{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,9]],"date-time":"2026-03-09T01:57:24Z","timestamp":1773021444844,"version":"3.50.1"},"reference-count":156,"publisher":"Springer Science and Business Media LLC","issue":"8","license":[{"start":{"date-parts":[[2006,8,1]],"date-time":"2006-08-01T00:00:00Z","timestamp":1154390400000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Nat Rev Genet"],"published-print":{"date-parts":[[2006,8]]},"DOI":"10.1038\/nrg1901","type":"journal-article","created":{"date-parts":[[2006,7,18]],"date-time":"2006-07-18T10:03:02Z","timestamp":1153216982000},"page":"632-644","source":"Crossref","is-referenced-by-count":303,"title":["Highly parallel genomic assays"],"prefix":"10.1038","volume":"7","author":[{"given":"Jian-Bing","family":"Fan","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mark S.","family":"Chee","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kevin L.","family":"Gunderson","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","reference":[{"key":"BFnrg1901_CR1","doi-asserted-by":"publisher","first-page":"531","DOI":"10.1126\/science.286.5439.531","volume":"286","author":"TR Golub","year":"1999","unstructured":"Golub, T. R. et al. Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science 286, 531\u2013537 (1999). This paper demonstrates the utility and power of whole-genome gene-expression profiling for cancer classification.","journal-title":"Science"},{"key":"BFnrg1901_CR2","doi-asserted-by":"publisher","first-page":"530","DOI":"10.1038\/415530a","volume":"415","author":"LJ van't Veer","year":"2002","unstructured":"van't Veer, L. J. et al. Gene expression profiling predicts clinical outcome of breast cancer. Nature 415, 530\u2013536 (2002).","journal-title":"Nature"},{"key":"BFnrg1901_CR3","doi-asserted-by":"publisher","first-page":"49","DOI":"10.1038\/ng1060","volume":"33","author":"S Ramaswamy","year":"2003","unstructured":"Ramaswamy, S., Ross, K. N., Lander, E. S. & Golub, T. R. A molecular signature of metastasis in primary solid tumors. Nature Genet. 33, 49\u201354 (2003).","journal-title":"Nature Genet."},{"key":"BFnrg1901_CR4","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1016\/j.cancergencyto.2004.02.010","volume":"155","author":"W Kildal","year":"2004","unstructured":"Kildal, W. et al. Evaluation of genomic changes in a large series of malignant ovarian germ cell tumors \u2014 relation to clinicopathologic variables. Cancer Genet. Cytogenet. 155, 25\u201332 (2004).","journal-title":"Cancer Genet. Cytogenet."},{"key":"BFnrg1901_CR5","doi-asserted-by":"publisher","first-page":"778","DOI":"10.1200\/JCO.2005.03.2375","volume":"24","author":"M Sanchez-Carbayo","year":"2006","unstructured":"Sanchez-Carbayo, M., Socci, N. D., Lozano, J., Saint, F. & Cordon-Cardo, C. Defining molecular profiles of poor outcome in patients with invasive bladder cancer using oligonucleotide microarrays. J. Clin. Oncol. 24, 778\u2013789 (2006).","journal-title":"J. Clin. Oncol."},{"key":"BFnrg1901_CR6","doi-asserted-by":"publisher","first-page":"1008","DOI":"10.1016\/0888-7543(92)90014-J","volume":"13","author":"EM Southern","year":"1992","unstructured":"Southern, E. M., Maskos, U. & Elder, J. K. Analyzing and comparing nucleic acid sequences by hybridization to arrays of oligonucleotides: evaluation using experimental models. Genomics 13, 1008\u20131017 (1992).","journal-title":"Genomics"},{"key":"BFnrg1901_CR7","doi-asserted-by":"publisher","first-page":"5022","DOI":"10.1073\/pnas.91.11.5022","volume":"91","author":"AC Pease","year":"1994","unstructured":"Pease, A. C. et al. Light-generated oligonucleotide arrays for rapid DNA sequence analysis. Proc. Natl Acad. Sci. USA 91, 5022\u20135026 (1994).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"BFnrg1901_CR8","doi-asserted-by":"publisher","first-page":"467","DOI":"10.1126\/science.270.5235.467","volume":"270","author":"M Schena","year":"1995","unstructured":"Schena, M., Shalon, D., Davis, R. W. & Brown, P. O. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270, 467\u2013470 (1995).","journal-title":"Science"},{"key":"BFnrg1901_CR9","doi-asserted-by":"publisher","first-page":"1675","DOI":"10.1038\/nbt1296-1675","volume":"14","author":"DJ Lockhart","year":"1996","unstructured":"Lockhart, D. J. et al. Expression monitoring by hybridization to high-density oligonucleotide arrays. Nature Biotechnol. 14, 1675\u20131680 (1996). The landmark paper that described high-density oligonucleotide arrays for gene-expression profiling.","journal-title":"Nature Biotechnol."},{"key":"BFnrg1901_CR10","doi-asserted-by":"publisher","first-page":"S5","DOI":"10.1038\/ng1558","volume":"37","author":"AC Syvanen","year":"2005","unstructured":"Syvanen, A. C. Toward genome-wide SNP genotyping. Nature Genet. 37, S5\u2013S10 (2005). This article provides an excellent background on genotyping technologies.","journal-title":"Nature Genet."},{"key":"BFnrg1901_CR11","doi-asserted-by":"publisher","first-page":"335","DOI":"10.1038\/nrg1325","volume":"5","author":"J Shendure","year":"2004","unstructured":"Shendure, J., Mitra, R. D., Varma, C. & Church, G. M. Advanced sequencing technologies: methods and goals. Nature Rev. Genet. 5, 335\u2013344 (2004). This article provides an excellent background on novel sequencing technologies.","journal-title":"Nature Rev. Genet."},{"key":"BFnrg1901_CR12","doi-asserted-by":"publisher","first-page":"89","DOI":"10.1038\/nrg1270","volume":"5","author":"KT Zondervan","year":"2004","unstructured":"Zondervan, K. T. & Cardon, L. R. The complex interplay among factors that influence allelic association. Nature Rev. Genet. 5, 89\u2013100 (2004).","journal-title":"Nature Rev. Genet."},{"key":"BFnrg1901_CR13","doi-asserted-by":"publisher","first-page":"95","DOI":"10.1038\/nrg1521","volume":"6","author":"JN Hirschhorn","year":"2005","unstructured":"Hirschhorn, J. N. & Daly, M. J. Genome-wide association studies for common diseases and complex traits. Nature Rev. Genet. 6, 95\u2013108 (2005).","journal-title":"Nature Rev. Genet."},{"key":"BFnrg1901_CR14","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/j.ygeno.2004.10.005","volume":"85","author":"TC Mockler","year":"2005","unstructured":"Mockler, T. C. et al. Applications of DNA tiling arrays for whole-genome analysis. Genomics 85, 1\u201315 (2005).","journal-title":"Genomics"},{"key":"BFnrg1901_CR15","doi-asserted-by":"publisher","first-page":"1663","DOI":"10.1073\/pnas.87.5.1663","volume":"87","author":"RN Van Gelder","year":"1990","unstructured":"Van Gelder, R. N. et al. Amplified RNA synthesized from limited quantities of heterogeneous cDNA. Proc. Natl Acad. Sci. USA 87, 1663\u20131667 (1990).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"BFnrg1901_CR16","doi-asserted-by":"publisher","first-page":"283","DOI":"10.1006\/meth.1996.0104","volume":"10","author":"J Phillips","year":"1996","unstructured":"Phillips, J. & Eberwine, J. H. Antisense RNA amplification: a linear amplification method for analyzing the mRNA population from single living cells. Methods 10, 283\u2013288 (1996).","journal-title":"Methods"},{"key":"BFnrg1901_CR17","doi-asserted-by":"publisher","first-page":"5","DOI":"10.1101\/gr.1.1.5","volume":"1","author":"F Barany","year":"1991","unstructured":"Barany, F. The ligase chain reaction in a PCR world. PCR Methods Appl. 1, 5\u201316 (1991).","journal-title":"PCR Methods Appl."