What Would You Do if You Could Sequence Everything?

Overview

Journal Nat Biotechnol

Specialty Biotechnology

Date 2008 Oct 11

PMID 18846086

Citations 82

Authors

Avak Kahvejian

John Quackenbush

John F Thompson

Affiliations

Soon will be listed here.

Abstract

It could be argued that the greatest transformative aspect of the Human Genome Project has been not the sequencing of the genome itself, but the resultant development of new technologies. A host of new approaches has fundamentally changed the way we approach problems in basic and translational research. Now, a new generation of high-throughput sequencing technologies promises to again transform the scientific enterprise, potentially supplanting array-based technologies and opening up many new possibilities. By allowing DNA/RNA to be assayed more rapidly than previously possible, these next-generation platforms promise a deeper understanding of genome regulation and biology. Significantly enhancing sequencing throughput will allow us to follow the evolution of viral and bacterial resistance in real time, to uncover the huge diversity of novel genes that are currently inaccessible, to understand nucleic acid therapeutics, to better integrate biological information for a complete picture of health and disease at a personalized level and to move to advances that we cannot yet imagine.

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References

Redon R, Ishikawa S, Fitch K, Feuk L, Perry G, Andrews T . Global variation in copy number in the human genome. Nature. 2006; 444(7118):444-54. PMC: 2669898. DOI: 10.1038/nature05329. View

Kim T, Ren B . Genome-wide analysis of protein-DNA interactions. Annu Rev Genomics Hum Genet. 2006; 7:81-102. DOI: 10.1146/annurev.genom.7.080505.115634. View

Levy S, Sutton G, Ng P, Feuk L, Halpern A, Walenz B . The diploid genome sequence of an individual human. PLoS Biol. 2007; 5(10):e254. PMC: 1964779. DOI: 10.1371/journal.pbio.0050254. View

Clark A, Eisen M, Smith D, Bergman C, Oliver B, Markow T . Evolution of genes and genomes on the Drosophila phylogeny. Nature. 2007; 450(7167):203-18. DOI: 10.1038/nature06341. View

Wood L, Parsons D, Jones S, Lin J, Sjoblom T, Leary R . The genomic landscapes of human breast and colorectal cancers. Science. 2007; 318(5853):1108-13. DOI: 10.1126/science.1145720. View

Myers A, Gibbs J, Webster J, Rohrer K, Zhao A, Marlowe L . A survey of genetic human cortical gene expression. Nat Genet. 2007; 39(12):1494-9. DOI: 10.1038/ng.2007.16. View

Yasui D, Peddada S, Bieda M, Vallero R, Hogart A, Nagarajan R . Integrated epigenomic analyses of neuronal MeCP2 reveal a role for long-range interaction with active genes. Proc Natl Acad Sci U S A. 2007; 104(49):19416-21. PMC: 2148304. DOI: 10.1073/pnas.0707442104. View

Rauch T, Zhong X, Wu X, Wang M, Kernstine K, Wang Z . High-resolution mapping of DNA hypermethylation and hypomethylation in lung cancer. Proc Natl Acad Sci U S A. 2007; 105(1):252-7. PMC: 2224196. DOI: 10.1073/pnas.0710735105. View

Yu W, Gius D, Onyango P, Muldoon-Jacobs K, Karp J, Feinberg A . Epigenetic silencing of tumour suppressor gene p15 by its antisense RNA. Nature. 2008; 451(7175):202-6. PMC: 2743558. DOI: 10.1038/nature06468. View

10.

Hirst M, Delaney A, Rogers S, Schnerch A, Persaud D, OConnor M . LongSAGE profiling of nine human embryonic stem cell lines. Genome Biol. 2007; 8(6):R113. PMC: 2394759. DOI: 10.1186/gb-2007-8-6-r113. View

11.

Kwan T, Benovoy D, Dias C, Gurd S, Provencher C, Beaulieu P . Genome-wide analysis of transcript isoform variation in humans. Nat Genet. 2008; 40(2):225-31. DOI: 10.1038/ng.2007.57. View

12.

Hillier L, Marth G, Quinlan A, Dooling D, Fewell G, Barnett D . Whole-genome sequencing and variant discovery in C. elegans. Nat Methods. 2008; 5(2):183-8. DOI: 10.1038/nmeth.1179. View

13.

Nardi V, Raz T, Cao X, Wu C, Stone R, Cortes J . Quantitative monitoring by polymerase colony assay of known mutations resistant to ABL kinase inhibitors. Oncogene. 2007; 27(6):775-82. DOI: 10.1038/sj.onc.1210698. View

14.

Huang Q, Gumireddy K, Schrier M, le Sage C, Nagel R, Nair S . The microRNAs miR-373 and miR-520c promote tumour invasion and metastasis. Nat Cell Biol. 2008; 10(2):202-10. DOI: 10.1038/ncb1681. View

15.

Feng H, Shuda M, Chang Y, Moore P . Clonal integration of a polyomavirus in human Merkel cell carcinoma. Science. 2008; 319(5866):1096-100. PMC: 2740911. DOI: 10.1126/science.1152586. View

16.

Broadbent H, Peden J, Lorkowski S, Goel A, Ongen H, Green F . Susceptibility to coronary artery disease and diabetes is encoded by distinct, tightly linked SNPs in the ANRIL locus on chromosome 9p. Hum Mol Genet. 2007; 17(6):806-14. DOI: 10.1093/hmg/ddm352. View

17.

Mardis E . The impact of next-generation sequencing technology on genetics. Trends Genet. 2008; 24(3):133-41. DOI: 10.1016/j.tig.2007.12.007. View

18.

Pop M, Salzberg S . Bioinformatics challenges of new sequencing technology. Trends Genet. 2008; 24(3):142-9. PMC: 2680276. DOI: 10.1016/j.tig.2007.12.006. View

19.

Palacios G, Druce J, Du L, Tran T, Birch C, Briese T . A new arenavirus in a cluster of fatal transplant-associated diseases. N Engl J Med. 2008; 358(10):991-8. DOI: 10.1056/NEJMoa073785. View

20.

Ellegren H, Sheldon B . Genetic basis of fitness differences in natural populations. Nature. 2008; 452(7184):169-75. DOI: 10.1038/nature06737. View