# US 2021/0280313 A1 · Polygenic risk score modifies risk of coronary artery disease conferred by low-density lipoprotein cholesterol

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- Number: US 2021/0280313 A1
- Document ID: US20210280313A1
- Status: Published application
- Kind: A1
- Application number: 17/191,004
- Filed: 2021-03-03
- Published: 2021-09-09
- Earliest claimed: 2020-03-04
- Applicants: ALLELICA S.r.l.
- Inventors: Giordano BOTTA'; Paolo DI DOMENICO; Alessandro BOLLI
- Web page: https://patentgrep.com/patent/US20210280313A1

## CPC

- G16H 50/20: for computer-aided diagnosis, e.g. based on medical expert systems
- G06N 20/00: Machine learning
- G16B 20/00: ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
- G16B 40/00: ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
- G16B 40/20: Supervised data analysis
- G16B 40/30: Unsupervised data analysis
- G16H 10/60: for patient-specific data, e.g. for electronic patient records
- G16H 50/30: for calculating health indices; for individual health risk assessment
- G16H: HEALTHCARE INFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR THE HANDLING OR PROCESSING OF MEDICAL OR HEALTHCARE DATA
- G06N: COMPUTING ARRANGEMENTS BASED ON SPECIFIC COMPUTATIONAL MODELS
- G16B: BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY

## Abstract

A method for a predictive prognosis of onset of a cardiovascular disease in an individual acquires/accesses low-density lipoprotein cholesterol level, calculating a risk value and determining an individualized risk value of onset of the cardiovascular disease, based on the calculated risk value. Calculating a risk value includes calculating the risk value representative for onset of the cardiovascular disease, based on operational values of a polygenic risk score and low-density lipoprotein cholesterol level, based on first, second and third risk parameters are representative of risk of onset of: the cardiovascular disease induced by the polygenic risk score, the cardiovascular disease induced by the low-density lipoprotein cholesterol level, and the cardiovascular disease induced by interaction of polygenic risk score and low-density lipoprotein cholesterol level. The risk parameters are calculated based on a pre-trained model and/or algorithm, to which the operational values of polygenic risk score and low-density lipoprotein cholesterol level are input.

## Claims

### Claim 1

A method for a predictive prognosis of onset of a cardiovascular disease in an individual, comprising the steps of:
acquiring or accessing data comprising the individual's low-density lipoprotein cholesterol level (LDL-Cp);
calculating at least one risk value (R), representative of a risk of onset of the cardiovascular disease in the individual, based on an operational value of a polygenic risk score (PRS) of the individual and an operational value of the individual's low-density lipoprotein cholesterol level (LDL-C), and also based on a first risk parameter (HR1) representative of a risk of onset of the cardiovascular disease induced by the polygenic risk score (PRS), of a second risk parameter (HR2) representative of a risk of onset of the cardiovascular disease induced by the low-density lipoprotein cholesterol level (LDL-C), and of a third risk parameter (HR3) representative of a risk of onset of the cardiovascular disease induced by the interaction of polygenic risk score (PRS) and low-density lipoprotein cholesterol level (LDL-C);
wherein said first risk parameter (HR1), said second risk parameter (HR2) and said third risk parameter (HR3) are calculated based on a pre-trained model and/or algorithm, to which said operational value of polygenic risk score (PRS) and said operational value of low-density lipoprotein cholesterol level (LDL-C) are provided in input;
determining and providing, as a prognostic result, an individualized risk value (Rp) of onset of the cardiovascular disease in an individual to be examined, based on said at least one calculated risk value (R);
wherein said step of calculating at least one risk value (R) comprises calculating a risk value (R) considering as the operational value of polygenic risk score (PRS) the value (PRSp) of the individual's polygenic risk score and as the operational value of the low-density lipoprotein cholesterol level (LDL-C) the individual's low-density lipoprotein cholesterol level (LDL-Cp); and
wherein the individualized risk value (Rp) of onset of cardiovascular disease corresponds to said calculated risk value (R).

### Claim 2 (depends on 1)

A method according to claim 1, wherein the pre-trained model and/or algorithm comprises an algorithm trained in a preliminary training step,
wherein the preliminary training step comprises training the algorithm by machine learning and/or artificial intelligence techniques, based on known data.

### Claim 3 (depends on 2)

A method according to claim 2, wherein the pre-trained model and/or algorithm comprises a regression model, which uses as covariates the polygenic risk score (PRS), low-density lipoprotein cholesterol level (LDL-C), combination of polygenic risk score and low-density lipoprotein cholesterol level (PRS×LDL-C); and
wherein the preliminary training step comprises training the regression model using as a reference dataset a first dataset of a population of individuals of which PRS and LDL-C are known, and for which the outcomes of onset of cardiovascular disease are known, for a first subset of individuals, or cases, or for which the non-onset of cardiovascular disease is known, after a predefined period of time, for a second subset of individuals or controls.

