US2013251677A1PendingUtilityA1
Genetic markers associated with interferon-alpha response
Est. expiryMay 21, 2029(~2.9 yrs left)· nominal 20-yr term from priority
Inventors:Arthur BertelsenJacques FellayDongliang GeDavid B. GoldsteinJohn G. MchutchisonPing QiuKevin ShiannaJason SimonAlexander J. ThompsonThomas Urban
A61P 43/00A61P 31/18G06F 17/18A61K 38/212C12Q 2600/172C12Q 1/6827C12Q 2600/106A61P 31/12C12Q 1/6883A61P 31/14C12Q 2600/156A61P 35/02A61P 35/00A61K 48/00
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Claims
Abstract
The present invention provides genetic markers on human chromosome 19 that are associated with a beneficial response to interferon alpha (IFN-α). These IFN-α response markers are useful, inter alia, to identify patients who are most likely to benefit from treatment with IFN-α pharmaceutical compositions and drug products, in methods of treating patients having a disease susceptible to treatment with an IFN-α, and in methods for selecting the most appropriate therapy for such patients.
Claims
exact text as granted — not AI-modifiedWe claim:
1 . A drug product which comprises a pharmaceutical composition and prescribing information,
wherein the pharmaceutical composition comprises an interferon alpha (IFN-α) and the prescribing information comprises a pharmacogenetic indication, wherein the pharmacogenetic indication comprises the treatment of a disease susceptible to treatment with the IFN-α in patients who test positive for at least one IFN-α response marker, wherein the IFN-α response marker is selected from the IFN-α response markers in Table 1 below.
TABLE 1
IFN-α Response Markers
Better
Heterozygous
Homozygous
Response
IFN-α Response
IFN-α Response
PS
SNP
Allele
Marker
Marker
rs12979860
T/C
C
C/T genotype
C/C genotype
rs28416813
G/C
G
G/C genotype
G/G genotype
rs8103142
A/G
A
A/G genotype
A/A genotype
rs12980275
A/G
A
A/G genotype
A/A genotype
rs8099917
A/C
A
A/C genotype
A/A genotype
rs12972991
T/G
T
T/G genotype
T/T genotype
rs8109886
A/C
C
C/A genotype
C/C genotype
rs4803223
T/C
T
T/C genotype
T/T genotype
rs12980602
A/G
A
A/G genotype
A/A genotype
2 . A method of testing an individual for the presence or absence of at least one IFN-α response marker, the method comprising obtaining a nucleic acid sample from the individual and assaying the nucleic acid sample to determine the individual's genotype at a polymorphic site (PS) in Table 1, wherein if the individual is heterozygous or homozygous for the better response allele for said PS, then the IFN-α response marker is present and if the individual is homozygous for the other allele for said PS, then the IFN-α response marker is absent.
3 . The method of claim 2 , which further comprises generating a test report that indicates the individual's genotype at said PS.
4 . The method of claim 2 , wherein the IFN-α response marker is selected from the homozygous IFN-α response marker genotypes in Table 1.
5 . A method of selecting a therapy for treating an individual having a disease susceptible to treatment with an interferon alpha (IFN-α), comprising obtaining the individual's genotype at a polymorphic site (PS) selected from the polymorphic sites in Table 1 and selecting a therapy based on the results of the determining step,
wherein if the individual is heterozygous or homozygous for the better response allele at the selected PS, then the selected therapy comprises initial treatment or continued treatment with the IFN-α, and
wherein if the individual is homozygous for the other allele at the selected PS, the selected therapy comprises administering the IFN-α in combination with at least one other therapeutic agent that is not an IFN-α or the selected therapy excludes IFN-α-based therapy.
6 . The method of claim 5 , wherein the disease susceptible to treatment with the interferon alpha is chronic infection with a hepatitis C virus (HCV).
