie S, Eng, Celeste, Fatkin, Diane, Fingerlin, Tasha, Forer, Lukas, Fornage, Myriam, Franceschini, Nora, Fuchsberger, Christian, Fullerton, Stephanie M, Germer, Soren, Gladwin, Mark T, Gottlieb, Daniel J, Guo, Xiuqing, Hall, Michael E, He, Jiang, Heard-Costa, Nancy L, Heckbert, Susan R, Irvin, Marguerite R, Johnsen, Jill M, Johnson, Andrew D, Kaplan, Robert, Kardia, Sharon LR, Kelly, Tanika, Kelly, Shannon, Kenny, Eimear E, Kiel, Douglas P, Klemmer, Robert, Konkle, Barbara A, Kooperberg, Charles, Köttgen, Anna, Lange, Leslie A, Lasky-Su, Jessica, Levy, Daniel, Lin, Xihong, Lin, Keng-Han, Liu, Chunyu, and Loos, Ruth JF

Subjects
Genetics, Biotechnology, Human Genome, Aetiology, 2.1 Biological and endogenous factors, Generic health relevance, Good Health and Well Being, Cytochrome P-450 CYP2D6, Genetic Variation, Genome, Human, Genomics, Haplotypes, Heterozygote, Humans, INDEL Mutation, Loss of Function Mutation, Mutagenesis, National Heart, Lung, and Blood Institute (U.S.), Phenotype, Polymorphism, Single Nucleotide, Population Density, Precision Medicine, Quality Control, Sample Size, United States, Whole Genome Sequencing, NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, General Science & Technology
Abstract

The Trans-Omics for Precision Medicine (TOPMed) programme seeks to elucidate the genetic architecture and biology of heart, lung, blood and sleep disorders, with the ultimate goal of improving diagnosis, treatment and prevention of these diseases. The initial phases of the programme focused on whole-genome sequencing of individuals with rich phenotypic data and diverse backgrounds. Here we describe the TOPMed goals and design as well as the available resources and early insights obtained from the sequence data. The resources include a variant browser, a genotype imputation server, and genomic and phenotypic data that are available through dbGaP (Database of Genotypes and Phenotypes)1. In the first 53,831 TOPMed samples, we detected more than 400 million single-nucleotide and insertion or deletion variants after alignment with the reference genome. Additional previously undescribed variants were detected through assembly of unmapped reads and customized analysis in highly variable loci. Among the more than 400 million detected variants, 97% have frequencies of less than 1% and 46% are singletons that are present in only one individual (53% among unrelated individuals). These rare variants provide insights into mutational processes and recent human evolutionary history. The extensive catalogue of genetic variation in TOPMed studies provides unique opportunities for exploring the contributions of rare and noncoding sequence variants to phenotypic variation. Furthermore, combining TOPMed haplotypes with modern imputation methods improves the power and reach of genome-wide association studies to include variants down to a frequency of approximately 0.01%.

Published
2021

4. Somatic whole genome dynamics of precancer in Barrett’s esophagus reveals features associated with disease progression

Author

Paulson, Thomas G., Galipeau, Patricia C., Oman, Kenji M., Sanchez, Carissa A., Kuhner, Mary K., Smith, Lucian P., Hadi, Kevin, Shah, Minita, Arora, Kanika, Shelton, Jennifer, Johnson, Molly, Corvelo, Andre, Maley, Carlo C., Yao, Xiaotong, Sanghvi, Rashesh, Venturini, Elisa, Emde, Anne-Katrin, Hubert, Benjamin, Imielinski, Marcin, Robine, Nicolas, Reid, Brian J., and Li, Xiaohong

Published
2022
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6. Whole-genome Studies of Malagasy People Uncover Novel Body Composition Associations

Author

Hamid, Iman, primary, Raveloson, Severine Nantenaina Stephie, additional, Spiral, Germain Jules, additional, Ravelonjanahary, Soanorolalao, additional, Raharivololona, Brigitte Marie, additional, Randria, Jose Mahenina, additional, Zafimaro, Mosa, additional, Randriambola, Tsiorimanitra Aimee, additional, Andriantsoa, Rota Mamimbahiny, additional, Andriamahefa, Tojo Julio, additional, Rafidison, Bodonomena Fitahiana Laza, additional, Mughal, Mehreen, additional, Emde, Anne-Katrin, additional, Hendershott, Melissa, additional, LeBaron von Baeyer, Sarah, additional, Wasik, Kaja A., additional, Ranaivoarisoa, Jean Freddy, additional, Yerges-Armstrong, Laura, additional, Castel, Stephane E., additional, and Rakotoarivony, Rindra, additional

Published
2023
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9. Correction to: Sequencing and curation strategies for identifying candidate glioblastoma treatments

