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Update from the NCMNS Genomics & Microbiology Lab: Meet Our New Little Friend, The MiSeq

January 2, 2015

This post is brought to you by Dr. Julie Urban, Assistant Director of the Museum’s Genomics and Microbiology Research Lab.

As a child, did you ever feel the overwhelming excitement portrayed by Ralphie, the character in the MGM movie A Christmas Story, obsessed with hopes of finding “an official Red Ryder, carbine action, two-hundred shot range model air rifle” under his tree? Many of us only experienced that kind of “I-can’t-sit-still” level of exhilaration as a kid, but not us scientists in the Genomics & Micro (G&M) Lab! We felt this level of gut-busting thrill just recently: Santa brought our lab a MiSeq:

The MiSeq DNA sequencing machine

Except it wasn’t Santa, it was National Science Foundation (NSF). And it wasn’t for Christmas, we got it back in October. But the same gut-busting thrill, nonetheless. What is this MiSeq? Why has it gotten us so excited? What does this mean for our research, specifically our citizen science research? And (as Ralphie had been repeatedly warned) should we be worried that we will shoot our eye out? Each of these, in turn.

The MiSeq, manufactured by Illumina, is a machine that sequences massive amounts of DNA. Several of us NCMNS scientists, led by G&M Director, Julie Horvath, submitted a grant proposal to NSF’s Major Research Instrumentation division requesting this instrument. After multiple submissions, our proposal was accepted this fall and, with the support of NCMNS and DENR administration, our lab was able to purchase the MiSeq.

Dr. Urban with the MiSeqThe MiSeq is a so-called “next-next generation” DNA sequencer. How this technology works is a cool story in itself (and will likely be the topic of a future blog post), the critical point is that this instrument allows us to generate millions of DNA sequences in one run, which means that we not only get more data cheaper and faster than before, but because of the way this machine works, it fundamentally changes (and vastly expands) the nature of the research questions we can use it to ask and to answer.

To put the cost savings into context, we also have a more traditional “first-generation” or Sanger sequencer in our lab. Sanger sequencing was the technology used to first sequence the human genome. Generating a DNA sequence using Sanger technology costs approximately $5 a sequence in our lab (we can generate up to 16 DNA sequences at a time; larger instruments can generate 96 sequences at a time for about the same price). For small projects (e.g., those requiring fewer than 200 DNA sequences) like those performed by many museum researchers and graduate students with minimal funding, Sanger sequencing remains the most cost-effective approach and this technology has not yet been replaced.

For projects that require sequencing of more DNA, two levels of technological advancement have driven the price down considerably. The first wave of advanced DNA sequencing, aka “next-generation” or pyrosequencing, is able to sequence ~500,000 sequences in one run, at the cost of <$0.01 per sequence. Because you still need to purchase a complete run, this ends up costing around $4000/run.

Loading samples into the MiSeqThe MiSeq uses second or “next-next-generation” sequencing, and generates 25,000,000 sequences in one run, at the cost of <$0.0001 per sequence. Therefore compared to the previous generation of sequencing, we can generate 50 times the number of DNA sequence data for one-half to one-third of the cost!! This is truly an amazing leap in technology, and it has all occurred within about the last 7 years. Larger next-next-generation machines using the similar technology as our MiSeq are able to deliver a sequenced human genome for ~$1,000.

Why would we need to generate so much data? Many research projects, including several in our lab, sequence DNA from microbes (primarily bacteria and fungi) to identify the number and identity of the immense variety of microbes living in various places. This is only now possible with this new technology. One of our lab projects used next-generation sequencing to determine what bacteria live in the armpits of citizen scientists, and to determine how underarm product use alters these communities. Another citizen science project, lead by postdoctoral scientist Dr. Julia Stevens, is part of the Students Discover collaboration with middle school teacher-scientists. It uses the MiSeq to identify the bacterial and fungal symbionts of the common dandelion using soils sampled by students throughout the state. In the first 44 samples she sequenced from the first cohort of Students Discover Kenan Fellows, she found over 1.1 million species of bacteria alone! Another Students Discover postdoc, Dr. Dan Fergus, used our MiSeq to sequence and identify the genes that are actively being used or “turned-on” in the genome (called the “transcriptome”) of the human face mite. This transcriptome will be used in several projects, including perhaps how the set of active genes may differ among healthy versus rosacea-suffering individuals. We have many, many more projects underway, including some of my own work on planthopper-associated bacteria and fungi and additional citizen science projects we hope you will participate in with us!

Dr. Fergus loads the MiSeqFinally, have we shot our eye out yet? It certainly felt like it in preparing my first planthopper run on the MiSeq, as this required multiple 11+ hour days at the lab bench, fueled mostly by coffee and atomic fireball candies. But given the completely novel insights that these data hold, using our MiSeq gives me that “I-can’t-sit-still” anticipation of discovery that to me, is what being a scientist is all about.

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