7 . A screening method for selecting individuals for initial treatment or continued treatment with an interferon alpha (IFN-α) from a group of individuals having a disease susceptible to treatment with the IFN-α, comprising testing each member of the disease group for the presence of at least one IFN-α response marker and selecting for treatment at least one individual testing positive for the IFN-α response marker, wherein a positive test for the IFN-α response marker is a heterozygous genotype or a homozygous genotype for the better response allele for at least one polymorphic site (PS) selected from the polymorphic sites in Table 1.
8 . A method of predicting whether an individual chronically infected with HCV genotype 1 will achieve a sustained viral response (SVR) to a combination therapy comprising an interferon alpha-2 and ribavirin, the method comprising:
obtaining a nucleic acid sample from the individual; assaying the nucleic acid sample to determine the patient's genotype for at least one polymorphic site (PS) in Table 1; and making a prediction based on the determined genotype, wherein if the patient's genotype is homozygous for the better response allele, then the prediction is that the individual is likely to achieve an SVR, and if the patient's genotype is heterozygous or homozygous for the other allele, then the prediction is that the individual is not likely to achieve an SVR.
9 . The method of claim 8 , wherein the interferon alpha-2 is a pegylated interferon alpha-2a protein, a pegylated interferon alpha-2b protein, an albumin-interferon alpha-2a fusion protein, or an albumin-interferon alpha-2b fusion protein.
10 . A method of treating an individual for chronic infection with HCV genotype 1, which comprises:
obtaining the individual's genotype for at least one polymorphic site (PS) in Table 1 and prescribing a treatment regimen based on the obtained genotype,
wherein if the genotype is homozygous for the better response allele, then the treatment regimen comprises administering to the individual an interferon alpha in combination with ribavirin and wherein if the individual's genotype is heterozygous or homozygous for the other allele, then the treatment regimen comprises administering to the individual an interferon alpha in combination with ribavirin and at least one antiviral agent that is not an interferon alpha or the treatment regimen excludes interferon-alfa based therapy.
11 . The method of claim 10 , wherein the interferon alpha is a pegylated interferon alpha-2a protein, a pegylated interferon alpha-2b protein, an albumin-interferon alpha-2a fusion protein, or an albumin-interferon alpha-2b fusion protein.
12 . The method of claim 11 , wherein the at least one antiviral agent is an HCV protease inhibitor.
13 . The method of claim 12 , wherein the HCV protease inhibitor is boceprevir or telaprevir.
14 . A method for estimating a probability that a patient having a chronic HCV genotype 1 infection will achieve a sustained viral response to combination therapy with a pegylated IFN-α-2 and ribavirin, the method comprising
obtaining a set of genetic and clinical response predictors of the patient's response,
inputting the obtained predictors into a computer that runs a logistic regression model on the inputted predictors to calculate the estimated probability, and
transmitting the estimated probability to the patient or to the patient's physician,
wherein the patient is self-identified as African American or Caucasian, and
wherein the set of genetic and clinical response predictors consists of the patient's genotype at the rs12979860 polymorphic site, the patient's baseline HCV viral load, the patient's self-identified ethnicity and the patient's METAVIR score for baseline fibrosis and wherein the logistic regression model is
P
=
1
1
+
-
[
(
1.4
×
G
)
+
(
1.7
×
V
)
+
(
1.1
×
E
)
+
(
1.1
×
F
)
-
3.8
]
,
where
P: Probability of achieving SVR;
G: rs12979860 genotype: TT=0, CT=1, CC=2;
V: Baseline viral load: >600,000 IU/mL=0, <600,000 IU/mL=1;
E: Ethnicity: African Ancestry=0, Caucasian=1; and
F: Baseline fibrosis: METAVIR F3-4=0, F0-2=1.
15 . A method of treating an individual diagnosed with acute hepatitis C, the method comprising obtaining the individual's genotype for the rs12979860 polymorphic site and making a treatment decision based on the obtained genotype,
wherein if the genotype is homozygous T, then the treatment decision is to start the patient on an antiviral therapy and wherein if the genotype is heterozygous C or homozygous C, the treatment decision is to withhold antiviral therapy until the individual is diagnosed with a chronic HCV infection.Cited by (0)
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