Mayo Clinic, OmniTier speed up de novo genome sequencing

In a joint study, Mayo Clinic and OmniTier have shown that de novo genome sequencing—which does not use a reference genome—can be used in whole genome sequencing without the need for “supercomputing-level resources,” making the speedier sequencing process more accessible.

The duo used OmniTier’s CompStor software to sequence the well-known genome NA12878, commonly used for benchmarking. They were able to assemble a 50x coverage genome—meaning that the sequencing reads each individual nucleotide base 50 times—in less than two hours, OmniTier said in a statement. Coverage requirements differ by application. For example, 10x to 30x coverage is recommended for the detection of human genome mutations, according to the sequencing giant Illumina. Generally, as coverage increases, genetic variants can be identified with higher degrees of confidence.

The CompStor software can be used with up to 800x coverage, a "dataset size previously considered too large for de novo techniques but necessary to reliably identify new and infrequent variants,” OmniTier said.

It improves upon variant-calling methods currently used in whole-genome sequencing. These methods rely on a reference genome against which sequenced reads are compared. However, this single-reference approach can lead to biases and missed variants. CompStor is designed to bridge a gap—while de novo methods do not use a reference and therefore avoid the biases that come with it, they are “too slow and expensive for mass deployment.”

De novo methods can now be used on platforms based on "standard, low-cost servers with next-generation software and memory—opening the door to hundreds of institutions globally that are eager to leverage next-generation sequencing techniques."

"De novo sequence assembly for better variant discovery and characterization has remained elusive due to the exceedingly long assembly times and resources requirement of existing assemblers. CompStor holds the promise to change that paradigm,” said Alexej Abyzov, Ph.D., a senior associate consultant and assistant professor of biomedical informatics at the Mayo Clinic.

Mayo Clinic plans to apply CompStor to the analysis of point substitution mutations, as well as insertion or deletion mutations and larger structural variants, Abyzov said.

CompStor is still in beta testing but is expected to be “generally available” in the fourth quarter. In the meantime, Abyzov’s lab, along with OmniTier scientists, will publish their observations in an upcoming peer-reviewed paper.

“Our current results in the joint study with the Mayo Clinic highlight the potential to integrate de novo assembly methodology in genomic medicine and achieve higher accuracy and shorter assembly times on affordable cloud or on-premise infrastructure,” said OmniTier CEO Hemant Thapar, Ph.D.