},{"key":"BFnrg1901_CR18","doi-asserted-by":"publisher","first-page":"2085","DOI":"10.1126\/science.7522346","volume":"265","author":"M Nilsson","year":"1994","unstructured":"Nilsson, M. et al. Padlock probes: circularizing oligonucleotides for localized DNA detection. Science 265, 2085\u20132088 (1994).","journal-title":"Science"},{"key":"BFnrg1901_CR19","doi-asserted-by":"publisher","first-page":"84","DOI":"10.1006\/meth.1996.0011","volume":"9","author":"U Landegren","year":"1996","unstructured":"Landegren, U., Samiotaki, M., Nilsson, M., Malmgren, H. & Kwiatkowski, M. Detecting genes with ligases. Methods 9, 84\u201390 (1996).","journal-title":"Methods"},{"key":"BFnrg1901_CR20","doi-asserted-by":"publisher","first-page":"5073","DOI":"10.1093\/nar\/26.22.5073","volume":"26","author":"J Baner","year":"1998","unstructured":"Baner, J., Nilsson, M., Mendel-Hartvig, M. & Landegren, U. Signal amplification of padlock probes by rolling circle replication. Nucleic Acids Res. 26, 5073\u20135078 (1998).","journal-title":"Nucleic Acids Res."},{"key":"BFnrg1901_CR21","doi-asserted-by":"publisher","first-page":"E116","DOI":"10.1093\/nar\/29.22.e116","volume":"29","author":"X Qi","year":"2001","unstructured":"Qi, X., Bakht, S., Devos, K. M., Gale, M. D. & Osbourn, A. L-RCA (ligation-rolling circle amplification): a general method for genotyping of single nucleotide polymorphisms (SNPs). Nucleic Acids Res. 29, E116 (2001).","journal-title":"Nucleic Acids Res."},{"key":"BFnrg1901_CR22","doi-asserted-by":"publisher","first-page":"4","DOI":"10.1186\/1471-2164-2-4","volume":"2","author":"AF Faruqi","year":"2001","unstructured":"Faruqi, A. F. et al. High-throughput genotyping of single nucleotide polymorphisms with rolling circle amplification. BMC Genomics 2, 4 (2001).","journal-title":"BMC Genomics"},{"key":"BFnrg1901_CR23","doi-asserted-by":"publisher","first-page":"S65","DOI":"10.1101\/gr.3.4.S65","volume":"3","author":"MC Edwards","year":"1994","unstructured":"Edwards, M. C. & Gibbs, R. A. Multiplex PCR: advantages, development, and applications. PCR Methods Appl. 3, S65\u2013S75 (1994).","journal-title":"PCR Methods Appl."},{"key":"BFnrg1901_CR24","doi-asserted-by":"publisher","first-page":"129","DOI":"10.1007\/BF02789108","volume":"3","author":"W Rychlik","year":"1995","unstructured":"Rychlik, W. Selection of primers for polymerase chain reaction. Mol. Biotechnol. 3, 129\u2013134 (1995).","journal-title":"Mol. Biotechnol."},{"key":"BFnrg1901_CR25","doi-asserted-by":"publisher","first-page":"333","DOI":"10.1007\/s00216-002-1683-2","volume":"375","author":"R Schoske","year":"2003","unstructured":"Schoske, R., Vallone, P. M., Ruitberg, C. M. & Butler, J. M. Multiplex PCR design strategy used for the simultaneous amplification of 10 Y chromosome short tandem repeat (STR) loci. Anal. Bioanal. Chem. 375, 333\u2013343 (2003).","journal-title":"Anal. Bioanal. Chem."},{"key":"BFnrg1901_CR26","doi-asserted-by":"publisher","first-page":"226","DOI":"10.2144\/04372ST03","volume":"37","author":"PM Vallone","year":"2004","unstructured":"Vallone, P. M. & Butler, J. M. AutoDimer: a screening tool for primer-dimer and hairpin structures. Biotechniques 37, 226\u201331 (2004).","journal-title":"Biotechniques"},{"key":"BFnrg1901_CR27","doi-asserted-by":"publisher","first-page":"2582","DOI":"10.1073\/pnas.93.6.2582","volume":"93","author":"Z Lin","year":"1996","unstructured":"Lin, Z., Cui, X. & Li, H. Multiplex genotype determination at a large number of gene loci. Proc. Natl Acad. Sci. USA 93, 2582\u20132587 (1996).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"BFnrg1901_CR28","doi-asserted-by":"publisher","first-page":"3235","DOI":"10.1093\/nar\/25.16.3235","volume":"25","author":"J Brownie","year":"1997","unstructured":"Brownie, J. et al. The elimination of primer\u2013dimer accumulation in PCR. Nucleic Acids Res. 25, 3235\u20133241 (1997).","journal-title":"Nucleic Acids Res."},{"key":"BFnrg1901_CR29","doi-asserted-by":"publisher","first-page":"610","DOI":"10.1126\/science.274.5287.610","volume":"274","author":"M Chee","year":"1996","unstructured":"Chee, M. et al. Accessing genetic information with high-density DNA arrays. Science 274, 610\u2013614 (1996).","journal-title":"Science"},{"key":"BFnrg1901_CR30","doi-asserted-by":"publisher","first-page":"1077","DOI":"10.1126\/science.280.5366.1077","volume":"280","author":"DG Wang","year":"1998","unstructured":"Wang, D. G. et al. Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome. Science 280, 1077\u20131082 (1998). References 29 and 30 represent the first application of high-density oligonucleotide arrays for large-scale genomic resequencing, SNP identification and genotyping.","journal-title":"Science"},{"key":"BFnrg1901_CR31","doi-asserted-by":"publisher","first-page":"853","DOI":"10.1101\/gr.10.6.853","volume":"10","author":"JB Fan","year":"2000","unstructured":"Fan, J. B. et al. Parallel genotyping of human SNPs using generic high-density oligonucleotide tag arrays. Genome Res. 10, 853\u2013860 (2000).","journal-title":"Genome Res."},{"key":"BFnrg1901_CR32","unstructured":"Adams, C. P. & Kron, S. J. Method for performing amplification of nucleic acid with two primers bound to a single solid support. US Patent 5,641,658 (1997)."},{"key":"BFnrg1901_CR33","doi-asserted-by":"publisher","first-page":"E87","DOI":"10.1093\/nar\/28.20.e87","volume":"28","author":"C Adessi","year":"2000","unstructured":"Adessi, C. et al. Solid phase DNA amplification: characterisation of primer attachment and amplification mechanisms. Nucleic Acids Res. 28, E87 (2000).","journal-title":"Nucleic Acids Res."},{"key":"BFnrg1901_CR34","doi-asserted-by":"publisher","first-page":"1926","DOI":"10.1101\/gr.205001","volume":"11","author":"MH Shapero","year":"2001","unstructured":"Shapero, M. H., Leuther, K. K., Nguyen, A., Scott, M. & Jones, K. W. SNP genotyping by multiplexed solid-phase amplification and fluorescent minisequencing. Genome Res. 11, 1926\u20131934 (2001).","journal-title":"Genome Res."},{"key":"BFnrg1901_CR35","doi-asserted-by":"publisher","first-page":"e5","DOI":"10.1093\/nar\/28.2.e5","volume":"28","author":"JD Andreadis","year":"2000","unstructured":"Andreadis, J. D. & Chrisey, L. A. Use of immobilized PCR primers to generate covalently immobilized DNAs for in vitro transcription\/translation reactions. Nucleic Acids Res. 28, e5 (2000).","journal-title":"Nucleic Acids Res."},{"key":"BFnrg1901_CR36","doi-asserted-by":"publisher","first-page":"276","DOI":"10.1101\/gr.2885205","volume":"15","author":"HY Wang","year":"2005","unstructured":"Wang, H. Y. et al. A genotyping system capable of simultaneously analyzing >1000 single nucleotide polymorphisms in a haploid genome. Genome Res. 15, 276\u2013283 (2005).","journal-title":"Genome Res."},{"key":"BFnrg1901_CR37","doi-asserted-by":"publisher","first-page":"673","DOI":"10.1038\/nbt821","volume":"21","author":"P Hardenbol","year":"2003","unstructured":"Hardenbol, P. et al. Multiplexed genotyping with sequence-tagged molecular inversion probes. Nature Biotechnol. 