Diagnostic tool for the identification of <i>MLL</i> rearrangements including unknown partner genes

<jats:p> Approximately 50 different chromosomal translocations of the human <jats:italic>MLL</jats:italic> gene are currently known and associated with high-risk acute leukemia. The large number of different <jats:italic>MLL</jats:italic> translocation partner genes makes a precise diagnosis a demanding task. After their cytogenetic identification, only the most common <jats:italic>MLL</jats:italic> translocations are investigated by RT-PCR analyses, whereas infrequent or unknown <jats:italic>MLL</jats:italic> translocations are excluded from further analyses. Therefore, we aimed at establishing a method that enables the detection of any <jats:italic>MLL</jats:italic> rearrangement by using genomic DNA isolated from patient biopsy material. This goal was achieved by establishing a universal long-distance inverse-PCR approach that allows the identification of any kind of <jats:italic>MLL</jats:italic> rearrangement if located within the breakpoint cluster region. This method was applied to biopsy material derived from 40 leukemia patients known to carry <jats:italic>MLL</jats:italic> abnormalities. Thirty-six patients carried known <jats:italic>MLL</jats:italic> fusions (34 with der(11) and 2 with reciprocal alleles), whereas 3 patients were found to carry novel <jats:italic>MLL</jats:italic> fusions to <jats:italic>ACACA, SELB</jats:italic> , and <jats:italic>SMAP1</jats:italic> , respectively. One patient carried a genomic fusion between <jats:italic>MLL</jats:italic> and <jats:italic>TIRAP</jats:italic> , resulting from an interstitial deletion. Because of this interstitial deletion, portions of the <jats:italic>MLL</jats:italic> and <jats:italic>TIRAP</jats:italic> genes were deleted, together with 123 genes located within the 13-Mbp interval between both chromosomal loci. Therefore, this previously undescribed diagnostic tool has been proven successful for analyzing any <jats:italic>MLL</jats:italic> rearrangement including previously unrecognized partner genes. Furthermore, the determined patient-specific fusion sequences are useful for minimal residual disease monitoring of <jats:italic>MLL</jats:italic> associated acute leukemias. </jats:p>