Genome-wide haplotype association study identify the FGFR2 gene as a risk gene for acute myeloid leukemia.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:27903959", "kind": "science-record", "revision": 7, "content_hash": "sha256:786777da65bad1d2b01ab4d28e3d05cb39cf476afcee151fd12637b213ee27fe", "created_at": "2026-11-01T15:40:21Z", "updated_at": "2026-11-01T21:20:44Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Genome-wide haplotype association study identify the FGFR2 gene as a risk gene for acute myeloid leukemia.", "doi": "10.18632/oncotarget.13631", "pmid": "27903959", "authors": ["Hongchao Lv", "Mingming Zhang", "Zhenwei Shang", "Jin Li", "Shanshan Zhang", "Duan Lian", "Ruijie Zhang"], "journal": "Oncotarget", "year": 2017, "abstract": "Acute myeloid leukemia (AML) is a cancer of the myeloid line of blood cells, and generally considered to be caused by environment and genetic factors. In this study, we combined a genome-wide haplotype association study (GWHAS) and gene prioritization strategy to mine AML-related genetic affect factors and understand its pathogenesis. A total of 175 AML patients were downloaded from the public GEO database (GSE32462) and 218 matched Caucasian controls were from the HapMap Project. We first identified the linkage disequilibrium (LD) blocks and performed a GWHAS to scan AML-related haplotypes. Then we mapped these haplotypes to the corresponding genes as candidate. And finally, we prioritized all the AML candidate genes based on the similarity with 38 known AML susceptibility genes. The results showed that 1754 haplotypes were significant associated with AML (P<1E-5) and mapped to 591 candidate genes. After prioritizing all 591 AML candidate genes, we obtained four genes ranking at the front as AML risk genes: RUNX1, JAK1, PDGFRA, and FGFR2. Among them, RUNX1, JAK1 and PDGFRA had been confirmed as AML risk genes. In particular, we found that the gene FGFR2 was a novel AML susceptibility gene with a haplotype TT (rs7090018 and rs2912759) showed significant association with AML (P-value = 7.07E-06). In a word, our findings might provide a new perspective to understand the pathogenesis of AML.", "claims": [{"id": "claim-method", "statement": "For each haplotype, we carried out a chi-square test to assess the relationship with AML risk.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:27903959", "locator": "sections[3] \"The results of genome-wide haplotype association study\" paragraph 2", "quote": "For each haplotype, we carried out a chi-square test to assess the relationship with AML risk."}], "state": "complete"}, {"id": "claim-data-access", "statement": "In this study, we downloaded all the original genotypes data of Caucasian CBF-AML patients from GEO database (accession GSE32462) under the chip platform GPL6801 (Affymetrix SNP 6.0 array), which contained 930,662 SNP markers.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:27903959", "locator": "sections[11] \"Datasets and Quality control\" paragraph 2", "quote": "In this study, we downloaded all the original genotypes data of Caucasian CBF-AML patients from GEO database (accession GSE32462) under the chip platform GPL6801 (Affymetrix SNP 6.0 array), which contained 930,662 SNP markers."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The results showed that 1754 haplotypes were significant associated with AML (P<1E-5) and mapped to 591 candidate genes.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:27903959", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "A total of 175 AML patients were downloaded from the public GEO database (GSE32462) and 218 matched Caucasian controls were from the HapMap Project."}, {"asset": "source:pmid:27903959", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "We first identified the linkage disequilibrium (LD) blocks and performed a GWHAS to scan AML-related haplotypes."}, {"asset": "source:pmid:27903959", "locator": "sections[3] \"The results of genome-wide haplotype association study\" paragraph 2", "quote": "For each haplotype, we carried out a chi-square test to assess the relationship with AML risk."}, {"asset": "source:pmid:27903959", "locator": "sections[3] \"The results of genome-wide haplotype association study\" paragraph 2", "quote": "After the quality control (detail see methods), our study obtained a total of 734,624 eligible autosomal SNPs."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The results showed that 1754 haplotypes were significant associated with AML (P<1E-5) and mapped to 591 candidate genes.", "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:27903959"], "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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