long reads


Clinicians Show High Demand for Single Cell Sequencing, Says Bobby Sebra of Mt. Sinai

If today's guest were a super hero, he'd be High Resolution Sequencing Man.

Bobby Sebra is the Director of Technology Development at the Icahn Institute of Genomics and Multiscale Biology at Mt Sinai in New York. He has the complete arsenal of DNA sequencers in his lab. He specializes in long read applications, and today he goes into several of those spaces, including infectious disease and oncology.

How has sequencing changed since we last had Bobby on a couple years ago, and how does he see it changing in the next two years?

Bobby says the technology hasn't so much changed as the sequencing user has. The user is becoming more savvy, more knowledgeable and familiar with the diversity of options. And the biggest trend has been the uptick in single cell sequencing. Beyond that, Bobby has been surprised that the highest demand for single cell sequencing has been coming from clinicians more than from other scientists.

"I wouldn't have predicted it. The clinical community is excited about seeing it come their way for applications like liquid biopsy and the progressive and prospective surveillance of an individual over time," he says.

Finally, one might think that being located in a city like New York would mean access to the greatest variety and range of data for genomics research. But of course there is better. Bobby and his colleagues have formed a new company they're calling Sema4, to open up the data gates to the rest of the world.

Will This New Nano Technology Be the Microarray of Genomic Structural Variation? Barrett Bready, Nabsys

Barrett Bready is back on the program. He’s the CEO of Nabsys, a company with some new technology for genome mapping.

Originally Nabsys had been working to develop nanopore sequencing, but after a recent reboot has become focused on scaling up scientists' ability to read structural genomic information. Barrett compares Nabsys’ new multiplex technology for genome mapping to the improvement of arrays over single nucleotide (SNP) detection.

"When we first started we were using solid state nanopores. And we realized that there were limitations to nanopores. Nanopores don’t multiplex well. If you have two nanopores very close to each other and a DNA molecule goes through nanopore number one, the signal in nanopore number two will be effected. So we developed our proprietary nano-detector that can be multiplexed at really high density.”

With long read sequencing now gone mainstream coupled with a growing interest among genome scientists in structural variation, Barrett says Nabsys has a chance to enter the marketplace competing on price and throughput and will have their instrument ready for beta testing early next year.

March 2016 with Nathan and Laura: Genomic Jenga and the Creator, the Anti-Abortion Lobby and Genetic Testing, and Theranos, Again

Which company offers the gold standard of sequencing? Nathan starts us out with a metaphor to compare linked reads with real long reads. Then it’s on to this month’s “knockout paper” that moves us yet further from a deterministic view of genetics. Or is this genomic Jenga part of the “proper design of the Creator”? Laura links a new Indiana law banning abortion due to chromosomal abnormalities such as Down Syndrome to a larger effort by the anti-abortion lobby to go after all genetic testing. Theranos plays the Donald Trump of our industry.

It’s the end of March and time to look back with Nathan Pearson of the New York Genome Center and Laura Hercher of Sarah Laurence College.

How Good are Linked Reads? Serge Saxonov, 10X Genomics

When 10X Genomics launched their GemCode sequencing instrument at last year’s AGBT conference, what they offered seemed too good to be true. 10X was promising researchers a machine that could generate long reads using Illumina’s short read technology at a price lower than what PacBio could offer with their “real” long read instruments. A year earlier, Illumina had announced they were buying Moleculo, a company that promised to offer long read data out of the short reads. But good data with the Moleculo platform failed to materialize.

10X Genomics hasn’t had that problem of Moleculo, and was in fact declared the “winner” at AGBT this year when they presented de novo human data.

Today, for the first time, the CEO of 10X, Serge Saxonov, joins us to talk about their technology and the company’s stellar rise.

The question everyone wants answered from Serge is how well the 10X linked reads stand up to so called “real” long reads. PacBio has spent years co-discovering with their customers applications where their long reads provide significant advantage over short reads, at a price. And even though PacBio released a cheaper-faster-better machine, the Sequel, late last year, some researchers have been wondering whether 10X might come through and "clean house" with their inexpensive system?

“Now you can get the information that people were hoping to access in maybe five or ten years--you can get it now. And in fact you don’t need to make a tremendous new investment and change your workflow radically,” says Serge.

While 10X is enabling Illumina customers to generate long reads, are there still limitations of the short read machines that can’t be overcome?

Serge and 10X have already launched a second system, the Chromium, which offers single cell analysis. How big is the single cell market, and what are Serge’s thoughts on the future of sequencing?

A Home Run on the First Hit: PacBio’s Jonas Korlach

Jonas Korlach is a natural storyteller—a rare trait in a scientist who is more comfortable presenting data than talking of himself. Jonas is the co-inventor of PacBio’s SMRT (single molecule, real time) sequencing, and we wanted to hear from him directly how it all got started, and also when the team realized that they had something big with long reads and close to 100X coverage. How many of us can boast of hitting it out of the park on our first try?

Sequencing in Space: Chris Mason, Cornell

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?

The Multi-Platform Approach to Clinical Sequencing with Bobby Sebra, Icahn School

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.

 

Improving the Backbone of Clinical Genomics : Valerie Schneider, NCBI

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 on the Future of Sequencing

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?

Eric Schadt on Long Read Sequencing and Clinical Genomics

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.



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