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(12) United States Patent (10) Patent No.: US 6,344,316 B1 L0ckhart Et Al

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(12) United States Patent (10) Patent No.: US 6,344,316 B1 L0ckhart Et Al USOO634.4316B1 (12) United States Patent (10) Patent No.: US 6,344,316 B1 L0ckhart et al. (45) Date of Patent: *Feb. 5, 2002 (54) NUCLEIC ACID ANALYSISTECHNIQUES 4,780,504 A 10/1988 Buendia et al. 4,812,512 A 3/1989 Buendia et al. (75) Inventors: David J. Lockhart, Santa Clara; Mark 4.820,630 A 4/1989 Taub Chee; Kevin Gunderson, both of Palo 4,833,092 A 5/1989 Geysen 4,849,513 A 7/1989 Smith et al. Alto; Lai Chaoqiang; Lisa Wodicka, 4,855.225 A 8/1989 Fung et al. both of Santa Clara; Maureen T. 4,868,103 A 9/1989 Stavrianopoulos et al. Cronin, Los Altos; Danny Lee; Huu 4,868,104 A 9/1989 Kurn et al. M. Tran, both of San Jose; Hajime 4,868,105 A 9/1989 Urdea et al. Matsuzaki, Palo Alto, all of CA (US) 4,874,500 A 10/1989 Madou et al. 4,921,805 A 5/1990 Gebeyehu et al. (73) Assignee: Affymetrix, Inc., Santa Clara, CA (US) 4,923,901 A 5/1990 Koester et al. 4,925,785 A 5/1990 Wang et al. (*) Notice: This patent issued on a continued pros ecution application filed under 37 CFR (List continued on next page.) 1.53(d), and is subject to the twenty year patent term provisions of 35 U.S.C. FOREIGN PATENT DOCUMENTS 154(a)(2). DE 3505287 9/1985 EP O63 810 11/1982 Subject to any disclaimer, the term of this EP O 132 621 6/1984 ............ C12O/1/68 patent is extended or adjusted under 35 EP O 159 719 10/1985 ............ C12O/1/68 U.S.C. 154(b) by 20 days. (List continued on next page.) (21) Appl. No.: 08/882,649 OTHER PUBLICATIONS (22) Filed: Jun. 25, 1997 Broude, Natalia E., et al., “Enhanced DNA Sequencing By Hybridization,” Proc. Natl. Acad. Sci. USA, Vol. 91, pp. Related U.S. Application Data 3072-3076, Apr. 1994. Chee, Robert, et al., “Accessing Genetic Information with (63) Continuation of application No. PCT/US97/01603, filed on High-Density DNA Arrays,” Science, vol. 274, Oct. 1996. Jan. 22, 1997. (60) Provisional application No. 60/035,170, filed on Jan. 9, Eggers, M., et al., “A Microchip for Quantitative Detection 1997, and provisional application No. 60/010,471, filed on of Molecules Utilizing Luminescent and Radioisotope Jan. 23, 1996. Reporter Groups.” BioTechniques, vol. 17, No. 3, 1994. (51) Int. Cl................................................... C12O 1/68 (List continued on next page.) (52) ... 435/6; 536/24.3 (58) Field of Search .............................. 435/6; 536/24.3 Primary Examiner Scott W. Houtteman (74) Attorney, Agent, or Firm Townsend and Townsend (56) References Cited and Crew LLP U.S. PATENT DOCUMENTS (57) ABSTRACT 3,730,844 A 5/1973 Gilham et al. The present invention provides a simplified method for 4,071,315 A 1/1978 Chateau identifying differences in nucleic acid abundances (e.g., 4,327,073. A 4/1982 Huang 4,373,071 A 2/1983 Itakura expression levels) between two or more samples. The meth 4,458,066 A 7/1984 Caruthers et al. ods involve providing an array containing a large number 4.483,920 A 11/1984 Gillespie et al. (e.g. greater than 1,000) of arbitrarily selected different 4,486,539 A 12/1984 Ranki et al. oligonucleotide probes where the Sequence and location of 4,500,707 A 2/1985 Caruthers et al. each different probe is known. Nucleic acid Samples (e.g. 4,542,102 A 9/1985 Dattagupta et al. mRNA) from two or more samples are hybridized to the 4,556,643 A 12/1985 Paau et al. probe arrays and the pattern of hybridization is detected. 