Frontiers of Engineering Reports on Leading-Edge Engineering from the 2010 Symposium (2011) / Chapter Skim
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The Current Status and Future Outlook for Genomic Technologies--Mostafa Ronaghi and Jeffrey Fisher
The Current Status and Future Outlook for Genomic Technologies--Mostafa Ronaghi and Jeffrey Fisher
Pages 129-138
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From page 129... ...
In addition, we discuss emerging applications and challenges to bringing genomics into the mainstream. BACkGROUND On the most fundamental level, sequencing the genome consists of just a handful of basic biochemical steps.
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From page 130... ...
, giving a total throughput per genome of 100 billion base pairs. The processing and reading of these immense amounts of information has been made possible by the adoption of engineering-based approaches to massive parallelization of the sequencing reactions.
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From page 131... ...
Although they are now larger than the initial single strand, the clusters remain immobile and physically separated from each other, making it possible to visually distinguish them during the readout step. The genetic sequence is then transformed into a visual signal by synthesizing a complementary strand, one base at a time, using nucleotides with four separate color tags (Figure 3a)
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From page 132... ...
The segment can then be "flipped over," and another 100 to 150 bases of sequence information can be read from the other end. Thus, the total amount of information that can be garnered from a single flow cell is directly proportional to the number of clusters and the read length per cluster, both of which represent targets for improvement as we continually increase system throughput.
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Cluster density has been increased by improving the optics and the algorithms that detect clusters. Total run time is regularly decreased by using faster chemistries, faster fluidics, faster optical scanning, and faster algorithms for image processing and base calling.
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From page 134... ...
Because there are huge archives of historical samples for which detailed patient outcomes are already known, researchers can use FFPE samples as resources to improve diagnosis by tracking down the genetic markers of disease. In addition, more accurate prognoses and more effective treatments are possible by studying the correlation between disease progression and genetic type in these earlier patients.
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During drug discovery, the pathways elucidated by genomic analysis lead to targeted development and shorter discovery cycles. The approval process will be facilitated by using genetic testing to define the patient populations involved in the testing of new drugs.
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From page 136... ...
To put this in perspective, a single machine can now produce the same amount of data in one week as the Human Genome Project produced in 10 years. Non-technical Challenges Some of the most significant challenges facing mainstream genomics are decidedly non-technical in nature.
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We predict that the cost of sequencing an entire genome will drop to a few hundred dollars in the next few years as throughput rises with increasing density, longer read length, and shorter cycle time. In a year or so, the cost of genome sequencing will be less than the cost of single-gene testing, which by itself has already brought significant cost savings to health care.
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From page 138... ...
benign and cancerous prostate tissues using universal bead arrays. Journal of Clinical Oncology 23(16S)
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