Human Genome Sequencing Using Unchained Base Reads on Self-Assembling DNA Nanoarrays

• Published in: Science (American Association for the Advancement of Science) Vol. 327; no. 5961; pp. 78 - 81
• Main Authors: Drmanac, Radoje, Sparks, Andrew B., Callow, Matthew J., Halpern, Aaron L., Burns, Norman L., Kermani, Bahram G., Carnevali, Paolo, Nazarenko, Igor, Nilsen, Geoffrey B., Yeung, George, Dahl, Fredrik, Fernandez, Andres, Staker, Bryan, Pant, Krishna P., Baccash, Jonathan, Borcherding, Adam P., Brownley, Anushka, Cedeno, Ryan, Chen, Linsu, Chernikoff, Dan, Cheung, Alex, Chirita, Razvan, Curson, Benjamin, Ebert, Jessica C., Hacker, Coleen R., Hartlage, Robert, Häuser, Brian, Huang, Steve, Jiang, Yuan, Karpinchyk, Vitali, Koenig, Mark, Kong, Calvin, Landers, Tom, Le, Catherine, Liu, Jia, McBride, Celeste E., Morenzoni, Matt, Morey, Robert E., Mutch, Karl, Perazich, Helena, Perry, Kimberly, Peters, Brock A., Peterson, Joe, Pethiyagoda, Charit L., Pothuraju, Kaliprasad, Richter, Claudia, Rosenbaum, Abraham M., Roy, Shaunak, Shafto, Jay, Sharanhovich, Uladzislau, Shannon, Karen W., Sheppy, Conrad G., Sun, Michel, Thakuria, Joseph V., Tran, Anne, Vu, Dylan, Zaranek, Alexander Wait, Wu, Xiaodi, Drmanac, Snezana, Oliphant, Arnold R., Banyai, William C., Martin, Bruce, Ballinger, Dennis G., Church, George M., Reid, Clifford A.
• Format: Journal Article
• Language: English
• Published: Washington, DC American Association for the Advancement of Science 01.01.2010; The American Association for the Advancement of Science
• Subjects: Base Sequence; Biological and medical sciences; Computational Biology; Costs and Cost Analysis; Databases, Nucleic Acid; Deoxyribonucleic acid; Diverse techniques; DNA; DNA - chemistry; DNA - genetics; Fundamental and applied biological sciences. Psychology; Genome, Human; Genomes; Genomic Library; Genomics; Genotype; Genotypes; Haplotypes; Human genetics; Human genome; Human Genome Project; Humans; Ligation; Male; Medical genetics; Microarray Analysis; Molecular and cellular biology; Nanostructures; Nanotechnology; Nucleic Acid Amplification Techniques; Polymerase chain reaction; Polymorphism, Single Nucleotide; Scientific method; Sequence Analysis, DNA - economics; Sequence Analysis, DNA - instrumentation; Sequence Analysis, DNA - methods; Sequence Analysis, DNA - standards; Sequencing; Software; Human; Self assembly; Method; Genome; Sequencing; DNA
• ISSN: 0036-8075; 1095-9203
• DOI: 10.1126/science.1181498

Genome sequencing of large numbers of individuals promises to advance the understanding, treatment, and prevention of human diseases, among other applications. We describe a genome sequencing platform that achieves efficient imaging and low reagent consumption with combinatorial probe anchor ligation chemistry to independently assay each base from patterned nanoarrays of self-assembling DNA nanoballs. We sequenced three human genomes with this platform, generating an average of 45-to 87-fold coverage per genome and identifying 3.2 to 4.5 million sequence variants per genome. Validation of one genome data set demonstrates a sequence accuracy of about 1 false variant per 100 kilobases. The high accuracy, affordable cost of $4400 for sequencing consumables, and scalability of this platform enable complete human genome sequencing for the detection of rare variants in large-scale genetic studies.