Genomic alterations in rectal tumors and response to neoadjuvant chemoradiotherapy: an exploratory study.

{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:22099067", "kind": "science-record", "revision": 4, "content_hash": "sha256:cf4185eaddea085f0a5c3f15cec4f077d1af6b721022fba13ff6f7e142e0d0ed", "created_at": "2026-11-01T15:40:02Z", "updated_at": "2026-11-01T21:19:39Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Genomic alterations in rectal tumors and response to neoadjuvant chemoradiotherapy: an exploratory study.", "doi": "10.1186/1748-717X-6-161", "pmid": "22099067", "authors": ["Chiara Molinari", "Michela Ballardini", "Nazario Teodorani", "Massimo Giannini", "Wainer Zoli", "Ermanno Emiliani", "Enrico Lucci", "Alessandro Passardi", "Paola Rosetti", "Luca Saragoni", "Massimo Guidoboni", "Dino Amadori", "Daniele Calistri"], "journal": "Radiation oncology (London, England)", "year": 2011, "abstract": "BACKGROUND: Neoadjuvant chemoradiotherapy is the treatment of choice in advanced rectal cancer, even though there are many patients who will not benefit from it. There are still no effective methods for predicting which patients will respond or not. The present study aimed to define the genomic profile of rectal tumors and to identify alterations that are predictive of response in order to optimize therapeutic strategies.\nMETHODS: Forty-eight candidates for neoadjuvant chemoradiotherapy were recruited and their pretherapy biopsies analyzed by array Comparative Genomic Hybridization (aCGH). Pathologic response was evaluated by tumor regression grade.\nRESULTS: Both Hidden Markov Model and Smoothing approaches identified similar alterations, with a prevalence of DNA gains. Non responsive patients had a different alteration profile from responsive ones, with a higher number of genome changes mainly located on 2q21, 3q29, 7p22-21, 7q21, 7q36, 8q23-24, 10p14-13, 13q12, 13q31-34, 16p13, 17p13-12 and 18q23 chromosomal regions.\nCONCLUSIONS: This exploratory study suggests that an in depth characterization of chromosomal alterations by aCGH would provide useful predictive information on response to neoadjuvant chemoradiotherapy and could help to optimize therapy in rectal cancer patients.The data discussed in this study are available on the NCBI Gene Expression Omnibus [GEO: GSE25885].", "claims": [{"id": "claim-method", "statement": "The Kruskal-Wallis non parametric test was used to assess the predictive relevance of genomic instability, expressed as the fraction of genome altered (FGA) in relation to response to therapy in different stage and age subgroups.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:22099067", "locator": "sections[7] \"Statistics\" paragraph 2", "quote": "The Kruskal-Wallis non parametric test was used to assess the predictive relevance of genomic instability, expressed as the fraction of genome altered (FGA) in relation to response to therapy in different stage and age subgroups."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data discussed in this study are available on the NCBI Gene Expression Omnibus [GEO: GSE25885].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:22099067", "locator": "sections[0] \"Abstract\" paragraph 5", "quote": "The data discussed in this study are available on the NCBI Gene Expression Omnibus [GEO: GSE25885]."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study used Hidden Markov Model and Smoothing analyses of pretherapy aCGH profiles from 48 rectal cancer candidates for neoadjuvant chemoradiotherapy, with the source data available through NCBI GEO accession GSE25885.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:22099067", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Both Hidden Markov Model and Smoothing approaches identified similar alterations, with a prevalence of DNA gains."}, {"asset": "source:pmid:22099067", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "Forty-eight candidates for neoadjuvant chemoradiotherapy were recruited and their pretherapy biopsies analyzed by array Comparative Genomic Hybridization (aCGH)."}, {"asset": "source:pmid:22099067", "locator": "sections[0] \"Abstract\" paragraph 5", "quote": "The data discussed in this study are available on the NCBI Gene Expression Omnibus [GEO: GSE25885]."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study used Hidden Markov Model and Smoothing analyses of pretherapy aCGH profiles from 48 rectal cancer candidates for neoadjuvant chemoradiotherapy, with the source data available through NCBI GEO accession GSE25885.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:22099067"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. 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