Source: https://patents.justia.com/patent/9695468
Timestamp: 2019-10-23 03:06:33
Document Index: 537811185

Matched Legal Cases: ['Application No. 61', 'Application No. 61', 'Application No. 61', 'Application No. 61', 'Application No. 61', 'Application No. 61']

US Patent for Methods for droplet-based sample preparation Patent (Patent # 9,695,468 issued July 4, 2017) - Justia Patents Search
Justia Patents Involving Nucleic AcidUS Patent for Methods for droplet-based sample preparation Patent (Patent # 9,695,468)
This application is a continuation of U.S. patent application Ser. No. 13/966,150, filed Aug. 13, 2013, which applications claim the benefit of U.S. Provisional Patent Application No. 61/683,192, filed Aug. 14, 2012; U.S. Provisional Patent Application No. 61/737,374, filed Dec. 14, 2012; U.S. Provisional Patent Application No. 61/762,435, filed Feb. 8, 2013; U.S. Provisional Patent Application No. 61/800,223, filed Mar. 15, 2013; U.S. Provisional Patent Application No. 61/840,403, filed Jun. 27, 2013; and U.S. Provisional Patent Application No. 61/844,804, filed Jul. 10, 2013, which applications are incorporated herein by reference in their entireties for all purposes.
“ ⁢ fraction ⁢ ⁢ multi ⁢ - ⁢ occupancy ” = 1 - [ ( 1 - 1 N ) + p N ] C
(a) providing at least 1,000,000 oligonucleotide molecules comprising barcode sequences, wherein said barcode sequences are the same sequence for said at least 1,000,000 oligonucleotide molecules, wherein said at least 1,000,000 oligonucleotide molecules are releasably attached to a bead, wherein said bead is porous;
(b) combining said at least 1,000,000 oligonucleotide molecules and a sample comprising a nucleic acid analyte each in an aqueous phase at a first junction of two or more channels of a microfluidic device to form an aqueous mixture comprising said at least 1,000,000 oligonucleotide molecules attached to said bead and said sample; and
(c) generating a droplet comprising said at least 1,000,000oligonucleotide molecules attached to said bead and said sample comprising said nucleic acid analyte by contacting said aqueous mixture with an immiscible continuous phase at a second junction of two or more channels of said microfluidic device.
2. The method of claim 1, further comprising, in (b), combining said at least 1,000,000 oligonucleotide molecules attached to said bead, said nucleic acid analyte and one or more reagents necessary for amplification of said nucleic acid analyte at said first junction to form said aqueous mixture comprising said at least 1,000,000 oligonucleotide molecules attached to said bead, said nucleic acid analyte and said one or more reagents.
3. The method of claim 2, wherein in (c), said droplet further comprises said one or more reagents.
4. The method of claim 3, wherein said one or more reagents comprises a polymerase.
5. The method of claim 4, wherein said polymerase is unable to recognize uracil.
6. The method of claim 1, wherein said bead comprises a polyacrylamide.
7. The method of claim 1, wherein said bead is a gel bead.
8. The method of claim 1, wherein said at least 1,000,000 oligonucleotide molecules comprise uracil.
9. The method of claim 1, wherein a given oligonucleotide molecule of said at least 1,000,000 oligonucleotide molecules comprises a region which functions as a primer.
10. The method of claim 9, wherein said region which functions as said primer has a sequence for random priming.
11. The method of claim 9, further comprising, after (c), amplifying said nucleic acid analyte with said primer.
12. The method of claim 1, wherein said nucleic acid analyte is selected from the group consisting of deoxyribonucleic acid (DNA), ribonucleic acid (RNA), amplicons, synthetic polynucleotides, polynucleotides, oligonucleotides, cDNA, dsDNA, ssDNA, plasmid DNA, cosmid DNA, High Molecular Weight (MW) DNA, chromosomal DNA, genomic DNA, viral DNA, bacterial DNA, mtDNA (mitochondrial DNA), mRNA, rRNA, tRNA, nRNA, siRNA, snRNA, snoRNA, scaRNA, microRNA, dsRNA, ribozyme, riboswitch and viral RNA.
13. The method of claim 1, wherein said at least 1,000,000 oligonucleotide molecules are attached to said bead via a chemical cross-linker.
14. The method of claim 1, wherein said at least 1,000,000 oligonucleotide molecules are attached to said bead via a disulfide bond.
15. The method of claim 1, wherein said at least 1,000,000 oligonucleotide molecules are attached to said bead via a covalent bond.
16. The method of claim 1, wherein said at least 1,000,000 oligonucleotide molecules are attached to said bead via a labile moiety.
17. The method of claim 1, wherein said bead is degradable upon application of a stimulus.
18. The method of claim 17, further comprising applying said stimulus to the droplet to release said at least 1,000,000 oligonucleotide molecules from said bead into said droplet.
19. The method of claim 18, wherein said stimulus is selected from the group consisting of a biological stimulus, a chemical stimulus, a thermal stimulus, an electrical stimulus, a magnetic stimulus, and a photo stimulus.
