{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,31]],"date-time":"2025-10-31T13:53:36Z","timestamp":1761918816066},"reference-count":36,"publisher":"Wiley","issue":"8","license":[{"start":{"date-parts":[[2006,5,15]],"date-time":"2006-05-15T00:00:00Z","timestamp":1147651200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Genes Chromosomes &amp; Cancer"],"published-print":{"date-parts":[[2006,8]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Panhandle PCR techniques to amplify known sequence flanked by unknown sequence have been useful for <jats:italic>MLL<\/jats:italic> genomic breakpoint junctions and fusion transcripts because <jats:italic>MLL<\/jats:italic> has a large number of partner genes. However, genomic panhandle PCR approaches are impeded when the restriction fragment that contains the breakpoint junction is too large to amplify. We devised new panhandle PCR approaches for <jats:italic>MLL<\/jats:italic> genomic breakpoint junctions that create the template from <jats:italic>Bgl<\/jats:italic>II restriction fragments by attaching <jats:italic>MLL<\/jats:italic> sequence to a <jats:italic>Bgl<\/jats:italic>II site in the partner gene. This leads to the annealing of <jats:italic>MLL<\/jats:italic> and its complement in the handle and creates an intrastrand loop containing the breakpoint junction sequence for amplification with primers all from <jats:italic>MLL. Bgl<\/jats:italic>II panhandle PCR for der(11) breakpoint junctions was accomplished by ligating a phosphorylated oligonucleotide containing a <jats:italic>Bgl<\/jats:italic>II overhang and sequence complementary to <jats:italic>MLL<\/jats:italic> exon 7 to the 3\u2032 ends of <jats:italic>Bgl<\/jats:italic>II digested DNA, and forming the template from the sense strand of DNA. In <jats:italic>Bgl<\/jats:italic>II reverse panhandle PCR for der(other) breakpoint junctions, a phosphorylated oligonucleotide containing a <jats:italic>Bgl<\/jats:italic>II overhang and the complement of antisense sequence in <jats:italic>MLL<\/jats:italic> exon 10 was ligated to the 3\u2032 ends of <jats:italic>Bgl<\/jats:italic>II digested DNA, and the template was formed from the antisense strand of DNA. These approaches amplified <jats:italic>5<\/jats:italic>\u2032\u2010<jats:italic>MLL\u2010MLLT4\u20103<\/jats:italic>\u2032 and <jats:italic>5<\/jats:italic>\u2032\u2010<jats:italic>AFF1\u2010MLL\u20103<\/jats:italic>\u2032 breakpoint junctions. The former is significant because few t(6;11) genomic breakpoint junctions have been sequenced. <jats:italic>Bgl<\/jats:italic>II panhandle PCR approaches increase the possibilities for cloning <jats:italic>MLL<\/jats:italic> genomic breakpoint junctions where there is heterogeneity in partner genes and breakpoint locations. \u00a9 2006 Wiley\u2010Liss, Inc.<\/jats:p>","DOI":"10.1002\/gcc.20336","type":"journal-article","created":{"date-parts":[[2006,5,15]],"date-time":"2006-05-15T16:25:33Z","timestamp":1147710333000},"page":"740-753","source":"Crossref","is-referenced-by-count":8,"title":["<i>Bgl<\/i>II\u2010based panhandle and reverse panhandle PCR approaches increase capability for cloning der(II) and der(other) genomic breakpoint junctions of <i>MLL<\/i> translocations"],"prefix":"10.1002","volume":"45","author":[{"given":"Blaine W.","family":"Robinson","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Diana 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