Nanopore Sequencing of Chronic Lymphocytic Leukemia

While splicing changes caused by somatic mutations in SF3B1 are known, identifying full-length isoform changes may better elucidate the functional consequences of these mutations. We have performed nanopore sequencing of full-length cDNA from CLL samples with and without SF3B1 mutation, as well as normal B cell samples. With long reads, we analyzed alternative splicing patterns associated with SF3B1 mutation at an isoform-level.]]>
Dr. Cathy Wu, senior author of the paper associated with the dbGaP study phs000435, gifted us with 5 CLL RNA samples from that study. We have resequenced them with the Oxford Nanopore PromethION 1D and MinION 2D cDNA long read sequencing. The Nanopore data consists of electrical current signal in fast5 format containing the basecalled sequences for each sequencing run. There were 9 subjects sequenced total. The RNA for all the subjects were collected by Cathy Wu's group and all sequenced at UCSC. The samples breakdown as follows: 6 CLL patients whose RNA were resequenced (3 patients with wildtype SF3B1 and 3 patients with the K700E mutation in SF3B1). These 6 patients were all sequenced with the PromethION. Two of these 6 patients (one wildtype SF3B1 and one mutant SF3B1) were also sequenced with the MinION. There is PromethION sequencing of B cells from 3 healthy donors and additional MinION sequencing of one of the donors. ]]>