{"ID": "PMID:37932252", "lab": {"uuid": "d3412190-317a-4837-823f-3892b9f641a4", "status": "current", "@id": "/labs/external-lab/", "title": "External Lab", "display_title": "External Lab", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.d3412190-317a-4837-823f-3892b9f641a4"]}}, "url": "https://www.ncbi.nlm.nih.gov/pubmed/37932252", "tags": ["4dn-external-reuse"], "award": {"display_title": "EXTERNAL AWARD", "name": "external-award", "status": "current", "@id": "/awards/external-award/", "uuid": "12a92962-8265-4fc0-b2f8-cf14f05db58b", "@type": ["Award", "Item"], "center_title": "External", "center": "External", "description": "Funding source is from outside 4DN.", "project": "External", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "title": "Tracing cancer evolution and heterogeneity using Hi-C.", "status": "current", "aliases": ["4dn-dcic-lab:PMID:37932252"], "authors": ["Erdmann-Pham DD", "Batra SS", "Turkalo TK", "Durbin J", "Blanchette M", "Yeh I", "Shain H", "Bastian BC", "Song YS", "Rokhsar DS", "Hockemeyer D"], "journal": "Nature communications", "abstract": "Chromosomal rearrangements can initiate and drive cancer progression, yet it has  been challenging to evaluate their impact, especially in genetically  heterogeneous solid cancers. To address this problem we developed HiDENSEC, a new  computational framework for analyzing chromatin conformation capture in  heterogeneous samples that can infer somatic copy number alterations,  characterize large-scale chromosomal rearrangements, and estimate cancer cell  fractions. After validating HiDENSEC with in silico and in vitro controls, we  used it to characterize chromosome-scale evolution during melanoma progression in  formalin-fixed tumor samples from three patients. The resulting comprehensive  annotation of the genomic events includes copy number neutral translocations that  disrupt tumor suppressor genes such as NF1, whole chromosome arm exchanges that  result in loss of CDKN2A, and whole-arm copy-number neutral loss of homozygosity  involving PTEN. These findings show that large-scale chromosomal rearrangements  occur throughout cancer evolution and that characterizing these events yields  insights into drivers of melanoma progression.", "date_created": "2024-02-13T21:59:30.904725+00:00", "published_by": "External", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2024-03-15T16:02:29.602092+00:00"}, "date_published": "2023-11-06", "public_release": "2024-03-15", "schema_version": "2", "project_release": "2024-03-15", "exp_sets_used_in_pub": [{"experimentset_type": "replicate", "@id": "/experiment-set-replicates/4DNES3JX38V5/", "status": "released", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "display_title": "4DNES3JX38V5", "uuid": "aa6f0d82-16c9-4109-a1f8-3fa0636a3560", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@id": "/publications/d23f7a68-6b66-493c-9011-d1bde9fcfd04/", "@type": ["Publication", "Item"], "uuid": "d23f7a68-6b66-493c-9011-d1bde9fcfd04", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "Erdmann-Pham DD et al. (2023) PMID:37932252", "external_references": [], "short_attribution": "Erdmann-Pham DD et al. (2023)", "@context": "/terms/", "aggregated-items": {}, "validation-errors": []}