### Claim 4 (depends on 3)

A method according to claim 3, wherein the pre-trained regression model is used to derive said first risk parameter (HR1), second risk parameter (HR2) and third risk parameter (HR3); and
wherein said preliminary training step comprises training the regression model with reference to said first risk parameter (HR1), said second risk parameter (HR2) and said third risk parameter (HR3) based on said reference dataset using as a dependent variable the cardiovascular disease onset or non-onset, obtainable from known data.

### Claim 5 (depends on 3)

A method according to claim 3, wherein the pre-trained regression model is used to calculate said at least one risk value (R); and
wherein said preliminary training step comprises training the regression model with reference to said at least one risk value (R) based on said reference dataset using as a dependent variable the cardiovascular disease onset or non-onset, obtainable from known data.

### Claim 6 (depends on 3)

A method according to claim 3, wherein the regression model is a Cox proportional hazards regression model.

### Claim 7 (depends on 1)

A method according to claim 1, adapted to perform a predictive prognosis which takes into account one or more further risk factors;
wherein said step of calculating at least one risk value (R) comprises calculating the at least one risk value (R) also based on an operational value of each of one or more further covariates (COVx) associated with a respective one of said one or more further risk factors;
wherein the pre-trained model and/or algorithm is configured to calculate said first risk parameter (HR1), said second risk parameter (HR2) and said third risk parameter (HR3) also based on the operational values of each of said one or more further covariates (COVx); and
wherein the method further comprises accessing data of the individual to be examined, including individual values (COVxp) of each of said one or more further covariates associated with the one or more further risk factors.

### Claim 8 (depends on 7)

A method according to claim 7, wherein the pre-trained model and/or algorithm comprises a regression model, which uses as covariates, in addition to the polygenic risk score (PRS) variable, a low-density lipoprotein cholesterol level (LDL-C) variable, a combination of polygenic risk score and low-density lipoprotein cholesterol level (PRS×LDL-C) variable, also said further variables (COVx) which encode the further risk factors; and
wherein the preliminary training step comprises training the regression model using as a reference dataset a second dataset of a population of individuals of which, in addition to PRS and CDC-L, also the individual values of each of said further covariates (COVx) is known.

### Claim 9 (depends on 7)

Method according to claim 7, wherein said further risk factors comprise any sub-set of one or more of the risk factors belonging to the following set:
age, gender, genotyping array, the first 4 principal components of ancestry, Townsend Deprivation Index (TDI), diabetes and smoking status, family history of heart disease, systolic blood pressure (SBP), Body Mass Index (BMI), Glycated hemoglobin, HbA1C, Triglycerides (TG), C-reactive protein (CRP), and dietary intake goals (DIG); and/or
wherein the logistic regression is adjusted or conditioned based on any sub-set of one or more of the risk factors belonging to said set comprising age, gender, genotyping array, the first 4 principal components of ancestry, Townsend Deprivation Index (TDI), diabetes and smoking status, family history of heart disease, systolic blood pressure (SBP), Body Mass Index (BMI), Glycated hemoglobin, HbA1C, Triglycerides (TG), C-reactive protein (CRP), and dietary intake goals (DIG).

### Claim 10 (depends on 1)

A method according to claim 1, wherein the risk value (R) is calculated based on a sum of products relating to different relevant variables, comprising at least said polygenic risk score (PRS) variable, low-density lipoprotein cholesterol level (LDL-C) variable, a combination of polygenic risk score and low-density lipoprotein cholesterol level (PRS×LDL-C) variable, wherein each product provides the multiplication of said first risk parameter (HR1), said second risk parameter (HR2) and said third risk parameter (HR3) for the difference between the operational value and the average value of the variables, respectively, polygenic risk score (PRS), low-density lipoprotein cholesterol level (LDL-C), combination of polygenic risk score and low-density lipoprotein cholesterol level (PRS×LDL-C).

### Claim 11 (depends on 1)

A method according to claim 1, wherein the determined or calculated risk value is a relative risk value, with respect to an average risk referring to a population; or
wherein the determined or calculated risk value is an absolute risk value, relating to the individual, and representative of an individual's risk of developing cardiovascular disease within a certain period of time, or at a given age.

### Claim 12 (depends on 1)

A method according to claim 1, wherein the cardiovascular disease is a coronary artery disease (CAD).

### Claim 13 (depends on 1)

A device adapted to perform a predictive prognosis of the onset of a cardiovascular disease, comprising:
acquisition means for acquiring a quantity of blood of an individual and determining the individual's low-density lipoprotein cholesterol level (LDL-C) based on a test of the quantity of blood acquired;
an electronic interface, adapted to receive in input a calculated value of the individual's polygenic risk score (PRS);
a processor configured to receive said low-density lipoprotein cholesterol level (LDL-C) and polygenic risk score (PRS) value of the individual, and to perform a method for a predictive prognosis of the onset of cardiovascular disease according to claim 1,
wherein said acquisition and determination means, said electronic interface and said processor are comprised in a single portable device.

### Claim 14 (depends on 1)

A method for providing a clinical evaluation or for deriving a therapeutic intervention, wherein said method is performed based on the results of a predictive prognosis method according to claim 1.