Diagnostics based on mass spectrometric detection of translated target polypeptides

• US 6,207,370 B1
• Filed: 09/02/1997
• Issued: 03/27/2001
• Est. Priority Date: 09/02/1997
• Status: Expired due to Term

• Current Assignee: Agena Bioscience Inc. (Mesa Laboratories Inc.)
• Original Assignee: Sequenom Incorporated (Laboratory Corporation Of America Holdings)
• Inventors: Higgins, Scott, Little, Daniel P., Köster, Hubert
• Primary Examiner(s): Campbell, Eggerton A.
• Application Number:
  US08/922,201
• Time in Patent Office: 1,302 Days
• Field of Search: 435/6, 435/91.2, 435/7.1, 436/89, 436/94
• US Class Current: 435/6.15
• CPC Class Codes: G01N 33/6818 Sequencing of polypeptides
• CPC Class Codes: G01N 33/6842 Proteomic analysis of subsets of protein mixtures with reduced complexity, e.g. membrane proteins, phosphoproteins, organelle proteins
• CPC Class Codes: G01N 33/6848 Methods of protein analysis involving mass spectrometry
• CPC Class Codes: G01N 33/6851 Methods of protein analysis involving laser desorption ionisation mass spectrometry
• CPC Class Codes: H01J 49/00 Particle spectrometers or separator tubes

Abstract

The invention provides a means of detecting and identifying mutations in a genetic region, and a means of quantifying the number of repeat units in, for example, a trinucleotide repeat, by transcription/translation of the genetic region into a target polypeptide. The method requires neither radioisotopic nor fluorescent labeling of the target polypeptide. In particular, the invention is based on mass spectrometric determination of the mass of the encoded target polypeptide and comparison of the mass of the polypeptide with its own expected mass or with the mass of a polypeptide of known identity. Depending on the target polypeptide to be identified, the processes can be used, for example, to diagnose a genetic disease or chromosomal abnormality; a predisposition to a disease or condition, infection by a pathogenic organism, or for determining identity or heredity.

Claims

1. A process for determining the genetic nature of a phenotype in a subject, comprising the steps of:

a) obtaining a target nucleic acid molecule from the subject;

b) preparing a target polypeptide from the nucleic acid molecule;

c) determining the molecular mass of the target polypeptide by mass spectrometry; and

d) comparing the target polypeptide with a reference polypeptide of known identity by comparing the molecular mass of the target polypeptide with the molecular mass of the reference polypeptide, thereby identifying an allelic variant of a polymorphic region of a chromosome in the subject.

2. The process of claim 1, wherein the polymorphic region is in a gene.

3. The process of claim 1, wherein the polymorphic region is not in a gene.

4. The process of claim 1, wherein the allelic variant comprises an abnormal number of nucleotide repeats.

5. The process of claim 4, wherein the nucleotide repeats are selected from the group consisting of dinucleotide, trinucleotide, tetranucleotide, and pentanucleotide repeats.

6. The process of claim 4, further comprising quantifying the number of nucleotide repeats.

7. The process of claim 4, wherein the phenotype is associated with a disease or condition, and wherein the nucleotide repeats are trinucleotide repeats.

8. The process of claim 7, wherein the disease or condition is selected from the group consisting of Huntington'"'"'s disease, prostate cancer, Fragile X syndrome type A, myotonic dystrophy type I, Kennedy disease, Machado-Joseph disease, dentatorubral and pallidolyusian atrophy, spino bulbar muscular atrophy and aging.

9. The process of claim 2, wherein the phenotype is associated with a disease or condition, and wherein the gene is selected from the group consisting of BRCA1, BRCA2, APC, dystrophin gene, β

-globin, Factor IX, Factor VIIc, ornithine-d-amino-transferase, hypoxanthine guanine phosphoribosyl transferase, CFTR, p53, and a proto-oncogene.

10. The process of claim 1, wherein the allelic variant is a point mutation.

11. The process of claim 1, wherein the phenotype is responsiveness of the subject to a medicament, and wherein the genetic nature of the phenotype is a polymorphic region of a chromosome associated with responsiveness to the medicament.

12. The process of claim 1, wherein the nucleic acid molecule encoding the target polypeptide comprises nucleotide repeats, and wherein the process is selected from the group consisting of genotyping the subject, forensic analysis, and paternity testing.

13. The process of claim 1, wherein the nucleic acid molecule is a mitochondrial gene.

14. A process for obtaining sequence information or the identity of a plurality of nucleic acid molecules by determining the identities of polypeptides encoded by the nucleic acid molecules, comprising the steps of:

a) obtaining nucleic acid molecules;

b) preparing a plurality of polypeptides from the nucleic acid molecules, wherein the plurality of polypeptides include mass modified polypeptides;

c) determining molecular masses of the differentially mass modified polypeptides by mass spectrometry; and

d) determining the identities of the polypeptides by comparing the molecular masses of the target polypeptides with the molecular mass of one or more reference polypeptides of known identity, thereby obtaining sequence information or sequence information of the nucleic acid molecules encoding the target polypeptides.

15. The process of claim 14, wherein the polypeptides are obtained by in vitro translation, or by in vitro transcription, followed by translation, of the nucleic acid molecules encoding the polypeptides.

16. The process of claim 14, further comprising, prior to step b), amplifying the nucleic acid molecules encoding the polypeptides.

17. The process of claim 16, wherein amplification is effected using a plurality of pairs of primers, wherein all amplification reactions are effected simultaneously or sequentially at a plurality of annealing temperatures.

18. A process for identifying an individual having spinal cerebellar ataxia-1, comprising detecting an abnormal number of trinucleotide repeats in a nucleic acid molecule obtained from the individual, said trinucleotide repeats comprising CAG trinucleotides and at least one GAG trinucleotide.

19. The process of claim 18, wherein said at least one GAG trinucleotide is detected by detecting a glycine residue encoded by the GAG trinucleotide.

20. The process of claim 19, wherein said glycine residue is detected by mass spectrometry.

21. A process for identifying the presence or absence of a mutation in a target nucleic acid sequence by determining the molecular mass of a polypeptide encoded by the nucleic acid sequence, comprising the steps of:

a) obtaining a nucleic acid molecule comprising a nucleic acid sequence suspected of containing a mutation;

b) preparing a polypeptide from a portion of the nucleic molecule comprising the nucleic acid sequence suspected of containing the mutation; and

c) determining the molecular mass of the polypeptide by mass spectrometry, whereby the molecular mass of the polypeptide identifies the presence or absence of a mutation in the nucleic acid sequence.

22. A process of claim 21, wherein the mutation is an abnormal number of nucleotide repeats, and wherein the molecular mass of the polypeptide identifies the number of nucleotide repeats in the nucleic acid sequence.

23. A process of claim 21, wherein:

the mutation results in a STOP codon that is identified by a molecular mass of the target polypeptide that is indicative of a truncated polypeptide.

24. A process of claim 21, wherein the identification of a mutation is diagnostic of a genetic disease or a predisposition to a genetic disease.