Direct haplotype-resolved 5-base HiFi sequencing for genome-wide profiling of hypermethylation outliers in a rare disease cohort

Autor: Warren A. Cheung, Adam F. Johnson, William J. Rowell, Emily Farrow, Richard Hall, Ana S. A. Cohen, John C. Means, Tricia N. Zion, Daniel M. Portik, Christopher T. Saunders, Boryana Koseva, Chengpeng Bi, Tina K. Truong, Carl Schwendinger-Schreck, Byunggil Yoo, Jeffrey J. Johnston, Margaret Gibson, Gilad Evrony, William B. Rizzo, Isabelle Thiffault, Scott T. Younger, Tom Curran, Aaron M. Wenger, Elin Grundberg, Tomi Pastinen

Publikováno v: Nature Communications, Vol 14, Iss 1, Pp 1-13 (2023)

Abstract Long-read HiFi genome sequencing allows for accurate detection and direct phasing of single nucleotide variants, indels, and structural variants. Recent algorithmic development enables simultaneous detection of CpG methylation for analysis o

Externí odkaz: https://doaj.org/article/10ee8f5178214fda98a06dc46647c12e

Identification of functional regulatory elements in the human genome using pooled CRISPR screens

Autor: Samantha M. Borys, Scott T. Younger

Publikováno v: BMC Genomics, Vol 21, Iss 1, Pp 1-15 (2020)

Abstract Background Genome-scale pooled CRISPR screens are powerful tools for identifying genetic dependencies across varied cellular processes. The vast majority of CRISPR screens reported to date have focused exclusively on the perturbation of prot

Externí odkaz: https://doaj.org/article/0e84aa26e45147cfa4c561f52f324ad6

SMAD4 represses FOSL1 expression and pancreatic cancer metastatic colonization

Autor: Chao Dai, Jonathan P. Rennhack, Taylor E. Arnoff, Maneesha Thaker, Scott T. Younger, John G. Doench, August Yue Huang, Annan Yang, Andrew J. Aguirre, Belinda Wang, Evan Mun, Joyce T. O’Connell, Ying Huang, Katherine Labella, Jessica A. Talamas, Ji Li, Nina Ilic, Justin Hwang, Andrew L. Hong, Andrew O. Giacomelli, Ole Gjoerup, David E. Root, William C. Hahn

Publikováno v: Cell Reports, Vol 36, Iss 4, Pp 109443- (2021)

Summary: Metastasis is a complex and poorly understood process. In pancreatic cancer, loss of the transforming growth factor (TGF)-β/BMP effector SMAD4 is correlated with changes in altered histopathological transitions, metastatic disease, and poor

Externí odkaz: https://doaj.org/article/576815dfcfd2415692f51077629b4730

Genomic answers for children: Dynamic analyses of >1000 pediatric rare disease genomes

Autor: Ana S.A. Cohen, Emily G. Farrow, Ahmed T. Abdelmoity, Joseph T. Alaimo, Shivarajan M. Amudhavalli, John T. Anderson, Lalit Bansal, Lauren Bartik, Primo Baybayan, Bradley Belden, Courtney D. Berrios, Rebecca L. Biswell, Pawel Buczkowicz, Orion Buske, Shreyasee Chakraborty, Warren A. Cheung, Keith A. Coffman, Ashley M. Cooper, Laura A. Cross, Tom Curran, Thuy Tien T. Dang, Mary M. Elfrink, Kendra L. Engleman, Erin D. Fecske, Cynthia Fieser, Keely Fitzgerald, Emily A. Fleming, Randi N. Gadea, Jennifer L. Gannon, Rose N. Gelineau-Morel, Margaret Gibson, Jeffrey Goldstein, Elin Grundberg, Kelsee Halpin, Brian S. Harvey, Bryce A. Heese, Wendy Hein, Suzanne M. Herd, Susan S. Hughes, Mohammed Ilyas, Jill Jacobson, Janda L. Jenkins, Shao Jiang, Jeffrey J. Johnston, Kathryn Keeler, Jonas Korlach, Jennifer Kussmann, Christine Lambert, Caitlin Lawson, Jean-Baptiste Le Pichon, James Steven Leeder, Vicki C. Little, Daniel A. Louiselle, Michael Lypka, Brittany D. McDonald, Neil Miller, Ann Modrcin, Annapoorna Nair, Shelby H. Neal, Christopher M. Oermann, Donna M. Pacicca, Kailash Pawar, Nyshele L. Posey, Nigel Price, Laura M.B. Puckett, Julio F. Quezada, Nikita Raje, William J. Rowell, Eric T. Rush, Venkatesh Sampath, Carol J. Saunders, Caitlin Schwager, Richard M. Schwend, Elizabeth Shaffer, Craig Smail, Sarah Soden, Meghan E. Strenk, Bonnie R. Sullivan, Brooke R. Sweeney, Jade B. Tam-Williams, Adam M. Walter, Holly Welsh, Aaron M. Wenger, Laurel K. Willig, Yun Yan, Scott T. Younger, Dihong Zhou, Tricia N. Zion, Isabelle Thiffault, Tomi Pastinen

Publikováno v: Genetics in Medicine. 24:1336-1348

This study aimed to provide comprehensive diagnostic and candidate analyses in a pediatric rare disease cohort through the Genomic Answers for Kids program.Extensive analyses of 960 families with suspected genetic disorders included short-read exome

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::0fae080f2e98a691a62cb07ca295bd7e
https://doi.org/10.1016/j.gim.2022.02.007

Supplementary Table S5 from Cells Lacking the RB1 Tumor Suppressor Gene Are Hyperdependent on Aurora B Kinase for Survival

Autor: William G. Kaelin, Simon T. Barry, Christopher J. Lord, Susan Ashton, David Pellman, Sabina Signoretti, David E. Root, Jon Travers, Kim Maratea, Elizabeth J. Pease, Colm J. Ryan, Stefano Cairo, Paula Taylor, Laura Brulle-Soumare, Quang-De Nguyen, Dennis M. Bonal, Glenn S. Cowley, Samuel K. McBrayer, Scott T. Younger, Elizabeth Buss, Aditi Gulati, Jesse S. Novak, Abdallah Flaifel, Rebecca B. Jennings, Alexander Spektor, Rachel Brough, Abhishek A. Chakraborty, Raquel Fonseca, Matthew G. Oser

Supplementary Table S5 shows RNA sequencing data and gene set enrichment analysis of NCI-H82 cells Dox-On pRB cells grown in the presence or absence of DOX and then treated with DMSO or AZD2811.

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::86489d55cf16ceed89defe77d5f66d58
https://doi.org/10.1158/2159-8290.22533007.v1