Adam C. Weiner

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.