Nanopore sequencing and liquid biopsy: copy number variation analysis of short cell-free DNA from plasma of lung cancer patients
Compared to tissue biopsies, ‘liquid biopsy is very very non-invasive, you can easily get out a lot of samples to strictly monitor the tumour evolution’– this is particularly important for personalised medicine in future.
Why Nanopore for sequencing cfDNA? Filippo explained its benefits: portability, low instrumentation costs, and real-time sequencing.
Filippo is investigating copy number variation (CNV), using shallow whole-genome nanopore sequencing, in cfDNA samples. Using the MinION or GridION devices, he sequenced samples from healthy control individuals and lung cancer patients, multiplexing 5 samples per flow cell (prepared using ligation sequencing and barcoding).
Only 2 M reads (out of the total 14 M reads) was sufficient to obtain a similar CNV profile, with 98% concordance to the 14 M read set. This could be achieved in 3 hours.
Nanopore real-time sequencing and analysis (NanoGLADIATOR) enables rapid CNV detection, in only 3 hours. This is ‘incredibly fast’ compared to short-read analysis which can take days.
See his recent publication on this research in the Resource Centre.