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These index cases were supplemented with whole transcriptome sequencing of three additional tumours and three cell lines. Unlike rhabdoid tumour (the other major group of <jats:styled-content style=\"fixed-case\">SMARCB1<\/jats:styled-content>\u2010negative cancers), epithelioid sarcoma shows a complex genome with a higher mutational rate, comparable to that of ovarian carcinoma. Despite this mutational burden, <jats:italic><jats:styled-content style=\"fixed-case\">SMARCB1<\/jats:styled-content><\/jats:italic> mutations remain the most frequently recurring event and are probably critical drivers of tumour formation. Several cases show heterozygous <jats:italic><jats:styled-content style=\"fixed-case\">SMARCB1<\/jats:styled-content><\/jats:italic> mutations without inactivation of the second allele, and we explore this further <jats:italic>in vitro<\/jats:italic>. Finding <jats:italic><jats:styled-content style=\"fixed-case\">CDKN2A<\/jats:styled-content><\/jats:italic> deletions in our discovery cohort, we evaluated <jats:styled-content style=\"fixed-case\">CDKN2A<\/jats:styled-content> protein expression in a tissue microarray. Six out of 16 cases had lost <jats:styled-content style=\"fixed-case\">CDKN2A<\/jats:styled-content> in greater than or equal to 90% of cells, while the remaining cases had retained the protein. Expression analysis of epithelioid sarcoma cell lines by transcriptome sequencing shows a unique profile that does not cluster with any particular tissue type or with other <jats:styled-content style=\"fixed-case\">SWI<\/jats:styled-content>\/<jats:styled-content style=\"fixed-case\">SNF<\/jats:styled-content>\u2010aberrant lines. Evaluation of the levels of members of the <jats:styled-content style=\"fixed-case\">SWI<\/jats:styled-content>\/<jats:styled-content style=\"fixed-case\">SNF<\/jats:styled-content> complex other than <jats:styled-content style=\"fixed-case\">SMARCB1<\/jats:styled-content> revealed that these proteins are expressed as part of a residual complex, similarly to previously studied rhabdoid tumour lines. This residual <jats:styled-content style=\"fixed-case\">SWI<\/jats:styled-content>\/<jats:styled-content style=\"fixed-case\">SNF<\/jats:styled-content> is susceptible to synthetic lethality and may therefore indicate a therapeutic opportunity. Copyright \u00a9 2015 Pathological Society of Great Britain and Ireland. Published by John Wiley &amp; Sons, Ltd.<\/jats:p>","DOI":"10.1002\/path.4636","type":"journal-article","created":{"date-parts":[[2015,9,14]],"date-time":"2015-09-14T07:53:59Z","timestamp":1442217239000},"page":"63-73","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":57,"title":["The genomic landscape of epithelioid sarcoma cell lines and tumours"],"prefix":"10.1002","volume":"238","author":[{"given":"Farzad","family":"Jamshidi","sequence":"first","affiliation":[{"name":"Genetic Pathology Evaluation Centre  Vancouver BC Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ali","family":"Bashashati","sequence":"additional","affiliation":[{"name":"BC Cancer Research Centre  Vancouver BC Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Karey","family":"Shumansky","sequence":"additional","affiliation":[{"name":"BC Cancer Research Centre  Vancouver BC 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