long reads

At the beginning of the year, we were all holding our breath for the future of PacBio. And by all, I mean all. It seems everyone has been rooting for this sequencing technology company.

And why? It’s simple. Pretty much everyone is in agreement that they have the highest quality reads on the market.

So why was their future in question? This could have been asked of many famous companies at one time or another. Apple computer faced their dark days. Disney overcame initial failure. A company’s success in the market does not always align perfectly with the quality of their product. There are other variables.

PacBio at the end of this year is a different company. They have raised two rounds of financing. They have released their Sequel IIe, and they have a new CEO, Christian Henry. From August to November, their stock tripled in price. So what happened? And what is Christian’s new vision for the company?

The main takeaway today is that Christian believes in PacBio’s existing core story: long reads will take science, medicine, and the world to new heights. He thinks this story has been undersold and plans to change that.

The last time we talked with Chris Mason of Weill Cornell Medical College the Supreme Court had just decided the controversial Myriad gene patent case. How forever ago two years can seem. Since then Chris has swabbed and sequenced the microbiome of New York City and began the project of sequencing in space.

His favorite research this year has been to longitudinally profile the genome, epigenome, transcriptome, metabolome and microbiome of identical twins, one in space and one on earth.

"We see that the gene expression changes dramatically as soon as you get into space, says Chris on today’s show. "What we’re looking for in particular are changes in RNA methylation--which has been related to circadian rhythm--and also RNA processing and stability. Really we’re looking at the epitranscriptomic changes of astronauts.”

Epitranscriptome? What’s that?

The second half of the interview is devoted to Chris’ assessment of the latest sequencing tools. Chris says he’s pleased with Oxford Nanopore’s MinION. Not only has he sequenced what he thinks is the longest continuous read (86 KB) on the MinION, he says the high error rate has come down and the GC bias is much improved. If this geneticist who sees his work as "a duty to the universe" had to choose one sequencer, which would it be?

Before Bobby Sebra became the Director of Technology Development at the Icahn School of Medicine at Mt Sinai in New York he worked at Pacific Biosciences, helping to develop their single molecule, long read (SMRT) sequencing technology.

In today's interview Bobby says he left PacBio to be free to use all of the available sequencing platforms to develop clinical solutions. At the Icahn School, he has been scaling up the facilities to include Illumina, Ion Torrent, PacBio and BioNano Genomics sequencers, as wells as researching some of the newer platforms such as 10X Genomics, and Oxford Nanopore Technologies. Bobby’s work includes matching these various platforms with the right project, often going back and forth between short read and long read technologies to get an adequate result.

Building on his familiarity with the PacBio system, one of Bobby's primary projects at Icahn is to take PacBio’s new long read technology and develop new clinical applications, such as looking at more polymorphic domains in the human genome at high throughput.

What are his big challenges? Bobby says that a single cell approach is the next important step for clinical sequencing, and he looks forward to a platform which integrates single cell analysis into one workflow. He is also pushing sequencing tool providers to be able to work with lower input, or smaller initial samples.

What clinical projects has Bobby excited, and what is his reaction to recent skepticism about the clinical potential for the study of genomics? Join us for a wide ranging discussion on the latest in clinical sequencing.

When President Bill Clinton stood with Francis Collins and Craig Venter in 2001 to announce the sequencing of the genome, the genome wasn’t really done.

So is it done now? And if not, when will it be done? What does ‘done’ even mean? That first human genome sequence that represented the work of Venter and Collins improved each year and became what geneticists refer to as the reference genome. In 2009 the Genome Reference Consortium, a group of various institutions, was set up for the purpose of finishing this reference genome. And every few years a new version is published. The latest goes by the sexy name of GRCh38.

Valerie Schneider, a scientist at the National Center for Biotechnology Information (NCBI), is the leader of the team working on the reference genome. In today’s interview, she tells us about the ongoing work to improve the reference genome, and why it’s important to science and medicine.

David Schwartz was focused on long read sequencing and the structural variations of the genome—the big picture—long before the current trend. His lab at the University of Wisconsin at Madison developed optical mapping and posted the first optical map of the human genome several years ago. And last year, they published the first optical map of a cancer genome.

David is the first guest in our second series to focus on long read sequencing. He was interested in structural variation even before the first human genome was published, an endeavor which he says changed the way we do biology.

How does he see sequencing developing?

“Sequencing will be electronic,” he says. “Ultimately we’ll use synthetic pores. Some sort of non-biomolecule based approach will reign supreme.”

With his illustrative history in genetics, we can’t help but ask David a couple of our favorite questions here at Mendelspod--such as, how much wet lab vs. dry lab for the new biologist?

Guest:

Eric Schadt, Professor & Chair Genetics and Genomic Sciences, Director Icahn Institute for Genomics and Multiscale Biology Bio and Contact Info

Listen (5:01) Getting buy-in from a few lead doctors

Listen (5:24) Do you see shift toward long read sequencing?

