Evaluating the analytical validity of circulating tumor DNA sequencing assays for precision oncology

Autor: Agda Karina Eterovic, Rebecca Ringler, Binsheng Gong, Jiashi Wang, Christopher E. Mason, Garima Kushwaha, Abhisek Ghosal, James C. Willey, Zhihong Zhang, Wenzhong Xiao, Natalia Novoradovskaya, Joshua Xu, Mary Yang, Zhiguang Li, Leihong Wu, Philippe Szankasi, Paul Rindler, Suman Verma, Simon Cawley, Daniel Stetson, Yilin Zhang, Fergal Casey, Nathan Haseley, Fujun Qiu, Paula Proszek, Mirna Jarosz, Ira W. Deveson, Kevin Lai, Donald J. Johann, Rebecca Kusko, Haowen Tan, Tim R. Mercer, Chia Jung Chang, Kristina Giorda, Tieliu Shi, Blake Burgher, Kyle Horvath, Leming Shi, Pierre R. Bushel, Guangchun Chen, Melissa Smith, Igor Stevanovski, Devin W. Close, Liang Feng, Lin-ya Tang, Liang-Chun Liu, Todd Richmond, Wendell D. Jones, Daniel Duncan, Andreas Scherer, Jorge Dinis, Chang Xu, Rita Shaknovich, Tom Morrison, Ping Song, Nikola Tom, Weida Tong, Quan Zhen Li, Lihyun Sun, Charles Ma, Dalila B. Megherbi, Robert Sebra, Sean Glenn, Narasimha Marella, Ambica Bhandari, Jennifer S. LoCoco, Zhichao Liu, Jeoffrey Schageman, Mehdi Pirooznia, Scott Happe, Hanane Arib, Maya Strahl, Dan Li, Hunter Best, Venkat J. Thodima, Amelia Raymond, Jeffrey Conroy, Mike Hubank, Piotr A. Mieczkowski, Carlos Pabón-Peña, James Blackburn, Li-Yuan Hung, Sa Zhang, Bindu Swapna Madala, Guangliang Zhang, Jonathan Choi

Publikováno v: Nature biotechnology

Circulating tumor DNA (ctDNA) sequencing is being rapidly adopted in precision oncology, but the accuracy, sensitivity, and reproducibility of ctDNA assays is poorly understood. Here we report the findings of a multi-site, cross-platform evaluation o

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::3f3d76ae77be6b6d242d19ba6f29eaf8
http://europepmc.org/articles/PMC8434938

Familial Immune Thrombocytopenia Associated With a Novel Variant in IKZF1

Autor: Qin Zhou, Devin W. Close, Panida Sriaroon, Boglarka Ujhazi, Hemant R. Joshi, Jolan E. Walter, Attila Kumánovics, Krisztian Csomos, Yenhui Chang

Publikováno v: Frontiers in Pediatrics
Frontiers in Pediatrics, Vol 7 (2019)

We report a novel variant in IKZF1 associated with IKAROS haploinsufficiency in a patient with familial immune thrombocytopenia (ITP). IKAROS, encoded by the IKZF1 gene, is a hematopoietic zinc-finger transcription factor that can directly bind to DN

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::f2fb31eee4f0bc2af272af87994d5aa4
https://doi.org/10.3389/fped.2019.00139

Algorithmic improvements for discovery of germline copy number variants in next-generation sequencing data

Autor: Lewis T, Devin W. Close, Jacob D. Durtschi, Brendan D. O'Fallon

Copy number variants (CNVs) play a significant role in human heredity and disease, however sensitive and specific characterization of CNVs from NGS data has remained challenging. Detection is especially problematic for hybridization-capture data in w

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::dc9bf85e8eaa5151dfb69a293b766a5b

A new family of β-helix proteins with similarities to the polysaccharide lyases

Autor: Devin W. Close, Sara D'Angelo, Andrew Bradbury

Publikováno v: Acta Crystallographica Section D Biological Crystallography. 70:2583-2592

Microorganisms that degrade biomass produce diverse assortments of carbohydrate-active enzymes and binding modules. Despite tremendous advances in the genomic sequencing of these organisms, many genes do not have an ascribed function owing to low seq

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::70db2b6fb089fd89faba1986743fb866
https://doi.org/10.1107/s1399004714015934

Discovery of DNA operators for TetR and MarR family transcription factors from Burkholderia xenovorans

Autor: Elizabeth Hong-Geller, Pat J. Unkefer, Yolanda E. Valdez, Tinh T. Nguyen, Kristy L. Nowak-Lovato, Andrew Bradbury, Tuhin S. Maity, John Dunbar, Devin W. Close, Ricardo Marti-Arbona

Publikováno v: Microbiology. 158:571-582

Determining transcription factor (TF) recognition motifs or operator sites is central to understanding gene regulation, yet few operators have been characterized. In this study, we used a protein-binding microarray (PBM) to discover the DNA recogniti

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::4f64d9984d5cf92e41a1749e74d3a4be
https://doi.org/10.1099/mic.0.055129-0