WO2021092226A1

WO2021092226A1 - Embryo transfer outcome prediction using endometrial organoids and spent embryo culture medium

Info

Publication number: WO2021092226A1
Application number: PCT/US2020/059185
Authority: WO
Inventors: Dusko Ilic; Ingvar HELGASON; Hugo VANKELECOM
Original assignee: Em-O-Em Diagnostics, Inc.
Priority date: 2019-11-05
Filing date: 2020-11-05
Publication date: 2021-05-14

Abstract

Described herein, in certain embodiments, are methods of determining an outcome of at least one embryo following transfer of the embryo to a recipient female, where the outcome is based on the expression of at least one gene in an endometrial organoid contacted with spent embryo culture medium used to culture the at least one embryo. Further described herein, in certain embodiments, are arrays of endometrial organoids and nucleic acid probe arrays for use in these methods.

Description

EMBRYO TRANSFER OUTCOME PREDICTION USING ENDOMETRIAL ORGANOIDS AND SPENT EMBRYO CULTURE MEDIUM

CROSS-REFERENCE

[0001] This application claims the benefit of U.S. Provisional Application No. 62/931,022, filed November 5, 2019 and U.S. Provisional Patent Application No. 62/947,180, filed December 12, 2019, which are incorporated herein by reference in their entireties for all purposes.

BACKGROUND

[0002] Assisted reproductive technologies, such as in vitro fertilization, can involve the transfer of an embryo into the uterus or fallopian tube of a woman experiencing reproductive complications, such as infertility. While approximately 40% or more of embryo transfers in women under 35 can result in a live birth, in certain cases seemingly healthy embryos can fail to implant following transfer.

[0003] Molecular cross-talk between embryos and maternal endometrial tissue can play an important role during implantation. However, molecules such as microRNA released by an embryo may interfere with the communication between the embryo and endometrium and contribute to failure of the embryo to implant. Improvements in the evaluation of embryos prior to transplantation can increase the success rate of in vitro fertilization, as well as further decreasing the emotional distress and financial burden in the women receiving these treatments.

SUMMARY

[0004] Described herein, in certain embodiments, are methods. In some embodiments, a method can comprise contacting an organoid with at least a portion of spent embryo culture medium used to culture an embryo. In some embodiments, a contacting can occur for at least 60 minutes, 90 minutes, 120 minutes, 150 minutes, or 180 minutes. In some embodiments, an organoid can be an endometrial organoid. In some embodiments, a organoid can be generated from a female individual. In some embodiments, a female individual can be a healthy female individual. In some embodiments, a healthy female individual can be selected from an individual who has not experienced a loss of a pregnancy, has not experienced a failure of an embryo to implant following in vitro fertilization, does not suffer from a reproductive system disorder or condition, and a combination thereof. In some embodiments, a reproductive system disorder or condition can be selected from the group of: endometriosis, uterine fibroids, polycystic ovary syndrome, premature ovarian failure, primary ovarian insufficiency, cancer of a reproductive organ, bacterial vaginosis, sexually transmitted disease, or a combination thereof. In some embodiments, a female individual can have a disease or condition. In some embodiments, a disease or condition can comprise endometriosis, uterine fibroids, polycystic ovary syndrome, premature ovarian failure, primary ovarian insufficiency, cancer of a reproductive organ, bacterial vaginosis, sexually transmitted disease, or a combination thereof. In some embodiments, a female individual can be a human. In some embodiments, a organoid can comprise a plurality of organoids. In some embodiments, a spent embryo culture medium can comprise a molecule secreted by an embryo. In some embodiments, a molecule secreted by an embryo can comprise at least one miRNA. In some embodiments, an embryo can be in a stage selected from cleavage, morula, or blastocyst. In some embodiments, an embryo can be a human embryo. In some embodiments, the method can comprise determining an expression of a gene in an organoid. In some embodiments, a gene can be differentially expressed in a first reference organoid contacted with a first reference spent embryo culture medium used to culture a first embryo resulting in confirmed positive outcome following transfer to a uterus of a first subject relative to a second reference organoid contacted with a second spent embryo culture medium used to culture a second embryo resulting in confirmed negative outcome following transfer to a uterus of a second subject. In some embodiments, determining an expression of a gene in an organoid can be carried out at least 12 hours, 24 hours, 36 hours, 48 hours, or 60 hours after a contacting. In some embodiments, an expression can indicate an outcome of an embryo following transfer of an embryo to a uterus of an individual. In some embodiments, an outcome can be a positive outcome or a negative outcome. In some embodiments, a positive outcome can be selected from a live birth or implantation. In some embodiments, a negative outcome can be no live birth or no implantation. In some embodiments an outcome can be a probability of a positive outcome or a negative outcome. In some embodiments, the method can comprise predicting a outcome. In some embodiments, predicting can comprise comparing an expression to a reference. In some embodiments, a reference can comprise a reference expression of a gene in a first reference organoid contacted with a first reference spent embryo culture medium used to culture a first reference embryo, wherein a first reference embryo resulted in a confirmed positive outcome following transfer to a uterus of a test subject. In some embodiments, a test subject can be a control. In some embodiments, an outcome can be predicted as a positive outcome if an expression can be similar to a reference expression. In some embodiments, an outcome can be predicted as a negative outcome if an expression can be different compared to a reference expression. In some embodiments, a reference can comprise a reference expression of a gene in a second reference organoid contacted with a second reference spent embryo culture medium used to culture a second reference embryo, wherein a second reference embryo resulted in a confirmed negative outcome following transfer to a uterus of a test subject. In some embodiments, an outcome can be predicted as a negative outcome if an expression can be similar to a reference expression. In some embodiments, an outcome can be predicted as a positive outcome if an expression can be different compared to a reference expression. In some embodiments, a predicting can comprise applying a classifier to an expression. In some embodiments, a classifier can be trained with gene expression data from a first reference organoid contacted with a first reference spent embryo culture medium used to culture a first reference embryo resulting in confirmed positive outcome following transfer to a uterus of a first test subject and a second reference organoid contacted with a second reference spent embryo culture medium used to culture a second reference embryo resulting in confirmed negative outcome following transfer to a uterus of a second test subject. In some embodiments, a classifier can be selected from the group of: Naive Bayes classifier, decision tree classifier, logistic regression classifier, K-nearest neighbor classifier, neural network classifier, or support vector machine classifier. In some embodiments, a method can comprise preserving an embryo when a outcome can be predicted as a positive outcome. In some embodiments, a preserving can comprise freezing. In some embodiments, a method can comprise transferring an embryo into a uterus of a recipient female when an outcome can be predicted as a positive outcome. In some embodiments, a method can comprise discarding an embryo when an outcome can be predicted as a negative outcome. In some embodiments, a method can comprise confirming a outcome. In some embodiments, a confirming can comprise measuring a first amount of human chorionic gonadotrophin (hCG). In some embodiments, a measuring a first amount of hCG can occur from 5 days to 9 days after transfer of an embryo into an individual. In some embodiments, a positive outcome can be confirmed when a first amount of hCG can be greater than about 5 IU of hCG/mL of blood. In some embodiments, a confirming can comprise measuring a second amount of hCG. In some embodiments, a measuring of a second amount of hCG can occur at least 5 hours, 10 hours, 15 hours, 24 hours, or 48 hours after a measuring a first amount of hCG. In some embodiments, a positive outcome can be confirmed when a second amount of hCG has doubled from a first amount of hCG for each of 48 hours passed since a measuring of a first amount of hCG. In some embodiments, a confirming can comprise performing an ultrasound on an individual. In some embodiments, a positive outcome can be confirmed when a ultrasounds shows visual evidence of a positive outcome. Further disclosed herein are compositions comprising an organoid wherein the organoid or a portion thereof was or is exposed to at least a portion of spent embryo culture medium.