21, 673\u2013678 (2003).","journal-title":"Nature Biotechnol."},{"key":"BFnrg1901_CR38","doi-asserted-by":"publisher","first-page":"69","DOI":"10.1101\/sqb.2003.68.69","volume":"68","author":"JB Fan","year":"2003","unstructured":"Fan, J. B. et al. Highly parallel SNP genotyping. Cold Spring Harb. Symp. Quant. Biol. 68, 69\u201378 (2003). References 37 and 38 describe two highly multiplexed SNP genotyping assays.","journal-title":"Cold Spring Harb. Symp. Quant. Biol."},{"key":"BFnrg1901_CR39","doi-asserted-by":"publisher","first-page":"1299","DOI":"10.1038\/nature04226","volume":"437","author":"D Altshuler","year":"2005","unstructured":"Altshuler, D. et al. A haplotype map of the human genome. Nature 437, 1299\u20131320 (2005). The seminal paper that described the results of the International HapMap Project.","journal-title":"Nature"},{"key":"BFnrg1901_CR40","doi-asserted-by":"publisher","first-page":"269","DOI":"10.1101\/gr.3185605","volume":"15","author":"P Hardenbol","year":"2005","unstructured":"Hardenbol, P. et al. Highly multiplexed molecular inversion probe genotyping: over 10,000 targeted SNPs genotyped in a single tube assay. Genome Res. 15, 269\u2013275 (2005).","journal-title":"Genome Res."},{"key":"BFnrg1901_CR41","doi-asserted-by":"publisher","first-page":"1072","DOI":"10.1126\/science.1105436","volume":"307","author":"DA Hinds","year":"2005","unstructured":"Hinds, D. A. et al. Whole-genome patterns of common DNA variation in three human populations. Science 307, 1072\u20131079 (2005).","journal-title":"Science"},{"key":"BFnrg1901_CR42","doi-asserted-by":"publisher","first-page":"1719","DOI":"10.1126\/science.1065573","volume":"294","author":"N Patil","year":"2001","unstructured":"Patil, N. et al. Blocks of limited haplotype diversity revealed by high-resolution scanning of human chromosome 21. Science 294, 1719\u20131723 (2001).","journal-title":"Science"},{"key":"BFnrg1901_CR43","doi-asserted-by":"publisher","first-page":"3645","DOI":"10.1093\/nar\/17.10.3645","volume":"17","author":"KW Kinzler","year":"1989","unstructured":"Kinzler, K. W. & Vogelstein, B. Whole genome PCR: application to the identification of sequences bound by gene regulatory proteins. Nucleic Acids Res. 17, 3645\u20133653 (1989).","journal-title":"Nucleic Acids Res."},{"key":"BFnrg1901_CR44","doi-asserted-by":"publisher","first-page":"946","DOI":"10.1126\/science.8438152","volume":"259","author":"N Lisitsyn","year":"1993","unstructured":"Lisitsyn, N. & Wigler, M. Cloning the differences between two complex genomes. Science 259, 946\u2013951 (1993).","journal-title":"Science"},{"key":"BFnrg1901_CR45","doi-asserted-by":"publisher","first-page":"4487","DOI":"10.1073\/pnas.95.8.4487","volume":"95","author":"R Lucito","year":"1998","unstructured":"Lucito, R. et al. Genetic analysis using genomic representations. Proc. Natl Acad. Sci. USA 95, 4487\u20134492 (1998).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"BFnrg1901_CR46","doi-asserted-by":"publisher","first-page":"2291","DOI":"10.1101\/gr.1349003","volume":"13","author":"R Lucito","year":"2003","unstructured":"Lucito, R. et al. Representational oligonucleotide microarray analysis: a high-resolution method to detect genome copy number variation. Genome Res. 13, 2291\u20132305 (2003).","journal-title":"Genome Res."},{"key":"BFnrg1901_CR47","doi-asserted-by":"publisher","first-page":"525","DOI":"10.1126\/science.1098918","volume":"305","author":"J Sebat","year":"2004","unstructured":"Sebat, J. et al. Large-scale copy number polymorphism in the human genome. Science 305, 525\u2013528 (2004).","journal-title":"Science"},{"key":"BFnrg1901_CR48","doi-asserted-by":"publisher","first-page":"1233","DOI":"10.1038\/nbt869","volume":"21","author":"GC Kennedy","year":"2003","unstructured":"Kennedy, G. C. et al. Large-scale genotyping of complex DNA. Nature Biotechnol. 21, 1233\u20131237 (2003).","journal-title":"Nature Biotechnol."},{"key":"BFnrg1901_CR49","doi-asserted-by":"publisher","first-page":"414","DOI":"10.1101\/gr.2014904","volume":"14","author":"H Matsuzaki","year":"2004","unstructured":"Matsuzaki, H. et al. Parallel genotyping of over 10,000 SNPs using a one-primer assay on a high-density oligonucleotide array. Genome Res. 14, 414\u2013425 (2004). References 48 and 49 describe the original development of whole genome sampling analysis (WGSA), which allows high-density genome-wide SNP analysis.","journal-title":"Genome Res."},{"key":"BFnrg1901_CR50","doi-asserted-by":"publisher","first-page":"109","DOI":"10.1038\/nmeth718","volume":"1","author":"H Matsuzaki","year":"2004","unstructured":"Matsuzaki, H. et al. Genotyping over 100,000 SNPs on a pair of oligonucleotide arrays. Nature Methods 1, 109\u2013111 (2004).","journal-title":"Nature Methods"},{"key":"BFnrg1901_CR51","doi-asserted-by":"publisher","first-page":"279","DOI":"10.1126\/science.1124779","volume":"312","author":"A Herbert","year":"2006","unstructured":"Herbert, A. et al. A common genetic variant is associated with adult and childhood obesity. Science 312, 279\u2013283 (2006).","journal-title":"Science"},{"key":"BFnrg1901_CR52","doi-asserted-by":"publisher","first-page":"385","DOI":"10.1126\/science.1109557","volume":"308","author":"RJ Klein","year":"2005","unstructured":"Klein, R. J. et al. Complement factor H polymorphism in age-related macular degeneration. Science 308, 385\u2013389 (2005).","journal-title":"Science"},{"key":"BFnrg1901_CR53","doi-asserted-by":"publisher","first-page":"549","DOI":"10.1038\/ng1547","volume":"37","author":"KL Gunderson","year":"2005","unstructured":"Gunderson, K. L., Steemers, F. J., Lee, G., Mendoza, L. G. & Chee, M. S. A genome-wide scalable SNP genotyping assay using microarray technology. Nature Genet. 37, 549\u2013554 (2005). This is the first paper that demonstrated the ability to conduct whole-genome genotyping on whole-genome amplified samples of full genome complexity.","journal-title":"Nature Genet."},{"key":"BFnrg1901_CR54","doi-asserted-by":"publisher","first-page":"31","DOI":"10.1038\/nmeth842","volume":"3","author":"FJ Steemers","year":"2006","unstructured":"Steemers, F. J. et al. Whole-genome genotyping with the single-base extension assay. Nature Methods 3, 31\u201333 (2006).","journal-title":"Nature Methods"},{"key":"BFnrg1901_CR55","doi-asserted-by":"publisher","first-page":"557","DOI":"10.1517\/14622416.3.4.557","volume":"3","author":"JP Langmore","year":"2002","unstructured":"Langmore, J. P. Rubicon Genomics, Inc. Pharmacogenomics 3, 557\u2013560 (2002).","journal-title":"Pharmacogenomics"},{"key":"BFnrg1901_CR56","doi-asserted-by":"publisher","first-page":"5261","DOI":"10.1073\/pnas.082089499","volume":"99","author":"FB Dean","year":"2002","unstructured":"Dean, F. B. et al. Comprehensive human genome amplification using multiple displacement amplification. Proc. Natl Acad. Sci. USA 99, 5261\u20135266 (2002).