Squeezing through the Channels
“We are looking at the genome holistically, taking into account changes all the way from individual base pair mutations to large chromosomal rearrangements on the haplotype level,” explained Michael Boyce-Jacino, Ph.D., president and CEO of BioNanomatrix. “In fact, we believe major structural changes, combined with single base pair mutations, are the basis of human genetic variability.”
The hardware of the company’s technology are chips fabricated from fused silica with 100 nm wide channels etched in them to form a highly organized surface providing maximum density. The channels are covered with a roof of sprayed silicon dioxide or a glass coverslip to form tiny tunnels that can be as narrow as 10 nanometers. The molecules are driven through this nanochannel array with low voltage electrical pulses.
The BioNanomatrix sorting strategy ensures maximum efficiency of space by driving the DNA molecules through the nanochannels, which are designed with a narrowing configuration reminiscent of a highway with the lanes merging together at a point where toll booths are placed. In such a landscape the cars are sorted and forced into narrower and narrower lanes. In a similar fashion the balled up DNA is forced to unravel as it flows through the device until it ends up as long, linear DNA molecules. To identify landmarks along the molecule they are tagged with fluorescent molecules that identify individual bases visually in order to arrive at a sequence.
The DNA-filled nanochannels have a number of applications such as genome mapping in which the molecules are digested with nicking enzymes and labeled, with the pattern of labels allowing identification of deletions, mutations, and translocations.
“To fill in the gaps we perform ultralong analysis, greater than 1 kb in length and up to the whole chromosome,” stated Dr. Boyce-Jacino. At this point we do not have a sequencing product, however, we are in the second year of a five-year NIST-ATP-funded collaboration with Complete Genomics to create a much lower cost sequencing solution.”
According to Dr. Boyce-Jacino, BioNanomatrix makes extensive use of DNA bar coding for identifying and classifying sequences. This is a technique for finding genes using short DNA sequences from standard and agreed-upon positions in the gene. Since DNA bar code sequences can be obtained quickly and cheaply they are of great value in ordering the sequencing information, especially in the case of large-scale analyses involving an entire genome.
The company’s initial focus on large-scale modifications of the genome at the cytogenetic level has been partly funded through SBIR grants from NIH, reflecting the fact that the commercial significance of cytogenetic changes is only now starting to be recognized.
BioNanomatrix and Complete Genomics have also combined their complementary technologies to collaborate under a five-year $8.8 million NIST-ATP grant with the aim of sequencing the entire human genome in eight hours at a cost of $100. Through this combination of public and private funding, the companies claim to be “on track to reach the goal of the $100 genome by 2012,” noted Dr. Boyce-Jacino.