Method of predicting rapid progression of fibrosis and therapy and reagents therefor

Patent metadata

Field	Value
Publication number	US-10939868-B2
Application number	US-201515325704-A
Country	US
Kind code	B2
Filing date	Jul 17, 2015
Priority date	Jul 18, 2014
Publication date	Mar 9, 2021
Grant date	Mar 9, 2021

Abstract

This invention relates to molecular diagnostics and, more specifically DNA-based tests for the prognosis and/or monitoring of fibrotic disease progression in humans, and processes for stratifying patients based on their likely rates of fibrotic disease progression. The invention also relates to the field of therapy for fibrotic disease, based on such prognoses, monitoring and stratification results, such as in monitoring and/or stratifying and/or treating patients having a higher likelihood of rapid fibrotic disease progression.

First claim

We claim:

1. A method of determining a likelihood that a subject having a medical condition associated with onset or progression of fibrosis is predisposed to developing fibrosis or is predisposed to progressing to a particular stage of fibrosis or is predisposed to a rapid progression of fibrosis, the method comprising:
(i) performing one or more genotyping assays on a DNA-containing sample obtained from the subject, wherein the one or more genotyping assays comprise contacting one or more nucleic acids configured to independently discriminate single nuclear polymorphism (SNP) genotypes in or at least linked to both the human IL28B gene and the human MERTK gene with the DNA-containing sample, wherein the SNP in or at least linked to human IL28B gene is rs12979860 and the SNP in or at least linked to human MERTK gene is rs4374383, wherein the assay results indicate a likelihood that the subject will develop fibrosis and/or progress to a particular stage of fibrosis and/or progress rapidly to a late-stage fibrosis; and
(ii) treating the fibrosis and/or the medical condition in a subject having a strong likelihood of developing fibrosis or progressing to a particular stage of fibrosis or progressing rapidly to a late-stage fibrosis based on the assay results at (i).

2. A method of determining a likelihood that a subject having a medical condition associated with onset or progression of fibrosis will develop fibrosis and/or progress to a particular stage of fibrosis and/or progress rapidly to a late-stage fibrosis, said method comprising:
(a) performing one or more genotyping assays on a DNA-containing sample obtained from the subject, wherein the one or more genotyping assays comprise contacting one or more nucleic acids configured to independently discriminate between different genotypes in or at least linked to both the human IL28B gene and the human MERTK gene with the DNA-containing sample, wherein the genotypes in or at least linked to the human IL28B gene are alleles of a single nuclear polymorphism (SNP) that is rs12979860, and wherein the genotypes in or at least linked to the human MERTK gene are alleles of a SNP that is rs4374383; and
(b) correlating the genotyping assay results to the likelihood that the subject will develop fibrosis or progress rapidly to a late-stage fibrosis, wherein a combination of the following genotypes (i) and (ii) indicates a strong likelihood (O.R.>4.0, p<0.01) that the subject will develop fibrosis and/or progress rapidly to a late-stage fibrosis:
(i) a CC genotype in rs12979860; and
(ii) an AG genotype or GG genotype in rs4374383,
thereby determining a likelihood that the subject will develop fibrosis and/or progress to a particular stage of fibrosis and/or progress rapidly to a late-stage fibrosis; and
(c) treating the fibrosis and/or the medical condition in a subject determined at (a) and (b) as having a strong likelihood of developing fibrosis or progressing to a particular stage of fibrosis or progressing rapidly to a late-stage fibrosis.

3. The method according to claim 1 , wherein the method comprises:
(a) performing the one or more genotyping assays, wherein the genotypes in the human IL28B gene are in the SNP rs12979860, and wherein the genotypes in the human MERTK gene are in the SNP rs4374383; and
(b) correlating the genotyping assay results to the likelihood that the subject will develop fibrosis or progress rapidly to a late-stage fibrosis, wherein a combination of the following genotypes (i) and (ii) indicates a strong likelihood (O.R.>4.0, p<0.01) that the subject will develop fibrosis and/or progress rapidly to a late-stage fibrosis:
(i) a CC genotype in rs12979860; and
(ii) an AG genotype or GG genotype in rs4374383.