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"BFnrg1901_CR57","doi-asserted-by":"publisher","first-page":"641","DOI":"10.2217\/14622416.7.4.641","volume":"7","author":"KL Gunderson","year":"2006","unstructured":"Gunderson, K. L. et al. Whole-genome genotyping of haplotype tag single nucleotide polymorphisms. Pharmacogenomics 7, 641\u2013648 (2006).","journal-title":"Pharmacogenomics"},{"key":"BFnrg1901_CR58","doi-asserted-by":"publisher","first-page":"818","DOI":"10.1126\/science.1359641","volume":"258","author":"A Kallioniemi","year":"1992","unstructured":"Kallioniemi, A. et al. Comparative genomic hybridization for molecular cytogenetic analysis of solid tumors. Science 258, 818\u2013821 (1992).","journal-title":"Science"},{"key":"BFnrg1901_CR59","doi-asserted-by":"publisher","first-page":"207","DOI":"10.1038\/2524","volume":"20","author":"D Pinkel","year":"1998","unstructured":"Pinkel, D. et al. High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nature Genet. 20, 207\u2013211 (1998). The first demonstration of array technology applied to high-resolution comparative genomic hybridization (CGH) applications.","journal-title":"Nature Genet."},{"key":"BFnrg1901_CR60","doi-asserted-by":"publisher","first-page":"41","DOI":"10.1038\/12640","volume":"23","author":"JR Pollack","year":"1999","unstructured":"Pollack, J. R. et al. Genome-wide analysis of DNA copy-number changes using cDNA microarrays. Nature Genet. 23, 41\u201346 (1999).","journal-title":"Nature Genet."},{"key":"BFnrg1901_CR61","doi-asserted-by":"publisher","first-page":"299","DOI":"10.1038\/ng1307","volume":"36","author":"AS Ishkanian","year":"2004","unstructured":"Ishkanian, A. S. et al. A tiling resolution DNA microarray with complete coverage of the human genome. Nature Genet. 36, 299\u2013303 (2004).","journal-title":"Nature Genet."},{"key":"BFnrg1901_CR62","doi-asserted-by":"publisher","first-page":"17765","DOI":"10.1073\/pnas.0407979101","volume":"101","author":"MT Barrett","year":"2004","unstructured":"Barrett, M. T. et al. Comparative genomic hybridization using oligonucleotide microarrays and total genomic DNA. Proc. Natl Acad. Sci. USA 101, 17765\u201317770 (2004).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"BFnrg1901_CR63","doi-asserted-by":"publisher","first-page":"644","DOI":"10.1136\/jcp.2003.013029","volume":"57","author":"B Carvalho","year":"2004","unstructured":"Carvalho, B., Ouwerkerk, E., Meijer, G. A. & Ylstra, B. High resolution microarray comparative genomic hybridisation analysis using spotted oligonucleotides. J. Clin. Pathol. 57, 644\u2013646 (2004).","journal-title":"J. Clin. Pathol."},{"key":"BFnrg1901_CR64","doi-asserted-by":"publisher","first-page":"305","DOI":"10.1002\/gcc.20243","volume":"44","author":"RR Selzer","year":"2005","unstructured":"Selzer, R. R. et al. Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44, 305\u2013319 (2005).","journal-title":"Genes Chromosomes Cancer"},{"key":"BFnrg1901_CR65","doi-asserted-by":"publisher","first-page":"445","DOI":"10.1093\/nar\/gkj456","volume":"34","author":"B Ylstra","year":"2006","unstructured":"Ylstra, B., van den Ijssel, P., Carvalho, B., Brakenhoff, R. H. & Meijer, G. A. BAC to the future! or oligonucleotides: a perspective for micro array comparative genomic hybridization (array CGH). Nucleic Acids Res. 34, 445\u2013450 (2006).","journal-title":"Nucleic Acids Res."},{"key":"BFnrg1901_CR66","doi-asserted-by":"publisher","first-page":"287","DOI":"10.1101\/gr.2012304","volume":"14","author":"GR Bignell","year":"2004","unstructured":"Bignell, G. R. et al. High-resolution analysis of DNA copy number using oligonucleotide microarrays. Genome Res. 14, 287\u2013295 (2004).","journal-title":"Genome Res."},{"key":"BFnrg1901_CR67","doi-asserted-by":"publisher","first-page":"287","DOI":"10.1186\/1479-7364-1-4-287","volume":"1","author":"J Huang","year":"2004","unstructured":"Huang, J. et al. Whole genome DNA copy number changes identified by high density oligonucleotide arrays. Hum. Genomics 1, 287\u2013299 (2004).","journal-title":"Hum. Genomics"},{"key":"BFnrg1901_CR68","doi-asserted-by":"publisher","first-page":"916","DOI":"10.1136\/jmg.2004.022855","volume":"41","author":"A Rauch","year":"2004","unstructured":"Rauch, A. et al. Molecular karyotyping using an SNP array for genomewide genotyping. J. Med. Genet. 41, 916\u2013922 (2004).","journal-title":"J. Med. Genet."},{"key":"BFnrg1901_CR69","doi-asserted-by":"publisher","first-page":"3060","DOI":"10.1158\/0008-5472.CAN-03-3308","volume":"64","author":"X Zhao","year":"2004","unstructured":"Zhao, X. et al. An integrated view of copy number and allelic alterations in the cancer genome using single nucleotide polymorphism arrays. Cancer Res. 64, 3060\u20133071 (2004).","journal-title":"Cancer Res."},{"key":"BFnrg1901_CR70","doi-asserted-by":"publisher","first-page":"5561","DOI":"10.1158\/0008-5472.CAN-04-4603","volume":"65","author":"X Zhao","year":"2005","unstructured":"Zhao, X. et al. Homozygous deletions and chromosome amplifications in human lung carcinomas revealed by single nucleotide polymorphism array analysis. Cancer Res. 65, 5561\u20135570 (2005).","journal-title":"Cancer Res."},{"key":"BFnrg1901_CR71","doi-asserted-by":"publisher","first-page":"847","DOI":"10.1136\/jmg.2005.032367","volume":"42","author":"S Bruce","year":"2005","unstructured":"Bruce, S. et al. Global analysis of uniparental disomy using high density genotyping arrays. J. Med. Genet. 42, 847\u2013851 (2005).","journal-title":"J. Med. Genet."},{"key":"BFnrg1901_CR72","doi-asserted-by":"publisher","first-page":"8597","DOI":"10.1158\/0008-5472.CAN-05-0842","volume":"65","author":"MT Teh","year":"2005","unstructured":"Teh, M. T. et al. Genomewide single nucleotide polymorphism microarray mapping in basal cell carcinomas unveils uniparental disomy as a key somatic event. Cancer Res. 65, 8597\u20138603 (2005).","journal-title":"Cancer Res."},{"key":"BFnrg1901_CR73","doi-asserted-by":"publisher","first-page":"e65","DOI":"10.1371\/journal.pcbi.0010065","volume":"1","author":"T LaFramboise","year":"2005","unstructured":"LaFramboise, T. et al. Allele-specific amplification in cancer revealed by SNP array analysis. PLoS Comput. Biol. 1, e65 (2005). This paper highlights the effects of high-level allele-specific amplification in cancer.","journal-title":"PLoS Comput. Biol."},{"key":"BFnrg1901_CR74","doi-asserted-by":"publisher","first-page":"10188","DOI":"10.1158\/0008-5472.CAN-05-2486","volume":"65","author":"EH Lips","year":"2005","unstructured":"Lips, E. H. et al. Reliable high-throughput genotyping and loss-of-heterozygosity detection in formalin-fixed, paraffin-embedded tumors using single nucleotide polymorphism arrays. Cancer Res. 65, 10188\u201310191 (2005).","journal-title":"Cancer Res."},{"key":"BFnrg1901_CR75","doi-asserted-by":"publisher","first-page":"298","DOI":"10.1016\/j.ygeno.2005.09.019","volume":"87","author":"SE Little","year":"2006","unstructured":"Little, S. E. et al. Array CGH using whole genome amplification of fresh-frozen and formalin-fixed, paraffin-embedded tumor DNA. Genomics 87, 298\u2013306 (2006).","journal-title":"Genomics"},{"key":"BFnrg1901_CR76","doi-asserted-by":"publisher","first-page":"171","DOI":"10.1016\/S1525-1578(10)60543-0","volume":"7","author":"M Bredel","year":"2005","unstructured":"Bredel, M. et al. Amplification of whole tumor genomes and gene-by-gene mapping of genomic aberrations from limited sources of fresh-frozen and paraffin-embedded DNA. J. Mol. Diagn. 