FusorSV: an algorithm for optimally combining data from multiple structural variation detection methods

Autor: Timothy Becker, Wan-Ping Lee, Joseph Leone, Qihui Zhu, Chengsheng Zhang, Silvia Liu, Jack Sargent, Kritika Shanker, Adam Mil-homens, Eliza Cerveira, Mallory Ryan, Jane Cha, Fabio C. P. Navarro, Timur Galeev, Mark Gerstein, Ryan E. Mills, Dong-Guk Shin, Charles Lee, Ankit Malhotra

Publikováno v: Genome Biology, Vol 19, Iss 1, Pp 1-14 (2018)

Abstract Comprehensive and accurate identification of structural variations (SVs) from next generation sequencing data remains a major challenge. We develop FusorSV, which uses a data mining approach to assess performance and merge callsets from an e

Externí odkaz: https://doaj.org/article/ed8fbd6184544edc8cdbff2d7a92587c

JAX-CNV: A Whole Genome Sequencing-based Algorithm for Copy Number Detection at Clinical Grade Level

Autor: Wan-Ping Lee, Qihui Zhu, Xiaofei Yang, Silvia Liu, Eliza Cerveira, Mallory Ryan, Adam Mil-Homens, Lauren Bellfy, Kai Ye, Charles Lee, Chengsheng Zhang

Publikováno v: Genomics, proteomicsbioinformatics.

We aimed to develop a whole-genome sequencing (WGS)-based copy number variant (CNV) calling algorithm with the potential of replacing chromosomal microarray assay (CMA) for clinical diagnosis. JAX-CNV is thus developed for CNV detection from WGS. The

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::db5d8cc7e42a2540b49f3d21204e70ec
https://pubmed.ncbi.nlm.nih.gov/35085778

Systematic analysis of copy number variation associated with congenital diaphragmatic hernia

Autor: Lauren Bellfy, Mallory Ryan, Mauro Longoni, Charles Lee, M. P. Joy, Patricia K. Donahoe, Chengsheng Zhang, Pooja Bhayani, Meaghan K. Russell, Eliza Cerveira, Caroline Coletti, Adam Mil-homens, Regis Hila, Qihui Zhu, Jay M. Wilson, Frances A. High

Publikováno v: Proceedings of the National Academy of Sciences of the United States of America

Significance This study describes the results of a large-scale case control analysis of copy number variants (CNVs) in a cohort of patients with congenital diaphragmatic hernia (CDH) and a large number of healthy population-matched controls. Using a

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::5c4dfc1dfadbde1c5d89e0a28a93232e
https://doi.org/10.1073/pnas.1714885115

Oncogenic extrachromosomal DNA functions as mobile enhancers to globally amplify chromosomal transcription

Autor: Meihong Li, Liang Gong, Yanfen Zhu, Chris Kuhlberg, Jihe Liu, Adam Mil-Homens, Ana C. deCarvalho, Chia-Lin Wei, Roel G.W. Verhaak, Yi-An Chen, Chew Yee Ngan, Yijun Ruan, Chee Hong Wong, Rahul Maurya, Eun Hee Yi, Harianto Tjong, Fanyue Sun, Amit D. Gujar, Hoon Kim

Publikováno v: Cancer Cell, 39(5), 694-707.e7. Cell Press
Zhu, Y, Gujar, A D, Wong, C-H, Tjong, H, Ngan, C Y, Gong, L, Chen, Y-A, Kim, H, Liu, J, Li, M, Mil-Homens, A, Maurya, R, Kuhlberg, C, Sun, F, Yi, E, deCarvalho, A C, Ruan, Y, Verhaak, R G W & Wei, C-L 2021, ' Oncogenic extrachromosomal DNA functions as mobile enhancers to globally amplify chromosomal transcription ', Cancer Cell, vol. 39, no. 5, pp. 694-707.e7 . https://doi.org/10.1016/j.ccell.2021.03.006

Extrachromosomal, circular DNA (ecDNA) is emerging as a prevalent yet less characterized oncogenic alteration in cancer genomes. We leverage ChIA-PET and ChIA-Drop chromatin interaction assays to characterize genome-wide ecDNA-mediated chromatin cont

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::5116bbf1cb60b3cb4ed253e327b6a932
https://doi.org/10.1016/j.ccell.2021.03.006