4. The method according to claim 1 , wherein performing one or more genotyping assays on the DNA-containing sample comprises performing the genotyping assays under conditions that discriminate between the following combinations of genotypes in the sample DNA:
(a) between homozygotes (CC), heterozygotes (CT) and alternate homozygotes (TT) at rs12979860; and
(b) between homozygotes (GG), heterozygotes (AG) and alternate homozygotes (AA) at rs4374383.

5. The method according to claim 1 , further comprising performing a genotype assay for a SNP selected from the group consisting of rs17175626 and rs6748256.

6. The method according to claim 1 , further comprising performing one or more additional genotyping assays on the DNA-containing sample obtained from the subject, wherein the one or more additional genotyping assays are configured to discriminate single nuclear polymorphism (SNP) genotypes in or at least linked to the human RNF7 gene, wherein the SNPs are selected from rs16851720 and a SNP in linkage disequilibrium with rs16851720.

7. The method according to claim 6 , wherein the method comprises performing one or more additional genotyping assays on the DNA-containing sample obtained from the subject, wherein the one or more additional genotyping assays are configured to discriminate between alleles at the SNP rs16851720, and wherein detection of an AA genotype in rs16851720 in combination with the SNPs in both the IL28B and MERTK genes indicates a strong likelihood that the subject will develop fibrosis and/or progress rapidly to a late-stage fibrosis.

8. The method according to claim 1 , wherein the assays comprise PCR assays and/or real-time PCR assays and/or minisequencing assays and/or next generation sequencing assays and/or isothermal nucleic acid sequence-based amplification assays (NASBA) and/or oligonucleotide ligation-PCR assays.

9. The method according to claim 1 , wherein the assays comprise multiplex assays for simultaneous discrimination between the SNPs in both the IL28B and MERTK genes.

10. The method according to claim 1 , wherein the combined SNP genotypes in the human IL28B gene and the human MERTK gene provide a stronger likelihood that a subject is predisposed to a rapid progression of fibrosis than a likelihood obtained by adding the separate effect of each of said genotypes.

11. The method according to claim 1 , further comprising the first step of providing a kit comprising nucleic acids that discriminate between different genotypes in the human IL28B and the human MERTK gene and the human RNF7 gene of the sample DNA, and then performing the one or more genotyping assays employing those nucleic acids.

12. The method according to claim 1 , wherein the fibrosis is liver fibrosis.

13. The method according to claim 1 , wherein the subject has a medical condition associated with progression of fibrosis selected from the group consisting of: a disease with secondary involvement of the liver, hemochromatosis, a congenital hepatic fibrosis, chronic hepatitis B, chronic hepatitis C, non-alcoholic steatohepatitis (NASH), primary biliary cirrhosis, primary sclerosing cholangitis, reduced hepatic blood flow, hepatic veno-occlusive disease, hepatocellular carcinoma, and scarring due to prior liver surgery.

14. A kit for performing the method according to claim 1 , said kit comprising two or more nucleic acids that independently discriminate between different single nuclear polymorphism (SNP) genotypes in or at least linked to the human IL28B gene and the human MERTK gene, wherein the SNP in or at least linked to the human IL28B is rs12979860 and the SNP in or at least linked to the human MERTK is rs4374383.

15. The kit according to claim 14 further comprising:
(i) one or more nucleic acids that independently discriminate between one or more further SNP genotypes in or at least linked to human IL28B, wherein the SNPs are selected from

Assignees

• Western Sydney Local Health Distr
• Univ Sydney

Inventors

• Booth David
• George Jacob
• Eslam Mohammed
• Ahlenstiel Golo
• O'Connor Kate

Classifications

• G16B20/40

  Population genetics; Linkage disequilibrium · CPC title

• G16B20/20 Primary

  Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection · CPC title

• C12Q1/6883

  for diseases caused by alterations of genetic material · CPC title

• C12Q1/68

  involving nucleic acids · CPC title

• G01N33/5308

  for analytes not provided for elsewhere, e.g. nucleic acids, uric acid, worms, mites · CPC title