FDA approves 'next gen' DNA sequencers

[deltasigma]

I don’t know that I’m understanding this correctly but this sounds like whole genome sequencing for personalized medicine. Hopefully there will be some splashy news stories on this.

Just for a moment, imagine a scenario in which you have an illness that has eluded diagnosis. The usual suspects have been ruled out and no one knows exactly what’s making you sick.

Using medical devices that FDA has now cleared for marketing, a laboratory could sequence your genome to look for any abnormalities in your genes that could be responsible for your illness. This information would be relayed to your doctor and used to determine the course of treatment.

This is called “next generation sequencing” because it’s another step towards a future in personalized medical care that few of us could have envisioned even a decade ago.

First, let’s define some terms. A genome is the complete set of genetic information in your body. This information is held in sequences of DNA, and gene sequencing from your whole blood allows laboratories to look for genetic variations that could hold the key to the causes of disease and the right treatment.

FDA is clearing the marketing of four gene-sequencing devices. Two of the devices make up the first test system authorized for marketing that allows laboratories to sequence a patient’s genome for any purpose. The software compares the patient’s sequence to a normal human genome sequence used for reference and identifies the differences.

The other two devices are used to detect changes in the CFTR gene, which can result in cystic fibrosis, a disease inherited through a faulty CFTR gene from both parents. More than 10 million Americans are carriers of cystic fibrosis (they have only one faulty copy), and one of these tests could be used to identify men and women with the faulty CFTR gene. The second test looks for other, perhaps unexpected, mutations in the CFTR gene that could be having an impact on the patient’s health

[Smeghead]

These sequencers have been in use for quite a while now - this is just the FDA approving them for certain commercial uses. It’s a regulatory advance more than a technology advance. If you link to the article, I might be able to better figure out what this means.

[deltasigma]

Sorry about that. I haven’t been as focused as usual lately. Long story.

FDA Voices: Perspectives From FDA Leadership and Experts

I imagine these sequencers have been around for a while but if you read this related story, maybe not. Isn’t this MIDAS tech fairly new?

[deltasigma]

Another thing is it looks like these will be use for whole genome sequencing, which I’d thought was still a few years away for medical purposes.

[JWT_Kottekoe]

Sequencing technology has been advancing extremely rapidly in the last decade. A number of systems have been commercialized since about 2005 that are now referred to as “next generation sequencers”. The news is not about a new sequencer, but about the FDA approving certain applications of these sequencers for use in medical diagnostics.

[dasmoocher]

From this link:

The Illumina MiSeqDx instrument platform and Illumina Universal Kit reagents together represent the first FDA-regulated test system that allows laboratories to develop and validate sequencing of any part of a patient’s genome. The kit reagents are used to isolate and copy DNA of interest from patient blood samples which is then sequenced and analysed using the MiSeqDx platform, comparing the genome sequence with a reference sequence and reporting differences between the two.

Review of these devices was via the de novo classification process, used for assessment of novel, low-to-moderate risk medical devices that are not substantially equivalent to an already legally marketed device.

The FDA has also approved two specialised applications that use the MiSeqDx system for cystic fibrosis carrier screening (testing for a panel of known CFTR gene variants) and clinical diagnosis (sequencing a large portion of the CFTR gene for comparison with a reference sequence).

Illumina has other NGS instruments, including the MiSeq, and other companies have their own NGS platforms and chemistry for research use only.

I was curious as to the difference between the MiSeq and the FDA-approved MiSeqDx and found this on their website:

Intended Use

The Illumina MiSeqDx is a sequencing instrument that measures fluorescence signals of labeled nucleotides through the use of instrument-specific reagents and flow cells (MiSeqDx Universal Kit 1.0), imaging hardware, and data analysis software. The MiSeqDx platform is intended for targeted sequencing of human genomic DNA from peripheral whole blood samples. The MiSeqDx platform is not intended for whole-genome or de novo sequencing. The MiSeqDx is intended to be used with Illumina-supplied IVD assays and reagent kits.

My emphasis.

I’ve never used a MiSeq, so I’m wondering if the Dx version is the same instrument just rebranded and that the disclaimer is for FDA approval.

