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REFERENCES

QUATITATIVE DIGITAL PCR

Beer NR, Wheeler EK, Lee-Houghton L, Watkins N, Nasarabadi S, Hebert N, Leung P, Arnold DW, Bailey CG, Colston BW. On-chip single-copy real-time reverse-transcription PCR in isolated picoliter droplets. Anal Chem. 2008 Mar 15;80(6):1854-8.

Diehl F, Schmidt K, Durkee KH, Moore KJ, Goodman SN, Shuber AP, Kinzler KW, Vogelstein B. Analysis of mutations in DNA isolated from plasma and stool of colorectal cancer patients. Gastroenterology. 2008 Aug;135(2):489-98. Epub 2008 May 15.

Dube S, Qin J, Ramakrishnan R. Mathematical analysis of copy number variation in a DNA sample using digital PCR on a nanofluidic device. PLoS ONE. 2008 Aug 6;3(8):e2876.

Lun FM, Chiu RW, Chan KC, Leung TY, Lau TK, Lo YM. Microfluidics Digital PCR Reveals a Higher than Expected Fraction of Fetal DNA in Maternal Plasma. Clin Chem. 2008 Aug 14.

McCaughan F, Darai-Ramqvist E, Bankier A, Konfortov B, Foster N, George P, Rabbitts T, Kost-Alimova M, Rabbitts P, Dear P.  Microdissection molecular copy-number counting (microMCC)-unlocking cancer archives with digital PCR. J Pathol. 2008 Jul 29.

Qin J, Jones RC, Ramakrishnan R. Studying copy number variations using a nanofluidic platform. Nucleic Acids Res. 2008 Aug 18.

Weisenberger DJ, Trinh BN, Campan M, Sharma S, Long TI, Ananthnarayan S, Liang G, Esteva FJ, Hortobagyi GN, McCormick F, Jones PA, Laird PW. DNA methylation analysis by digital bisulfite genomic sequencing and digital MethyLight. Nucleic Acids Res. 2008 Aug;36(14):4689-98.

Diehl F, Diaz LA Jr.  Digital quantification of mutant DNA in cancer patients. Curr Opin Oncol. 2007 Jan;19(1):36-42.

Lo YM, Lun FM, Chan KC, Tsui NB, Chong KC, Lau TK, Leung TY, Zee BC, Cantor CR, Chiu RW. Digital PCR for the molecular detection of fetal chromosomal aneuploidy.  Proc Natl Acad Sci U S A. 2007 Aug 7;104(32):13116-21.

Rago C, Huso DL, Diehl F, Karim B, Liu G, Papadopoulos N, Samuels Y, Velculescu VE, Vogelstein B, Kinzler KW, Diaz LA Jr. Serial assessment of human tumor burdens in mice by the analysis of circulating DNA. Cancer Res. 2007 Oct 1;67(19):9364-70.

Schmidt K, Diehl F. A blood-based DNA test for colorectal cancer screening. Discov Med. 2007 Feb;7(37):7-12.

Li M, Diehl F, Dressman D, Vogelstein B, Kinzler KW. BEAMing up for detection and quantification of rare sequence variants. Nat Methods. 2006 Feb;3(2):95-7.

Ottesen EA, Hong JW, Quake SR, Leadbetter JR. Microfluidic digital PCR enables multigene analysis of individual environmental bacteria. Science. 2006 Dec 1;314(5804):1464-7.

Rübben A, Bausch B, Nikkels A. Somatic deletion of the NF1 gene in a neurofibromatosis type 1-associated malignant melanoma demonstrated by digital PCR. Mol Cancer. 2006 Sep 10;5:36.

Matsubara Y, Kerman K, Kobayashi M, Yamamura S, Morita Y, Tamiya E. Microchamber array based DNA quantification and specific sequence detection from a single copy via PCR in nanoliter volumes. Biosens Bioelectron. 2005 Feb 15;20(8):1482-90.

Matsubara Y, Kerman K, Kobayashi M, Yamamura S, Morita Y, Takamura Y, Tamiya E. On-chip nanoliter-volume multiplex TaqMan polymerase chain reaction from a single copy based on counting fluorescence released microchambers.  Anal Chem. 2004 Nov 1;76(21):6434-9.

Pohl G, Shih IeM. Principle and applications of digital PCR. Expert Rev Mol Diagn. 2004 Jan;4(1):41-7.

