Evolutionary tracking of cancer haplotypes at single-cell resolution

Autor: Nicholas Ceglia, Diljot Grewal, Justina Biele, Weiner Ac, Brimhall J, Peter Eirew, Samuel Aparicio, Ciara H. O'Flanagan, Havasov E, Masud T, Hakwoo Lee, Beatty S, Samantha Leung, Florian Uhlitz, Abrams D, Ignacio Vázquez-García, Marc J Williams, Damian Yap, Daniel Lai, Salehi S, Sohrab P. Shah, Ting J, Wang B, Farhia Kabeer, Nicole Rusk, Bojilova, Tyler Funnell, Jenifer Pham, Andrew McPherson

Cancer genomes exhibit extensive chromosomal copy number changes and structural variation, yet how allele specific alterations drive cancer genome evolution remains unclear. Here, through application of a new computational approach we report allele s

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::bfe906a55569752a1cc9c03c621e85ce
https://doi.org/10.1101/2021.06.04.447031

Inferring replication timing and proliferation dynamics from single-cell DNA sequencing data.

Autor: Weiner AC; Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.; Tri-Institutional PhD Program in Computational Biology and Medicine, Weill Cornell Medicine, New York, NY, USA., Williams MJ; Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA., Shi H; Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.; Gerstner Sloan Kettering Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, USA., Vázquez-García I; Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA., Salehi S; Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA., Rusk N; Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA., Aparicio S; Department of Molecular Oncology, British Columbia Cancer, Vancouver, BC, Canada.; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada., Shah SP; Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA. shahs3@mskcc.org., McPherson A; Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA. mcphera1@mskcc.org.

Publikováno v: Nature communications [Nat Commun] 2024 Oct 01; Vol. 15 (1), pp. 8512. Date of Electronic Publication: 2024 Oct 01.

Single-cell mtDNA dynamics in tumors is driven by coregulation of nuclear and mitochondrial genomes.

Autor: Kim M; Tri-Institutional PhD Program in Computational Biology & Medicine, Weill Cornell Medicine, New York City, NY, USA.; Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York City, NY, USA., Gorelick AN; Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York City, NY, USA.; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York City, NY, USA., Vàzquez-García I; Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York City, NY, USA., Williams MJ; Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York City, NY, USA., Salehi S; Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York City, NY, USA., Shi H; Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York City, NY, USA., Weiner AC; Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York City, NY, USA., Ceglia N; Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York City, NY, USA., Funnell T; Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York City, NY, USA., Park T; Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York City, NY, USA., Boscenco S; Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York City, NY, USA., O'Flanagan CH; Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada., Jiang H; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York City, NY, USA., Grewal D; Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York City, NY, USA., Tang C; Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York City, NY, USA., Rusk N; Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York City, NY, USA., Gammage PA; Institute of Cancer Sciences, University of Glasgow, Glasgow, UK.; CRUK Beatson Institute, Glasgow, UK., McPherson A; Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York City, NY, USA., Aparicio S; Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada., Shah SP; Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York City, NY, USA. shahs3@mskcc.org., Reznik E; Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York City, NY, USA. reznike@mskcc.org.

Publikováno v: Nature genetics [Nat Genet] 2024 May; Vol. 56 (5), pp. 889-899. Date of Electronic Publication: 2024 May 13.

Single-cell DNA replication dynamics in genomically unstable cancers.

Autor: Weiner AC; Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.; Tri-Institutional PhD Program in Computational Biology and Medicine, Weill Cornell Medicine, New York, NY, USA., Williams MJ; Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA., Shi H; Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.; Gerstner Sloan Kettering Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, USA., Vázquez-García I; Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA., Salehi S; Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA., Rusk N; Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA., Aparicio S; Department of Molecular Oncology, British Columbia Cancer, Vancouver, BC, Canada.; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada., Shah SP; Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA., McPherson A; Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.

Publikováno v: BioRxiv : the preprint server for biology [bioRxiv] 2023 Sep 23. Date of Electronic Publication: 2023 Sep 23.

Single-cell genomic variation induced by mutational processes in cancer.

Autor: Funnell T; Tri-Institutional PhD Program in Computational Biology and Medicine, Weill Cornell Medicine, New York, NY, USA.; Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA., O'Flanagan CH; Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada., Williams MJ; Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA. william1@mskcc.org., McPherson A; Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA., McKinney S; Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada., Kabeer F; Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada.; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada., Lee H; Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada.; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada., Salehi S; Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA., Vázquez-García I; Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA., Shi H; Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA., Leventhal E; Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA., Masud T; Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada., Eirew P; Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada., Yap D; Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada., Zhang AW; Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada., Lim JLP; Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA., Wang B; Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada., Brimhall J; Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada., Biele J; Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada., Ting J; Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada., Au V; Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada., Van Vliet M; Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada., Liu YF; Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada., Beatty S; Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada., Lai D; Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada.; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada., Pham J; Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada., Grewal D; Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA., Abrams D; Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA., Havasov E; Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA., Leung S; Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA., Bojilova V; Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA., Moore RA; Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada., Rusk N; Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA., Uhlitz F; Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA., Ceglia N; Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA., Weiner AC; Tri-Institutional PhD Program in Computational Biology and Medicine, Weill Cornell Medicine, New York, NY, USA.; Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA., Zaikova E; Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada., Douglas JM; Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada., Zamarin D; GYN Medical Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA., Weigelt B; Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA., Kim SH; Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA., Da Cruz Paula A; Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA., Reis-Filho JS; Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA., Martin SD; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada., Li Y; Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada., Xu H; Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada., de Algara TR; Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada., Lee SR; Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada., Llanos VC; Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada., Huntsman DG; Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada.; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada., McAlpine JN; Department of Gynecology and Obstetrics, University of British Columbia, Vancouver, British Columbia, Canada., Shah SP; Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA. shahs3@mskcc.org., Aparicio S; Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada. saparicio@bccrc.ca.; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada. saparicio@bccrc.ca.

Publikováno v: Nature [Nature] 2022 Dec; Vol. 612 (7938), pp. 106-115. Date of Electronic Publication: 2022 Oct 26.