7, 171\u2013182 (2005).","journal-title":"J. Mol. Diagn."},{"key":"BFnrg1901_CR77","doi-asserted-by":"publisher","first-page":"1143","DOI":"10.1126\/science.1072545","volume":"297","author":"H Yan","year":"2002","unstructured":"Yan, H., Yuan, W., Velculescu, V. E., Vogelstein, B. & Kinzler, K. W. Allelic variation in human gene expression. Science 297, 1143 (2002). The first systematic cataloguing of allele-specific expression in human genes.","journal-title":"Science"},{"key":"BFnrg1901_CR78","doi-asserted-by":"crossref","first-page":"149","DOI":"10.1007\/s00439-003-0956-y","volume":"113","author":"NJ Bray","year":"2003","unstructured":"Bray, N. J., Buckland, P. R., Owen, M. J. & O'Donovan, M. C. Cis-acting variation in the expression of a high proportion of genes in human brain. Hum. Genet. 113, 149\u2013153 (2003).","journal-title":"Hum. Genet."},{"key":"BFnrg1901_CR79","doi-asserted-by":"publisher","first-page":"469","DOI":"10.1038\/ng1124","volume":"33","author":"JC Knight","year":"2003","unstructured":"Knight, J. C., Keating, B. J., Rockett, K. A. & Kwiatkowski, D. P. In vivo characterization of regulatory polymorphisms by allele-specific quantification of RNA polymerase loading. Nature Genet. 33, 469\u2013475 (2003).","journal-title":"Nature Genet."},{"key":"BFnrg1901_CR80","doi-asserted-by":"publisher","first-page":"647","DOI":"10.1126\/science.1101659","volume":"306","author":"T Pastinen","year":"2004","unstructured":"Pastinen, T. & Hudson, T. J. Cis-acting regulatory variation in the human genome. Science 306, 647\u2013650 (2004).","journal-title":"Science"},{"key":"BFnrg1901_CR81","doi-asserted-by":"publisher","first-page":"284","DOI":"10.1101\/gr.2850605","volume":"15","author":"J Ronald","year":"2005","unstructured":"Ronald, J. et al. Simultaneous genotyping, gene-expression measurement, and detection of allele-specific expression with oligonucleotide arrays. Genome Res. 15, 284\u2013291 (2005).","journal-title":"Genome Res."},{"key":"BFnrg1901_CR82","doi-asserted-by":"publisher","first-page":"1855","DOI":"10.1101\/gr.885403","volume":"13","author":"HS Lo","year":"2003","unstructured":"Lo, H. S. et al. Allelic variation in gene expression is common in the human genome. Genome Res. 13, 1855\u20131862 (2003).","journal-title":"Genome Res."},{"key":"BFnrg1901_CR83","doi-asserted-by":"publisher","first-page":"24","DOI":"10.1186\/1472-6750-4-24","volume":"4","author":"U Liljedahl","year":"2004","unstructured":"Liljedahl, U., Fredriksson, M., Dahlgren, A. & Syvanen, A. C. Detecting imbalanced expression of SNP alleles by minisequencing on microarrays. BMC Biotechnol. 4, 24 (2004).","journal-title":"BMC Biotechnol."},{"key":"BFnrg1901_CR84","doi-asserted-by":"publisher","first-page":"e183","DOI":"10.1093\/nar\/gni177","volume":"33","author":"Y Wang","year":"2005","unstructured":"Wang, Y. et al. Allele quantification using molecular inversion probes (MIP). Nucleic Acids Res. 33, e183 (2005).","journal-title":"Nucleic Acids Res."},{"key":"BFnrg1901_CR85","doi-asserted-by":"publisher","first-page":"331","DOI":"10.1101\/gr.4559106","volume":"16","author":"PV Pant","year":"2006","unstructured":"Pant, P. V. et al. Analysis of allelic differential expression in human white blood cells. Genome Res. 16, 331\u2013339 (2006).","journal-title":"Genome Res."},{"key":"BFnrg1901_CR86","doi-asserted-by":"publisher","first-page":"3963","DOI":"10.1093\/hmg\/ddi420","volume":"14","author":"T Pastinen","year":"2005","unstructured":"Pastinen, T. et al. Mapping common regulatory variants to human haplotypes. Hum. Mol. Genet. 14, 3963\u20133971 (2005). An excellent review article that describes the origin, measurements and effects of cis -acting regulatory polymorphisms on transcription.","journal-title":"Hum. Mol. Genet."},{"key":"BFnrg1901_CR87","doi-asserted-by":"publisher","first-page":"900","DOI":"10.1021\/ac00208a003","volume":"62","author":"H Drossman","year":"1990","unstructured":"Drossman, H., Luckey, J. A., Kostichka, A. J., D'Cunha, J. & Smith, L. M. High-speed separations of DNA sequencing reactions by capillary electrophoresis. Anal. Chem. 62, 900\u2013903 (1990).","journal-title":"Anal. Chem."},{"key":"BFnrg1901_CR88","doi-asserted-by":"publisher","first-page":"1194","DOI":"10.1126\/science.281.5380.1194","volume":"281","author":"EA Winzeler","year":"1998","unstructured":"Winzeler, E. A. et al. Direct allelic variation scanning of the yeast genome. Science 281, 1194\u20131197 (1998).","journal-title":"Science"},{"key":"BFnrg1901_CR89","doi-asserted-by":"publisher","first-page":"e35","DOI":"10.1093\/nar\/gng035","volume":"31","author":"TJ Albert","year":"2003","unstructured":"Albert, T. J. et al. Light-directed 5\u2032\u2013>3\u2032 synthesis of complex oligonucleotide microarrays. Nucleic Acids Res. 31, e35 (2003).","journal-title":"Nucleic Acids Res."},{"key":"BFnrg1901_CR90","doi-asserted-by":"publisher","first-page":"1767","DOI":"10.1101\/gr.3770505","volume":"15","author":"ML Metzker","year":"2005","unstructured":"Metzker, M. L. Emerging technologies in DNA sequencing. Genome Res. 15, 1767\u20131776 (2005).","journal-title":"Genome Res."},{"key":"BFnrg1901_CR91","doi-asserted-by":"publisher","first-page":"e34","DOI":"10.1093\/nar\/27.24.e34","volume":"27","author":"RD Mitra","year":"1999","unstructured":"Mitra, R. D. & Church, G. M. In situ localized amplification and contact replication of many individual DNA molecules. Nucleic Acids Res. 27, e34 (1999).","journal-title":"Nucleic Acids Res."},{"key":"BFnrg1901_CR92","doi-asserted-by":"publisher","first-page":"55","DOI":"10.1016\/S0003-2697(03)00291-4","volume":"320","author":"RD Mitra","year":"2003","unstructured":"Mitra, R. D., Shendure, J., Olejnik, J., Edyta Krzymanska, O. & Church, G. M. Fluorescent in situ sequencing on polymerase colonies. Anal. Biochem. 320, 55\u201365 (2003). References 91 and 92 describe the original polony approach and associated fluorescent in situ sequencing.","journal-title":"Anal. Biochem."},{"key":"BFnrg1901_CR93","doi-asserted-by":"publisher","first-page":"e11","DOI":"10.1093\/nar\/gnh184","volume":"33","author":"A Pemov","year":"2005","unstructured":"Pemov, A., Modi, H., Chandler, D. P. & Bavykin, S. DNA analysis with multiplex microarray-enhanced PCR. Nucleic Acids Res. 33, e11 (2005).","journal-title":"Nucleic Acids Res."},{"key":"BFnrg1901_CR94","doi-asserted-by":"publisher","first-page":"225","DOI":"10.1038\/898","volume":"19","author":"PM Lizardi","year":"1998","unstructured":"Lizardi, P. M. et al. Mutation detection and single-molecule counting using isothermal rolling-circle amplification. Nature Genet. 19, 225\u2013232 (1998).","journal-title":"Nature Genet."},{"key":"BFnrg1901_CR95","doi-asserted-by":"publisher","first-page":"8817","DOI":"10.1073\/pnas.1133470100","volume":"100","author":"D Dressman","year":"2003","unstructured":"Dressman, D., Yan, H., Traverso, G., Kinzler, K. W. & Vogelstein, B. Transforming single DNA molecules into fluorescent magnetic particles for detection and enumeration of genetic variations. Proc. Natl Acad. Sci. USA 100, 8817\u20138822 (2003). This paper describes the use of emulsion PCR for cloning on beads (BEAMing).