A C T G T Ta G Cta a Tt G G-1 Ref

USOO6309823B1 (12) United States Patent (10) Patent No.: US 6,309,823 B1 Cronin et al. (45) Date of Patent: *Oct. 30, 2001 (54) ARRAYS OF NUCLEC ACID PROBES FOR (56) References Cited ANALYZING BIOTRANSFORMATION U.S. PATENT DOCUMENTS GENES AND METHODS OF USING THE SAME 4,656,127 4/1987 Mundy ..................................... 435/6 (75) Inventors: Maureen T. Cronin, Los Altos, (List continued on next page.) Charles G. Miyada, San Jose; Earl A. FOREIGN PATENT DOCUMENTS Hubbell, Los Angeles; Mark Chee; Stephen P. A. Fodor, both of Palo WO 89/10977 11/1989 (WO) .............................. C12O/1/68 Alto; Xiaohua C. Huang, Mountain WO 89/11548 11/1989 (WO) .............................. C12O/1/68 View; Robert J. Lipshutz, Palo Alto; (List continued on next page.) Peter E. Lobban, Mountain View; OTHER PUBLICATIONS MacDonald S. Morris, Felton; Edward Chee et al., “Towards sequencing mitochondrial DNA poly L. Sheldon, San Diego, all of CA (US) morphisms by hybridization to a custom oligonucleotide (73) Assignee: Affymetrix, Inc., Santa Clara, CA (US) probe array,' poster, American Society of Human Genetics, 43rd Annual Meeting, Oct. 5-9, 1993, New Orleans, LA (*) Notice: Subject to any disclaimer, the term of this patent is extended or adjusted under 35 (abstract). U.S.C. 154(b) by 0 days. (List continued on next page.) Primary Examiner Ardin H. Marschel This patent is Subject to a terminal dis (74) Attorney, Agent, or Firm Townsend and Townsend claimer. and Crew LLP (21) Appl. No.: 08/778,794 (57) ABSTRACT (22) Filed: Jan. 3, 1997 The invention provides arrays of immobilized probes, and methods employing the arrays, for detecting mutations in the Related U.S. Application Data biotransformation genes, such as cytochromes P450. For example, one Such array comprises four probe Sets. A first (63) Continuation-in-part of application No. 08/544,381, filed on probe Set comprises a plurality of probes, each probe com Oct. 10, 1995, now Pat. No. 6,027,880, which is a continu ation-in-part of application No. 08/510,521, filed on Aug. 2, prising a Segment of at least three nucleotides exactly 1995, which is a continuation-in-part of application No. complementary to a Subsequence of a reference Sequence PCT/US94/12305, filed on Oct. 26, 1994, which is a con from a biotransformation gene, the Segment including at tinuation-in-part of application No. 08/284,064, filed on least one interrogation position complementary to a corre Aug. 2, 1994, now abandoned, which is a continuation-in sponding nucleotide in the reference Sequence. Second, third part of application No. 08/143,312, filed on Oct. 26, 1993, and fourth probe Sets each comprise a corresponding probe now abandoned. for each probe in the first probe set. The probes in the Second, third and fourth probe Sets are identical to a Sequence comprising the corresponding probe from the first (51) Int. Cl. ................................................ C12O 1/68 probe Set or a Subsequece of at least three nucleotides thereof that includes the at least one interrogation position, except (52) U.S. Cl. ................................. 435/6; 422/50; 422/68.1 that the at least one interrogation position is occupied by a different nucleotide in each of the four corresponding probes from the four probe sets. (58) Field of Search ......................... 