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This study evaluated the applicability of panel-based RNA sequencing and array CGH within the diagnostic workflow of the German study group of the international AIEOP-BFM ALL 2017 trial. In a consecutive cohort of 117 children with B cell precursor (BCP) ALL, array analysis identified twelve cases with an\n                    <jats:italic>IKZF1<\/jats:italic>\n                    <jats:sup>plus<\/jats:sup>\n                    profile of gene deletions and one case of masked hypodiploidy. Genetic markers\n                    <jats:italic>BCR<\/jats:italic>\n                    -\n                    <jats:italic>ABL1<\/jats:italic>\n                    (\n                    <jats:italic>n<\/jats:italic>\n                    \u2009=\u20091),\n                    <jats:italic>ETV6<\/jats:italic>\n                    -\n                    <jats:italic>RUNX1<\/jats:italic>\n                    (\n                    <jats:italic>n<\/jats:italic>\n                    \u2009=\u200925), and rearrangements involving\n                    <jats:italic>KMT2A<\/jats:italic>\n                    (\n                    <jats:italic>n<\/jats:italic>\n                    \u2009=\u20093) or\n                    <jats:italic>TCF3<\/jats:italic>\n                    (n\u2009=\u20093) were assessed by established conventional techniques such as karyotyping, FISH, and RT-PCR. Comparison of these results with RNA sequencing analysis revealed overall consistency in\n                    <jats:italic>n<\/jats:italic>\n                    =115\/117 cases, albeit with one undetected\n                    <jats:italic>AFF1<\/jats:italic>\n                    -\n                    <jats:italic>KMT2A<\/jats:italic>\n                    fusion in RNA sequencing and one undetected\n                    <jats:italic>ETV6<\/jats:italic>\n                    -\n                    <jats:italic>RUNX1<\/jats:italic>\n                    fusion in conventional analyses. The combined application of RNA sequencing, FISH, and CGH+SNP array reliably detected all genetic markers necessary for risk stratification and will be used as the diagnostic standard workflow for BCP-ALL patients enrolled in the AIEOP-BFM ALL 2017 study. Prospectively, consistent collection of genome-wide CGH+SNP array as well as RNA sequencing data will be a valuable source to elucidate new prognostic lesions beyond established markers of pediatric ALL. In this respect, RNA sequencing identified various gene fusions in up to half of the\n                    <jats:italic>IKZF1<\/jats:italic>\n                    <jats:sup>plus<\/jats:sup>\n                    (\n                    <jats:italic>n<\/jats:italic>\n                    \u2009=\u20096\/12) and B-other (\n                    <jats:italic>n<\/jats:italic>\n                    \u2009=\u200919\/36) cases but not in cases with hyperdiploid karyotypes (\n                    <jats:italic>n<\/jats:italic>\n                    \u2009=\u200935). Among these fusions, this study reports several previously undescribed in frame\n                    <jats:italic>PAX5<\/jats:italic>\n                    fusions, including\n                    <jats:italic>PAX5-MYO1G<\/jats:italic>\n                    and\n                    <jats:italic>PAX5-NCOA6<\/jats:italic>\n                    .\n                  <\/jats:p>","DOI":"10.1007\/s00277-020-03953-3","type":"journal-article","created":{"date-parts":[[2020,2,20]],"date-time":"2020-02-20T02:02:58Z","timestamp":1582164178000},"page":"809-818","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":34,"title":["Implementation of RNA sequencing and array CGH in the diagnostic workflow of the AIEOP-BFM ALL 2017 trial on acute lymphoblastic leukemia"],"prefix":"10.1007","volume":"99","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5878-0546","authenticated-orcid":false,"given":"Maximilian","family":"Schieck","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jana","family":"Lentes","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kathrin","family":"Thomay","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Winfried","family":"Hofmann","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yvonne Lisa","family":"Behrens","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maike","family":"Hagedorn","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Juliane","family":"Ebersold","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Colin F.","family":"Davenport","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Grazia","family":"Fazio","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anja","family":"M\u00f6ricke","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Swantje","family":"Buchmann","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Julia","family":"Alten","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gunnar","family":"Cario","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Martin","family":"Schrappe","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anke Katharina","family":"Bergmann","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Martin","family":"Stanulla","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Doris","family":"Steinemann","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Brigitte","family":"Schlegelberger","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Giovanni","family":"Cazzaniga","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gudrun","family":"G\u00f6hring","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2020,2,20]]},"reference":[{"issue":"6","key":"3953_CR1","doi-asserted-by":"publisher","first-page":"440","DOI":"10.1016\/S2352-4642(18)30066-X","volume":"2","author":"CH Pui","year":"2018","unstructured":"Pui CH, Yang JJ, Bhakta N, Rodriguez-Galindo C (2018) Global efforts toward the cure of childhood acute lymphoblastic leukaemia. 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