{"doi":"10.1101/2022.11.25.517982","title":"SlideCNA: Spatial copy number alteration detection from Slide-seq-like spatial transcriptomics data","abstract":"Abstract Solid tumors are spatially heterogeneous in their genetic, molecular and cellular composition, and this variation can be meaningful for diagnosis, prognosis and therapy. Recent spatial profiling studies have mostly charted genetic and RNA variation in tumors separately. To leverage the potential of RNA to identify copy number alterations (CNAs), we developed SlideCNA, a computational tool to extract sparse spatial CNA signals from spatial transcriptomics data, using expression-aware spatial binning. We test SlideCNA on simulated and real Slide-seq data of metastatic breast cancer (MBC) and demonstrate its potential for spatial sub-clone detection.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2022,"id":313362,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":0,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.8596,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2022-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":3618,"name":"Åsa Segerstolpe","orcid":"0000-0002-3700-9661","position":1,"is_corresponding":false},{"id":2274,"name":"Michal Slyper","orcid":"0000-0002-3002-0366","position":2,"is_corresponding":false},{"id":2275,"name":"Julia Waldman","orcid":"0000-0002-0584-5833","position":3,"is_corresponding":false},{"id":35220,"name":"Evan Murray","orcid":"0000-0002-9195-7478","position":4,"is_corresponding":false},{"id":3739,"name":"Ofir Cohen","orcid":"0000-0002-0043-6838","position":5,"is_corresponding":false},{"id":2691,"name":"Orr Ashenberg","orcid":"0000-0002-7802-8834","position":6,"is_corresponding":false},{"id":20801,"name":"Daniel L. Abravanel","orcid":"0000-0002-0129-1618","position":7,"is_corresponding":false},{"id":25071,"name":"Judit Jané‐Valbuena","orcid":"0000-0002-5651-1745","position":8,"is_corresponding":false},{"id":35223,"name":"Simon Mages","orcid":"0000-0003-1447-6811","position":9,"is_corresponding":false},{"id":35224,"name":"Ana Lako","orcid":"0000-0003-2931-6212","position":10,"is_corresponding":false},{"id":20794,"name":"Karla Helvie","orcid":"0000-0002-3514-0332","position":11,"is_corresponding":false},{"id":2697,"name":"Orit Rozenblatt–Rosen","orcid":"0000-0001-6313-3570","position":12,"is_corresponding":false},{"id":3736,"name":"Scott J. Rodig","orcid":"0000-0003-1761-9769","position":13,"is_corresponding":false},{"id":24055,"name":"Fei Chen","orcid":"0000-0003-2308-3649","position":14,"is_corresponding":false},{"id":3754,"name":"Nikhil Wagle","orcid":"0000-0003-3332-9438","position":15,"is_corresponding":false},{"id":104370,"name":"Aviv Regev","orcid":"0000-0003-3293-3158","position":16,"is_corresponding":false},{"id":472,"name":"Johanna Klughammer","orcid":"0000-0002-3628-9278","position":17,"is_corresponding":false},{"id":35219,"name":"Diane Zhang","orcid":"0000-0002-0268-4413","position":0,"is_corresponding":true}],"reference_count":20,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-07-19T00:33:44.454239Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}