Versatility of 454 Sequencing™ Demonstrated in Three Publications in Science this Week
Variety of new applications spans paleogenomics, paired-end mapping, and gene expression analysis
The three publications span a number of research fields, genomic applications, and even 454 Sequencing protocols. The diversity of the publications illustrate the flexibility of 454 Sequencing and its ability to deliver scientifically relevant results in any research field employing DNA sequencing. The studies relied on long, highly accurate reads and long paired reads exclusive to 454 Sequencing.
Previous studies of human genomic variation tended to look at changes called single nucleotide polymorphism (SNP), variations that involve just one nucleotide. However, the study, "Paired-End Mapping Reveals Extensive Genomic Structural Variation in Humans," published today suggests that structural variation is responsible for a larger number of differences between the genomes of two individuals than SNPs. Furthermore, structural variation may have notable physical effects on an individual. The role that SV plays in human variability has not been well understood because of imprecise technology used in previous research. The novel approach described today in Science, called Paired End Mapping (PEM), used 454 Sequencing to comprehensively study SV at an unmatched level of resolution, detecting most of the structural variation in the human genome.
The presence of worker wasps that forgo reproduction and care for their siblings is a defining feature of eusociality and a major challenge for evolutionary theory. In the study, "Wasp Brain Gene Expression Supports an Evolutionary Link between Maternal Behavior and Eusociality," researchers used 454 Sequencing to examine messenger RNA from the brains of wasps and correlate different expression patterns to different social behaviors. Insulin-related genes were among those genes showing a distinct pattern, suggesting that the evolution of eusociality involved major nutritional and reproductive pathways.
The study entitled "Whole-Genome Shotgun Sequencing of Mitochondria from Ancient Hair Shafts" combines a novel approach of preparing ancient DNA with 454 Sequencing to quickly and affordably sequencing the complete mitochondria from 10 individual mammoths. To put this new study in perspective, only seven mitochondrial genomes from extinct animals had been previously published, four from ancient birds, two mammoths and one of the mastodon, a distant relative of mammoths. The method for obtaining ancient DNA, as described in today’s paper, uses hair shafts and not live cells. Hair from many extinct species is available in museum collections around the world. The new protocol, along with 454 Seqeuncing, opens the door to sequence many ancient species.
"Three diverse publications appearing in Science the same week and utilizing 454 Sequencing is a testament to the system’s flexibility and applicability to life science research," explained Michael Egholm, Ph.D., co-author of two studies and vice president of research and development at 454 Life Sciences. "Researchers were able to sequence ancient and degraded DNA, obtain a paired-end map of structural variation throughput the human genome at unprecedented resolution, and analyze the role of gene expression in the evolution of eusociality. All of this in one week in Science is outstanding."
454 Life Sciences develops and commercializes novel instrumentation for high-throughput DNA sequencing. Specific applications include whole-genome sequencing, RNA analysis and ultra-deep sequencing of target genes. The hallmarks of 454 Sequencing™ are its simple, unbiased sample preparation and massively parallel sequencing, which makes large-scale scientific projects feasible and more affordable. During the last months, the technology proved its suitability in a lot of application examples, in cancer research, infectious diseases research, drug discovery, marine biology, anthropology, paleontology, and many more.