Author

Frank, Mayu O., Koyama, Takahiko, Rhrissorrakrai, Kahn, Robine, Nicolas, Utro, Filippo, Emde, Anne-Katrin, Chen, Bo-Juen, Arora, Kanika, Shah, Minita, Geiger, Heather, Felice, Vanessa, Dikoglu, Esra, Rahman, Sadia, Fang, Xiaolan, Vacic, Vladimir, Bergmann, Ewa A., Moore Vogel, Julia L., Reeves, Catherine, Khaira, Depinder, Calabro, Anthony, Kim, Duyang, Lamendola-Essel, Michelle F., Esteves, Cecilia, Agius, Phaedra, Stolte, Christian, Boockvar, John, Demopoulos, Alexis, Placantonakis, Dimitris G., Golfinos, John G., Brennan, Cameron, Bruce, Jeffrey, Lassman, Andrew B., Canoll, Peter, Grommes, Christian, Daras, Mariza, Diamond, Eli, Omuro, Antonio, Pentsova, Elena, Orange, Dana E., Harvey, Stephen J., Posner, Jerome B., Michelini, Vanessa V., Jobanputra, Vaidehi, Zody, Michael C., Kelly, John, Parida, Laxmi, Wrzeszczynski, Kazimierz O., Royyuru, Ajay K., and Darnell, Robert B.

Published
2019
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10. Sequencing and curation strategies for identifying candidate glioblastoma treatments

Author

Frank, Mayu O., Koyama, Takahiko, Rhrissorrakrai, Kahn, Robine, Nicolas, Utro, Filippo, Emde, Anne-Katrin, Chen, Bo-Juen, Arora, Kanika, Shah, Minita, Geiger, Heather, Felice, Vanessa, Dikoglu, Esra, Rahman, Sadia, Fang, Alice, Vacic, Vladimir, Bergmann, Ewa A., Vogel, Julia L. Moore, Reeves, Catherine, Khaira, Depinder, Calabro, Anthony, Kim, Duyang, Lamendola-Essel, Michelle F., Esteves, Cecilia, Agius, Phaedra, Stolte, Christian, Boockvar, John, Demopoulos, Alexis, Placantonakis, Dimitris G., Golfinos, John G., Brennan, Cameron, Bruce, Jeffrey, Lassman, Andrew B., Canoll, Peter, Grommes, Christian, Daras, Mariza, Diamond, Eli, Omuro, Antonio, Pentsova, Elena, Orange, Dana E., Harvey, Stephen J., Posner, Jerome B., Michelini, Vanessa V., Jobanputra, Vaidehi, Zody, Michael C., Kelly, John, Parida, Laxmi, Wrzeszczynski, Kazimierz O., Royyuru, Ajay K., and Darnell, Robert B.

Published
2019
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11. PGBD5 promotes site-specific oncogenic mutations in human tumors

Author

Henssen, Anton G, Koche, Richard, Zhuang, Jiali, Jiang, Eileen, Reed, Casie, Eisenberg, Amy, Still, Eric, MacArthur, Ian C, Rodríguez-Fos, Elias, Gonzalez, Santiago, Puiggròs, Montserrat, Blackford, Andrew N, Mason, Christopher E, de Stanchina, Elisa, Gönen, Mithat, Emde, Anne-Katrin, Shah, Minita, Arora, Kanika, Reeves, Catherine, Socci, Nicholas D, Perlman, Elizabeth, Antonescu, Cristina R, Roberts, Charles W M, Steen, Hanno, Mullen, Elizabeth, Jackson, Stephen P, Torrents, David, Weng, Zhiping, Armstrong, Scott A, and Kentsis, Alex

Published
2017
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12. Author Correction: PGBD5 promotes site-specific oncogenic mutations in human tumors

Author

Henssen, Anton G., Koche, Richard, Zhuang, Jiali, Jiang, Eileen, Reed, Casie, Eisenberg, Amy, Still, Eric, MacArthur, Ian C., Rodríguez-Fos, Elias, Gonzalez, Santiago, Puiggròs, Montserrat, Blackford, Andrew N., Mason, Christopher E., de Stanchina, Elisa, Gönen, Mithat, Emde, Anne-Katrin, Shah, Minita, Arora, Kanika, Reeves, Catherine, Socci, Nicholas D., Perlman, Elizabeth, Antonescu, Cristina R., Roberts, Charles W. M., Steen, Hanno, Mullen, Elizabeth, Jackson, Stephen P., Torrents, David, Weng, Zhiping, Armstrong, Scott A., and Kentsis, Alex

Published
2020
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16. Diverse tumorigenic consequences of human papillomavirus integration in primary oropharyngeal cancers

Author

Symer, David E., primary, Akagi, Keiko, additional, Geiger, Heather M., additional, Song, Yang, additional, Li, Gaiyun, additional, Emde, Anne-Katrin, additional, Xiao, Weihong, additional, Jiang, Bo, additional, Corvelo, André, additional, Toussaint, Nora C., additional, Li, Jingfeng, additional, Agrawal, Amit, additional, Ozer, Enver, additional, El-Naggar, Adel K., additional, Du, Zoe, additional, Shewale, Jitesh B., additional, Stache-Crain, Birgit, additional, Zucker, Mark, additional, Robine, Nicolas, additional, Coombes, Kevin R., additional, and Gillison, Maura L., additional

Published
2021
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17. Whole-Exome Sequencing of Metastatic Cancer and Biomarkers of Treatment Response

