Over the past decade, rapid advancements in next-generation sequencing products have enabled research scientists to design experiments and produce results that were previously out of reachopening up the field of genomics to greater possibilities for breakthroughs, both big and small.

In the past year, many scientists have published their findings demonstrating these possibilities. To celebrate these scientific breakthroughs, we have awarded Ms. Anna Cubula from Center for Biotechnology and Genomic Medicine, Georgia Regents University with the Ion Torrent™ Breakthrough Award, 2013. Ms. Cubula is the nominated author for the publication “Thymus-derived regulatory T cells contribute to tolerance to commensal microbiota,” published in the May 2013 edition of Nature.

The finalists for the Ion Torrent™ Breakthrough Award were selected by a panel of Ion Torrent™ team members with experience in next-generation sequencing technology applications. The finalists were evaluated by a panel including Ion Torrent™ team members and two external judges, Prof. Leonid L. Moroz, Ph.D. and Mr. Joseph Boland, M.S., and the winner was announced at Ion World 2013. A nominated author from the winning publication will awarded with trophy and a cash prize.

 

The finalists were:

Cebula A, Seweryn M, Rempala GA, et al. (2013)

Thymus-derived regulatory T cells contribute to tolerance to commensal microbiota. Nature 497:258–262.

Research using semiconductor sequencing helped elucidate how immune tolerance of commensal microbes and autoimmune diseases such as colitis are regulated by a poorly defined population of peripheral T cells called intestinal regulatory T cells (Treg). Using the Ion PGM™ System, sequencing of the T cell receptor (TCR) demonstrated in peripheral tissues, such as the lymphoid organs, intestine, and colon, that thymus-derived Treg cells are predominant. In contrast to previous studies suggesting induced Treg cells control the immune tolerance to intestinal antigens, this paper provides new insight into thymic Treg control of intestinal inflammation and tolerance of antigens produced by intestinal commensal bacteria.

 

Stolle E and Moritz RFA (2013)

RESTseq–efficient benchtop population genomics with RESTriction fragment sequencing. PLoS ONE 8(5):e63960.

Genotyping by sequencing (GBS) is a rapidly expanding NGS method that can be applied to a diversity of research fields such as ecology, agricultural breeding and selection, and other efforts to understand genotype-phenotype relationships. GBS can be used to perform large population-based studies and is useful for analyzing complex genomes or for investigations involving species that lack a reference genome. In this paper, the Ion PGM™ System was used as part of a novel method called restriction fragment sequencing (RESTseq). RESTseq is a reduced complexity sequencing method that can be applied to a wide range of studies that involve SNP detection or SNP genotyping; this includes fine-scale linkage mapping and population genetics/genomics in non-model organisms. To illustrate, the paper compares two honeybee and several stingless bee samples.

 

Kimoto M, Yamashige R, Matsunaga Ki, et al. (2013)

Generation of high-affinity DNA aptamers using an expanded genetic alphabet. Nat Biotech 31:453–457.

DNA aptmers are nucleic acids used to target proteins and cells with potential uses as diagnostic and therapeutic agents. Typically the refinement of DNA aptmer targeting occurs through iterative rounds of in vitro selection and amplification (systematic evolution of ligands by exponential enrichment (SELEX)). In this paper the authors use unnatural bases, Ds, along with natural nucleotides to improve the affinity and selectivity of DNA aptmers against two human target proteins: vascular endothelial growth factor-165 (VEGF-165) and interferon-γ (IFN-γ). Following seven rounds of selection using barcoded samples, the enriched DNA library was PCR-amplified in the presence of the natural dNTPs and a substrate was used to replace the Ds bases in the DNA fragments with the natural bases (mainly A or T). All amplified DNA fragments were sequenced with the Ion PGM™ System to determine the barcode recognition tag and the position of Ds in the sequence followed by subsequent selection to obtain the best aptamers.

 

Nikiforova MN, Wald AI, Roy S, et al. (2013)

Targeted next-generation sequencing panel (ThyroSeq) for detection of mutations in thyroid cancer. J Clin Endocrinol Metab. Published online before print August 26, 2013.

Thyroid cancer usually develops from thyroid nodules, and accurate discrimination between malignant and benign nodules is of strong scientific importance. Cytological examination of nodule samples obtained using fine-needle aspiration (FNA) is the standard used to assess nonmalignant status. However, in ~25% of nodules, cytological examination is not definitive, with improved classification possible via molecular methods. To this end, a research study was developed using an Ion AmpiSeq™ Custom Panel (ThyroSeq) which was designed to target 12 cancer genes with 284 mutational hotspots with sequencing performed using the Ion PGM™ System. The authors found 100% analytical accuracy for mutation detection with 3–5% sensitivity for the mutant allele. Importantly for FNA samples, the panel required an input of only 5-10 ng of DNA for successful analysis of 99.6% of samples (n=229).

 

Hall-Mendelin S, Allcock R, Kresoje N, et al. (2013)

Detection of arboviruses and other micro-organisms in experimentally infected mosquitoes using massively parallel sequencing. PLoS ONE 8(2):e58026.

As the vector for dengue (DENV), yellow fever (YFV) and chikungunya (CHIKV) viruses, control of the mosquito, Aedes aegypti, is an important public health objective. A novel approach to controlling A. aegypti involved the release in northern Queensland, Australia of an experimentally-generated mosquito line carrying a bacterium (Wolbachia spp.) that significantly reduces the replication of DENV, CHIKV, and YFV. To monitor the mosquito populations and perform viral surveillance, a shotgun sequencing approach was developed using the Ion PGM™ System. Using experimentally-infected mosquitos, the method described in this paper generated near full-length viral genome assemblies, facilitated detection of other microorganisms, and proved potentially applicable for post-release monitoring of Wolbachia in mosquito populations.


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