The rapid advances in DNA sequencing technology are beginning to affect how human diseases are diagnosed, and will soon affect significant numbers of people in the developed world. Because this technology will fundamentally alter many fields of biological research, students even in freshman biology courses should become aware of the technology and its potential impact. I think stories of children with mystery diseases, who are diagnosed by genome sequencing and successfully treated as a result, will make a compelling learning experience and lead students to questions that address most aspects of genomics appropriate for a college-level introductory biology course.
Isn’t sequencing a human genome prohibitively expensive and time consuming?
The graph below from the National Human Genome Research Institute shows that the cost of DNA sequencing has plummeted in recent years. The $1,000 human genome sequence is within sight.
The rapid decline in cost of sequencing resulted from the advent of next-generation sequencing platforms such as Roche 454 (a YouTube playlist for a number of different sequencing technologies: (http://www.youtube.com/view_play_list?p=1B2FEA81FFAD1748). The development of massively parallel high-throughput sequencing technologies, coupled with single-molecule sequencing (the so-called third generation), in a highly competitive marketplace, continues to lower the cost of obtaining a whole human genome sequence. Illumina announced in a June 8, 2011 press release a huge price drop for a human whole genome sequence, from $19,500 to $9,500 (Illumina 6/08/2011), along with release of a personal genome browser app for the iPad. In 2014, Illumina claimed that Hi-SeqX Ten lowers the cost to $1,000 per genome.
What does this mean for ordinary people? It means that the era of personalized genomic medicine has arrived. Instead of individual genetic tests, it will become cost-effective for each person to have his or her own genome sequence. Here is a series of excellent articles in the Milwaukee Journal Sentinel about the first published use of genome sequencing to diagnose and identify a cure for a boy, Nicholas Volker, suffering from a previously unknown disease:
In this case, rather than sequencing the entire genome, the researchers sequenced the boy’s exome, the 2% of the genome that encodes proteins. Their paper was published in March 2011 in Genetics in Medicine (http://dx.doi.org/10.1097/GIM.0b013e3182088158) – a proof is freely downloadable here with an accompanying commentary.
So what do you get when your DNA is sequenced?
Too much information? A bunch of As, Gs, Cs and Ts, in strings of 100-200 letters. Your DNA sample is shredded and random fragments are sequenced. To get 99% of the target DNA sequenced at least once, the researchers sequenced Nic’s exome to an average of 34-fold. Individual sequence strings are matched against the human reference genome and differences noted. For Nic Volker’s exome, Worthey et al. found more than 16,000 differences from the reference human sequence. Which of these, if any, is causing the boy’s disease? The paper by Worthey et al. describes the process of sifting through the chaff to identify candidate gene mutations.
Question #1 for student discussion: given this long list of differences from the reference sequence, how can we identify the most likely candidate mutations? What criteria should be used to eliminate or include mutations?
DNA sequencing gives you hypotheses, not necessarily answers.
Question #2 for student discussion: In what way, or under what circumstances, would exome sequencing fail to discover the cause of a rare disease?
See story by Ed Yong: “Under 3 layers of junk, the secret to a rare brain disease” (Update 7/17/12) and this excellent summary of how exome sequencing analyses can miss the cause of even a Mendelian disease: http://massgenomics.org/2012/07/6-causes-of-elusive-mendelian-disease-genes.html Really, the decision to sequence his exome was a gamble born of desperation.
Question #3 for student discussion: What are possible ethical, legal and social considerations for human genome sequencing?
Genome sequencing has collateral consequences, in the form of answers to questions not asked, and possibly not wanted. (Update 8/25/2012: NY Times piece on the ethical quandaries encountered when sequencing human gneomes: http://www.nytimes.com/2012/08/26/health/research/with-rise-of-gene-sequencing-ethical-puzzles.html)
Added April 2015: I’ve created a case with discussion/clicker questions on the Nic Volker story. Click the title below to download the ppt slides (updated July 2015):
Student Inquiry Activity: NCBI Tutorial/Practical on human genetic variation and disease using hemochromatosis and sickle cell ftp://ftp.ncbi.nlm.nih.gov/pub/FieldGuide/FGPlus/NLMDecember2007/DiseaseGenes/disease_fgplusnlm_HO_2007.pdf
A highly reduced subset of actual patient sequence data would be ideal, but this tutorial goes through all the steps, from BLAST, to identification of the gene, dbSNP, OMIM, and visualizing the altered amino acid on the 3-D structure of the protein in Cn3D. Update 11/16/2011: Although most individual human genome sequences on NCBI require authorization to access, human cell line DNA sequences are available. One example of 454 exome sequencing of human cell lines is this project on the NCBI trace archive: http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?study=ERP000265 (end update 11/16/2011)
Additional stories about Nicholas Volker: http://blogs.forbes.com/matthewherper/2011/03/02/sequencing-a-childs-dna-and-convincing-an-insurance-company-to-pay/ http://www.technologyreview.com/biomedicine/35068/?a=f
A new story about pinpointing the cause of a rare genetic disorder in a Utah family by exome sequencing: http://www.nature.com/news/2011/110623/full/news.2011.382.html
Emory U. researchers use exome sequencing to identify cause of glycosylation defect: http://www.sciencedaily.com/releases/2012/02/120203182621.htm
Ed Yong’s blog post about discovering a mutation associated with a rare, fatal neural disorder; the mutation is located within a transposable element nested inside another transposable element located within an intron: http://blogs.discovermagazine.com/notrocketscience/2012/03/12/under-three-layers-of-junk-the-secret-to-a-fatal-brain-disease/
A news story about the impact of 23andMe SNP genotyping for consumers: http://roswell.patch.com/articles/at-home-dna-test-changes-roswell-womans-life
NIH launches a new genetic testing registry, with information about over 2,500 genetic tests: story on Genome Web: NIH launches genetic testing registry
Blog post by Daniel MacArthur on new NCBI browser for GWAS studies. http://www.wired.com/wiredscience/2011/02/the-disease-ridden-genome/
NCBI’s genome-wide association studies browser: http://www.ncbi.nlm.nih.gov/projects/gapplusprev/sgap_plus.htm
(Update 7/17/12) My blog post about my own exome sequence: https://jchoigt.wordpress.com/2012/07/02/a-first-look-at-my-exome-variants-from-23andme/
(Update 11/20/12) A new video about genome sequencing for lay audiences:
And of course, genetics is NOT fate: http://www.genomesunzipped.org/2012/04/identical-twins-usually-do-not-die-from-the-same-thing.php