TP53 gene mutation analysis in chronic lymphocytic leukemia by nanopore MinION sequencing

Background

The assessment of TP53 mutational status is becoming a routine clinical practice for chronic lymphocytic leukemia patients (CLL). A broad spectrum of molecular techniques has been employed so far, including both direct Sanger sequencing and next generation sequencing. Oxford Nanopore Technologies recently released the MinION an USB-interfaced sequencer. In this paper we report our experience, with the MinION technology for the detection of the TP53 gene mutation in CLL patients.

Twelve CLL patients at diagnosis were included in this study. All except one patient showed the TP53 gene deletion in Fluorescence In Situ Hybridization experiments.

Patients were investigated for TP53 mutation by Sanger and by MinION sequencing.

Analysis by Sanger was performed according with the IARC protocol.

Analysis by MinION was performed adopting a strategy based on long template PCR, read error correction, and post variant calling filtering.

Results

Due to the high error rate of nanopore technology, sequence data were both used directly and before correction with two different in silico methods: ALEC and nanocorrect. A mean error rate of 15 % was detected before correction that was reduced to 4-5 % after correction.

Analysis by Sanger sequencing was able to detect four patients mutated for TP53. MinION analysis detected one more mutated patient previously not detected from Sanger.

Conclusion

In our hands, the Nanopore technology shows correlation with Sanger sequencing but more sensitive, manageable and less expensive, and therefore has proven to be a useful tool for TP53 gene mutation detection.

additional keywords: cancer, cancer research, oncology