{"corpus_id":25667413,"paper_sha":"cae74fd389a0872de3592d1e7dc52ffd9b62f7bf","doi":"10.1182/blood-2009-07-230722","arxiv_id":null,"pmid":19797517,"pmcid":null,"mag_id":2046882226,"dblp_id":null,"acl_id":null,"title":"Classification of amyloidosis by laser microdissection and mass spectrometry-based proteomic analysis in clinical biopsy specimens.","year":2009,"publication_date":"2009-12-03","venue":"Blood","journal":{"name":"Blood","pages":"\n          4957-9\n        ","volume":"114 24"},"journal_issn":null,"journal_title":null,"publication_types":["JournalArticle"],"pubmed_pub_types":["Journal Article"],"s2_fields_of_study":["Medicine"],"reference_count":21,"citation_count":815,"influential_citation_count":13,"is_open_access":true,"arxiv_categories":null,"arxiv_license":null,"arxiv_journal_ref":null,"mesh_headings":[{"d":"Amyloidosis","mj":false,"qs":[{"q":"classification","mj":true,"ui":"Q000145"}],"ui":"D000686"},{"d":"Female","mj":false,"ui":"D005260"},{"d":"Humans","mj":false,"ui":"D006801"},{"d":"Lasers","mj":false,"ui":"D007834"},{"d":"Male","mj":false,"ui":"D008297"},{"d":"Microdissection","mj":false,"qs":[{"q":"methods","mj":true,"ui":"Q000379"}],"ui":"D042282"},{"d":"Proteomics","mj":false,"qs":[{"q":"methods","mj":true,"ui":"Q000379"}],"ui":"D040901"},{"d":"Sensitivity and Specificity","mj":false,"ui":"D012680"},{"d":"Tandem Mass Spectrometry","mj":false,"qs":[{"q":"methods","mj":false,"ui":"Q000379"}],"ui":"D053719"}],"chemicals":null,"comments_corrections":null,"source_flags":5,"s2_open_access_pdf_url":"https://ashpublications.org/blood/article-pdf/114/24/4957/1320138/zh804909004957.pdf","s2_open_access_landing_url":"https://www.semanticscholar.org/paper/cae74fd389a0872de3592d1e7dc52ffd9b62f7bf","s2_open_access_license":null,"s2_open_access_status":"BRONZE","pmc_open_access_pdf_url":null,"pmc_open_access_landing_url":null,"pmc_open_access_license":null,"pmc_open_access_status":null,"unpaywall_open_access_pdf_url":null,"unpaywall_open_access_landing_url":null,"unpaywall_open_access_license":null,"unpaywall_open_access_status":null,"abstract":"The clinical management of amyloidosis is based on the treatment of the underlying etiology, and accurate identification of the protein causing the amyloidosis is of paramount importance. Current methods used for typing of amyloidosis such as immunohistochemistry have low specificity and sensitivity. In this study, we report the development of a highly specific and sensitive novel test for the typing of amyloidosis in routine clinical biopsy specimens. Our approach combines specific sampling by laser microdissection (LMD) and analytical power of tandem mass spectrometry (MS)-based proteomic analysis. We studied 50 cases of amyloidosis that were well-characterized by gold standard clinicopathologic criteria (training set) and an independent validation set comprising 41 cases of cardiac amyloidosis. By use of LMD/MS, we identified the amyloid type with 100% specificity and sensitivity in the training set and with 98% in validation set. Use of the LMD/MS method will enhance our ability to type amyloidosis accurately in clinical biopsy specimens.","claims":[{"public_id":"cl_d119cd5975a89dbfc8523dd021022950","status":"active","text":"A laser microdissection and tandem mass spectrometry-based proteomic approach provides highly specific and sensitive typing of amyloidosis in routine clinical biopsy specimens.","confidence":0.98,"contributors":[{"id":1,"public_id":"12632b8b5f","public_label":"Anonymous (12632b8b5f)","roles":["extraction"],"url":"https://sah.borca.ai/u/12632b8b5f"}],"url":"https://sah.borca.ai/claims/cl_d119cd5975a89dbfc8523dd021022950"},{"public_id":"cl_355ae579f509e38dc8510c893ba2374d","status":"active","text":"The