REVIEWSThe resounding success of the Human Genome Project(HGP) is largely the result of early investments in thedevelopment of cost-effective sequencing methods.Over the course of a decade, through the parallelization,automation and refinement of established sequencingmethods, the HGP motivated a 100-fold reduction insequencing costs, from US $10 per finished base to 10finished bases per US $1 (REF. 1; BOX 1).The relevance andutility of high-throughput sequencing and sequencingcentres in the wake of the HGP has been a subject ofrecent debate. Nonetheless, several academic and com-mercial efforts are developing new ultra-low-costsequencing (ULCS) technologies that aim to reduce thecost of DNA sequencing by several orders of magni-tude2,3.Here, we discuss the motivations for ULCS andreview a sample of the technologies themselves.Until recently, the motivations for pursuing ULCStechnologies have generally been defined in terms of theneeds and goals of the biomedical and bioagriculturalresearch communities. This list is long, diverse andpotentially growing (BOX 2).In more recent years, the pri-mary justification for these efforts has shifted to the ideathat the technology could become so affordable thatsequencing the full genomes of individual patients wouldbe warranted from a health-care perspective4–7.‘Full indi-vidual genotyping’ has great potential to influencehealth care, through its contributions to clinical diag-nostics and prognostics, risk assessment and diseaseprevention. Here, we use the phrase ‘personal genomeproject’ (PGP) to describe this goal. As we contemplatethe routine sequencing of individual human genomes,we must consider the economic, social, legal and ethicalissues that are raised by this technology. What are thepotential health-care benefits? At what cost thresholddoes the PGP become viable? What risks does the PGPpose with respect to issues such as consent, confidential-ity, discrimination and patient psychology? In additionto reviewing technologies, we try to address severalaspects of these questions.Why continue sequencing?As a community, we have already sequenced tens of bil-lions of bases and are putting the finishing touches onthe canonical human genome. Is a new sequencingtechnology necessary? Is there anything interesting leftto sequence?Comparative genomics. Through comparative genomics,we are learning a great deal about our own molecularprogramme, as well as those of other organisms8,9.Atpresent, there are more than 3×1010bases in internationaldatabases10; the genomes of more than 180 organismsADVANCED SEQUENCINGTECHNOLOGIES: METHODS ANDGOALSJay Shendure*, Robi D. Mitra‡, Chris Varma* and George M. Church*Nearly three decades have passed since the invention of electrophoretic methods for DNAsequencing. The exponential growth in the cost-effectiveness of sequencing has been drivenby automation and by numerous creative refinements of Sanger sequencing, rather thanthrough the invention of entirely new methods. Various novel sequencing technologies arebeing developed, each aspiring to reduce costs to the point at which the genomes ofindividual humans could be sequenced as part of routine health care. Here, we review thesetechnologies, and discuss the potential impact of such a ‘personal genome project’ on boththe research community and on society.NATURE REVIEWS | GENETICS VOLUME 5 | MAY 2004 | 335*Harvard Medical School,77 Avenue Louis Pasteur,Boston, Massachusetts02115, USA.‡Deptartment of Genetics,Washington UniversitySchool of Medicine,4566 Scott Avenue,St.Louis, Missouri 63110,USA.Correspondence to G.M.C.e-mail address can be foundon the following web page:http://arep.med.harvard.edu/gmcdoi:10.1038/nrg1325BERMUDA PRINCIPLES A commitment that was made inBermuda (February 1996) by aninternational assortment ofgenome-research sponsors to theprinciples of public sharing andthe rapid release of humangenome sequence information.‘COMMON’SINGLE NUCLEOTIDEPOLYMORPHISMS (SNPs). Those single-nucleotidesubstitutions that occur with anallelic frequency of more than1% in a given population.HAPLOTYPE MAPPING A technique that involves the useof combinations of ‘common’DNA polymorphisms to findblocks of association withphenotypic traits.GENETIC HETEROGENEITY Describes situations in which asimilar phenotype can resultfrom various genetic defects.SYNTHETIC BIOLOGY A discipline that embraces theemerging ability to design,synthesize and evolve newgenomes or biomimetic systems.336 | MAY 2004 | VOLUME 5 www.nature.com/reviews/geneticsREVIEWSmore quickly from a haplotype that is linked to a pheno-type to the causative SNPs. Diseases that are confoundedby GENETIC HETEROGENEITY could be investigated by sequenc-ing specific candidate loci, or whole genomes, across pop-ulations of affected individuals17,18.It is possible that thecost of accurately genotyping tens of thousands of indi-viduals (for example, US $5,000 for 500,000 SNPs19and/or 30,000 genes) will make more sense in the contextof routine health care than as stand-alone epidemiology.Whether it occurs by using SNPs or personal genomes,this project will require high levels of informed consentand security20.Another broad area that ULCS could influence signifi-cantly is cancer biology21,22.The ability to sequence andcompare complete genomes from many normal, neoplas-tic and malignant cells would allow us to exhaustively cat-alogue the molecular pathways and checkpoints that aremutated in cancer. Such a comprehensive approachwould help us to more fully decipher the combinations ofmutations that together give rise to cancer, and wouldtherefore facilitate a deeper understanding of the cellularfunctions that are perturbed during tumorigenesis.ULCS also has the potential to facilitate new researchmodels. Mutagenesis in model and non-model organ-isms would be more powerful if large genomic regions orcomplete genomes across large panels of mutant pedi-grees could be inexpensively sequenced. In studyingacquired immunity, sequencing the rearranged B-celland T-cell receptor loci in a large panel of lymphocytescould become routine, rather than a large undertaking.ULCS would also benefit the emerging fields ofSYNTHETICBIOLOGYand genome engineering, both of which arebecoming powerful tools for perturbing or designinghave been fully sequenced, as well as parts of the genomesof more than 100,000 taxonomic species11,12.It is bothhumbling and amusing to compare these numbers withthe full complexity of the
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