de novo assembly

When Long Reads are Double the Price of Short Reads, Short Reads Are Dead, Says Evan Eichler

Each year at this time, sequencing tools leader, Illumina, generates another round of sequencing buzz in the industry, this year by announcing the $100 genome is around the corner with their latest boxes. But more and more, people are asking just what they will get with that $100. Indeed, what do they get today with a $1,500 genome?

Illumina sells short read sequencing technology which is unable to characterize much of the human genome, particularly complex regions which are responsible for many of the known and unknown diseases.

Today’s guest has made his career studying structural variation of the genome. He’s done it with the rapidly improving long read sequencing technology, mostly on instruments produced by Pacific Biosciences. He says researchers have been seduced by the ability to sequence thousands and tens of thousands of genomes as opposed to understanding five or ten genomes really well.

Evan Eichler is a professor of genomics at the University of Washington and first made his name known back with the original Human Genome Project. In the final days of the project, he was brought into the NIH to analyze the genome for structural variation repeats. Neither the private Venter enterprise nor the public attempt had the ability to see them at the time, and with what Evan calls his “young, stupid naivety," he waded into the project. He was able to compare data from the two groups without getting too caught up in the politics and ended up making an important contribution to the final output. Today Evan has established himself so well in the structural variation space that it is said no project into structural variation can be conceived without him.

“Work that we have done over the past couple years has shown that if you apply a new sequencing technology like long reads, you basically uncover 90% of the structural variation that is missed by short read sequencing technology.”

That’s a big number.

“That is a big number,” says Evan, “so the question is, how important are structural variations? That’s open to debate.”

Evan says there is data which shows that structural variant level changes are likely to be more impactful than those of single nucleotide variants (SNVs). He compares SNVs to little tremors and structural changes to earthquakes when it comes to regulating the genome.

As with his mentor, Jim Lupski, (featured on the program here), Evan is adamant that we must stop using short read technology and aligning to a reference genome. Rather, he says, we must get to the place where we are doing de novo assembly of each genome. We can do that in the research setting now, but we must do that clinically as well.

“If we’re still aligning sequences to a reference genome, and that’s our only way for understanding genetic variation ten years from now, clinically we’ve failed. What we need to think about is how to do this right, and that means understanding all the variation from stem to stern in these genomes."

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