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"BFnrg1901_CR96","doi-asserted-by":"publisher","first-page":"95","DOI":"10.1093\/bfgp\/1.1.95","volume":"1","author":"J Reinartz","year":"2002","unstructured":"Reinartz, J. et al. Massively parallel signature sequencing (MPSS) as a tool for in-depth quantitative gene expression profiling in all organisms. Brief. Funct. Genomic. Proteomic. 1, 95\u2013104 (2002).","journal-title":"Brief. Funct. Genomic. Proteomic."},{"key":"BFnrg1901_CR97","doi-asserted-by":"publisher","first-page":"630","DOI":"10.1038\/76469","volume":"18","author":"S Brenner","year":"2000","unstructured":"Brenner, S. et al. Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nature Biotechnol. 18, 630\u2013634 (2000).","journal-title":"Nature Biotechnol."},{"key":"BFnrg1901_CR98","doi-asserted-by":"publisher","first-page":"484","DOI":"10.1126\/science.270.5235.484","volume":"270","author":"VE Velculescu","year":"1995","unstructured":"Velculescu, V. E., Zhang, L., Vogelstein, B. & Kinzler, K. W. Serial analysis of gene expression. Science 270, 484\u2013487 (1995). The original paper that described serial analysis of gene expression (SAGE).","journal-title":"Science"},{"key":"BFnrg1901_CR99","doi-asserted-by":"publisher","first-page":"16156","DOI":"10.1073\/pnas.202610899","volume":"99","author":"TL Wang","year":"2002","unstructured":"Wang, T. L. et al. Digital karyotyping. Proc. Natl Acad. Sci. USA 99, 16156\u201316161 (2002).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"BFnrg1901_CR100","doi-asserted-by":"publisher","first-page":"1728","DOI":"10.1126\/science.1117389","volume":"309","author":"J Shendure","year":"2005","unstructured":"Shendure, J. et al. Accurate multiplex polony sequencing of an evolved bacterial genome. Science 309, 1728\u20131732 (2005).","journal-title":"Science"},{"key":"BFnrg1901_CR101","doi-asserted-by":"publisher","first-page":"376","DOI":"10.1038\/nature03959","volume":"437","author":"M Margulies","year":"2005","unstructured":"Margulies, M. et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437, 376\u2013380 (2005). References 100 and 101 were the first two papers to describe the sequencing of bacterial genomes using highly parallel array-based sequencing assays.","journal-title":"Nature"},{"key":"BFnrg1901_CR102","unstructured":"Tsien, R. Y., Ross, P., Fahnestock, M. & Johnston, A. J. DNA sequencing. PCT Patent WO 91\/06678 (1991)."},{"key":"BFnrg1901_CR103","doi-asserted-by":"publisher","first-page":"4259","DOI":"10.1093\/nar\/22.20.4259","volume":"22","author":"ML Metzker","year":"1994","unstructured":"Metzker, M. L. et al. Termination of DNA synthesis by novel 3\u2032-modified-deoxyribonucleoside 5\u2032-triphosphates. Nucleic Acids Res. 22, 4259\u20134267 (1994).","journal-title":"Nucleic Acids Res."},{"key":"BFnrg1901_CR104","doi-asserted-by":"publisher","first-page":"3960","DOI":"10.1073\/pnas.0230489100","volume":"100","author":"I Braslavsky","year":"2003","unstructured":"Braslavsky, I., Hebert, B., Kartalov, E. & Quake, S. R. Sequence information can be obtained from single DNA molecules. Proc. Natl Acad. Sci. USA 100, 3960\u20133964 (2003).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"BFnrg1901_CR105","doi-asserted-by":"publisher","first-page":"363","DOI":"10.1126\/science.281.5375.363","volume":"281","author":"M Ronaghi","year":"1998","unstructured":"Ronaghi, M., Uhlen, M. & Nyren, P. A sequencing method based on real-time pyrophosphate. Science 281, 363\u2013365 (1998).","journal-title":"Science"},{"key":"BFnrg1901_CR106","doi-asserted-by":"publisher","first-page":"373","DOI":"10.1517\/14622416.6.4.373","volume":"6","author":"ST Bennett","year":"2005","unstructured":"Bennett, S. T., Barnes, C., Cox, A., Davies, L. & Brown, C. Toward the $1000 human genome. Pharmacogenomics 6, 373\u2013382 (2005).","journal-title":"Pharmacogenomics"},{"key":"BFnrg1901_CR107","doi-asserted-by":"publisher","first-page":"331","DOI":"10.2144\/000112111","volume":"40","author":"SJ Tebbutt","year":"2006","unstructured":"Tebbutt, S. J. et al. Deoxynucleotides can replace dideoxynucleotides in minisequencing by arrayed primer extension. Biotechniques 40, 331\u2013338 (2006).","journal-title":"Biotechniques"},{"key":"BFnrg1901_CR108","unstructured":"Macevicz, S. C. DNA sequencing by parallel oligonucleotide extensions. US Patent 6,306,597 (2001)."},{"key":"BFnrg1901_CR109","doi-asserted-by":"publisher","first-page":"9236","DOI":"10.1073\/pnas.96.16.9236","volume":"96","author":"B Vogelstein","year":"1999","unstructured":"Vogelstein, B. & Kinzler, K. W. Digital PCR. Proc. Natl Acad. Sci. USA 96, 9236\u20139241 (1999).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"BFnrg1901_CR110","doi-asserted-by":"publisher","first-page":"41","DOI":"10.1586\/14737159.4.1.41","volume":"4","author":"G Pohl","year":"2004","unstructured":"Pohl, G. & Shih I.-M. Principle and applications of digital PCR. Expert Rev. Mol. Diagn. 4, 41\u201347 (2004).","journal-title":"Expert Rev. Mol. Diagn."},{"key":"BFnrg1901_CR111","doi-asserted-by":"publisher","first-page":"15718","DOI":"10.1073\/pnas.2536670100","volume":"100","author":"H Matsumura","year":"2003","unstructured":"Matsumura, H. et al. Gene expression analysis of plant host\u2013pathogen interactions by SuperSAGE. Proc. Natl Acad. Sci. USA 100, 15718\u201315723 (2003).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"BFnrg1901_CR112","doi-asserted-by":"publisher","first-page":"11","DOI":"10.1111\/j.1462-5822.2004.00478.x","volume":"7","author":"H Matsumura","year":"2005","unstructured":"Matsumura, H. et al. SuperSAGE. Cell. Microbiol. 7, 11\u201318 (2005).","journal-title":"Cell. Microbiol."},{"key":"BFnrg1901_CR113","doi-asserted-by":"publisher","first-page":"e121","DOI":"10.1093\/nar\/gnh120","volume":"32","author":"T Tengs","year":"2004","unstructured":"Tengs, T. et al. Genomic representations using concatenates of Type IIB restriction endonuclease digestion fragments. Nucleic Acids Res. 32, e121 (2004).","journal-title":"Nucleic Acids Res."},{"key":"BFnrg1901_CR114","doi-asserted-by":"publisher","first-page":"1567","DOI":"10.1126\/science.1114112","volume":"309","author":"C Lu","year":"2005","unstructured":"Lu, C. et al. Elucidation of the small RNA component of the transcriptome. Science 309, 1567\u20131569 (2005).","journal-title":"Science"},{"key":"BFnrg1901_CR115","doi-asserted-by":"publisher","first-page":"95","DOI":"10.1038\/nmeth850","volume":"3","author":"M Li","year":"2006","unstructured":"Li, M., Diehl, F., Dressman, D., Vogelstein, B. & Kinzler, K. W. BEAMing up for detection and quantification of rare sequence variants. Nature Methods 3, 95\u201397 (2006).","journal-title":"Nature Methods"},{"key":"BFnrg1901_CR116","doi-asserted-by":"publisher","first-page":"16368","DOI":"10.1073\/pnas.0507904102","volume":"102","author":"F Diehl","year":"2005","unstructured":"Diehl, F. et al. Detection and quantification of mutations in the plasma of patients with colorectal tumors. Proc. Natl Acad. Sci. USA 102, 16368\u201316373 (2005).