Author

Beltran, Himisha, Eng, Kenneth, Mosquera, Juan Miguel, Sigaras, Alexandros, Romanel, Alessandro, Rennert, Hanna, Kossai, Myriam, Pauli, Chantal, Faltas, Bishoy, Fontugne, Jacqueline, Park, Kyung, Banfelder, Jason, Prandi, Davide, Madhukar, Neel, Zhang, Tuo, Padilla, Jessica, Greco, Noah, McNary, Terra J., Herrscher, Erick, Wilkes, David, MacDonald, Theresa Y., Xue, Hui, Vacic, Vladimir, Emde, Anne-Katrin, Oschwald, Dayna, Tan, Adrian Y., Chen, Zhengming, Collins, Colin, Gleave, Martin E., Wang, Yuzhuo, Chakravarty, Dimple, Schiffman, Marc, Kim, Robert, Campagne, Fabien, Robinson, Brian D., Nanus, David M., Tagawa, Scott T., Xiang, Jenny Z., Smogorzewska, Agata, Demichelis, Francesca, Rickman, David S., Sboner, Andrea, Elemento, Olivier, and Rubin, Mark A.

Published
2015
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19. Additional file 1 of Mid-pass whole genome sequencing enables biomedical genetic studies of diverse populations

Author

Emde, Anne-Katrin, Phipps-Green, Amanda, Cadzow, Murray, Gallagher, C. Scott, Major, Tanya J., Merriman, Marilyn E., Topless, Ruth K., Takei, Riku, Dalbeth, Nicola, Murphy, Rinki, Stamp, Lisa K., de Zoysa, Janak, Wilcox, Philip L., Fox, Keolu, Wasik, Kaja A., Merriman, Tony R., and Castel, Stephane E.

Abstract

Additional file 1: Figure S1. Benchmarking of libraries generated with low-pass kits sequenced at intermediate coverage levels. a) Mean coverage across the library types. b) Per-sample duplicate rate over (deduplicated) sequencing coverage. c) Genotype quality (GQ) as a function of mean GQ (averaged over 2 �� 12 samples). Fraction of variant calls that overlap between replicates (d), and their genotype concordance (e) at either all variants (GQ > 0) or high-confidence variants (GQ > 20). f) Recall, g) Precision and h) Non-reference concordance rates computed per sample against the 1000 Genomes high coverage call set [32] as ���truth���. The single HP4 sample with coverage>10x was excluded from this comparison. Figure S2. a) Overview of data types available for participants and how they overlap. b) Distribution of de-duplicated sequencing coverage per sample for low-pass samples, c) TruSeq PCR-free high-coverage samples, d) TruSeq Nano high-coverage samples. e) Distribution of sequencing duplicate rates per sample for low-pass samples, f) for TruSeq PCR-free samples, and g) for TruSeq Nano samples. h) Breakdown of number of individuals by self-reported ethnicity and sequencing type. Figure S3. Effect of GQ filtering on indel calling performance. a) Recall, b) Precision, and c) NCR for indels over varying GQ thresholds. Figure S4. Accuracy of flagged sites by flag type. a) Overview of the different flag types that characterize variants by comparing (filtered) sequencing-based genotype with genotype after imputation. A call is flagged with IM = 0 if sequencing-based genotype and imputed genotype agree fully. Given low coverage, we consider the lack of sequencing data evidence for an imputed allele as ���not inconsistent��� while the disappearance of an allele after imputation is categorized as ���inconsistent���. IM = 1 therefore flags imputed calls that are not inconsistent with the sequencing-based call (either because it was missing or we may have only observed one of two alleles in sequencing). IM = 2 and IM = 3 flag sites that are inconsistent between sequencing-based and imputed calls, where IM = 2 calls were heterozygous in sequencing (potentially due to sequencing or mapping artifacts or contamination, or an error in imputation) and IM = 3 calls were homozygous for the opposite allele. b) Fraction of SNV calls in each IM flag category. c) Fraction of indel calls in each IM flag category. d) Recall (normalized to each individual���s overall SNV recall), e) Precision, and f) NCR of SNVs. g) Normalized recall, h) Precision, and i) NCR of indels. Figure S5. Detailed performance (recall, precision, and NCR) of SNV and indel calling both genomewide (including repetitive regions) as well as in high-confidence regions only, shown over coverage. a) SNVs genomewide, b) SNVs in high-confidence regions, c) Indels genomewide, d) Indels in high-confidence regions. Figure S6. Performance comparison across different pipeline stages/runs. a) Overview of tested call sets. ���Single��� refers to individually called mid-pass data (GQ > 17). ���MP��� and ���MP-HP��� refer to the joint-called (���joint���) and imputed (���imp���) call sets using mid-pass data from 1510 individuals (MP) and mid-pass data from 1410 individuals plus high-pass data from 100 high-pass individuals (MP-HP) For more details see methods. b) Recall, c) Precision, and d) NCR for SNVs. e) Recall, f) Precision, and g) NCR for indels. Figure S7. Analysis of European admixture in the study cohort. ADMIXTURE was run assuming two populations on the cohort with 91 British individuals from 1000 Genomes (GBR) included to capture European ancestry. Shown are the proportions of ancestry estimated (population 1 = red, population 2 = orange). Individuals are ordered by cohort (GBR/Polynesian). Analysis of PC1 from PC analysis versus proportion of population 1 ancestry from ADMIXTURE analysis found that PC1 is highly correlated with the degree of estimated European ancestry (Spearman���s �� = ��� 0.89, p 5%) variants in the study cohort that are either absent from (a) or rare in (b) 1000 Genomes. Indels located in high-confidence regions of the genome and all SNVs were included in the analysis.

