Retrotransposon instability dominates the acquired mutation landscape of mouse induced pluripotent stem cells

Authors: Patricia Gerdes, Sue Mei Lim, Adam D. Ewing, Michael R. Larcombe, Dorothy Chan, Francisco J. Sanchez-Luque, Lucinda Walker, Alexander L. Carleton, Cini James, Anja S. Knaupp, Patricia E. Carreira, Christian M. Nefzger, Ryan Lister, Sandra R. Richardson, Jose M. Polo, Geoffrey J. Faulkner

Source: Nature Communications, Vol 13, Iss 1, Pp 1-18 (2022)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/b8c17138d7be4d378e40d7894f019bb7

Long-read cDNA sequencing identifies functional pseudogenes in the human transcriptome

Authors: Robin-Lee Troskie, Yohaann Jafrani, Tim R. Mercer, Adam D. Ewing, Geoffrey J. Faulkner, Seth W. Cheetham

Source: Genome Biology, Vol 22, Iss 1, Pp 1-15 (2021)

Subject Terms: Pseudogene, PacBio, Long-read, lncRNA, CRISPR, Biology (General), QH301-705.5, Genetics, QH426-470

File Description: electronic resource

Relation: https://doaj.org/toc/1474-760X

Access URL: https://doaj.org/article/3702d87f702146c4889888e2897d0e4b

Whole genome investigation of an atypical autism case identifies a novel ANOS1 mutation with subsequent diagnosis of Kallmann syndrome

Authors: Paul A. Dawson, Soohyun Lee, Adam D. Ewing, Johannes B. Prins, Helen S. Heussler

Source: Molecular Genetics and Metabolism Reports, Vol 23, Iss , Pp - (2020)

Subject Terms: Autism, Kallmann syndrome, Whole-genome sequencing, Secondary findings, Medicine (General), R5-920, Biology (General), QH301-705.5

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2214426920300392; https://doaj.org/toc/2214-4269

Access URL: https://doaj.org/article/320529a3ed7948b4a5e6aa509d846d3b

Combining accurate tumor genome simulation with crowdsourcing to benchmark somatic structural variant detection

Authors: Anna Y. Lee, Adam D. Ewing, Kyle Ellrott, Yin Hu, Kathleen E. Houlahan, J. Christopher Bare, Shadrielle Melijah G. Espiritu, Vincent Huang, Kristen Dang, Zechen Chong, Cristian Caloian, Takafumi N. Yamaguchi, ICGC-TCGA DREAM Somatic Mutation Calling Challenge Participants, Michael R. Kellen, Ken Chen, Thea C. Norman, Stephen H. Friend, Justin Guinney, Gustavo Stolovitzky, David Haussler, Adam A. Margolin, Joshua M. Stuart, Paul C. Boutros

Source: Genome Biology, Vol 19, Iss 1, Pp 1-15 (2018)

Subject Terms: Somatic mutations, Simulation, Structural variants, Benchmarking, Cancer genomics, Whole-genome sequencing, Biology (General), QH301-705.5, Genetics, QH426-470

File Description: electronic resource

Relation: http://link.springer.com/article/10.1186/s13059-018-1539-5; https://doaj.org/toc/1474-760X

Access URL: https://doaj.org/article/fca34c67ffed4790a306c9523e251762

L1 Retrotransposon Heterogeneity in Ovarian Tumor Cell Evolution

Authors: Thu H.M. Nguyen, Patricia E. Carreira, Francisco J. Sanchez-Luque, Stephanie N. Schauer, Allister C. Fagg, Sandra R. Richardson, Claire M. Davies, J. Samuel Jesuadian, Marie-Jeanne H.C. Kempen, Robin-Lee Troskie, Cini James, Elizabeth A. Beaven, Tristan P. Wallis, Jermaine I.G. Coward, Naven P. Chetty, Alexander J. Crandon, Deon J. Venter, Jane E. Armes, Lewis C. Perrin, John D. Hooper, Adam D. Ewing, Kyle R. Upton, Geoffrey J. Faulkner

Source: Cell Reports, Vol 23, Iss 13, Pp 3730-3740 (2018)

Subject Terms: Biology (General), QH301-705.5

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2211124718308714; https://doaj.org/toc/2211-1247

Access URL: https://doaj.org/article/02b2c6ba831b4bec8988f6149861dbe1

Germline contamination and leakage in whole genome somatic single nucleotide variant detection

Authors: Dorota H. Sendorek, Cristian Caloian, Kyle Ellrott, J. Christopher Bare, Takafumi N. Yamaguchi, Adam D. Ewing, Kathleen E. Houlahan, Thea C. Norman, Adam A. Margolin, Joshua M. Stuart, Paul C. Boutros

Source: BMC Bioinformatics, Vol 19, Iss 1, Pp 1-9 (2018)

Subject Terms: Cancer genomics, Next-generation sequencing, Mutation calling, Germline contamination, Germline leakage, Patient identifiability, Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5

File Description: electronic resource

Relation: http://link.springer.com/article/10.1186/s12859-018-2046-0; https://doaj.org/toc/1471-2105

Access URL: https://doaj.org/article/ab0b15f9663d47eca47e4595ae0cd171

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