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"BFnrg1901_CR117","doi-asserted-by":"publisher","first-page":"8046","DOI":"10.1073\/pnas.95.14.8046","volume":"95","author":"J Jing","year":"1998","unstructured":"Jing, J. et al. Automated high resolution optical mapping using arrayed, fluid-fixed DNA molecules. Proc. Natl Acad. Sci. USA 95, 8046\u20138051 (1998).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"BFnrg1901_CR118","doi-asserted-by":"publisher","first-page":"297","DOI":"10.1016\/S0167-7799(99)01326-8","volume":"17","author":"C Aston","year":"1999","unstructured":"Aston, C., Mishra, B. & Schwartz, D. C. Optical mapping and its potential for large-scale sequencing projects. Trends Biotechnol. 17, 297\u2013302 (1999).","journal-title":"Trends Biotechnol."},{"key":"BFnrg1901_CR119","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/j.ab.2004.09.043","volume":"337","author":"A Ramanathan","year":"2005","unstructured":"Ramanathan, A., Pape, L. & Schwartz, D. C. High-density polymerase-mediated incorporation of fluorochrome-labeled nucleotides. Anal. Biochem. 337, 1\u201311 (2005).","journal-title":"Anal. Biochem."},{"key":"BFnrg1901_CR120","doi-asserted-by":"publisher","first-page":"5293","DOI":"10.1021\/ac0496401","volume":"76","author":"ET Dimalanta","year":"2004","unstructured":"Dimalanta, E. T. et al. A microfluidic system for large DNA molecule arrays. Anal. Chem. 76, 5293\u20135301 (2004).","journal-title":"Anal. Chem."},{"key":"BFnrg1901_CR121","doi-asserted-by":"publisher","first-page":"1045","DOI":"10.1038\/nature04689","volume":"440","author":"MC Zody","year":"2006","unstructured":"Zody, M. C. et al. DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage. Nature 440, 1045\u20131049 (2006).","journal-title":"Nature"},{"key":"BFnrg1901_CR122","doi-asserted-by":"crossref","unstructured":"The ENCODE Project Consortium. The ENCODE (ENCyclopedia Of DNA Elements) Project. Science 306, 636\u2013640 (2004).","DOI":"10.1126\/science.1105136"},{"key":"BFnrg1901_CR123","doi-asserted-by":"publisher","first-page":"123","DOI":"10.1101\/gr.4074106","volume":"16","author":"GE Crawford","year":"2005","unstructured":"Crawford, G. E. et al. Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS). Genome Res. 16, 123\u2013131 (2005).","journal-title":"Genome Res."},{"key":"BFnrg1901_CR124","doi-asserted-by":"publisher","first-page":"105","DOI":"10.1038\/nmeth733","volume":"2","author":"P Ng","year":"2005","unstructured":"Ng, P. et al. Gene identification signature (GIS) analysis for transcriptome characterization and genome annotation. Nature Methods 2, 105\u2013111 (2005).","journal-title":"Nature Methods"},{"key":"BFnrg1901_CR125","doi-asserted-by":"publisher","first-page":"922","DOI":"10.1038\/35057141","volume":"409","author":"DD Shoemaker","year":"2001","unstructured":"Shoemaker, D. D. et al. Experimental annotation of the human genome using microarray technology. Nature 409, 922\u2013927 (2001).","journal-title":"Nature"},{"key":"BFnrg1901_CR126","doi-asserted-by":"publisher","first-page":"1149","DOI":"10.1126\/science.1108625","volume":"308","author":"J Cheng","year":"2005","unstructured":"Cheng, J. et al. Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science 308, 1149\u20131154 (2005).","journal-title":"Science"},{"key":"BFnrg1901_CR127","doi-asserted-by":"publisher","first-page":"916","DOI":"10.1126\/science.1068597","volume":"296","author":"P Kapranov","year":"2002","unstructured":"Kapranov, P. et al. Large-scale transcriptional activity in chromosomes 21 and 22. Science 296, 916\u2013919 (2002).","journal-title":"Science"},{"key":"BFnrg1901_CR128","doi-asserted-by":"publisher","first-page":"830","DOI":"10.1101\/gr.3430605","volume":"15","author":"TH Kim","year":"2005","unstructured":"Kim, T. H. et al. Direct isolation and identification of promoters in the human genome. Genome Res. 15, 830\u2013839 (2005).","journal-title":"Genome Res."},{"key":"BFnrg1901_CR129","doi-asserted-by":"publisher","first-page":"2306","DOI":"10.1126\/science.290.5500.2306","volume":"290","author":"B Ren","year":"2000","unstructured":"Ren, B. et al. Genome-wide location and function of DNA binding proteins. Science 290, 2306\u20132309 (2000). The first study that used a ChIP-on-chip approach for genome-wide mapping and functional analysis of DNA-binding proteins.","journal-title":"Science"},{"key":"BFnrg1901_CR130","doi-asserted-by":"publisher","first-page":"876","DOI":"10.1038\/nature03877","volume":"436","author":"TH Kim","year":"2005","unstructured":"Kim, T. H. et al. A high-resolution map of active promoters in the human genome. Nature 436, 876\u2013880 (2005).","journal-title":"Nature"},{"key":"BFnrg1901_CR131","doi-asserted-by":"publisher","first-page":"1559","DOI":"10.1126\/science.1112014","volume":"309","author":"P Carninci","year":"2005","unstructured":"Carninci, P. et al. The transcriptional landscape of the mammalian genome. Science 309, 1559\u20131563 (2005).","journal-title":"Science"},{"key":"BFnrg1901_CR132","doi-asserted-by":"publisher","first-page":"33","DOI":"10.1016\/j.cell.2005.05.008","volume":"122","author":"JS Carroll","year":"2005","unstructured":"Carroll, J. S. et al. Chromosome-wide mapping of estrogen receptor binding reveals long-range regulation requiring the forkhead protein FoxA1. Cell 122, 33\u201343 (2005).","journal-title":"Cell"},{"key":"BFnrg1901_CR133","doi-asserted-by":"publisher","first-page":"393","DOI":"10.1016\/j.molcel.2005.12.016","volume":"21","author":"AS Cheng","year":"2006","unstructured":"Cheng, A. S. et al. Combinatorial analysis of transcription factor partners reveals recruitment of c-MYC to estrogen receptor-\u03b1 responsive promoters. Mol. Cell 21, 393\u2013404 (2006).","journal-title":"Mol. Cell"},{"key":"BFnrg1901_CR134","doi-asserted-by":"publisher","first-page":"8164","DOI":"10.1073\/pnas.1332764100","volume":"100","author":"Z Li","year":"2003","unstructured":"Li, Z. et al. A global transcriptional regulatory role for c- Myc in Burkitt's lymphoma cells. Proc. Natl Acad. Sci. USA 100, 8164\u20138169 (2003).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"BFnrg1901_CR135","doi-asserted-by":"publisher","first-page":"2479","DOI":"10.1093\/hmg\/11.20.2479","volume":"11","author":"C Plass","year":"2002","unstructured":"Plass, C. Cancer epigenomics. Hum. Mol. Genet. 11, 2479\u20132488 (2002).","journal-title":"Hum. Mol. Genet."},{"key":"BFnrg1901_CR136","doi-asserted-by":"publisher","first-page":"S18","DOI":"10.1038\/ng1559","volume":"37","author":"B van Steensel","year":"2005","unstructured":"van Steensel, B. Mapping of genetic and epigenetic regulatory networks using microarrays. Nature Genet. 37, S18\u2013S24 (2005).","journal-title":"Nature Genet."