It seems we just can’t get enough of genomics conferences! This week, Sage Science is proud to be a sponsor of the Sequencing, Finishing, and Analysis in the Future conference hosted by Los Alamos National Laboratory (May 28-30). We’ll be heading to Santa Fe to get our fill of great presentations and posters on what happens after the sequencing run: new methods and best practices for data analysis.
The agenda is built around several useful topics, including: genome sequencing and assembly, finishing tools, genome analysis, and clinical applications of next-gen sequencing. This year’s keynote speakers include Rick Wilson, director of the Genome Institute at Washington University; Deanna Church, senior director of genomics and content at Personalis; and Stephan Schuster, research director at the Singapore Centre on Environmental Life Sciences Engineering.
Talks at SFAF will cover a good mix of sequencing platforms and applications, from metagenomics to clinical to forensic. There will also be many posters — judging from the terrific abstracts, we’ll be spending a lot of time at the poster sessions.
So why is a sample prep company interested in a data analysis meeting? As we’ve carved out our niche in the DNA size selection space, we have found that the people who are most insistent about using Pippin tools are actually the bioinformaticians. They routinely see the difference in quality between assemblies generated from libraries with and without automated size selection and have determined that data from Pippin-sized libraries comes together into cleaner, more accurate assemblies. Never doubt that your sample prep choices have a significant downstream impact!
Earlier this week, thousands of microbiologists descended on Boston for the annual meeting of the American Society for Microbiology. The Sage Science team was thrilled to be part of the festivities. Many thanks to all of the scientists who visited our booth to learn more about targeted DNA sizing with Pippin and whole-sample fractionation with our new SageELF.
Genomics has steadily increased its presence at ASM over the years. At this meeting, many of the researchers we spoke with were using next-gen sequencers to learn more about their bugs of interest. We heard from many PacBio users interested in improving their average read lengths with Pippin, and from Illumina users eager to construct libraries with multiple insert sizes to generate a better assembly.
There were some general themes at this year’s ASM, including emerging pathogens, big data, and of course the challenge of studying microbes that can’t be cultured. Experts predicted the next pathogen global threats, and one team noted that microbes can live for a week or longer on surfaces found in any airplane. (We’ll be flying in full hazmat suits from now on, thank you very much.) Scientists including George Church and Joachim Messing spoke about the increasing need to merge massive data sets and study them in combination. And several researchers reported on how the “dark matter” of the microbial world, or the organisms that are uncultivable, appear to be impacted by climate change and other stressors. We also heard about the world’s first stool bank designed for fecal transplants, and learned that urine is not bacteria-free, as we always thought it was.
And now it’s back to our regular jobs. It was great to hang out with the microbiology crowd — we’re already looking forward to ASM 2015!
Scientists from the Mayo Clinic, Institute for Systems Biology, and University of Illinois recently published a study investigating the effects of vitamin D on microRNA regulation of gene expression in zebrafish. The team used our Pippin Prep together with the NEBNext Multiplex Small RNA Kit from New England Biolabs to enrich their samples for miRNAs.
Lead authors Theodore Craig and Yuji Zhang performed RNA-seq with Illumina to look across the zebrafish transcriptome at which genes’ activity are changed by vitamin D. They found that by the seventh day of development, the zebrafish larvae have 2,500 protein-coding genes that are up- or down-regulated by vitamin D. The authors looked closely at the miRNAs involved in this process, finding that both known and novel miRNAs play a role. “The differentially expressed miRNAs are predicted to potentially alter mRNAs for metabolic enzymes, transcription factors, growth factors, and Jak-STAT signaling,” the authors write.
The scientists hypothesize that the higher number of miRNAs involved by day 7 of development is probably “due to the increased complexity of organs and the need for fine tuning of mRNA expression.”
You can view the paper, “Detection of 1,25-Dihydroxyvitamin D-Regulated miRNAs in Zebrafish by Whole Transcriptome Sequencing,” in the journal Zebrafish.
To learn more about the use of Pippin size selection to enrich miRNA selection with the NEBNext Multiplex Small RNA Kit, check out this app note.
Several diseases, many of them involving neurological symptoms, have been linked to expansions of trinucleotide repeat sequences. These repeat expansion disorders include Fragile X syndrome, Huntington’s disease, and various forms of epilepsy and ataxia. In Fragile X, for example, a CGG pattern in the FMR1 gene is associated with the disease: people with 45 CGG copies or fewer are unaffected, while people with more than 200 copies have the syndrome.
This was the foundation for a fascinating project by researchers in France who used a transcription activator-like effector nuclease (TALEN) to target a CAG/CTG repeat in yeast cells, introducing a double-strand break at that location. By doing so, the repeat was deleted; multiple rounds of the TALEN genome editing activity led to repeat tracts with far fewer copies of the trinucleotides. Had these been human cells, the reduction in repeat size would have been enough to shorten a pathogenic region into a harmless region.
“Highly Specific Contractions of a Single CAG/CTG Trinucleotide Repeat by TALEN in Yeast,” published in PLoS One (Guy-Franck Richard et al.), details the promising results of using a TALEN for this type of work. It offers the first evidence that a TALEN can shrink a repeat expansion region, which could prove quite promising for biomedical researchers aiming to help people with repeat expansion disorders.
We were glad to see that the scientists used Pippin Prep for their size selection prior to sequencing on the Illumina platform. It’s an honor to be part of such a great effort!
Here at Sage Science headquarters, we’ll be spending April 25th celebrating DNA Day. If you’re not familiar, the day honors double milestones of the original publication of the structure of DNA in 1953 as well as the ceremonial completion of the Human Genome Project fifty years later.
Of course, thinking about DNA is nothing new for our team. After all, it takes a special kind of person to join a company like Sage, where success is measured by how well we can practice the art of sample prep. From our scientists to our sales representatives, we are constantly sharing ideas and feedback on ways to ensure that the highest-quality DNA is moved from sample to sequencer.
We’d love to take our technology back in time to Francis Crick and the rest of the lab in 1953 and see that extraordinary team react to what we take for granted today: completely automated, highly reproducible tools for selecting the exact DNA needed for study. Of course, their reliance on what we consider rudimentary tools to determine the structure of DNA makes the finding even more remarkable.
This year, perhaps DNA Day is a good time to consider what’s most needed in the life sciences field. Perhaps it’s sample prep standards as we move toward routine use of genomics in the clinic, or maybe it’s better legislation to improve on the nondiscrimination efforts of GINA. Feel free to share your own ideas below, and enjoy DNA Day