Published
2021
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20. Robust consensus computation

Author

Emde Anne-Katrin, Rausch Tobias, and Reinert Knut

Subjects
Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5
Published
2008
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23. Distinct Classes of Complex Structural Variation Uncovered across Thousands of Cancer Genome Graphs

Author

Hadi, Kevin, primary, Yao, Xiaotong, additional, Behr, Julie M., additional, Deshpande, Aditya, additional, Xanthopoulakis, Charalampos, additional, Tian, Huasong, additional, Kudman, Sarah, additional, Rosiene, Joel, additional, Darmofal, Madison, additional, DeRose, Joseph, additional, Mortensen, Rick, additional, Adney, Emily M., additional, Shaiber, Alon, additional, Gajic, Zoran, additional, Sigouros, Michael, additional, Eng, Kenneth, additional, Wala, Jeremiah A., additional, Wrzeszczyński, Kazimierz O., additional, Arora, Kanika, additional, Shah, Minita, additional, Emde, Anne-Katrin, additional, Felice, Vanessa, additional, Frank, Mayu O., additional, Darnell, Robert B., additional, Ghandi, Mahmoud, additional, Huang, Franklin, additional, Dewhurst, Sally, additional, Maciejowski, John, additional, de Lange, Titia, additional, Setton, Jeremy, additional, Riaz, Nadeem, additional, Reis-Filho, Jorge S., additional, Powell, Simon, additional, Knowles, David A., additional, Reznik, Ed, additional, Mishra, Bud, additional, Beroukhim, Rameen, additional, Zody, Michael C., additional, Robine, Nicolas, additional, Oman, Kenji M., additional, Sanchez, Carissa A., additional, Kuhner, Mary K., additional, Smith, Lucian P., additional, Galipeau, Patricia C., additional, Paulson, Thomas G., additional, Reid, Brian J., additional, Li, Xiaohong, additional, Wilkes, David, additional, Sboner, Andrea, additional, Mosquera, Juan Miguel, additional, Elemento, Olivier, additional, and Imielinski, Marcin, additional

Published
2020
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26. Mid-pass whole genome sequencing enables biomedical genetic studies of diverse populations.

Author

Emde, Anne-Katrin, Phipps-Green, Amanda, Cadzow, Murray, Gallagher, C. Scott, Major, Tanya J., Merriman, Marilyn E., Topless, Ruth K., Takei, Riku, Dalbeth, Nicola, Murphy, Rinki, Stamp, Lisa K., de Zoysa, Janak, Wilcox, Philip L., Fox, Keolu, Wasik, Kaja A., Merriman, Tony R., and Castel, Stephane E.

Subjects
*WHOLE genome sequencing, *GENETIC variation, *HUMAN genetic variation, *HEALTH equity, *GENETICISTS
Abstract

Background: Historically, geneticists have relied on genotyping arrays and imputation to study human genetic variation. However, an underrepresentation of diverse populations has resulted in arrays that poorly capture global genetic variation, and a lack of reference panels. This has contributed to deepening global health disparities. Whole genome sequencing (WGS) better captures genetic variation but remains prohibitively expensive. Thus, we explored WGS at "mid-pass" 1-7x coverage. Results: Here, we developed and benchmarked methods for mid-pass sequencing. When applied to a population without an existing genomic reference panel, 4x mid-pass performed consistently well across ethnicities, with highc recall (98%) and precision (97.5%). Conclusion: Compared to array data imputed into 1000 Genomes, mid-pass performed better across all metrics and identified novel population-specific variants with potential disease relevance. We hope our work will reduce financial barriers for geneticists from underrepresented populations to characterize their genomes prior to biomedical genetic applications. [ABSTRACT FROM AUTHOR]

Published
2022
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28. Novel patterns of complex structural variation revealed across thousands of cancer genome graphs

Author

Hadi, Kevin, primary, Yao, Xiaotong, additional, Behr, Julie M., additional, Deshpande, Aditya, additional, Xanthopoulakis, Charalampos, additional, Rosiene, Joel, additional, Darmofal, Madison, additional, Tian, Huasong, additional, DeRose, Joseph, additional, Mortensen, Rick, additional, Adney, Emily M., additional, Gajic, Zoran, additional, Eng, Kenneth, additional, Wala, Jeremiah A., additional, Wrzeszczyński, Kazimierz O., additional, Arora, Kanika, additional, Shah, Minita, additional, Emde, Anne-Katrin, additional, Felice, Vanessa, additional, Frank, Mayu O., additional, Darnell, Robert B., additional, Ghandi, Mahmoud, additional, Huang, Franklin, additional, Maciejowski, John, additional, De Lange, Titia, additional, Setton, Jeremy, additional, Riaz, Nadeem, additional, Reis-Filho, Jorge S., additional, Powell, Simon, additional, Knowles, David, additional, Reznik, Ed, additional, Mishra, Bud, additional, Beroukhim, Rameen, additional, Zody, Michael C., additional, Robine, Nicolas, additional, Oman, Kenji M., additional, Sanchez, Carissa A., additional, Kuhner, Mary K., additional, Smith, Lucian P., additional, Galipeau, Patricia C., additional, Paulson, Thomas G., additional, Reid, Brian J., additional, Li, Xiaohong, additional, Wilkes, David, additional, Sboner, Andrea, additional, Mosquera, Juan Miguel, additional, Elemento, Olivier, additional, and Imielinski, Marcin, additional