422/50, 68.1; 435/6; 935/77, 78 32 Claims, 22 Drawing Sheets CORRESPONDING NUCLEOTIDE A C T G T TA G CTA A TT G G-1 REF. SEQ. CA ATCC AN-NPROBE FROM FIRST SET CA AICC G A Y CORRESPONDING PROBES CA A C GA FROM SECOND, THIRD CA A C GA AND FOURTH PROBE SETS N INTERROGATION POSITION US 6,309,823 B1 Page 2 U.S. PATENT DOCUMENTS Lockhart et al., “DNA sequencing by hybridization on high density probe arrays: enzymatic enhancement and Sequence 4,683,195 7/1987 Mullis et al. ............................ 435/6 5,002,867 3/1991 Macevicz ....... ... 435/6 reconstruction, poster, American Society of Human Genet 5,143,854 9/1992 Pirrung et al. 436/518 ics 44th Annual Meeting, Oct. 18-22, 1994, Montreal, 5,202,231 4/1993 Drmanac et al. ........................ 435/6 Quebec (abstract). 5,273,632 12/1993 Stockham et al. 204/108.1 Luo et al., “Cellular protein modulates effects of human 5,472,842 12/1995 Stokke et al. ............................ 435/6 immunodeficiency virus type 1 rev,” J. Virol. 68:3850-3856 5,527,681 6/1996 Holmes .................................... 435/6 (1994). 5,670,314 9/1997 Christman et al. ... 435/6 Maxam et al., “A new method for sequencing DNA,” Proc. 5,690,894 11/1997 Pinkel et al. ....... ... 422/68.1 Natl. Acad. Sci. USA, 74:560–564 (1977). 5,837,832 * 11/1998 Chee et al...... ... 536/22.1 Maxam et al., “Sequencing end-labeled DNA with 5,861,242 1/1999 Chee et al. ............................... 435/6 base-specific chemical cleavages,” Methods in Enzymology, 65:499–560 (1980). FOREIGN PATENT DOCUMENTS Miyada et al., “Detection of cystic fibrosis mutations in a WO 90/OO626 1/1990 (WO) .............................. C12O/1/68 GeneChipTM assay format,” poster, Amerian Society of WO 90/03382 4/1990 (WO). CO7H/21/OO Human Genetics 44th Annual Meeting, Oct., 1994, Mont WO 92/10092 6/1992 (WO). ... AO1NA1/02 real, Quebec (abstract). WO 92/10588 6/1992 (WO). ... C12O/1/68 Querat et al., “Nucleotide sequence analysis of SA-OMVV, WO 93/17126 9/1993 (WO). ... C12O/1/68 a Visna-related Ovine lentivirus: phylogenetic history of WO95/11995 5/1995 (WO). ... C12O/1/68 lentiviruses,” Virology, 175:434–447 (1990). WO95/26973 10/1995 (WO) ............................ CO7H/21/04 Ratner et al., “Complete nucleotide sequence of the AIDS virus, HTLV-III,” Nature, 313:227–284 (1985). OTHER PUBLICATIONS Sambrook et al., “Molecular cloning,” Cold Spring Harbor Press, pp. 1145-1147 (1989). Chee et al., “Genetic analysis by hybridization to Sequenc Sanger et al., “DNA sequencing with chain-terminating e-Specific DNA arrays, poster, American Society of Human inhibitors,” Proc. Natl. Acad. Sci. USA, 74:5463-5467 Genetics, 43rd Annual Meeting, Oct. 5–9, 1993, New (1977). Orleans, LA (abstract). Southern et al., “Analyzing and comparing nucleic acid Chee et al., “Sequence analysis by hybridization: the human Sequences by hybridization to arrays of oligonucleotides: mitochondrial genome on a chip, poster and Slide presen evaluation using experimental models, GeOnmics, tation, Genome Sequencing and Analysis Conference V, 13:1008-1017 (1992). Sep. 17–21, 1994, Hilton Head, SC (abstract). Stratagene 1988 Catalog, “Gene Characterization Kits,” p. Chee et al., “Sequencing mitochondrial DNA polymoriph 39. isms by hybridization,' Slide presentation, American Society Wain-Hobson et al., “Nucleotide sequence of the AIDS of Human Genetics 44th Annual Meeting, Oct. 