SYSTEMS AND METHODS FOR DETERMINING THE PROBABILITY OF A PREGNANCY AT A SELECTED POINT IN TIME

• US 20160078172A1
• Filed: 09/18/2015
• Published: 03/17/2016
• 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
• Granted Patent: US 10,580,516 B2
• Time in Patent Office: Days
• US Class Current: 1/1
• 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 system for determining a probability of achieving a pregnancy at a selected point in time, the system comprising:

a central processing unit (CPU); and

storage coupled to said CPU for storing instructions that when executed by the CPU cause the CPU to;

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

provide a probability of achieving a pregnancy at a selected point in time as a result of running an algorithm on said input data, the algorithm having 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, wherein the algorithm accounts for any woman who ceases pregnancy attempts prior to reaching a live birth outcome.

2. The system of claim 1, wherein the pregnancy results in a live birth.

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

4. The system of claim 1, wherein said 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 system of claim 1, wherein said 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 system of claim 5, wherein said sample is a human tissue or bodily fluid.

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

8. The system of claim 7, wherein the reference set of data from the plurality of women further comprises fertility-associated genotypic traits.

9. The system 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 system according to claim 9, wherein the assay is selected from the group consisting of:

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

11. The system 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 system of claim 7, wherein the genotype traits are reflective of expression levels of one or more fertility-associated genes.

13. The system of claim 1, wherein the fertility-associated phenotypic trait is a trait selected from Table 1.

14. The system of claim 1, wherein the algorithm is stored at a remote location and the CPU communicates across a network to access said algorithm.

15. The system of claim 1, wherein the algorithm is stored locally within the CPU and the CPU accesses the algorithm within the CPU.

16. The system of claim 1, wherein the algorithm accounts for any woman who ceases pregnancy attempts without reaching a live birth outcome by weighting the remaining women in the reference set.

17. The system of claim 16, wherein the weighting is determined by modeling the likelihood of dropout.

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

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

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

providing a probability of achieving a pregnancy at a selected point in time as a result of running an algorithm on said input data, the algorithm having 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, wherein the algorithm accounts for any woman who ceases pregnancy attempts prior to reaching a live birth outcome.

20. The method of claim 19, wherein the pregnancy results in a live birth.

21. The method of claim 19, wherein said fertility-associated traits are adjusted per pre-specified time interval or fertility-associated medical intervention.

22. The method of claim 19, wherein said 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.

23. The method of claim 19, wherein said 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.

24. The method of claim 23, wherein said sample is a human tissue or bodily fluid.

25. The method of claim 19, wherein the data of the female subject further comprises fertility-associated genotypic traits of the female subject.

26. The method of claim 25, wherein the reference set of data from the plurality of women further comprises fertility-associated genotypic traits.

27. The method of claim 25, 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.

28. The method according to claim 27, wherein the assay is selected from the group consisting of:

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

29. The method of claim 27, 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.

30. The method of claim 25, wherein the genotype traits are reflective of expression levels of one or more fertility-associated genes.

31. The method of claim 19, wherein the fertility-associated phenotypic trait is a trait selected from Table 1.

32. The method of claim 19, wherein the data further comprises a plurality of fertility-associated phenotypic traits of a male subject.

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

inputting data representative of a plurality of fertility-associated phenotypic traits of a female subject into a computer; and

causing the computer to provide a probability of achieving a pregnancy at a selected point in time as a result of running an algorithm on the inputted data, the algorithm having 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, wherein the algorithm accounts for any woman who ceases pregnancy attempts prior to reaching a live birth outcome.

34-40. -40. (canceled)