Published
2019
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29. Abstract 2870: Genetic mechanisms of primary chemotherapy resistance in pediatric acute myeloid leukemia

Author

McNeer, Nicole, primary, Philip, John, additional, Geiger, Heather, additional, Ries, Rhonda E., additional, Lavallee, Vincent-Philippe, additional, Walsh, Michael, additional, Shah, Minita, additional, Arora, Kanika, additional, Emde, Anne-Katrin, additional, Robine, Nicolas, additional, Alonzo, Todd A., additional, Kolb, E. Anders, additional, Gamis, Alan S., additional, Smith, Malcom, additional, Gerhard, Daniela Se, additional, Guidry-Auvil, Jaime, additional, Meshinchi, Soheil, additional, and Kentsis, Alex, additional

Published
2019
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30. A novel and well-defined benchmarking method for second generation read mapping

Author

Weese David, Emde Anne-Katrin, Holtgrewe Manuel, and Reinert Knut

Subjects
Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5
Abstract

Abstract Background Second generation sequencing technologies yield DNA sequence data at ultra high-throughput. Common to most biological applications is a mapping of the reads to an almost identical or highly similar reference genome. The assessment of the quality of read mapping results is not straightforward and has not been formalized so far. Hence, it has not been easy to compare different read mapping approaches in a unified way and to determine which program is the best for what task. Results We present a new benchmark method, called Rabema (Read Alignment BEnchMArk), for read mappers. It consists of a strict definition of the read mapping problem and of tools to evaluate the result of arbitrary read mappers supporting the SAM output format. Conclusions We show the usefulness of the benchmark program by performing a comparison of popular read mappers. The tools supporting the benchmark are licensed under the GPL and available from http://www.seqan.de/projects/rabema.html.

Published
2011
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31. Human papillomavirus and the landscape of secondary genetic alterations in oral cancers

Author

Gillison, Maura L., primary, Akagi, Keiko, additional, Xiao, Weihong, additional, Jiang, Bo, additional, Pickard, Robert K.L., additional, Li, Jingfeng, additional, Swanson, Benjamin J., additional, Agrawal, Amit D., additional, Zucker, Mark, additional, Stache-Crain, Birgit, additional, Emde, Anne-Katrin, additional, Geiger, Heather M., additional, Robine, Nicolas, additional, Coombes, Kevin R., additional, and Symer, David E., additional

Published
2018
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32. Analytical model of peptide mass cluster centres with applications

Author

Lehrach Hans, Emde Anne-Katrin, Farrow Malcolm, Wolski Witold E, Lalowski Maciej, and Reinert Knut

Subjects
Cytology, QH573-671
Abstract

Abstract Background The elemental composition of peptides results in formation of distinct, equidistantly spaced clusters across the mass range. The property of peptide mass clustering is used to calibrate peptide mass lists, to identify and remove non-peptide peaks and for data reduction. Results We developed an analytical model of the peptide mass cluster centres. Inputs to the model included, the amino acid frequencies in the sequence database, the average length of the proteins in the database, the cleavage specificity of the proteolytic enzyme used and the cleavage probability. We examined the accuracy of our model by comparing it with the model based on an in silico sequence database digest. To identify the crucial parameters we analysed how the cluster centre location depends on the inputs. The distance to the nearest cluster was used to calibrate mass spectrometric peptide peak-lists and to identify non-peptide peaks. Conclusion The model introduced here enables us to predict the location of the peptide mass cluster centres. It explains how the location of the cluster centres depends on the input parameters. Fast and efficient calibration and filtering of non-peptide peaks is achieved by a distance measure suggested by Wool and Smilansky.

Published
2006
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33. Genetic mechanisms of primary chemotherapy resistance in pediatric acute myeloid leukemia: A report from the TARGET initiative

Author

McNeer, Nicole A., primary, Philip, John, additional, Geiger, Heather, additional, Ries, Rhonda E., additional, Lavallée, Vincent-Philippe, additional, Walsh, Michael, additional, Shah, Minita, additional, Arora, Kanika, additional, Emde, Anne-Katrin, additional, Robine, Nicolas, additional, Alonzo, Todd A, additional, Kolb, E. Anders, additional, Gamis, Alan S, additional, Smith, Malcolm, additional, Gerhard, Daniela Se, additional, Guidry-Auvil, Jaime, additional, Meshinchi, Soheil, additional, and Kentsis, Alex, additional

Published
2018
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34. Analytical Validation of Clinical Whole-Genome and Transcriptome Sequencing of Patient-Derived Tumors for Reporting Targetable Variants in Cancer