},{"key":"BFnrg1901_CR137","doi-asserted-by":"publisher","first-page":"517","DOI":"10.1016\/j.cell.2005.06.026","volume":"122","author":"DK Pokholok","year":"2005","unstructured":"Pokholok, D. K. et al. Genome-wide map of nucleosome acetylation and methylation in yeast. Cell 122, 517\u2013527 (2005).","journal-title":"Cell"},{"key":"BFnrg1901_CR138","doi-asserted-by":"publisher","first-page":"169","DOI":"10.1016\/j.cell.2005.01.001","volume":"120","author":"BE Bernstein","year":"2005","unstructured":"Bernstein, B. E. et al. Genomic maps and comparative analysis of histone modifications in human and mouse. Cell 120, 169\u2013181 (2005).","journal-title":"Cell"},{"key":"BFnrg1901_CR139","doi-asserted-by":"publisher","first-page":"346","DOI":"10.2144\/03352rv01","volume":"35","author":"B van Steensel","year":"2003","unstructured":"van Steensel, B. & Henikoff, S. Epigenomic profiling using microarrays. Biotechniques 35, 346\u2013357 (2003).","journal-title":"Biotechniques"},{"key":"BFnrg1901_CR140","doi-asserted-by":"publisher","first-page":"e405","DOI":"10.1371\/journal.pbio.0020405","volume":"2","author":"VK Rakyan","year":"2004","unstructured":"Rakyan, V. K. et al. DNA methylation profiling of the human major histocompatibility complex: a pilot study for the human epigenome project. PLoS Biol. 2, e405 (2004). This work represents the first large-scale bisulphite sequencing effort for a large genomic region.","journal-title":"PLoS Biol."},{"key":"BFnrg1901_CR141","doi-asserted-by":"publisher","first-page":"11241","DOI":"10.1158\/0008-5472.CAN-05-3865","volume":"65","author":"PA Jones","year":"2005","unstructured":"Jones, P. A. & Martienssen, R. A blueprint for a Human Epigenome Project: The AACR Human Epigenome Workshop. Cancer Res 65, 11241\u201311246 (2005).","journal-title":"Cancer Res"},{"key":"BFnrg1901_CR142","doi-asserted-by":"publisher","first-page":"R3","DOI":"10.1093\/hmg\/ddi110","volume":"14","author":"A Murrell","year":"2005","unstructured":"Murrell, A., Rakyan, V. K. & Beck, S. From genome to epigenome. Hum. Mol. Genet. 14, R3\u2013R10 (2005).","journal-title":"Hum. Mol. Genet."},{"key":"BFnrg1901_CR143","doi-asserted-by":"publisher","first-page":"311","DOI":"10.1038\/30613","volume":"393","author":"TH Bestor","year":"1998","unstructured":"Bestor, T. H. Gene silencing. Methylation meets acetylation. Nature 393, 311\u2013312 (1998).","journal-title":"Nature"},{"key":"BFnrg1901_CR144","doi-asserted-by":"publisher","first-page":"2042","DOI":"10.1056\/NEJMra023075","volume":"349","author":"JG Herman","year":"2003","unstructured":"Herman, J. G. & Baylin, S. B. Gene silencing in cancer in association with promoter hypermethylation. N. Engl. J. Med. 349, 2042\u20132054 (2003).","journal-title":"N. Engl. J. Med."},{"key":"BFnrg1901_CR145","doi-asserted-by":"publisher","first-page":"158","DOI":"10.1101\/gr.202801","volume":"12","author":"RS Gitan","year":"2002","unstructured":"Gitan, R. S., Shi, H., Chen, C. M., Yan, P. S. & Huang, T. H. Methylation-specific oligonucleotide microarray: a new potential for high-throughput methylation analysis. Genome Res. 12, 158\u2013164 (2002).","journal-title":"Genome Res."},{"key":"BFnrg1901_CR146","doi-asserted-by":"publisher","first-page":"e21","DOI":"10.1093\/nar\/30.5.e21","volume":"30","author":"P Adorjan","year":"2002","unstructured":"Adorjan, P. et al. Tumour class prediction and discovery by microarray-based DNA methylation analysis. Nucleic Acids Res. 30, e21 (2002).","journal-title":"Nucleic Acids Res."},{"key":"BFnrg1901_CR147","doi-asserted-by":"publisher","first-page":"383","DOI":"10.1101\/gr.4410706","volume":"16","author":"M Bibikova","year":"2006","unstructured":"Bibikova, M. et al. High-throughput DNA methylation profiling using universal bead arrays. Genome Res. 16, 383\u2013393 (2006).","journal-title":"Genome Res."},{"key":"BFnrg1901_CR148","doi-asserted-by":"publisher","first-page":"282","DOI":"10.1101\/gr.4181406","volume":"16","author":"YW Cheng","year":"2006","unstructured":"Cheng, Y. W., Shawber, C., Notterman, D., Paty, P. & Barany, F. Multiplexed profiling of candidate genes for CpG island methylation status using a flexible PCR\/LDR\/Universal Array assay. Genome Res. 16, 282\u2013289 (2006).","journal-title":"Genome Res."},{"key":"BFnrg1901_CR149","doi-asserted-by":"publisher","first-page":"219","DOI":"10.1038\/nmeth0305-219","volume":"2","author":"Z Lippman","year":"2005","unstructured":"Lippman, Z., Gendrel, A. V., Colot, V. & Martienssen, R. Profiling DNA methylation patterns using genomic tiling microarrays. Nature Methods 2, 219\u2013224 (2005).","journal-title":"Nature Methods"},{"key":"BFnrg1901_CR150","doi-asserted-by":"publisher","first-page":"528","DOI":"10.1093\/nar\/gkj461","volume":"34","author":"A Schumacher","year":"2006","unstructured":"Schumacher, A. et al. Microarray-based DNA methylation profiling: technology and applications. Nucleic Acids Res. 34, 528\u2013542 (2006).","journal-title":"Nucleic Acids Res."},{"key":"BFnrg1901_CR151","doi-asserted-by":"publisher","first-page":"2952","DOI":"10.1093\/nar\/gki582","volume":"33","author":"LE Heisler","year":"2005","unstructured":"Heisler, L. E. et al. CpG Island microarray probe sequences derived from a physical library are representative of CpG Islands annotated on the human genome. Nucleic Acids Res. 33, 2952\u20132961 (2005).","journal-title":"Nucleic Acids Res."},{"key":"BFnrg1901_CR152","doi-asserted-by":"publisher","first-page":"853","DOI":"10.1038\/ng1598","volume":"37","author":"M Weber","year":"2005","unstructured":"Weber, M. et al. Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells. Nature Genet. 37, 853\u2013862 (2005).","journal-title":"Nature Genet."},{"key":"BFnrg1901_CR153","doi-asserted-by":"publisher","first-page":"57","DOI":"10.1016\/S0092-8674(00)81683-9","volume":"100","author":"D Hanahan","year":"2000","unstructured":"Hanahan, D. & Weinberg, R. A. The hallmarks of cancer. Cell 100, 57\u201370 (2000).","journal-title":"Cell"},{"key":"BFnrg1901_CR154","doi-asserted-by":"publisher","first-page":"S31","DOI":"10.1038\/ng1570","volume":"37","author":"DR Rhodes","year":"2005","unstructured":"Rhodes, D. R. & Chinnaiyan, A. M. Integrative analysis of the cancer transcriptome. Nature Genet. 37, S31\u2013S37 (2005).","journal-title":"Nature Genet."},{"key":"BFnrg1901_CR155","doi-asserted-by":"publisher","first-page":"579","DOI":"10.1038\/ng1578","volume":"37","author":"DR Rhodes","year":"2005","unstructured":"Rhodes, D. R. et al. Mining for regulatory programs in the cancer transcriptome. Nature Genet. 37, 579\u2013583 (2005).","journal-title":"Nature Genet."},{"key":"BFnrg1901_CR156","doi-asserted-by":"publisher","first-page":"870","DOI":"10.1101\/gr.2255804","volume":"14","author":"KL Gunderson","year":"2004","unstructured":"Gunderson, K. L. et al. Decoding randomly ordered DNA arrays. Genome Res. 14, 870\u2013877 (2004).","journal-title":"Genome Res."}],"container-title":["Nature Reviews Genetics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/www.nature.com\/articles\/nrg1901.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/www.nature.com\/articles\/nrg1901","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/www.nature.com\/articles\/nrg1901.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,5,19]],"date-time":"2023-05-19T04:02:45Z","timestamp":1684468965000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/nrg1901"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2006,8]]},"references-count":156,"journal-issue":{"issue":"8","published-print":{"date-parts":[[2006,8]]}},"alternative-id":["BFnrg1901"],"URL":"https:\/\/doi.org\/10.1038\/nrg1901","relation":{},"ISSN":["1471-0056","1471-0064"],"issn-type":[{"value":"1471-0056","type":"print"},{"value":"1471-0064","type":"electronic"}],"subject":[],"published":{"date-parts":[[2006,8]]}}}