Sohrab P. Shah

Sep 30, 2024 | nature.com | Adam C. Weiner |Marc Williams |Nicole Rusk |Samuel Aparicio |Sohrab P. Shah

AbstractDysregulated DNA replication is a cause and a consequence of aneuploidy in cancer, yet the interplay between copy number alterations (CNAs), replication timing (RT) and cell cycle dynamics remain understudied in aneuploid tumors. We developed a probabilistic method, PERT, for simultaneous inference of cell-specific replication and copy number states from single-cell whole genome sequencing (scWGS) data.

May 13, 2024 | nature.com | Alexander N Gorelick |Ignacio Vázquez-García |Marc Williams |Adam C. Weiner |Tyler Funnell |Tricia Park | +5 more

AbstractThe extent of cell-to-cell variation in tumor mitochondrial DNA (mtDNA) copy number and genotype, and the phenotypic and evolutionary consequences of such variation, are poorly characterized. Here we use amplification-free single-cell whole-genome sequencing (Direct Library Prep (DLP+)) to simultaneously assay mtDNA copy number and nuclear DNA (nuDNA) in 72,275 single cells derived from immortalized cell lines, patient-derived xenografts and primary human tumors.

May 5, 2024 | nature.com | Nicholas W Bateman |Tamara Abulez |Dale W. Garsed |Pang-ning Teng |Clifton L. Dalgard |Mariaelena Pierobon | +5 more

Correction to: npj Precision Oncology https://doi.org/10.1038/s41698-024-00519-8, published online 13 March 2024In the original version of this article, the wrong file was inadvertently supplied for Supplementary Data 15. The original article has been corrected.

Mar 12, 2024 | nature.com | Nicholas W Bateman |Tamara Abulez |Dale W. Garsed |Pang-ning Teng |Clifton L. Dalgard |Mariaelena Pierobon | +5 more

AbstractWe performed a deep proteogenomic analysis of bulk tumor and laser microdissection enriched tumor cell populations from high-grade serous ovarian cancer (HGSOC) tissue specimens spanning a broad spectrum of purity.

Jul 20, 2023 | nature.com | Nicole Rusk |Andrew Chow |Benjamin D. Greenbaum |Sohrab P. Shah

Dataset preprocessingEach single cell RNA-seq dataset in this study was processed using the Scanpy python library7. All highly variable gene selection was performed using the Seurat V36 method implemented in Scanpy. We performed cell type classification on 23,764 cells from the Tumor Immune Cell Atlas (TICA)20 using raw read counts from 2,000 highly variable after removal of non-protein coding genes.