method achieved 98% accuracy in the independent validation set of 41 cardiac amyloidosis cases.","confidence":0.95,"contributors":[{"id":1,"public_id":"12632b8b5f","public_label":"Anonymous (12632b8b5f)","roles":["extraction"],"url":"https://sah.borca.ai/u/12632b8b5f"}],"url":"https://sah.borca.ai/claims/cl_355ae579f509e38dc8510c893ba2374d"},{"public_id":"cl_2afe3bafd5bb78145c338bba3e077581","status":"active","text":"The method identified the amyloid type with 100% specificity and sensitivity in the training set of 50 well-characterized cases.","confidence":0.97,"contributors":[{"id":1,"public_id":"12632b8b5f","public_label":"Anonymous (12632b8b5f)","roles":["extraction"],"url":"https://sah.borca.ai/u/12632b8b5f"}],"url":"https://sah.borca.ai/claims/cl_2afe3bafd5bb78145c338bba3e077581"}],"concepts":[{"public_id":"co_0248ede69fdb0470ccbfc14b76ed04ae","status":"active","name":"proteomic analysis","description":"The large-scale analysis of proteins present in a biological sample.","types":["method"],"aliases":["proteomic profiling"],"contributors":[{"id":1,"public_id":"12632b8b5f","public_label":"Anonymous (12632b8b5f)","roles":["extraction"],"url":"https://sah.borca.ai/u/12632b8b5f"}],"url":"https://sah.borca.ai/concepts/co_0248ede69fdb0470ccbfc14b76ed04ae"},{"public_id":"co_0b8ac602b1dd8ffe09235dc658ecf94b","status":"active","name":"gold standard clinicopathologic criteria","description":"Established clinical and pathological criteria used to characterize the amyloidosis cases.","types":["reference standard"],"aliases":["gold standard criteria"],"contributors":[{"id":1,"public_id":"12632b8b5f","public_label":"Anonymous (12632b8b5f)","roles":["extraction"],"url":"https://sah.borca.ai/u/12632b8b5f"}],"url":"https://sah.borca.ai/concepts/co_0b8ac602b1dd8ffe09235dc658ecf94b"},{"public_id":"co_1313e30d439e0e389ccec856ba54284d","status":"active","name":"routine clinical biopsy specimens","description":"Biopsy tissue samples obtained in routine clinical practice.","types":["specimen"],"aliases":["clinical biopsy specimens"],"contributors":[{"id":1,"public_id":"12632b8b5f","public_label":"Anonymous (12632b8b5f)","roles":["extraction"],"url":"https://sah.borca.ai/u/12632b8b5f"}],"url":"https://sah.borca.ai/concepts/co_1313e30d439e0e389ccec856ba54284d"},{"public_id":"co_37ed700771d6d4642c3a463894c52b00","status":"active","name":"immunohistochemistry","description":"An antibody-based tissue staining method used for typing amyloidosis.","types":["method"],"aliases":["IHC"],"contributors":[{"id":1,"public_id":"12632b8b5f","public_label":"Anonymous (12632b8b5f)","roles":["extraction"],"url":"https://sah.borca.ai/u/12632b8b5f"}],"url":"https://sah.borca.ai/concepts/co_37ed700771d6d4642c3a463894c52b00"},{"public_id":"co_5924e7a04502af6edd2e0fac4eb89ce5","status":"active","name":"tandem mass spectrometry","description":"An analytical mass spectrometry technique used to identify proteins in the dissected tissue samples.","types":["method"],"aliases":["MS"],"contributors":[{"id":1,"public_id":"12632b8b5f","public_label":"Anonymous (12632b8b5f)","roles":["extraction"],"url":"https://sah.borca.ai/u/12632b8b5f"}],"url":"https://sah.borca.ai/concepts/co_5924e7a04502af6edd2e0fac4eb89ce5"},{"public_id":"co_6a6d336e29ca1820895789cfc6177721","status":"active","name":"independent validation set","description":"The separate cohort of 41 cases used to test the method after training.","types":["dataset"],"aliases":["validation set"],"contributors":[{"id":1,"public_id":"12632b8b5f","public_label":"Anonymous (12632b8b5f)","roles":["extraction"],"url":"https://sah.borca.ai/u/12632b8b5f"}],"url":"https://sah.borca.ai/concepts/co_6a6d336e29ca1820895789cfc6177721"},{"public_id":"co_b2c7aa7f248a016e5ce16c7c7a263834","status":"active","name":"training set","description":"The set of 50 amyloidosis cases used to develop and assess the method.","types":["dataset"],"aliases":[],"contributors":[{"id":1,"public_id":"12632b8b5f","public_label":"Anonymous (12632b8b5f)","roles":["extraction"],"url":"https://sah.borca.ai/u/12632b8b5f"}],"url":"https://sah.borca.ai/concepts/co_b2c7aa7f248a016e5ce16c7c7a263834"},{"public_id":"co_b8ff5e3719fb1254e74ab600055f2fea","status":"active","name":"amyloidosis","description":"A disease characterized by deposition of misfolded amyloid proteins in tissues.","types":["disease"],"aliases":[],"contributors":[{"id":1,"public_id":"12632b8b5f","public_label":"Anonymous (12632b8b5f)","roles":["extraction"],"url":"https://sah.borca.ai/u/12632b8b5f"}],"url":"https://sah.borca.ai/concepts/co_b8ff5e3719fb1254e74ab600055f2fea"},{"public_id":"co_c18b81fe9b2c6a858c8560bf6c155ed7","status":"active","name":"cardiac amyloidosis","description":"Amyloidosis affecting the heart, used here as the independent validation cohort.","types":["disease"],"aliases":[],"contributors":[{"id":1,"public_id":"12632b8b5f","public_label":"Anonymous (12632b8b5f)","roles":["extraction"],"url":"https://sah.borca.ai/u/12632b8b5f"}],"url":"https://sah.borca.ai/concepts/co_c18b81fe9b2c6a858c8560bf6c155ed7"},{"public_id":"co_c3545546bb2474df3242d3ffd3eba2ce","status":"active","name":"laser microdissection","description":"A sample preparation technique used to isolate specific microscopic regions from biopsy tissue.","types":["method"],"aliases":["LMD"],"contributors":[{"id":1,"public_id":"12632b8b5f","public_label":"Anonymous (12632b8b5f)","roles":["extraction"],"url":"https://sah.borca.ai/u/12632b8b5f"}],"url":"https://sah.borca.ai/concepts/co_c3545546bb2474df3242d3ffd3eba2ce"}],"external_ids":{"DOI":"10.1182/blood-2009-07-230722","ArXiv":null,"PubMed":19797517,"PubMedCentral":null,"MAG":2046882226,"DBLP":null,"ACL":null},"open_access":{"is_open_access":true,"pdf_url":"https://ashpublications.org/blood/article-pdf/114/24/4957/1320138/zh804909004957.pdf","landing_url":"https://www.semanticscholar.org/paper/cae74fd389a0872de3592d1e7dc52ffd9b62f7bf","source":"semantic_scholar","pdf_url_source":"semantic_scholar_open_access_pdf","license":null,"status":"BRONZE","reason":null},"reference_availability":{"status":"available","references_indexed":true,"full_text_available":false,"full_text_source":null,"count_basis":"semantic_scholar_metadata","extraction_status":"not_applicable","reason":null},"source":{"provider":"episteme2","base_corpus":"semantic_scholar_dump","freshness_mode":"unknown","basis":["semantic_scholar_metadata","postgres_metadata"],"limits":["paper metadata is based on indexed upstream scholarly datasets","claims and concepts are available only for extracted papers","absence of claims or concepts means no extracted graph data is available in this response"],"status":"available","degraded":false,"degraded_reasons":[],"diagnostics":{"status":"available","degraded":false,"degraded_reasons":[],"metadata_status":"available","graph_status":"available","abstract_status":"available"},"source_flags":5},"paper_id":632375,"paper_uid":"c82f77c6-e7ae-4e97-8bb6-52cb394d2cae","canonical_identity":{"paper_id":632375,"paper_uid":"c82f77c6-e7ae-4e97-8bb6-52cb394d2cae","identity_status":"available","lookup_basis":"semantic_scholar_external_id","compatibility_path":"corpus_id"},"url":"https://sah.borca.ai/papers/25667413"}