Methods for polymorphism identification and profiling

• US 20030054393A1
• Filed: 08/27/2002
• Published: 03/20/2003
• Est. Priority Date: 06/25/1993
• Status: Abandoned Application

• Current Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Original Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Inventors: Lipshutz, Robert J., Fodor, Stephen
• Application Number:
  US10/229,319
• Publication Number:
  US 20030054393A1
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: B01J 19/0046 Sequential or parallel reactions, e.g. for the synthesis of polypeptides or polynucleotides; Apparatus and devices for combinatorial chemistry or for making molecular arrays synthesis methods per se C40B50/00
• CPC Class Codes: B01J 2219/00432 Photolithographic masks
• CPC Class Codes: B01J 2219/00529 DNA chips
• CPC Class Codes: B01J 2219/00596 Solid-phase processes
• CPC Class Codes: B01J 2219/00605 the compounds being directly bound or immobilised to solid supports
• CPC Class Codes: B01J 2219/00608 DNA chips
• CPC Class Codes: B01J 2219/00659 Two-dimensional arrays
• CPC Class Codes: B01J 2219/00689 using computers
• CPC Class Codes: B01J 2219/00711 Light-directed synthesis
• CPC Class Codes: B01J 2219/00722 Nucleotides
• CPC Class Codes: B82Y 30/00 Nanotechnology for materials or surface science, e.g. nanocomposites
• CPC Class Codes: C07B 2200/11 Compounds covalently bound to a solid support
• CPC Class Codes: C07H 21/00 Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
• CPC Class Codes: C12Q 1/6827 for detection of mutation or polymorphism
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 1/6874 involving nucleic acid arrays, e.g. sequencing by hybridisation
• CPC Class Codes: C12Q 2525/179 incorporating arbitrary or random nucleotide sequences
• CPC Class Codes: C12Q 2565/501 being an array of oligonucleotides
• CPC Class Codes: C12Q 2565/515 characterised by the interaction between or sequential use of two or more arrays
• CPC Class Codes: C40B 40/06 Libraries containing nucleotides or polynucleotides, or derivatives thereof
• CPC Class Codes: C40B 60/14 : for creating libraries
• CPC Class Codes: Y02A 90/10 : Information and communication technologies [ICT] supporting adaptation to climate change, e.g. for weather forecasting or climate simulation

Abstract

The invention provides methods of using probe arrays for polymorphism identification and profiling. Such methods entail constructing a first array of probes that span and are complementary to one or more known DNA sequences. This array is hybridized with nucleic acid samples from different individuals to identify a collection of polymorphisms. A second array is then constructed to determine a polymorphic profile of an individual at the collection of polymorphic sites. The polymorphic profile is useful for, e.g., genetic mapping, epidemiology, diagnosis and forensics.

Claims

1. A method of polymorphism analysis, comprising:

(a) constructing a first array of probes spanning and complementary to one or more known DNA sequences;

(b) hybridizing the first array of probes with nucleic acid samples from different individuals, whereby differences in the hybridization pattern of the samples to the probes among the different individuals indicate the location of one or more polymorphic sites in the one or more DNA sequences;

(c) repeating (a) and (b) as needed until a collection of polymorphic sites in known DNA sequences has been identified;

(d) constructing a second array of probes comprising a first set of probes spanning each of the polymorphic sites in the collection and complementary to polymorphic forms present in the known sequences, and a second set of probes spanning each of the polymorphic sites in the collection and complementary to polymorphic forms absent in the known DNA sequences;

(e) hybridizing the second array of probes to a nucleic acid sample from a further individual, and analyzing the hybridization intensities of probes in the first and second sets of probes to determine a profile of polymorphic forms present in the further individual.

2. The method of claim 1, wherein the further individual in step (e) has a known characteristic whose presence or absence is unknown in the different individuals in step (b).

3. The method of claim 1, further comprising retrieving the known DNA sequences from a computer database whereby the probes spanning the known DNA sequences are selected.