20. The method of claim 19, wherein said stimulus is a chemical stimulus that is a reducing agent.
21. The method of claim 1, wherein subsequent to generating said droplet in (c), a given oligonucleotide molecule of said at least 1,000,000 oligonucleotide molecules attaches to said nucleic acid analyte, and wherein said given oligonucleotide molecule attached to said given nucleic acid analyte is subjected to nucleic acid amplification to yield a barcoded nucleic acid analyte.
22. The method of claim 1, wherein said bead comprises a chemical cross-linker.
23. The method of claim 22, wherein said chemical cross-linker is a disulfide bond.
8986286 March 24, 2015 Tanghoj et al.
20160024558 January 28, 2016 Hardenbol
Aaron P. Esser-Kahn, Triggered Release from Polymer Capsules, 2011, Macromolecules, 44, 5539-5553.
Chaudhary “A rapid method of cloning functioNal variable-region antibody genese in Escherichia coli as single-chain imrnunotoxins” Proc. Nat!. Acad. Sci USA 87: 1066-1070 (Feb. 1990).
Demirci, et al. Single cell epitaxy by acoustic picolitre droplets. Lab Chip. 2007 Sep;7(9):1139-45. Epub Jul. 10, 2007.
Kim, et al. Albumin loaded microsphere of amphiphilic poly(ethylene glycol)/ poly(alpha-ester) multiblock copolymer. Eur J Pharm Sci. Nov. 2004;23(3):245-51.
Office action dated Oct. 9, 2015 for US Appl. No. 14/680,808.
Chung, et al. Structural and molecular interrogation of intact biological systems. Nature. May 16, 2013;497(7449):332-7. doi: 10.1038/nature12107. Epub Apr. 10, 2013.
Dekker, et al. Capturing chromosome conformation. Science. Feb. 15, 2002;295(5558):1306-11.
Karmakar, et al. Organocatalytic removal of formaldehyde adducts from RNA and DNA bases. Nat Chem. Sep. 2015;7(9):752-8. doi: 10.1038/nchem.2307. Epub Aug. 3, 2015.
Anonymous: “Viscosity-Basic concepts” (2004) XP055314117, Retrieved from the Internet: URL:http://lhtc.epfl.ch/webdav/site/Ihtc/shared/import/migration/2 VISCOSITY.pdf.
Christiansen et al. “The Covalent Eukaryotic Topoisomerase I-DNA Intermediate Catalyzes pH-dependent Hydrolysis and Alcholysis” J Biol Chem (Apr. 14, 1994) 269(15):11367-11373.
Guo, et al. Droplet microfluidics for high-throughput biological assays. Lab Chip. Jun. 21, 2012;12(12):2146-55. doi: 10.1039/c21c21147e. Epub Feb. 9, 2012.
Ioannidis, N. Manufacturing of Agarose-Based Chromatographic Adsorbents With Controlled Pore and Particle Sizes. A thesis submitted to The University of Birmingham for the degree of Doctor of Philosophy. 2009.
Klein, et al. Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells. Cell. May 21, 2015;161(5):1187-201. doi: 10.1016/j.ce11.2015.04.044.
Macosko, et al. Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets. Cell. May 21, 2015;161(5)1202-14. doi: 10.1016/j.ce11.2015.05.002.
Mozhanova, A.A. et al. “Local elastic properties of biological materials studied by SFM” (2003) XP055314108, Retrieved from the Internet: URL:http://www.ntmdt.com/data/media/files/publications/2003/08.08—a.a.mozhanova—nin—english.pdf.
Patel, et al. Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma. Science. Jun. 20, 2014;244(6190):1396-401. doi: 10.1126/science.1254257. Epub Jun. 12, 2014.
Ram, et al. Strategy for microbiome analysis using 16S rRNA gene sequence analysis on the Illumina sequencing platform. Syst Biol Reprod Med. Jun. 2011;57(3):162-70. doi: 10.3109/19396368.2011.555598. Epub Mar. 1, 2011.
Tayyab, S. et al. “Size exclusion chromatography and size exclusion HPLC of proteins” Biochem Ed, Pergamon, (1991) 19(3):149-152.
Tonelli, et al. Perfluoropolyether functional oligomers: unusual reactivity in organic chemistry. Journal of fluorine chemistry. 2002; 118(1)″107-121.
“Dressman et al. Transforming single DNA molecules into fluorescent magnetic particles for detection and enumeration of genetic variations. Proc. Natl. Acad. Sci. 2003. 100(15):8817-8822.”
Patent number: 9695468
Patent Publication Number: 20150225778
Application Number: 14/624,473
International Classification: C12Q 1/68 (20060101); C12P 19/34 (20060101); C07H 21/04 (20060101); G01N 15/06 (20060101); C40B 50/14 (20060101); C12N 15/10 (20060101); B01L 3/00 (20060101); B01J 19/00 (20060101);