Methods and systems for assessing infertility and related pathologies

• US 10,208,350 B2
• Filed: 07/17/2015
• Issued: 02/19/2019
• Est. Priority Date: 07/17/2014
• Status: Active Grant

• Current Assignee: Celmatix Inc.
• Original Assignee: Celmatix Inc.
• Inventors: Beim, Piraye Yurttas, Parfitt, David Emlyn, Elashoff, Michael
• Primary Examiner(s): Hibbert, Catherine S
• Application Number:
  US14/802,609
• Publication Number:
  US 20160017426A1
• Time in Patent Office: 1,313 Days
• Field of Search: None
• CPC Class Codes: C12Q 1/6883 for diseases caused by alterations of genetic material
• CPC Class Codes: C12Q 2600/112 Disease subtyping, staging or classification
• CPC Class Codes: C12Q 2600/158 Expression markers
• CPC Class Codes: G16B 25/00 ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
• CPC Class Codes: G16B 25/10 Gene or protein expression profiling; Expression-ratio estimation or normalisation

Abstract

Methods for assessing infertility and related pathologies and informing treatment type and timing thereof are provided. According to certain embodiments, methods of the invention include determining levels of one or more transcripts present in a sample obtained from a subject suspected of having endometriosis, identifying transcript levels that correspond to a regulation pattern specific to a time-point in a uterine cycle, and characterizing endometriosis of the subject based upon the identified transcript levels. The invention includes methods for assessing age-associated increase in aneuploidy rates based on FSH levels and IVF success rates based on obesity in PCOS patients.

Claims

1. A method for assessing endometriosis, the method comprising:

sequencing nucleic acid obtained from a tissue sample to determine levels of transcripts of a plurality of genes present in a tissue sample obtained from a subject suspected of having endometriosis, the plurality of genes comprising CCL 3L 1, CCL 3, FAM 180A, THBS 2, PDGFRL, FN 1, CLE 11A, CCNA 2, KIF 20A, BUB 1B, HSD 17B 6, HSD 11B 1, C 7, C 3, CXCL 2, CXCL 12, CXCL 13, PDGFC, CXCL 14, ACTA 2, TAGLN, ROBO 3, MT 1M, and SORBS 1;

analyzing said levels against a reference regulation pattern specific to a time-point in a uterine cycle using a computer system having a processor, thereby to generate a patient-specific signature;

preparing a report characterizing an endometriosis status of the subject based upon said patient-specific signature; and

treating the subject with an effective amount of drugs specific to the patient-specific signature;

wherein the reference regulation pattern is generated using gene expression data obtained from the plurality of genes across each phase of the uterine cycle from a reference population that includes both normal patients and endometriosis patients.

2. The method of claim 1, wherein the time-point comprises a phase in the uterine cycle.

3. The method of claim 2, wherein the phase is selected from the group consisting of the menstruation phase, the proliferative phase, the early secretory phase, the mid-secretory phase, and the late secretory phase.

4. The method of claim 1, wherein the tissue comprises endometrial tissue.

5. The method of claim 4, wherein the endometrial tissue is ectopic, eutopic, or both.

6. The method of claim 5, wherein the regulation pattern is specific to ectopic tissue, eutopic tissue, or both.

7. The method of claim 1 , wherein the regulation pattern comprises one or more transcripts selected from the group consisting of de-regulated transcripts, up-regulated transcripts, and combinations thereof.

8. The method of claim 1, wherein the characterizing step comprises determining the subject'"'"'s phase in the uterine cycle.

9. The method of claim 8, wherein the treatment is based on the subject'"'"'s phase in the uterine cycle.

10. A method for assessing endometriosis in a subject, the method comprising:

sequencing nucleic acid obtained from a blood sample to determine levels of transcripts of a plurality of genes expressed by the subject across different time-points of the subject'"'"'s uterine cycle, the plurality of genes comprising CCL 3L 1, CCL 3, FAM 180A, THBS 2, PDGFRL, FN 1, CLE 11A, CCNA 2, KIF 20A, BUB 1B, HSD 17B 6, HSD 11B 1, C 7, C 3, CXCL 2, CXCL 12, CXCL 13, PDGFC, CXCL 14, ACTA 2, TAGLN, ROBO 3, MT 1M, and SORBS 1;

analyzing the determined transcript levels against reference transcript signatures corresponding to the different time-points of the uterine cycle using a computer system having a processor, wherein the reference transcript signatures are generated using gene expression data obtained from the plurality of genes across each phase of the uterine cycle from a reference population that includes both normal patients and endometriosis patients;

generating, using the computer system, a patient-specific genetic signature for endometriosis at each time-point based on differential transcripts of the genes determined from the analyzing step;

classifying endometriosis based on the patient-specific genetic signature; and

treating the subject with a treatment specific to the patient-specific signature, wherein the treatment comprises administering an effective amount of vitamins or drugs.

11. The method of claim 10, wherein the different time-points comprise the phases of the subject'"'"'s uterine cycle.

12. The method of claim 11, wherein the different phases are selected from the group consisting of the menstruation phase, the proliferative phase, the early secretory phase, the midsecretory phase, and the late secretory phase.

13. The method of claim 10, wherein the classifying step comprises determining the type of the endometriosis.

14. The method of claim 13, wherein the type of endometriosis is selected from the group consisting of subtle, typical, cystic ovarian, and deep.

15. The method of claim 10, wherein the treatment comprises applying a therapy during a time-point in which a differential transcript was identified.

16. The method of claim 10 wherein the sample comprises endometrial tissue.

17. The method of claim 16, wherein the endometrial tissue is ectopic, eutopic or both.