Author

Wrzeszczynski, Kazimierz O., primary, Felice, Vanessa, additional, Abhyankar, Avinash, additional, Kozon, Lukasz, additional, Geiger, Heather, additional, Manaa, Dina, additional, London, Ferrah, additional, Robinson, Dino, additional, Fang, Xiaolan, additional, Lin, David, additional, Lamendola-Essel, Michelle F., additional, Khaira, Depinder, additional, Dikoglu, Esra, additional, Emde, Anne-Katrin, additional, Robine, Nicolas, additional, Shah, Minita, additional, Arora, Kanika, additional, Basturk, Olca, additional, Bhanot, Umesh, additional, Kentsis, Alex, additional, Mansukhani, Mahesh M., additional, Bhagat, Govind, additional, and Jobanputra, Vaidehi, additional

Published
2018
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35. Next-Generation Rapid Autopsies Enable Tumor Evolution Tracking and Generation of Preclinical Models

Author

Pisapia, David J., primary, Salvatore, Steven, additional, Pauli, Chantal, additional, Hissong, Erika, additional, Eng, Ken, additional, Prandi, Davide, additional, Sailer, Verena-Wilbeth, additional, Robinson, Brian D., additional, Park, Kyung, additional, Cyrta, Joanna, additional, Tagawa, Scott T., additional, Kossai, Myriam, additional, Fontugne, Jacqueline, additional, Kim, Robert, additional, Sigaras, Alexandros, additional, Rao, Rema, additional, Pancirer, Danielle, additional, Faltas, Bishoy, additional, Bareja, Rohan, additional, Molina, Ana M., additional, Nanus, David M., additional, Rajappa, Prajwal, additional, Souweidane, Mark M., additional, Greenfield, Jeffrey, additional, Emde, Anne-Katrin, additional, Robine, Nicolas, additional, Elemento, Olivier, additional, Sboner, Andrea, additional, Demichelis, Francesca, additional, Beltran, Himisha, additional, Rubin, Mark A., additional, and Mosquera, Juan Miguel, additional

Published
2017
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36. Erratum: PGBD5 promotes site-specific oncogenic mutations in human tumors

Author

Henssen, Anton G, primary, Koche, Richard, additional, Zhuang, Jiali, additional, Jiang, Eileen, additional, Reed, Casie, additional, Eisenberg, Amy, additional, Still, Eric, additional, MacArthur, Ian C, additional, Rodríguez-Fos, Elias, additional, Gonzalez, Santiago, additional, Puiggròs, Montserrat, additional, Blackford, Andrew N, additional, Mason, Christopher E, additional, de Stanchina, Elisa, additional, Gönen, Mithat, additional, Emde, Anne-Katrin, additional, Shah, Minita, additional, Arora, Kanika, additional, Reeves, Catherine, additional, Socci, Nicholas D, additional, Perlman, Elizabeth, additional, Antonescu, Cristina R, additional, Roberts, Charles W M, additional, Steen, Hanno, additional, Mullen, Elizabeth, additional, Jackson, Stephen P, additional, Torrents, David, additional, Weng, Zhiping, additional, Armstrong, Scott A, additional, and Kentsis, Alex, additional

Published
2017
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38. Comparing sequencing assays and human-machine analyses in actionable genomics for glioblastoma

Author

Wrzeszczynski, Kazimierz O., primary, Frank, Mayu O., additional, Koyama, Takahiko, additional, Rhrissorrakrai, Kahn, additional, Robine, Nicolas, additional, Utro, Filippo, additional, Emde, Anne-Katrin, additional, Chen, Bo-Juen, additional, Arora, Kanika, additional, Shah, Minita, additional, Vacic, Vladimir, additional, Norel, Raquel, additional, Bilal, Erhan, additional, Bergmann, Ewa A., additional, Moore Vogel, Julia L., additional, Bruce, Jeffrey N., additional, Lassman, Andrew B., additional, Canoll, Peter, additional, Grommes, Christian, additional, Harvey, Steve, additional, Parida, Laxmi, additional, Michelini, Vanessa V., additional, Zody, Michael C., additional, Jobanputra, Vaidehi, additional, Royyuru, Ajay K., additional, and Darnell, Robert B., additional

Published
2017
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39. Abstract 2714: Analytical validation of clinical whole genome and transcriptome sequencing of patient derived tumors: clinical application of whole genome sequencing for reporting targetable variants in cancer

Author

Wrzeszczynski, Kazimierz O., primary, Abhyankar, Avinash, additional, Felice, Vanessa, additional, Dikoglu, Esra, additional, Kozon, Lukasz, additional, Robine, Nicolas, additional, Emde, Anne-Katrin, additional, Basturk, Olca, additional, Bhanot, Umesh K., additional, Kentsis, Alex, additional, Mansukhani, Mahesh, additional, Bhagat, Govind, additional, and Jobanputra, Vaidehi, additional

Published
2017
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40. Abstract 4888: Human PGBD5 DNA transposase promotes site-specific oncogenic mutations in rhabdoid tumors

