UW electrical engineering Assistant Professor Sreeram Kannan leads a $1.2 million collaborative National Science Foundation (NSF) Communications and Information Foundations (CIF) Grant. The research aims to design new algorithms for sequencing DNA using nanopore readers.
Fast and inexpensive DNA sequencing technology is beginning to impact society through applications ranging from personalized medicine to the understanding of ecological systems. However, existing DNA sequencing methods are limited in the length of DNA that can be analyzed. These systems can read only short strands of DNA, limiting the ability of algorithms to resolve and analyze regions of the genome which have repeating motifs.
Nanopore sequencing is a new and emerging technology, where DNA is transmigrated through a pore, and the induced electrical current variations are measured to infer the DNA sequence. In addition to having the ability to sequence long stretches of DNA, nanopore sequencers are also relatively inexpensive and offer high mobility for testing and rapid processing of samples.
An algorithm, called base-caller, is used to infer the DNA sequence from the observed current waveform. Current base-calling methods suffer from high measurement noise. Kannan and his team of collaborators seek to address this problem. In a recent paper, they have quantified the amount of information that can be extracted by the process of nanopore sequencing, establishing interesting parallels to a classical problem studied in communication theory. A telecommunication system is mathematically characterized by the probabilistic mapping between the transmitted signal and the received signal. Analogously, the mapping between the DNA sequence and the observed current waveform can be thought of as a communication channel whose information rates can be characterized using information-theoretic methods.
This project develops a holistic approach for the nanopore sequencing problem, using tools from information theory and bio-informatics to build more representative mathematical models and better algorithms for inferring the DNA sequence, as well as to explore potential applications in DNA forensics, phasing and assembly.
Kannan is the PI on the four-year grant. Co-PIs include UW Department of Physics Professor Jens Gundlach and UCLA electrical engineering Professor Suhas Diggavi.