Traverso G, Shuber A, Levin B, Johnson C, Olsson L, Schoetz DJ Jr, Hamilton SR, Boynton K, Kinzler KW, Vogelstein B. Detection of APC mutations in fecal DNA from patients with colorectal tumors. N Engl J Med. 2002 Jan 31;346(5):311-20. PMID: 11821507.

Dong SM, Traverso G, Johnson C, Geng L, Favis R, Boynton K, Hibi K, Goodman SN, D'Allessio M, Paty P, Hamilton SR, Sidransky D, Barany F, Levin B, Shuber A, Kinzler KW, Vogelstein B, Jen J. Detecting colorectal cancer in stool with the use of multiple genetic targets. J Natl Cancer Inst. 2001 Jun 6;93(11):858-65.

Zhou W, Galizia G, Lieto E, Goodman SN, Romans KE, Kinzler KW, Vogelstein B, Choti MA, Montgomery EA. Counting alleles reveals a connection between chromosome 18q loss and vascular invasion. Nat Biotechnol. 2001 Jan;19(1):78-81. Erratum in: Nat Biotechnol 2001 Mar;19(3):277.

Vogelstein B, Kinzler KW. Digital PCR. Proc Natl Acad Sci U S A. 1999 Aug 3;96(16):9236-41.

Kalinina O, Lebedeva I, Brown J, Silver J. Nanoliter scale PCR with TaqMan detection.Nucleic Acids Res. 1997

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SECOND GENERATION SEQUENCING

Droege M, Hill B. The Genome Sequencer FLXtrade mark System-Longer reads, more applications, straight forward bioinformatics and more complete data sets. J Biotechnol. 2008 Aug 31;136(1-2):3-10.

Huang W, Marth G. EagleView: a genome assembly viewer for next-generation sequencing technologies. Genome Res. 2008 Sep;18(9):1538-43.

Mardis ER. The impact of next-generation sequencing technology on genetics.  Trends Genet. 2008 Mar;24(3):133-41.

Smith AD, Xuan Z, Zhang MQ. Using quality scores and longer reads improves accuracy of Solexa read mapping. BMC Bioinformatics. 2008 Feb 28;9:128.

Lasken RS. Single-cell genomic sequencing using Multiple Displacement Amplification.  Curr Opin Microbiol. 2007 Oct;10(5):510-6.


Issued Patents

6,391,559	Method of sampling, amplifying and quantifying segment of nucleic acid, polymerase chain reaction assembly having nanoliter-sized sample chambers, and method of filling assembly
6,143,496	Method of sampling, amplifying and quantifying segment of nucleic acid, polymerase chain reaction assembly having nanoliter-sized sample chambers, and method of filling assembly

Published Patent Applications

20080213766	METHOD AND DEVICE FOR DETECTING THE PRESENCE OF A SINGLE TARGET NUCLEIC ACID IN SAMPLES
20080171382	METHOD AND DEVICE FOR DETECTING THE PRESENCE OF A SINGLE TARGET NUCLEIC ACID IN A SAMPLE
20080171380	MICROFLUIDIC ASSEMBLY WITH REAGENT
20080171327	METHOD AND DEVICE FOR DETECTING THE PRESENCE OF A SINGLE TARGET NUCLEIC ACID IN A SAMPLE
20080171326	METHOD AND DEVICE FOR DETECTING THE PRESENCE OF A SINGLE TARGET NUCLEIC ACID IN A SAMPLE
20080171325	METHOD AND DEVICE FOR DETECTING THE PRESENCE OF A SINGLE TARGET NUCLEIC ACID IN A SAMPLE
20080171324	METHOD FOR QUANTIFYING NUMBER OF MOLECULES OF TARGET NUCLEIC ACID CONTAINED IN A SAMPLE
20080169184	DEVICE HAVING REGIONS OF DIFFERING AFFINITIES TO FLUID, METHODS OF MAKING SUCH DEVICES, AND METHODS OF USING SUCH DEVICES
20080160525	METHOD AND DEVICE FOR DETECTING THE PRESENCE OF A SINGLE TARGET NUCLEIC ACID IN A SAMPLE
20080153091	METHOD AND DEVICE FOR DETECTING THE PRESENCE OF TARGET NUCLEIC ACIDS IN A SAMPLE, AND MICROFLUIDIC DEVICE FOR USE IN SUCH METHODS
20080138815	METHOD OF LOADING SAMPLE INTO A MICROFLUIDIC DEVICE
20040171055	Method for detecting the presence of a single target nucleic acid in a sample
20020164820	Method of sampling, amplifying and quantifying segment of nucleic acid, polymerase chain reaction assembly having nanoliter-sized sample chambers, and method of filling assembly

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