Next-generation sequencing (NGS), also known as massively parallel sequencing, is revolutionizing genomic research. NGS technologies have made whole genome sequencing fast and easy, leading to dramatic advances in evolutionary biology and phylogenetics, personalized medicine and forensic science. Why is NGS such a hot topic right now?
While there are more than a dozen next-generation sequencing platforms, they all have the same goal: inexpensive high-throughput sequencing. With these new technologies, DNA sequencing costs are lower than ever. In September of 2001, the National Human Genome Research Institute Genome Sequencing Program estimated the cost to sequence 1Mbases of DNA at $5292.39; by April of 2014, that cost had dropped to $0.0547. While costs dropped, throughput soared. Today, NGS instruments can generate gigabases (Gb) of sequence in a single day, and they do so in small increments—read lengths are less than 200bp. For example, the Illumina HiSeq® 2500 System can sequence ~100Gb in 40 hours, with a read length of 100–150bp. That level of throughput is critical when you think about the size of some of the genomes being sequenced. The human genome is 3 × 109 base pairs in length. If you printed the human genome at 5,000 bases per printed page, that translates to 600,000 pages or 120 boxes of paper (at 5,000 pages per box). Factor in the fact that the target DNA must be sequenced at least 6 times (sixfold coverage) to ensure accuracy, sequencing the human genome is the equivalent of shredding 720 boxes of printed pages, then reassembling them to form the original sequence. Wow!
OK. NGS is powerful. What are scientists doing with that string of nucleotides? If we know how to interpret that string of letters (and that can be a big if), a genome sequence is the key to understanding physiology and evolutionary history at the species level. When taken to the individual level, genome sequencing can uncover genetic differences that influence phenotype, behavior, health and other important aspects of an individual. In humans, next-generation sequencing is making whole genome sequencing a viable option to open up whole new avenues of investigation. Two of the most promising are personalized medicine and forensic science.
I have already discussed the use of whole genome sequencing in personalized medicine when I wrote about a keynote speech that Kevin Davies gave at the 24th International Symposium on Human Identification in 2013. See Learning About the $1,000 Genome . In that blog post, I gave two examples of young children who underwent whole genome sequencing to identify the cause of significant medical problems. One child was successfully diagnosed and treated for autoimmune disease that resulted from a cysteine to tyrosine mutation at position 203 of the XIAP gene, and the other child was diagnosed with a mutation in the titin gene, which encodes a ~3,700kDa protein important for muscle contraction. DNA sequencing also has the potential to assess genetic predisposition to diseases such as cancer.
Another big upcoming application for next-generation sequencing is forensic science. NGS can be used to sequence the genome of pathogenic agents that might be used as biological weapons, such as Bacillus anthracis (anthrax), and help track the origin of the material. This has created a whole new forensic disclipline: microbial forensics . In addition to microbial identification, NGS can be applied to human identification. Currently, forensic science uses short tandem repeat (STR) regions, and to lesser extent single-nucleotide polymorphisms (SNPs), within DNA to try to identify people who may have been involved in a crime. STRs and SNPs are powerful approaches to discriminate between individuals based on their DNA, so the use of NGS to perform whole genome sequencing and increase the power of discrimination is not a big advantage in many cases. However, complicated cases would benefit greatly from NGS; this includes cases involving DNA mixtures, which are notoriously difficult to interpret, or familial searching, where analysts are looking for genetic near matches in a database to help identify the perpetrator based on a familial relationship. Finally, NGS would be a boon for forensic phenotyping, a fairly new and controversial forensic field where SNPs are analyzed to gain information about the physical description of an alleged criminal or his ancestry or biogeographical origins. An individual’s whole genome sequence would provide us with much more information that an arsenal of SNPs. There has been much excitement in the forensic community about adding next-generation sequencing to the forensic analyst’s toolbox for solving crimes.
Considering the volumes of information that can be obtained from a single NGS run, I think it is safe to say that a lot of people are excited about the potential of NGS. As the price continues to drop, I expect to see whole genome sequencing become commonplace, not only in laboratories—medical, criminal or otherwise—but also in people’s everyday lives. Already, there are commercial companies that are advertising genome sequencing and analysis for an array of reasons such as genealogical investigations and ancestry determination. In the future, individuals may decide to use information generated through NGS to assess medical risks. Of course, there are all sort of ethical considerations that surround the power of NGS, begging the question “Yes we can, but should we?” Because this is a short blog entry and not a book, I won’t start an ethical debate here. Just remember: With power comes responsibility.