Category Archives: pub_2020

Genomic Profiling of Prostate Cancers from Men with African and European Ancestry

Yusuke Koga, Hanbing Song, Zachary R. Chalmers, Justin Newberg, Eejung Kim, Jian Carrot-Zhang, Daphnee Piou, Paz Polak, Sarki A. Abdulkadir, Elad Ziv, Matthew Meyerson, Garrett M. Frampton, Joshua D. Campbell and Franklin W. Huang. Abstract Purpose: African American (AFR) men have the highest mortality rate from prostate cancer (PCa) compared with men of other racial/ancestral groups. Differences in the spectrum of somatic genome alterations in tumors between AFR men and other populations have not been well-characterized due to a lack of inclusion of significant ……

Decontamination of ambient RNA in single-cell RNA-seq with DecontX

Shiyi Yang, Sean E. Corbett, Yusuke Koga, Zhe Wang, W. Evan Johnson, Masanao Yajima, Joshua D. Campbell. Abstract Droplet-based microfluidic devices have become widely used to perform single-cell RNA sequencing (scRNA-seq). However, ambient RNA present in the cell suspension can be aberrantly counted along with a cell’s native mRNA and result in cross-contamination of transcripts between different ……