Gold nanoparticles for high-throughput genotyping of long-range haplotypes

Nature Nanotechnology

Volumn 6, Issue 10, 2011, Pages 639-644

  Chen, Peng ^a   Pan, Dun ^b   Fan, Chunhai ^a,b   Chen, Jianhua ^a   Huang, Ke ^a   Wang, Dongfang ^b   Zhang, Honglu ^b   Li, You ^a   Feng, Guoyin ^a   Liang, Peiji ^a   He, Lin ^a,c,d   Shi, Yongyong ^a,e  

^a SHANGHAI JIAO TONG UNIVERSITY   (China)

^b SHANGHAI INSTITUTE OF APPLIED PHYSICS   (China)

^c Shanghai Jiao Tong University Affiliated Sixth People s Hospital   (China)

^d FUDAN UNIVERSITY   (China)

^e Changning Mental Health Center   (China)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; DRUG DELIVERY; FIBER OPTIC SENSORS; GENE ENCODING; METAL NANOPARTICLES; POLYMERASE CHAIN REACTION;

AGE-RELATED MACULAR DEGENERATION; COMPLEX TRAITS; DNA VARIATIONS; DRUG RESISTANCE; GENETIC ANALYSIS; HIGH THROUGHPUT; HIGH THROUGHPUT GENOTYPING; HUMAN GENOME PROJECT;

GOLD NANOPARTICLES;

GENOMIC DNA; GOLD NANOPARTICLE;

ARTICLE; CAPILLARY; DISEASE ASSOCIATION; DNA SEQUENCE; DRUG RESISTANCE; GENETIC ANALYSIS; GENETIC SUSCEPTIBILITY; GENOTYPE; HAPLOTYPE; HUMAN; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PSORIASIS; RETINA MACULA AGE RELATED DEGENERATION;

EID: 80455155017     PISSN: 17483387     EISSN: 17483395     Source Type: Journal    
DOI: 10.1038/nnano.2011.141     Document Type: Article

References (30)

1. McPherson, J. D. et al. A physical map of the human genome. Nature 409, 934-941 (2001). (Pubitemid 32165348)
2. Frazer, K. A. & Consortium, T. I. H. A second generation human haplotype map of over 3.1 million SNPs. Nature 449, 851-861 (2007). (Pubitemid 47598626)
3. Douglas, J. A., Boehnke, M., Gillanders, E., Trent, J. M. & Gruber, S. B. Experimentally-derived haplotypes substantially increase the efficiency of linkage disequilibrium studies. Nature Genet. 28, 361-364 (2001). (Pubitemid 32702426)
4. Xiao, M., et al. Direct determination of haplotypes from single DNA molecules. Nature Methods 6, 199-201 (2009).
5. Kwok, P. Y. & Xiao, M. Single-molecule analysis for molecular haplotyping. Hum. Mutat. 23, 442-446 (2004). (Pubitemid 38569216)
6. DeWan, A., et al. HTRA1 promoter polymorphism in wet age-related macular degeneration. Science 314, 989-992 (2006).
7. Fritsche, L. G. et al. Age-related macular degeneration is associated with an unstable ARMS2 (LOC387715) mRNA. Nature Genet. 40, 892-896 (2008). (Pubitemid 351913654)
8. Kanda, A., et al. A variant of mitochondrial protein LOC387715/ARMS2, not HTRA1, is strongly associated with age-related macular degeneration. Proc. Natl Acad. Sci. USA 104, 16227-16232 (2007). (Pubitemid 350099389)
9. Zhang, X. J. et al. Psoriasis genome-wide association study identifies susceptibility variants within LCE gene cluster at 1q21. Nature Genet. 41, 205-210 (2009).
10. Collins, F. S., Guyer, M. S. & Chakravarti, A. Variations on a theme: cataloging human DNA sequence variation. Science 278, 1580-1581 (1997). (Pubitemid 27516268)
11. Folstein, S. & Rutter, M. Genetic influences and infantile autism. Nature 265, 726-728 (1977). (Pubitemid 8039452)
12. Collins, F. S., Brooks, L. D. & Chakravarti, A. A DNA polymorphism discovery resource for research on human genetic variation. Genome Res. 8, 1229-1231 (1998). (Pubitemid 29039095)
13. Kwok, P. Y. Methods for genotyping single nucleotide polymorphisms. Annu. Rev. Genom. Hum. Genet. 2, 235-258 (2001).
14. Beaudet, A. L. & Belmont, J.W. Array-based DNA diagnostics: let the revolution begin. Ann. Rev. Med. 59, 113-129 (2008). (Pubitemid 351287927)
15. Rosi, N. L. & Mirkin, C. A. Nanostructures in biodiagnostics. Chem. Rev. 105, 1547-1562 (2005). (Pubitemid 40596871)
16. Lu, Y. & Liu, J. Smart nanomaterials inspired by biology: dynamic assembly of error-free nanomaterials in response to multiple chemical stimuli. Acc. Chem. Res. 40, 315-323 (2007).
17. Li, H., et al. Nanoparticle PCR: nanogold-assisted PCR with enhanced specificity. Angew. Chem. Int. Ed. 44, 5100-5103 (2005). (Pubitemid 41188553)
18. Li, M., Lin, Y. C., Wu, C. C. & Liu, H. S. Enhancing the efficiency of a PCR using gold nanoparticles. Nucleic Acids Res. 33, e184 (2005).
19. Mi, L., et al. Modulation of DNA polymerases with gold nanoparticles and their applications in hot-start PCR. Small 5, 2597-2600 (2009).
20. Rosi, N. L. et al. Smart nanomaterials inspired by biology: dynamic assembly of error-free nanomaterials in response to multiple chemical stimuli. Science 312, 1027-1030 (2006).
21. Li, H. & Rothberg, L. Colorimetric detection of DNA sequences based on electrostatic interactions with unmodified gold nanoparticles. Proc. Natl Acad. Sci. USA 101, 14036-14039 (2004). (Pubitemid 39305025)
22. Sharma, J., et al. Control of self-assembly of DNA tubules through integration of gold nanoparticles. Science 323, 112-116 (2009).
23. Herdt, A. R., Drawz, S. M., Kang, Y. & Taton, T. A. DNA dissociation and degradation at gold nanoparticle surfaces. Colloid. Surface. B 51, 130-139 (2006). (Pubitemid 44234081)
24. Tost, J., et al. Molecular haplotyping at high throughput. Nucleic Acids Res. 30, e96 (2002).
25. Voelkerding, K. V., Dames, S. & Durtschi, J. D. Next generation sequencing for clinical diagnostics-principles and application to targeted resequencing for hypertrophic cardiomyopathy. J. Mol. Diag. 12, 539-551 (2010).
26. Shendure, J. & Ji, H. Next-generation DNA sequencing. Nature Biotechnol. 26, 1146-1153 (2008).
27. Stephens, M., Smith, N. J. & Donnelly, P. A new statistical method for haplotype reconstruction from population data. Am. J. Hum. Genet. 68, 978-989 (2001). (Pubitemid 32289743)
28. Levenstien, M. A., Ott, J. & Gordon, D. Are molecular haplotypes worth the time and expense? A cost-effective method for applying molecular haplotypes. PLOS Genet. 2, e127 (2006).
29. Fan, H. C., Wang, J., Potanina, A. & Quake, S. R. Whole-genome molecular haplotyping of single cells. Nature Biotechnol. 29, 51-57 (2010).
30. Kitzman, J. O. et al. Haplotype-resolved genome sequencing of a Gujarati Indian individual. Nature Biotechnol. 29, 59-63 (2010).