[Smeghead]

I’d suspect the technology is the same, but it’s being very carefully packaged in a way that makes it clear that you’re not supposed to use it for whole genomes. I used to work in a clinical genetics lab, testing human DNA for mutations, and we used kits all the time that said “For research purposes only. Not for clinical use.” In practice, all that meant was that our company was responsible for validating that our tests worked, instead of the company that made the kits.

Regulations are weird.

[lazybratsche]

How can a next-gen sequencer even do anything resembling “targeted sequencing”? Does the software just throw out the non-target sequences? Or are there “nothing to see hear, move along” annotations across 99% of the genome?

[Smeghead]

Proprietary targeted primers, perhaps?

[dasmoocher]

I suspect it’s the same instrument and it’s a branding/regulation thing. It looks like the same instrument in the pictures on their website. I haven’t really taken a deeper look, but why make two MiSeq instruments? I think the MiSeq is the smaller and cheaper version of their HiSeq platform. The MiSeq is advertized as being able to do “small genomes”, probably because the total input to be sequenced is smaller than what the HiSeq can do.

There’s another thread about 23and me and the recent FDA ruling came up (although that’s genotyping by microarray and not NGS). Basically, the FDA told them to stop selling their genome testing service and making health recommendations because the FDA had not approved it for that purpose.

@lazybratsche

How can a next-gen sequencer even do anything resembling “targeted sequencing”? Does the software just throw out the non-target sequences? Or are there “nothing to see hear, move along” annotations across 99% of the genome?

I believe you can target specific regions when the cDNA library that will be sequenced is made. You make the library from your source DNA–adding sequences that can act as PCR primers and barcodes to sheared fragments of the preferential size, basically, and it’s this library DNA that is sequenced.

Using their Nextera Rapid Capture Custom Enrichment Kit, they say you can:

Nextera Rapid Capture Custom Enrichment provides unparalleled access to genomic regions of interest. This custom assay allows researchers to sequence precious samples faster and more efficiently than ever before, using as little as 50 ng of input DNA. The kit offers add-on functionality to refine content over time, or add regions of unique interest to established panels like Nextera Rapid Capture Exome or TruSight content sets. Nextera Rapid Capture Custom Enrichment allows researchers to:

Generate ~0.5 – 15 Mbps of custom content in a single enrichment assay
Evolve a custom assay over time with add-on capability
Design a preferred assay using an intuitive, user-friendly, online tool

Rapidly interrogate key areas of specific research
With Nextera Rapid Capture Custom Enrichment, researchers can rapidly interrogate those portions of the human genome most important to their project. They can densely pack hybridization probes into a region as small as 0.5 Mbps, or space them more liberally to enrich up to 15 Mbps of fully custom content. Nextera Rapid Capture Custom Enrichment offers maximum flexibility to address specific needs.

So, you don’t have to sequence the whole genome, but instead you can look at regions of interest that you “enriched” in making your library:

Researchers can define custom content for this workflow using Nextera Rapid Capture Custom Enrichment. This custom assay allows researchers to rapidly interrogate those portions of the human genome most important to their specific research. Choose from a fully custom design or start from a defined content set, such as Nextera Rapid Capture Exome, and include areas of interest using add-on functionality.

So, for this FDA-approved assay, it looks like you sequence the region containing the CFTR gene.

This make sense for a assay looking for variants in a particular gene. Instead of wasting reagents on the rest of the genome, you sequence the same region many, many times. Errors are made in making the libraries–noise, due to the error rate of the enzymes, and with deeper coverage you can get a stronger signal to address whether that SNP is a mis-incorporation of an nucleotide by the polymerase, or a real variant that shows up multiple times in the exact same spot.

I haven’t done NGS myself, but I image early errors would be more noisy, though.

[deltasigma]

@dasmoocher

This make sense for a assay looking for variants in a particular gene. Instead of wasting reagents on the rest of the genome, you sequence the same region many, many times. Errors are made in making the libraries–noise, due to the error rate of the enzymes, and with deeper coverage you can get a stronger signal to address whether that SNP is a mis-incorporation of an nucleotide by the polymerase, or a real variant that shows up multiple times in the exact same spot.

I haven’t done NGS myself, but I image early errors would be more noisy, though.

I don’t think that’s the only point. The article mentions that the same gene can be expressed differently in different tissues. From my MIDASlink earlier.

