Genome-wide haplotype association study identify TNFRSF1A, CASP7, LRP1B, CDH1 and TG genes associated with Alzheimer's disease in Caribbean Hispanic individuals.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:26621834", "kind": "science-record", "revision": 7, "content_hash": "sha256:9fdf3eac4592798447fd6a67a0edb4d0250339179078514d3ee8712f9da05699", "created_at": "2026-11-01T15:40:14Z", "updated_at": "2026-11-01T21:20:17Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Genome-wide haplotype association study identify TNFRSF1A, CASP7, LRP1B, CDH1 and TG genes associated with Alzheimer's disease in Caribbean Hispanic individuals.", "doi": "10.18632/oncotarget.6391", "pmid": "26621834", "authors": ["Zhenwei Shang", "Hongchao Lv", "Mingming Zhang", "Lian Duan", "Situo Wang", "Jin Li", "Guiyou Liu", "Zhang Ruijie", "Yongshuai Jiang"], "journal": "Oncotarget", "year": 2015, "abstract": "Alzheimer's disease (AD) is an acquired disorder of cognitive and behavioral impairment. It is considered to be caused by variety of factors, such as age, environment and genetic factors. In order to identify the genetic affect factors of AD, we carried out a bioinformatic approach which combined genome-wide haplotype-based association study with gene prioritization. The raw SNP genotypes data was downloaded from GEO database (GSE33528). It contains 615 AD patients and 560 controls of Caribbean Hispanic individuals. Firstly, we identified the linkage disequilibrium (LD) haplotype blocks and performed genome-wide haplotype association study to screen significant haplotypes that were associated with AD. Then we mapped these significant haplotypes to genes and obtained candidate genes set for AD. At last, we prioritized AD candidate genes based on their similarity with 36 known AD genes, so as to identify AD related genes. The results showed that 141 haplotypes on 134 LD blocks were significantly associated with AD (P<1E-4), and these significant haplotypes were mapped to 132 AD candidate genes. After prioritizing these candidate genes, we found seven AD related genes: APOE, APOC1, TNFRSF1A, LRP1B, CDH1, TG and CASP7. Among these genes, APOE and APOC1 are known AD risk genes. For the other five genes TNFRSF1A, CDH1, CASP7, LRP1B and TG, this is the first genetic association study which showed the significant association between these five genes and AD susceptibility in Caribbean Hispanic individuals. We believe that our findings can provide a new perspective to understand the genetic affect factors of AD.", "claims": [{"id": "claim-method", "statement": "For each haplotype, we carried out a chi-square test to obtain its statistical significance.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26621834", "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 obtain its statistical significance."}], "state": "complete"}, {"id": "claim-data-access", "statement": "In our study, the raw SNP genotypes data was downloaded from GEO database (http://www.ncbi.nlm.nih.gov/geo), the GEO accession is GSE33528. It was released on May 01, 2012. The purpose of original study was to survey large rare copy number variations in late-onset AD, and they had found some meaningful results [56]. The datasets include 615 patients with late-onset AD and 560 controls of unrelated Caribbean Hispanic individuals. Its SNP chip platform is GPL14932 which includes 662,841 SNP markers.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26621834", "locator": "sections[13] \"Datasets\" paragraph 2", "quote": "In our study, the raw SNP genotypes data was downloaded from GEO database (http://www.ncbi.nlm.nih.gov/geo), the GEO accession is GSE33528. It was released on May 01, 2012. The purpose of original study was to survey large rare copy number variations in late-onset AD, and they had found some meaningful results [56]. The datasets include 615 patients with late-onset AD and 560 controls of unrelated Caribbean Hispanic individuals. Its SNP chip platform is GPL14932 which includes 662,841 SNP markers."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Using chi-square testing of genome-wide haplotypes from GSE33528, the study identified 141 haplotypes on 134 LD blocks significantly associated with Alzheimer’s disease at P < 1E-4.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:26621834", "locator": "sections[3] \"The results of genome-wide haplotype association study\" paragraph 2", "quote": "At last, we found 141 haplotypes that were significantly associated with AD (P < 1E-4, see Supplementary Table 2 in the website: http://www.bioapp.org/research/ADhaplotype). The 141 significant haplotypes were located on 134 block regions."}, {"asset": "source:pmid:26621834", "locator": "sections[14] \"Genome-wide haplotype association analysis\" paragraph 3", "quote": "Here we used the software Haploview to identify the LD blocks and performed association analysis. The method of identify LD blocks was Four Gamete Tests (FGT) which combined the impact of genetic factors into block construction. Then the Maximum Likelihood Estimation and Expectation Maximization algorithm were used to estimate the haplotypes and their frequencies. At last, the statistically significant haplotypes that associated with AD were obtained by chi-square test [57, 58]. A haplotype was considered associated with AD, if its P value of chi-square test was less than 1.0E-4."}, {"asset": "source:pmid:26621834", "locator": "sections[3] \"The results of genome-wide haplotype association study\" paragraph 2", "quote": "In this study, we carried out a genome-wide haplotype association study using SNP genotypes data of 1,175 Caribbean Hispanic individuals (GSE33528)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Using chi-square testing of genome-wide haplotypes from GSE33528, the study identified 141 haplotypes on 134 LD blocks significantly associated with Alzheimer’s disease at P < 1E-4.", "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:26621834"], "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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It was released on May 01, 2012. The purpose of original study was to survey large rare copy number variations in late-onset AD, and they had found some meaningful results [56]. The datasets include 615 patients with late-onset AD and 560 controls of unrelated Caribbean Hispanic individuals. Its SNP chip platform is GPL14932 which includes 662,841 SNP markers.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "In our study, the raw SNP genotypes data was downloaded from GEO database (http://www.ncbi.nlm.nih.gov/geo), the GEO accession is GSE33528. It was released on May 01, 2012. The purpose of original study was to survey large rare copy number variations in late-onset AD, and they had found some meaningful results [56]. The datasets include 615 patients with late-onset AD and 560 controls of unrelated Caribbean Hispanic individuals. 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null, "platform": "14932", "taxon": "Homo sapiens", "title": "Genome-wide survey of large rare copy number variations in Alzheimer’s disease   among Caribbean Hispanics", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:26621834:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:990593eaa2576a5d93e32509c90420a722db79b2d2561b3a7c036b6fdc7c32d4", "bytes": 549, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[4]/table-wrap[1]#T1", "version": null, "note": "The top seven AD related genes of prioritization", "structure": {"pmcid": "PMC4767448", "section_index": 4, "section_title": "Mapping and prioritizing the AD candidate genes", "row_count": 8, "column_count": 4}, "table": {"label": "Table 1", "caption": 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The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE33528"], "resolved_accessions": ["GSE33528"], "statements": ["In our study, the raw SNP genotypes data was downloaded from GEO database (http://www.ncbi.nlm.nih.gov/geo), the GEO accession is GSE33528. It was released on May 01, 2012. The purpose of original study was to survey large rare copy number variations in late-onset AD, and they had found some meaningful results [56]. The datasets include 615 patients with late-onset AD and 560 controls of unrelated Caribbean Hispanic individuals. Its SNP chip platform is GPL14932 which includes 662,841 SNP markers."], "basis": "The paper names GSE33528 in GEO database (http://www.ncbi.nlm.nih.gov/geo) and the accession resolves in the repository. 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