{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,7]],"date-time":"2026-10-07T06:57:59Z","timestamp":1791356279867,"version":"4.3.1"},"reference-count":27,"publisher":"Wiley","issue":"4","license":[{"start":{"date-parts":[[2010,5,6]],"date-time":"2010-05-06T00:00:00Z","timestamp":1273104000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"}],"funder":[{"DOI":"10.13039\/501100000925","name":"NHMRC","doi-asserted-by":"crossref","award":["145684"],"award-info":[{"award-number":["145684"]}],"id":[{"id":"10.13039\/501100000925","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100000925","name":"NHMRC","doi-asserted-by":"crossref","award":["288704"],"award-info":[{"award-number":["288704"]}],"id":[{"id":"10.13039\/501100000925","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100000925","name":"NHMRC","doi-asserted-by":"crossref","award":["454508"],"award-info":[{"award-number":["454508"]}],"id":[{"id":"10.13039\/501100000925","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100001026","name":"National Breast Cancer Foundation","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100001026","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100000925","name":"National Health and Medical Research Council","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100000925","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Queensland Cancer Fund"}],"content-domain":{"domain":["pathsocjournals.onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["The Journal of Pathology"],"published-print":{"date-parts":[[2010,8]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Tissue sample acquisition is a limiting step in many studies. There are many thousands of formalin\u2010fixed, paraffin\u2010embedded archival blocks collected around the world, but in contrast relatively few fresh frozen samples in tumour banks. Once samples are fixed in formalin, the RNA is degraded and traditional methods for gene expression profiling are not suitable. In this study, we have evaluated the ability of the whole genome DASL (c<jats:styled-content>D<\/jats:styled-content>NA\u2010mediated <jats:styled-content>A<\/jats:styled-content>nnealing, <jats:styled-content>S<\/jats:styled-content>election, extension, and <jats:styled-content>L<\/jats:styled-content>igation) assay from Illumina to perform transcriptomic analysis of archived breast tumour tissue in formalin\u2010fixed, paraffin\u2010embedded (FFPE) blocks. We profiled 76 familial breast tumours from cases carrying a <jats:italic>BRCA1, BRCA2<\/jats:italic> or <jats:italic>ATM<\/jats:italic> mutation, or from non\u2010<jats:italic>BRCA1\/2<\/jats:italic> families. We found that replicate samples correlated well with each other (<jats:italic>r<\/jats:italic><jats:sup>2<\/jats:sup> = 0.9\u20130.98). In 12\/15 cases, the matched formalin\u2010fixed and frozen samples predicted the same tumour molecular subtypes with confidence. These results demonstrate that the whole genome DASL assay is a valuable tool to profile degraded RNA from archival FFPE material. This assay will enable transcriptomic analysis of a large number of archival samples that are stored in pathology archives around the globe and consequently will have the potential to improve our understanding and characterization of many diseases. Copyright \u00a9 2010 Pathological Society of Great Britain and Ireland. Published by John Wiley &amp; Sons, Ltd.<\/jats:p>","DOI":"10.1002\/path.2728","type":"journal-article","created":{"date-parts":[[2010,5,6]],"date-time":"2010-05-06T13:03:34Z","timestamp":1273151014000},"page":"452-461","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":64,"title":["Gene expression profiling of formalin\u2010fixed, paraffin\u2010embedded familial breast tumours using the whole genome\u2010DASL assay"],"prefix":"10.1002","volume":"221","author":[{"given":"Nic","family":"Waddell","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sibylle","family":"Cocciardi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Julie","family":"Johnson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sue","family":"Healey","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anna","family":"Marsh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joan","family":"Riley","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Leonard da","family":"Silva","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ana Cristina","family":"Vargas","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lynne","family":"Reid","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peter T","family":"Simpson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sunil R","family":"Lakhani","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Georgia","family":"Chenevix\u2010Trench","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2010,7]]},"reference":[{"key":"e_1_2_7_2_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0002-9440(10)63435-9"},{"key":"e_1_2_7_3_2","doi-asserted-by":"publisher","DOI":"10.1007\/978-1-59745-188-8_11"},{"key":"e_1_2_7_4_2","doi-asserted-by":"publisher","DOI":"10.1101\/gr.2167504"},{"key":"e_1_2_7_5_2","doi-asserted-by":"publisher","DOI":"10.1186\/1479-5876-7-65"},{"key":"e_1_2_7_6_2","doi-asserted-by":"publisher","DOI":"10.1158\/1078-0432.CCR-09-1631"},{"key":"e_1_2_7_7_2","doi-asserted-by":"publisher","DOI":"10.2144\/000112703"},{"key":"e_1_2_7_8_2","doi-asserted-by":"publisher","DOI":"10.1097\/PAS.0b013e318158d6c5"},{"key":"e_1_2_7_9_2","doi-asserted-by":"publisher","DOI":"10.1007\/s00432-009-0692-3"},{"key":"e_1_2_7_10_2","doi-asserted-by":"publisher","DOI":"10.1186\/1472-6890-6-9"},{"key":"e_1_2_7_11_2","doi-asserted-by":"publisher","DOI":"10.1038\/labinvest.2008.11"},{"key":"e_1_2_7_12_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0008162"},{"key":"e_1_2_7_13_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.ygyno.2009.04.002"},{"key":"e_1_2_7_14_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.96.16.9212"},{"key":"e_1_2_7_15_2","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2164-7-96"},{"key":"e_1_2_7_16_2","doi-asserted-by":"publisher","DOI":"10.1038\/35021093"},{"key":"e_1_2_7_17_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.191367098"},{"key":"e_1_2_7_18_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0932692100"},{"key":"e_1_2_7_19_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1732912100"},{"key":"e_1_2_7_20_2","doi-asserted-by":"publisher","DOI":"10.1038\/415530a"},{"key":"e_1_2_7_21_2","doi-asserted-by":"publisher","DOI":"10.1056\/NEJMoa0900212"},{"key":"e_1_2_7_22_2","doi-asserted-by":"publisher","DOI":"10.1007\/s10549-009-0653-1"},{"key":"e_1_2_7_23_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btn224"},{"key":"e_1_2_7_24_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btg385"},{"key":"e_1_2_7_25_2","doi-asserted-by":"publisher","DOI":"10.1101\/gr.2739104"},{"key":"e_1_2_7_26_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gnh071"},{"key":"e_1_2_7_27_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.ajhg.2009.08.018"},{"key":"e_1_2_7_28_2","doi-asserted-by":"publisher","DOI":"10.1038\/modpathol.3800969"}],"container-title":["The Journal of Pathology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.wiley.com\/onlinelibrary\/tdm\/v1\/articles\/10.1002%2Fpath.2728","content-type":"unspecified","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.wiley.com\/onlinelibrary\/tdm\/v1\/articles\/10.1002%2Fpath.2728","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/pathsocjournals.onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/path.2728","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,21]],"date-time":"2025-10-21T14:48:05Z","timestamp":1761058085000},"score":1,"resource":{"primary":{"URL":"https:\/\/pathsocjournals.onlinelibrary.wiley.com\/doi\/10.1002\/path.2728"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2010,7]]},"references-count":27,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2010,8]]}},"alternative-id":["10.1002\/path.2728"],"URL":"https:\/\/doi.org\/10.1002\/path.2728","archive":["Portico"],"relation":{},"ISSN":["0022-3417","1096-9896"],"issn-type":[{"value":"0022-3417","type":"print"},{"value":"1096-9896","type":"electronic"}],"subject":[],"published":{"date-parts":[[2010,7]]},"assertion":[{"value":"2010-02-08","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2010-04-27","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2010-07-01","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}