Systems and methods for determining the probability of a pregnancy at a selected point in time

• US 10,580,516 B2
• Filed: 09/18/2015
• Issued: 03/03/2020
• Est. Priority Date: 10/17/2012
• Status: Active Grant

• Current Assignee: Celmatix Inc.
• Original Assignee: Celmatix Inc.
• Inventors: Elashoff, Michael, Karvir, Hrishikesh, Beim, Piraye Yurttas
• Primary Examiner(s): Lin, Jerry
• Application Number:
  US14/858,540
• Publication Number:
  US 20160078172A1
• Time in Patent Office: 1,628 Days
• Field of Search: 702 19
• CPC Class Codes: G16B 20/00 ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• CPC Class Codes: G16B 20/20 Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
• CPC Class Codes: 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
• CPC Class Codes: G16B 50/00 ICT programming tools or database systems specially adapted for bioinformatics

Abstract

The present invention generally relates to systems and methods for determining the probability of a pregnancy at a selected point in time. Systems and methods of the invention employ an algorithm that has been trained on a reference set of data from a plurality of women for whom at least one of fertility-associated phenotypic traits, fertility-associated medical interventions, or pregnancy outcomes are known, in which the algorithm accounts for any woman who ceases pregnancy attempts prior to reaching a live birth outcome.

Claims

1. A method for determining a probability of achieving a pregnancy at a selected point in time, the method comprising:

training a prognosis predictor, using training data from a population that includes women who ceased pregnancy attempts after one or more reproductive cycles without conception and women who continued pregnancy attempts until live birth, to determine a correlation between fertility-associated characteristics and known pregnancy outcomes, the fertility-associated characteristics comprising phenotypic traits, fertility-associated interventions, and pregnancy outcomes;

accepting as input, data representative of a plurality of fertility-associated phenotypic traits of a female subject;

analyzing the input data using the prognosis predictor;

providing, based on the analysis, a probability of achieving a pregnancy at a selected point in time; and

treating the female subject with a fertility treatment based on the probability of achieving a pregnancy.

2. The method of claim 1, wherein the pregnancy of the female subject results in a live birth.

3. The method of claim 1, wherein said fertility-associated traits are adjusted per pre-specified time interval or fertility-associated medical intervention.

4. The method of claim 1, wherein said input data are obtained from at least one selected from the group consisting of:

a questionnaire, a medical history of said subject, a family medical history of said subject, and a combination thereof.

5. The method of claim 1, wherein said input data are obtained by analyzing a sample collected from a person selected from the group consisting of:

said female subject, intimate partners of said subject, blood-related relatives of said subject, gamete donors, embryo donors, gestational carriers, and a combination thereof.

6. The method of claim 5, wherein said sample is a human tissue or bodily fluid.

7. The method of claim 1, wherein the input data further comprises fertility-associated genotypic traits of the female subject.

8. The method of claim 7, wherein the training data further comprises fertility-associated genotypic traits.

9. The method of claim 7, wherein the genotypic traits of the subject are obtained by conducting an assay on a sample from the subject to determine the presence or absence of a genetic variation that is associated with infertility.

10. The method of claim 9, wherein the assay is selected from the group consisting of:

sequencing, hybridization to an array, and an amplification reaction.

11. The method of claim 9, wherein the genetic variation is selected from the group consisting of:

a single nucleotide polymorphism, a deletion, an insertion, a rearrangement, a copy number variation, and a combination thereof.

12. The method of claim 7, wherein the genotypic traits are reflective of expression levels of one or more fertility-associated genes.

13. The method of claim 1, wherein the fertility-associated phenotypic traits comprise a trait selected from Table 1.

14. The method of claim 1, wherein the input data further comprises a plurality of fertility-associated phenotypic traits of a male subject.

15. A method for determining a probability of achieving a pregnancy at a selected point in time, the method comprising:

using at least one computer to train a prognosis predictor using training data from a population that includes women who ceased pregnancy attempts after one or more reproductive cycles without conception and women who continued pregnancy attempts until live birth, to determine a correlation between fertility-associated characteristics and known pregnancy outcomes, the fertility-associated characteristics comprising phenotypic traits, fertility-associated interventions, and pregnancy outcomes;

inputting data representative of a plurality of fertility-associated phenotypic traits of a female subject into the at least one computer;

analyzing the input data using the prognosis predictor;

causing the at least one computer to provide a probability of achieving a pregnancy at a selected point in time based on the analysis; and

treating the female subject with a fertility treatment based on the probability of achieving a pregnancy.