The team tested MIDAS on an individual bacterium and showed that it enabled them to read significantly more of the genome sequence than they could when using the single cell sequencing methods currently available. Furthermore, when they used MIDAS to examine the genomes of individual nerve cells from human brains,** they detected significant differences between cells—even between neurons in an individual, healthy brain.** This is consistent with a string of surprising findings that suggests that genomes in our body may vary from cell to cell, because of changes that occur as DNA is copied during cell division.

[dasmoocher]

@deltasigma

I don’t think that’s the only point. The article mentions that the same gene can be expressed differently in different tissues. From my MIDASlink earlier.

Gene expression is something very different than genome sequencing. Of course genes are expressed differently in different tissues–that’s why they are different tissues; the cells that make them up express different genes. And the same gene can certainly show different expression levels in cells within and between tissues. Some gene expression varies by time of day.

Sequencing can potentially tell you why genes are expressed differently–does a tumor suppressor gene promoter have a deletion that makes it disfunctional, or does an expressed protein have a mutation that makes it too active, or has a region of DNA been duplicated and is expressing a gene from multiple copies?

It don’t have access to Nature Biotechnology, and the article came out this month:

Nat Biotechnol. 2013 Nov 10. doi: 10.1038/nbt.2720. [Epub ahead of print]
Massively parallel polymerase cloning and genome sequencing of single cells using nanoliter microwells.
Gole J, Gore A, Richards A, Chiu YJ, Fung HL, Bushman D, Chiang HI, Chun J, Lo YH, Zhang K.
Source

Department of Bioengineering, Institute for Genomic Medicine and Institute of Engineering in Medicine, University of California at San Diego, La Jolla, California, USA.
Abstract

Genome sequencing of single cells has a variety of applications, including characterizing difficult-to-culture microorganisms and identifying somatic mutations in single cells from mammalian tissues. A major hurdle in this process is the bias in amplifying the genetic material from a single cell, a procedure known as polymerase cloning. Here we describe the microwell displacement amplification system (MIDAS), a massively parallel polymerase cloning method in which single cells are randomly distributed into hundreds to thousands of nanoliter wells and their genetic material is simultaneously amplified for shotgun sequencing. MIDAS reduces amplification bias because polymerase cloning occurs in physically separated, nanoliter-scale reactors, facilitating the de novo assembly of near-complete microbial genomes from single Escherichia coli cells. In addition, MIDAS allowed us to detect single-copy number changes in primary human adult neurons at 1- to 2-Mb resolution. MIDAS can potentially further the characterization of genomic diversity in many heterogeneous cell populations.

This is great, but not what the FDA has approved for genetic testing. As they say themselves in the last sentence, it may have potentially further applications.

One application that immediately comes to mind is the genomes of cells in a tumor, which can be notoriously heterogeneous.

[deltasigma]

I do understand the difference between sequencing and expression. Did I say something to make you think otherwise or do you assume everyone who is a layperson is clueless? Just curious? Not to brag but I happen to have 2 advanced degrees they just don’t happen to be in scientific areas (if you’d like to check my profile).

My point was that a particular gene can be implicated in more than one type of disease, can’t it? So let’s say you find disease X correlates with disease Y and they both have a genetic component. You might very well want to do genomic testing on both types of tissue - right? These machines might be very handy for that since there might very well be differences in the genomes of the the two tissues, contrary to what used to be accepted dogma.

[dasmoocher]

@deltasigma

I do understand the difference between sequencing and expression. Did I say something to make you think otherwise or do you assume everyone who is a layperson is clueless? Just curious? Not to brag but I happen to have 2 advanced degrees they just don’t happen to be in scientific areas (if you’d like to check my profile). My point was that a particular gene can be implicated in more than one type of disease, can’t it? So let’s say you find disease X correlates with disease Y and they both have a genetic component. You might very well want to do genomic testing on both types of tissue - right? These machines might be very handy for that since there might very well be differences in the genomes of the the two tissues, contrary to what used to be accepted dogma.

Since you’re “just curious”, I was addressing the technical question of targeting a specific region of the genome for sequencing since it was asked. But in your reply to my comment you said “The article mentions that the same gene can be expressed differently in different tissues.” and then bolded “they detected significant differences between cells—even between neurons in an individual, healthy brain.” in your linked quote.