Listen (6:35) Scaling up for the clinic

Listen (6:03) PacBio leading on quality

Listen (4:07) The genome fractal? Using math in biology

Three years ago, Eric Schadt left the sequencing company, Pacific Biosciences, as their CSO to go be guru of genomic medicine at Mt Sinai in New York City. Backed with terrific funding and leadership, Eric has the resources to be in the vanguard of translating our latest understanding of genomics into real world benefits for patients.

Today he updates us on his work at Mt Sinai, detailing his strategy and the obstacles that he faces. He then weighs in on the rising importance of long read sequencing, not just for microbial research, but for practical human genomics. Eric comments here on the journey of PacBio from a company that was overhyped and under delivering to one that is setting the mark for quality in human genome sequencing today.

“It’s very exciting to see the quality of the PacBio data,” he says. “The utility is just beyond compare, whether you're assembling a bacterial genome de novo, or looking at structural features in the fragile X region of the [human] genome, or looking at methylation simultaneously. ”

Eric has a Ph D in biomathematics. We end by discussing how math will help in deciphering biology.

“We don’t know the language yet of biology. So we’re trying to learn how to write the book without really understanding all the words or knowing how to string the words together into sentences," he says at the conclusion of the interview.

Podcast brought to you by: Pacific Biosciences - providers of long read sequencing solutions based on their Single Molecule Real Time technology.

Guest:

George Church, Professor of Genetics, Harvard Medical School 

Listen (6:11) Church's Law

Listen (6:45) Colbert, Der Spiegel and Regenesis

Listen (2:49) Do you have a hobby?

Listen (8:22) The promise of 3D sequencing

Listen (4:42) Is long reads the NGS story of the year?

Listen (6:02) Have you heard any good arguments against GMOs?

Listen (5:46) How much wet lab vs. coding for the new biologist?

Listen (2:57) 60th Birthday Bash

If we have celebrities in the life science industry, George Church of Harvard is one of them. Author, professor, entrepreneur, advisor—the list goes on and on. One of the special things about George is his commitment to advocate for science to the larger community. With everything else he has going on, he makes time to talk on programs like ours.

We launched Mendelspod with a George Church interview. Three years later, it’s a treat to have him on again to talk about his work, career, philosophy, and take a few questions from the audience.

Thanks to IDT for underwriting this show.

Podcast Sponsor: Integrated DNA Technologies - providing custom double-stranded gBlocks Gene Fragments of up to 2 kb, for easy gene construction.

Guest:

Dan Geraghty, Researcher, Fred Hutchinson Cancer Center; CEO, Scisco Genetics Bio and Contact Info

Listen (4:43) Unable so far to find causal linkages in MHC region of the genome

Listen (4:43) Illumina vs. PacBio

Listen (9:27) Major sequencing projects should be done with long reads

Listen (9:32) Is the message about long reads getting out there?

Listen (3:15) What projects will you pursue with long read technology?

Dan Geraghty has a message for anyone looking for genetic causes of disease.

A researcher at the Fred Hutchinson Cancer Center, Dan has been working at characterizing the difficult region of the genome known as MHC, or major histocompatibility complex. This region controls a major part of the immune system and is linked with many common diseases. Until now, Dan says, researchers have so far been unable to find causal linkages to common diseases, such as diabetes, celiac disease, and rheumatoid arthritis in the MHC region because they haven't been able to look at long enough pieces of DNA.

Unlike with Mendelian diseases where a single mutation is linked directly to the disease, the regions in the MHC that are linked to disease often include long "flanking" sequences which play a part. Until now, to get a complete look at a long genetic region, researchers have used Illumina's short read technology and then had a lot of data analysis and finishing work to do. First of all, that finishing takes hours and hours. And secondly it doesn't give an accurate picture.

"The finishing is really prohibitive for a modest research effort," says Dan.

Enter new long read technology. Recently Dan worked with PacBio where he was able to get 40kb read lengths. Contrast that with the 300bp reads of the Illumina technology. There's just no comparison, he says. And the error rate for the long reads: one in a million.

"This is really high quality data," Dan says of the PacBio reads. "This is the kind of zero error rate where you can compare your cases and controls and easily validate them and have high confidence that what you're seeing is accurate."

What does this mean for genomic research going forward? Take the 1,000 Genome Project of the NHGRI. Shouldn't researchers be using long reads to get the most accurate data possible?

And just what projects is Dan pursuing with what he calls the "breakthrough" technology?

"We're hot on the trail," he says. "We basically can see the entire picture. We're not looking under a lamppost for the keys. It's daylight, and we can see the whole neighborhood. So we're gonna find the keys."

Podcast brought to you by: Pacific Biosciences - providers of long read sequencing solutions based on their Single Molecule Real Time technology.