Chemistry: molecular biology and microbiology – Measuring or testing process involving enzymes or... – Involving nucleic acid
Reexamination Certificate
2006-05-01
2008-11-18
Whisenant, Ethan (Department: 1634)
Chemistry: molecular biology and microbiology
Measuring or testing process involving enzymes or...
Involving nucleic acid
C536S023100, C536S024300
Reexamination Certificate
active
07452671
ABSTRACT:
The present invention provides methods for reducing the complexity of a nucleic acid sample to interrogate a collection of target sequences. Complexity reduction can be accomplished by fragmenting the nucleic acid sample with a restriction enzyme that has at least one variable position in the recognition sequence. In some aspects adaptors that ligate to some but not all possible overhangs generated by digestion are ligated to the fragments. Selective adaptor ligation allows for selective amplification of a subset of the fragments using primers complementary to the adaptor sequence. In another aspect primers that are complementary to a subset of the fragments after adaptor ligation are used for amplification. Reduced complexity samples generated by the disclosed methods may be interrogated for the genotypes of SNPs in the sample.
REFERENCES:
patent: 5002867 (1991-03-01), Macevicz
patent: 5143854 (1992-09-01), Pirrung et al.
patent: 5202231 (1993-04-01), Drmanac et al.
patent: 5387505 (1995-02-01), Wu
patent: 5492806 (1996-02-01), Drmanac et al.
patent: 5498535 (1996-03-01), Fomenkov et al.
patent: 5501964 (1996-03-01), Wigler et al.
patent: 5508169 (1996-04-01), Deugau et al.
patent: 5580730 (1996-12-01), Okamoto
patent: 5582989 (1996-12-01), Caskey et al.
patent: 5624825 (1997-04-01), Walker et al.
patent: 5667972 (1997-09-01), Drmanac et al.
patent: 5695940 (1997-12-01), Drmanac et al.
patent: 5700637 (1997-12-01), Southern
patent: 5700642 (1997-12-01), Monforte et al.
patent: 5710000 (1998-01-01), Sapolsky et al.
patent: 5776753 (1998-07-01), Hillman et al.
patent: 5854033 (1998-12-01), Lizardi
patent: 5858656 (1999-01-01), Deugau et al.
patent: 5972693 (1999-10-01), Rothberg et al.
patent: 5994068 (1999-11-01), Guilfoyle et al.
patent: 6045994 (2000-04-01), Zabeau et al.
patent: 6100030 (2000-08-01), McCasky Feazel et al.
patent: 6197510 (2001-03-01), Vinayagamoorthy
patent: 6232066 (2001-05-01), Felder et al.
patent: 6258539 (2001-07-01), Hunkapiller et al.
patent: 6280935 (2001-08-01), Macevicz
patent: 6280950 (2001-08-01), Lipshutz et al.
patent: 6322971 (2001-11-01), Chetverin et al.
patent: 6352828 (2002-03-01), Brenner
patent: 6355431 (2002-03-01), Chee et al.
patent: 6361947 (2002-03-01), Dong et al.
patent: 6509160 (2003-01-01), Sapolsky et al.
patent: 6703228 (2004-03-01), Landers et al.
patent: 6720179 (2004-04-01), Macevicz
patent: 6773886 (2004-08-01), Kaufman et al.
patent: 6777187 (2004-08-01), Makarov et al.
patent: 6812005 (2004-11-01), Fan et al.
patent: 7108976 (2006-09-01), Jones et al.
patent: 2003/0036069 (2003-02-01), Su
patent: 2004/0067493 (2004-04-01), Matsuzaki et al.
patent: 2004/0110153 (2004-06-01), Dong et al.
patent: 2005/0100911 (2005-05-01), Patil et al.
patent: 2005/0148004 (2005-07-01), Wober et al.
patent: 2006/0063158 (2006-03-01), Dong et al.
patent: 2006/0073501 (2006-04-01), Van Den Boom et al.
patent: 2006/0246457 (2006-11-01), Dirks et al.
patent: 2007/0065816 (2007-03-01), Dong et al.
patent: 0534858 (1993-03-01), None
patent: 1350853 (2003-10-01), None
patent: WO 96/41893 (1996-12-01), None
patent: WO 01/88174 (2001-11-01), None
Unrau et al. Non-cloning amplification of specific DNBA fragments from whole genomic DNA digests using DNA ‘indexers’ Gene 145 : 163-169 (1994).
Szybalski et al. Class-IIS restriction enzymes—a review Gene 100 : 13-26 (1991).
Smith DR. Ligation Mediated PCR of restriction fragments from large DNA molecules. PCR Methods and Applications 2 : 21-27 (1992).
Patel et al. A novel and rapid method for isolating sequences adjacent to rare cutting sites and their use in physical mapping. Nucleic Acids Research 19 (16) : 4371-4375 (1991).
Broude et al., High Level Multiplex DNA Amplification;Antisense&Nucleic Acid Drug Development, 2001, 11: 327-332.
Broude et al., Multiplex Allele-Specific Target Amplifcation Based on PCR Suppression,PNA, Jan. 2, 2001, 98:1, 206-2111.
Craig et al., Removal of Repetitive Sequences from FISH probes using PCR-assisted affinity chromatography; Human Genetics, vol. 100, No. 3-4, 1997, pp. 472-476.
Durm et al., Fast-painting of Human Metaphase Spreads Using a Chromosome-Specific, Repeat-Depleted DNA Library Probe; Biotechniques, Eaton Publishing; Vo. 24; No. 5; May 1988; pp. 820-825.
Siebert et al., An Improved PCR Method for Walking an Uncloned Genomic DNA,Nucleic Acids Research, 1995, 23:6, 1087-1088.
Jones Keith W.
Shapero Michael H.
Affymetrix Inc.
Wells Sandra E.
Whisenant Ethan
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