Those were differences in the sequence they were talking about, not gene expression.

Congratulations on your advanced degrees and insight, but other people reading the thread may not know what the difference between “gene expression” and “genomic sequencing” is.

If your point was hopefully MIDAS or a related protocol will allow FDA-approved NGS sequencing of single cells in the future, I agree that would be great.

But you had to add “or do you assume everyone who is a layperson is clueless?”, didn’t you?

That seems like a clueless assumption and probably explains this Pit thread: obstinate ignorance + obnoxious cockiness = Deltasigma.

[deltasigma]

@dasmoocher

Gene expression is something very different than genome sequencing. Of course genes are expressed differently in different tissues–that’s why they are different tissues; the cells that make them up express different genes. And the same gene can certainly show different expression levels in cells within and between tissues. Some gene expression varies by time of day.

Sequencing can potentially tell you why genes are expressed differently–does a tumor suppressor gene promoter have a deletion that makes it disfunctional, or does an expressed protein have a mutation that makes it too active, or has a region of DNA been duplicated and is expressing a gene from multiple copies?

It don’t have access to Nature Biotechnology, and the article came out this month:

This is great, but not what the FDA has approved for genetic testing. As they say themselves in the last sentence, it may have potentially further applications.

One application that immediately comes to mind is the genomes of cells in a tumor, which can be notoriously heterogeneous.

My quote was NOT about expression since it specifically talks about differences in the GENOMES themselves. Even obnoxious little old me understands that means a difference in the DNA itself - not even epigenetic changes would count there since they are NOT changes to the base pairs, but hey, nice try at saving face.

[dasmoocher]

@deltasigma

My quote was NOT about expression since it specifically talks about differences in the GENOMES themselves.

Originally Posted by deltasigma
I don’t think that’s the only point. The article mentions that the same gene can be expressed differently in different tissues. From my MIDAS link earlier.

So, your quote about “the same gene can be expressed differently” is NOT about expression?

Or, are you saying that to make a point about gene expression, you cited a NIH web article quote that was NOT about expression?

The MIDAS article does NOT mention that genes are expressed differently, which is what you said it did, but that different cells can have different genomes.

but hey, nice try at saving face.

I’m pretty sure that anyone reading this thread would probably not think I’m the one trying to save face.

[deltasigma]

That was a poor choice of words in post 11 - I admit that. But would have thought it subsequently became clear what I meant and despite my improper use of the word ‘expression’ there you would have eventually realized from the context that what I meant was that the actual genomes of different cells were different - you know, since that’s what I kept saying.

I’m not sure why you decided to keep focusing on my original error rather than trying to adapt, but you know what, I don’t especially care .

[deltasigma]

edit: I’d also point out that the article I cited wasn’t talking about expression so maybe that could have been a clue for you too rather simply assuming that I was a moron, but I guess that was just an expression of your obvious bias huh?

[Smeghead]

Firstly, there is a legitimate point in sequencing the CFTR gene. There have been hundreds of documented mutations in the CFTR gene, each of which is enough to contribute toward cystic fibrosis. However, most of these mutations have only ever been seen in a single individual. Most tests these days look for the one or two dozen most common mutations, which covers something like 95% of cases (number pulled out of my rear). However, sequencing allows you to eliminate the possibility of a rare mutation with absolute certainty.

Secondly, gene expression is certainly a very different test from genomic sequencing. Genomic information looks at the sequence of the cells’ DNA. Gene expression testing measures relative levels of specific mRNAs. Extracting RNA from a sample and counting it is a very different process from extracting DNA and reading it. Expression testing lets you see, for instance, that sample X has twice as many CFTR mRNAs per cell than sample Y. That’s informative for some diseases, like cancer, but not really for something like CF.

Edit: You could, also, look at DNA samples for epigenetic marks, which would tell you something about how that gene is being expressed, but I don’t think our understanding of those systems are good enough for this to really tell us anything clinically important at this point.

[dasmoocher]

@deltasigma

edit: I’d also point out that the article I cited wasn’t talking about expression so maybe that could have been a clue for you too rather simply assuming that I was a moron, but I guess that was just an expression of your obvious bias huh?

Whatever. Is your next act going to be telling a statistician what the word “significant” means?