4,562,157 A 12/1985 Lowe et al. Differences in the hybridization patterns between the 4,563,419 A 1/1986 Ranki et al. Samples indicates differences in expression of various genes 4,584.277 A 4f1986 Ullman et al. 4,591,570 A 5/1986 Chang between those Samples. This invention also provides a 4,613,566 A 9/1986 Potter method of end-labeling a nucleic acid. In one embodiment, 4,670,380 A 6/1987 Dattagupta the method involves providing a nucleic acid, providing a 4,677,054 A 6/1987 White et al. labeled oligonucleotide and then enzymatically ligating the 4,683,195 A 7/1987 Mullis et al. oligonucleotide to the nucleic acid. Thus, for example, 4,683.202 A 7/1987 Mullis where the nucleic acid is an RNA, a labeled oligoribonucle 4,689.405 A 8/1987 Frank otide can be ligated using an RNA ligase. In another 4,704,353 A 11/1987 Humphries et al. embodiment, the end labeling can be accomplished by 4,711.955 A 12/1987 Ward et al. providing a nucleic acid, providing labeled nucleoside 4,716,106 A 12/1987 Chiswell triphosphates, and attaching the nucleoside triphosphates to 4,728,591 A 3/1988 Clark et al. 4,731,325 A 3/1988 Palva et al. the nucleic acid using a terminal transferase. 4,755.458 A 7/1988 Rabbani et al. 4,767,700 A 8/1988 Wallace 28 Claims, 47 Drawing Sheets US 6,344,316 B1 Page 2 U.S. PATENT DOCUMENTS 5,807,522 A 9/1998 Brown et al. 5.830,645. A 11/1998 Pinkel et al. 4,981,783 A 1/1991 Augenlicht .................... 435/6 5,972,619 A 10/1999 Drmanac et al. 4,987,065. A 1/1991 Stavrianopoulos et al. 6,018,041 A 1/2000 Drmanac et al. 4.988,617 A 1/1991 Landegren et al. 6,025,136 A 2/2000 Drmanac et al. 4992,383 A 2/1991 Farnsworth 6,030,788 A 2/2000 Gerhold ......................... 435/6 4,994,373 A 2/1991 Stavrianopoulos et al. 6,040,138 A 3/2000 Lockhart et al. 5,002,867 A 3/1991 Macevicz ...................... 435/6 6,054,270 A 4/2000 Southern 5,013,669 A 5/1991 Peters, Jr. et al. 6,110,426 A 8/2000 Shalon et al. 5,021,550 A 6/1991 Zeiger 5,026,840 A 6/1991 Dattagupta et al. FOREIGN PATENT DOCUMENTS 5,028,525 A 7/1991 Gray et al. 5,028,545 A 7/1991 Soini EP 171 150 2/1986 5,043,265 A 8/1991 Tanke et al. EP 173339 3/1986 5,047,524 A 9/1991 Andrus et al. EP 185547 6/1986 5,064,754 A 11/1991 Mills EP 225807 6/1987 5,082,830 A 1/1992 Brakel et al. EP 232967 8/1987 5,091,652 A 2/1992 Mathies et al. EP 235 726 9/1987 5,100,777 A 3/1992 Chang EP 237 362 9/1987 5,141,813 A 8/1992 Nelson EP 281927 9/1988 5,143,854 A 9/1992 Pirrung et al. .............. 436/518 EP O 266 787 11/1988 ... C12O/1/68 5,153,319 A 10/1992 Caruthers et al. EP O 320 308 6/1989 ... C12O/1/68 5,173,260 A 12/1992 Zander et al. EP O322 311 6/1989 C12O/1/68 5,185.243 A 2/1993 Ullman et al. EP O 336 731 10/1989 C12O/1/68 5,188.963 A 2/1993 Stapleton EP 337 498 10/1989 5,200,051 A 4/1993 Cozzette EP 392,546 10/1990 5,200,312 A 4/1993 Oprandy EP 535 242 A1 4/1993 .... ... C12O/1/68 5,202.231 A 4/1993 Drmanac et al. .............. 435/6 EP O 717 113 A2 6/1996 ............ C12O/1/68 5,204.268 A 4/1993 Matsumoto EP 721 O16 7/1996 5,215,882 A 6/1993 Bahl et al. EP O 721 O16 A2 7/1996 ............ C12O/1/68 5,232,829 A 8/1993 Longiaru et al. FR 2559.783 2/1985 5,242.974 A 9/1993 Holmes GB 2156O74 10/1985 5,252.296 A 10/1993 Zuckerman et al. JP 63-223,557 9/1989 5,252,743 A 10/1993 Barrett et al. WO WO84/03151 8/1984 5,256,549 A 10/1993 Urdea WO WO85/O1051 3/1985 5,310,893 A 5/1994 Erlich et al. WO WO89/10977 5/1989 5,324,633 A 6/1994 Fodor et al. ................... 435/6 WO 89/10977 11/1989 ............ C12O/1/68 5,328,824 A 7/1994 Ward et al. WO WO89/11548 11/1989 5,338,688 A 8/1994 Deeg et al. WO 90/OO626 1/1990 ............ C12O/1/68 5,348.855 A 9/1994 Duttagupta et al. WO WO90/03382 4/1990 5,389,512 A 2/1995 Sninsky et al. WO 90/O4652 5/1990 ............ C12O/1/68 5,412,087 A 5/1995 McGall et al. WO 90/15070 12/1990 ............ CO7K/1/04 5,422,241 A 6/1995 Goldrick et al. ............... 435/6 WO 92/10092 6/1992 ............ AO1N/1/02 5.434,049 A 7/1995 Okano et al. WO WO92/10588 6/1992 5,436,327 A 7/1995 Southern et al. WO 92/10588 6/1992 ............ C12O/1/68 5,445,934 A 8/1995 Fodor et al. ................... 435/6 WO WO93/11262 6/1993 5,447.841 A 9/1995 Gray et al. WO 93/17126 9/1993 ............ C12O/1/68 5,472,842 A 12/1995 Stokke et al. 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