18-22, 1994, virus, LAV," Cell, 40:9–17 (1985). Montreal, Quebec (abstract). Cronin et al. Abstract: Comparison of CY2D6 Genotyping Chee, “Resequencing DNA by hybidization to oligonucle by Oligonucleotide Array Hybridization and a PCR Based otide arrays,” slide presentation, Western Biotech Confer Method, International Society for the Study of Xenobiotics ence, Oct. 18-21, 1995, San Diego, CA abstract. Meeting, Oct. 24–26, 1996. Lin et al. Abstract: A Method for Genotyping CYP2D6 and Cronin et al., “Hybridzation to arrays of olignucleotides,” CYP2C19 Genotyping Using Oligonucleptide Array poster, Nucleic Acids in Medical Applications Conference Hybridization, International Society for the Study of Xeno sponsored by AACC, Jan., 1993, Cancun, Mexico (abstract). biotics Meeting, Oct. 24-26, 1996. Cronin et al., “Detection of cystic fibrosis gene mutations by Laan et al., “Solide-Phase Minisequencing Confirmed by hybridization to GeneChipTM probe arrays,” poster, Nucleic FISH Analysis in Determination of Gene Copy Number.” Acids in Medical Applications Conference sponsored by Human Genetics, vol. 96, pp. 275-280, 1995. AACC, Nov., 1993, Cancun, Mexico (abstract). Stickland et al., “Quantification of Oncogene Dosage in Cronin et al., “GeneChipTM Screening assay for cystic fibro Tumors by Simultaneous Dual Label Hybridization,” Onco sis mutations, poster, American Society of Human Genetics gene, vol. 8, pp. 223-227, 1993. Meeting, Oct., 1994, Montreal, Canada (abstract). Tully et al., “Analysis of 6 VNTR Loci by Multiplex PCR Croninet al., “Detecting cystic fibrosis mutations by hybrid and Automated Florescent Detection.” Human Genetics, vol. ization to DNA probe arrays,” slide presentation, UCSF 92, pp. 554–562, 1993. School of Medicine Symposium: Molecular Approaches to Chee et al., “Accessing Genetic Information with High Laboratory Diagnosis, Feb., 1995 (abstract). Density DNA Arrays,” Science, vol. 274, pp. 610-614, Oct. Elder, “Analysis of DNA oligonucleotide hybridization data 25, 1996. by maximum entropy,” Maxium Entropy and Bayesian Lipshutz et al., “Using Oligonucleotide Probe Arrays to Methods, pp. 1-10, Paris (1992). Access Gentic Diversity,” Biotechniques, vol. 19, No. 3, pp. Lipschutz, “Likelihood DNA sequencing by hybridization,” 442-447, 1995. J. of Biomolecular Structure & Dynamics, 11:637-653 Rudert et al., “Rapid Detection of Sequence Variations (1993). Using Polymers of Specific Oligonucleotides,” Nucleic Lipshutz, “Oligonucleotide arrays for hybridization analy Acids Research, vol. 20, No. 5, p. 1146, Mar. 11, 1992. Hacia et al., “Detection of Heterozygous Mutations in sis,” poster, Genome Sequencing and Analysis Conference BRCA1. Using High Density Oligonucleotide Arrays and V. Oct. 23–27, 1993, Hilton Head, SC (abstract). Two-Colour Fluorescence Analysis,” Nature Genetics, vol. Lobban et al., “DNA chips for genetic analysis,” poster, 14, pp. 441–447, Dec. 1996. Genome Sequencing and Analysis Conference V, Oct. 23–27, 1993, Hilton Head, SC (abstract). * cited by examiner U.S. Patent Oct. 30, 2001 Sheet 1 of 22 US 6,309,823 B1 CORRESPONDING NUCLEOTIDE A C T G T TAN G CTA A TT G G-1 REF. SEQ. CA ATCC AN-1NPROBE FROM FIRST SET CA AICC G A Y CORRESPONDING PROBES CA AGC G A - FROM SECOND, THIRD CAAAIC GAJ AND FOURTH PROBE SETS N INTERROGATION POSITION FIG.

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