Author

Henssen, Anton G., primary, Koche, Richard, additional, Zhuang, Jiali, additional, Jiang, Eileen, additional, Reed, Casie, additional, Eisenberg, Amy, additional, Still, Eric, additional, Rodríguez-Fos, Elias, additional, Gonzalez, Santiago, additional, Puiggròs, Montserrat, additional, Blackford, Andrew N., additional, Mason, Christopher E., additional, Stanchina, Elisa de, additional, Gönen, Mithat, additional, Emde, Anne-Katrin, additional, Shah, Minita, additional, Arora, Kanika, additional, Reeves, Catherine, additional, Socci, Nicholas D., additional, Perlman, Elizabeth, additional, Antonescu, Cristina R., additional, Roberts, Charles W., additional, Steen, Hanno, additional, Mullen, Elizabeth, additional, Jackson, Stephen P., additional, Torrents, David, additional, Weng, Zhiping, additional, Armstrong, Scott A., additional, and Kentsis, Alex, additional

Published
2017
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41. Human PGBD5 DNA transposase promotes site-specific oncogenic mutations in rhabdoid tumors

Author

Henssen, Anton G., primary, Koche, Richard, additional, Zhuang, Jiali, additional, Jiang, Eileen, additional, Reed, Casie, additional, Eisenberg, Amy, additional, Still, Eric, additional, MacArthur, Ian C., additional, Rodríguez-Fos, Elias, additional, Gonzalez, Santiago, additional, Puiggròs, Montserrat, additional, Blackford, Andrew N., additional, Mason, Christopher E., additional, de Stanchina, Elisa, additional, Gönen, Mithat, additional, Emde, Anne-Katrin, additional, Shah, Minita, additional, Arora, Kanika, additional, Reeves, Catherine, additional, Socci, Nicholas D., additional, Perlman, Elizabeth, additional, Antonescu, Cristina R., additional, Roberts, Charles W. M., additional, Steen, Hanno, additional, Mullen, Elizabeth, additional, Jackson, Stephen P., additional, Torrents, David, additional, Weng, Zhiping, additional, Armstrong, Scott A., additional, and Kentsis, Alex, additional

Published
2017
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42. Abstract 4497: NYGC glioblastoma clinical outcomes pilot study: Discovering therapeutic potential in glioblastoma through integrative genomics

Author

Wrzeszczynski, Kazimierz O., primary, Robine, Nicolas, additional, Vacic, Vladimir, additional, Emde, Anne-Katrin, additional, Chen, Bo-Juen, additional, Liao, Will, additional, Arora, Kanika, additional, Shah, Minita, additional, Grabowska, Ewa A., additional, Felice, Vanessa, additional, Dikoglu, Esra, additional, Reeves, Catherine, additional, Frank, Mayu, additional, Jobanputra, Vaidehi, additional, Zody, Michael C., additional, Bloom, Toby, additional, and Darnell, Robert B., additional

Published
2016
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43. Abstract 4498: RNA-Seq in the NYGC GBM Clinical Outcomes Pilot Study

Author

Chen, Bo-Juen R., primary, Robine, Nicolas, additional, Wrzeszczynski, Kazimierz, additional, Vacic, Vladimir, additional, Emde, Anne Katrin, additional, Arora, Kanika, additional, Shah, Minita, additional, Grabowska, Ewa A., additional, Felice, Vanessa, additional, Dikoglu, Esra, additional, Reeves, Catherine, additional, Frank, Mayu, additional, Jobanputra, Vaidehi, additional, Zody, Michael C., additional, Bloom, Toby, additional, and Darnell, Robert, additional

Published
2016
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44. Next-generation sequencing algorithms : from read mapping to variant detection

Author

Emde, Anne-Katrin

Subjects
Bioinformatics, Variant Detection, Sequence Analysis, Algorithms, Alignment
Abstract

Next-Generation-Sequencing (NGS) has brought on a revolution in sequence analysis with its broad spectrum of applications ranging from genome resequencing to transcriptomics or metagenomics, and from fundamental research to diagnostics. The tremendous amounts of data necessitate highly efficient computational analysis tools for the wide variety of NGS applications. This thesis addresses a broad range of key computational aspects of resequencing applications, where a reference genome sequence is known and heavily used for interpretation of the newly sequenced sample. It presents tools for read mapping and benchmarking, for partial read mapping of small RNA reads and for structural variant/indel detection, and finally tools for detecting and genotyping SNVs and short indels. Our tools efficiently scale to large NGS data sets and are well-suited for advances in sequencing technology, since their generic algorithm design allows handling of arbitrary read lengths and variable error rates. Furthermore, they are implemented within the robust C++ library SeqAn, making them open-source, easily available, and potentially adaptable for the bioinformatics community. Among other applications, our tools have been integrated into a large-scale analysis pipeline and have been applied to large datasets, leading to interesting discoveries of human retrocopy variants and insights into the genetic causes of X-linked intellectual disabilities., Neuste DNA-Sequenzieungstechnologien (kurz genannt NGS Technologien) ermöglichen revolutionäre neue Anwendungen, die sowohl von Genomresequenzierung über Transkriptomsequenzierung zu Metagenomik als auch von Grundlagenforschung zu Diagnostik reichen. Problematisch ist dabei die Flut an Daten, die eine grosse Herausforderung für die Bionformatik darstellt. Hocheffiziente Analysesoftware ist von enormer Wichtigkeit für das breite Spektrum von NGS Anwendungen. Diese Arbeit adressiert mehrere Schlüsselaspekte der Analyse von Resequenzierungsdaten, bei der ein bereits sequenziertes Referenzgenom als Grundlage für die Interpretation eines neu sequenzierten Datensatzes dient. Es werden Algorithmen und Programme präsentiert für das sogenannte Read Mapping Problem und für die Auswertung der Güte seiner Lösung, für partielles Read Mapping, welches in miRNA Studien und bei der Suche nach strukturellen Variationen Anwendung findet, sowie letztlich zum Auffinden und Genotypisieren von Basenmutationen und kurzen Insertionen/Deletionen im Genom. Die vorgestellten Algorithmen sind effizient und so gestaltet, dass sie auch bei Fortschritten in Sequenzierungstechnologien weiterhin anwendbar und skalierbar bleiben. Zudem sind sie in der robusten C++ Bibliothek SeqAn implementiert, was sie leicht zugänglich und adaptierbar macht. Unter anderem wurden unsere Tools in eine Hochdurchsatz-Analysepipeline integriert und auf grosse Datensaetze angewendet, wodurch interessante biologische Erkenntnisse (vorallem im Zusammenhang X-Chromosom gebundener geistiger Behinderung) gewonnen werden konnten.

