PACLseq: A Standalone Diagnostic Method for Ph‐Like Acute Lymphoblastic Leukemia Using Nanopore Sequencing

Timely and accurate detection of Philadelphia chromosome–like acute lymphoblastic leukemia (Ph‐like ALL)‐related fusion gene is essential for treatment decisions. However, due to the complexity of possible gene fusion combinations of Ph‐like ALL, current diagnostic workflows face critical limitations: prolonged turnaround (7–14 days), high costs, and deficiency in degraded specimens. In this study, we introduce Partial Anchored Capture and Long‐Read Sequencing (PACLseq), a nanopore‐sequencing‐technology‐based approach. We designed a detection panel associated with Ph‐like ALL, specifically ABL2 , CSF1R , PDGFRB , JAK2 , ABL1 , EPOR , and CRLF2 as target genes. Validated on 47 clinical samples, PACLseq achieved 93.3% sensitivity and 100% specificity in 26 degraded RNA samples (RIN > 3). Crucially, PACLseq maintained detection accuracy in nine low‐RIN samples (RIN ≤ 3) with fragmented transcripts. The method requires only 10 ng of RNA input, delivers results in 3 days (vs. 7–14 days for conventional methods), and reduces costs by 50%. By offering rapid and accurate fusion detection, PACLseq has the potential to significantly improve diagnostic efficiency, facilitate timely treatment decisions, and enhance patient outcomes in the management of Ph‐like ALL.