4. The method of claim 3, wherein the known DNA sequences are of unknown function.

5. The method of claim 3, wherein the known DNA sequences are expressed sequence tags.

6. The method of claim 2, wherein the known characteristic is the presence of a disease.

7. The method of claim 2, wherein the known characteristic is the absence of a disease.

8. The method of claim 2, wherein the known characteristic is being suspected of perpetrating a crime.

9. The method of claim 1, wherein the known DNA sequences comprise at least 100 sequences.

10. The method of claim 9, wherein the known sequences occur on a least 2 chromosomes.

11. The method of claim 9, wherein the known sequences occur on each of the 23 human chromosomes.

12. The method of claim 9, wherein at least 10 of the known sequences are unlinked.

13. The method of claim 1, wherein the hybridization pattern of a sample from one of the individuals shows a footprint in which probes spanning a polymorphism hybridize with reduced hybridization intensity relative to the hybridization pattern or a sample from another individual.

14. The method of claim 1, wherein there are at least 10 different individuals in step (b).

15. The method of claim 1, wherein the further nucleic acid sample is RNA or cDNA.

16. The method of claim 15, further comprising determining from the hybridization intensities of probes in the second array a subset of polymorphic sites in a subset of known sequences which are expressed in the further nucleic acid sample.

17. The method of claim 16, further comprising:

(f) constructing a third array of probes comprising first subset of probes spanning each of the subset of polymorphic sites in the collection and complementary to polymorphic forms present in the subset of known sequences, and a second set of probes spanning each of the subset of polymorphic sites in the collection and complementary to polymorphic forms absent in the subset of known DNA sequences; and

(g) hybridizing the third array of probes to an RNA sample from a third individual, and analyzing the hybridization intensities of probes in the first and second sets of probes to determine a profile of polymorphic forms present in the third individual.

18. The method of claim 17, wherein the RNA sample is obtained without amplification.

19. A method of polymorphism analysis, comprising:

retrieving multiple versions of a nucleic acid sequence from a published source;

comparing the multiple versions to identify point(s) of diversion;

designing an array comprising probes spanning and complementary to part(s) of the nucleic acid sequence spanning the point(s) of diversion; and

hybridizing nucleic acid samples from multiple individuals to the array, whereby the existence of difference(s) in the hybridization intensity of probes spanning a point of diversion among the individuals indicates a polymorphism at the point of diversion, and lack of difference in hybridization intensity of probes spanning a point of diversion among the individuals indicates the point of diversion was due to a sequencing error.

20. The method of claim 19, wherein the published source is a computer database.

21. The method of claim 19, wherein the multiple versions of the nucleic acid sequence are retrieved as trace profiles.

22. A method of polymorphism analysis comprising:

providing an immobilized array of probes comprising a first set of probes spanning each of a collection of polymorphic sites in known sequences and complementary to a first allelic forms of the sites and a second set of probes spanning each of the polymorphic sites in the collection and complementary to second allelic forms of the sites, wherein the collection of polymorphic sites includes at least 10 unlinked polymorphic sites;

hybridizing a nucleic acid sample from an individual to the array of probes and analyzing the hybridization intensities of probes in the first and second probe sets to determine a profile of polymorphic forms present in the individual.

23. The method of claim 22, wherein the collection of polymorphic sites includes a polymorphic site on each of the 23 human chromosomes.

24. The method of claim 22, wherein the collection of polymorphic sites includes an least 100 polymorphic sites.

25. The method of claim 22, wherein the hybridizing step is repeated for nucleic acid samples from a population of individuals, each of whom is characterized for the presence or absence of a phenotype, to determine a profile of polymorphic forms present in each individual in the population, and the method further comprises correlating profiles of polymorphic forms with the presence or absence of the phenotype in the population.

26. The method of claim 22, wherein the nucleic acid sample is RNA or cDNA.

27. The method of claim 26, further comprising enriching for transcripts of the known sequences in the nucleic acid sample by contacting the nucleic acid sample with probes complementary to the transcripts, whereby the probes hybridize to the transcripts to form complexes, isolating the complexes and dissociating the transcripts of the known sequences from the probes.

28. The method of claim 22, wherein the nucleic acid sample is a genomic DNA sample.

29. The method of claim 22, wherein the nucleic acid sample is prepared by amplification with random primers.