Published
2013

45. Human papillomavirus and the landscape of secondary genetic alterations in oral cancers

Author

Gillison, Maura L., Akagi, Keiko, Xiao, Weihong, Jiang, Bo, Pickard, Robert K.L., Li, Jingfeng, Swanson, Benjamin J., Agrawal, Amit D., Zucker, Mark, Stache-Crain, Birgit, Emde, Anne-Katrin, Geiger, Heather M., Robine, Nicolas, Coombes, Kevin R., and Symer, David E.

Abstract

Human papillomavirus (HPV) is a necessary but insufficient cause of a subset of oral squamous cell carcinomas (OSCCs) that is increasing markedly in frequency. To identify contributory, secondary genetic alterations in these cancers, we used comprehensive genomics methods to compare 149 HPV-positive and 335 HPV-negative OSCC tumor/normal pairs. Different behavioral risk factors underlying the two OSCC types were reflected in distinctive genomic mutational signatures. In HPV-positive OSCCs, the signatures of APOBEC cytosine deaminase editing, associated with anti-viral immunity, were strongly linked to overall mutational burden. In contrast, in HPV-negative OSCCs, T>C substitutions in the sequence context 5′-ATN-3′ correlated with tobacco exposure. Universal expression of HPV E6*1and E7oncogenes was a sine qua non of HPV-positive OSCCs. Significant enrichment of somatic mutations was confirmed or newly identified in PIK3CA, KMT2D, FGFR3, FBXW7, DDX3X, PTEN, TRAF3, RB1, CYLD, RIPK4, ZNF750, EP300, CASZ1, TAF5, RBL1, IFNGR1, and NFKBIA. Of these, many affect host pathways already targeted by HPV oncoproteins, including the p53 and pRB pathways, or disrupt host defenses against viral infections, including interferon (IFN) and nuclear factor kappa B signaling. Frequent copy number changes were associated with concordant changes in gene expression. Chr 11q (including CCND1) and 14q (including DICER1and AKT1) were recurrently lost in HPV-positive OSCCs, in contrast to their gains in HPV-negative OSCCs. High-ranking variant allele fractions implicated ZNF750, PIK3CA, and EP300mutations as candidate driver events in HPV-positive cancers. We conclude that virus-host interactions cooperatively shape the unique genetic features of these cancers, distinguishing them from their HPV-negative counterparts.

Published
2019
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48. Comparative sequencing analysis reveals high genomic concordance between matched primary and metastatic colorectal cancer lesions

Author

Brannon, A Rose, primary, Vakiani, Efsevia, additional, Sylvester, Brooke E, additional, Scott, Sasinya N, additional, McDermott, Gregory, additional, Shah, Ronak H, additional, Kania, Krishan, additional, Viale, Agnes, additional, Oschwald, Dayna M, additional, Vacic, Vladimir, additional, Emde, Anne-Katrin, additional, Cercek, Andrea, additional, Yaeger, Rona, additional, Kemeny, Nancy E, additional, Saltz, Leonard B, additional, Shia, Jinru, additional, D’Angelica, Michael I, additional, Weiser, Martin R, additional, Solit, David B, additional, and Berger, Michael F, additional

Published
2014
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49. Disease variants in genomes of 44 centenarians

Author

Freudenberg‐Hua, Yun, primary, Freudenberg, Jan, additional, Vacic, Vladimir, additional, Abhyankar, Avinash, additional, Emde, Anne‐Katrin, additional, Ben‐Avraham, Danny, additional, Barzilai, Nir, additional, Oschwald, Dayna, additional, Christen, Erika, additional, Koppel, Jeremy, additional, Greenwald, Blaine, additional, Darnell, Robert B., additional, Germer, Soren, additional, Atzmon, Gil, additional, and Davies, Peter, additional

Published
2014
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