[0005] Disclosed herein, in certain embodiments, can be methods of determining an expression of a gene in an organoid, wherein an expression indicates an outcome of an embryo following transfer of an embryo to a uterus of an individual. In some embodiments, an embryo can be cultured in a culture medium. In some embodiments, a culture medium can be spent culture medium following contact with an embryo. In some embodiments, a organoid or a portion thereof can be contacted with at least a portion of a spent culture medium prior to a determining. In some embodiments, a organoid can be an endometrial organoid. In some embodiments, an outcome can be a positive outcome or a negative outcome. In some embodiments, a positive outcome can be selected from live birth or implantation. In some embodiments, a negative outcome can be no live birth or no implantation. In some embodiments, an outcome can be determined by comparing an expression to a reference. In some embodiments, a reference can comprise a reference expression of a gene in a first reference organoid contacted with a first reference spent embryo culture medium used to culture a first reference embryo, wherein a first reference embryo resulted in a confirmed positive outcome following transfer to a uterus of an individual. In some embodiments, an outcome can be a positive outcome if an expression can be similar to a reference expression. In some embodiments, an outcome can be a negative outcome if an expression can be different compared to a reference expression. In some embodiments, a reference comprises a reference expression of a gene in a second reference organoid contacted with a second reference spent embryo culture medium used to culture a second reference embryo, wherein a second reference embryo resulted in a negative outcome following transfer to a uterus to an individual. In some embodiments, an outcome can be a negative outcome if an expression can be similar to a reference expression. In some embodiments, an outcome can be a positive outcome if an expression can be different compared to a reference expression. In some embodiments, an outcome can be determined by applying a classifier to an expression. In some embodiments, a classifier can be trained with gene expression data from a first reference organoid contacted with a first reference spent embryo culture medium used to culture a first reference embryo resulting in a confirmed positive outcome following transfer to a uterus of an individual and a second reference organoid contacted with a second reference spent embryo culture medium used to culture a second reference embryo resulting in a confirmed negative outcome following transfer to a uterus of an individual. In some embodiments, a classifier can be selected from: Naive Bayes classifier, decision tree classifier, logistic regression classifier, K- nearest neighbor classifier, neural network classifier, or support vector machine classifier. In some embodiments, a gene can be differentially expressed in a first reference organoid contacted with a first reference spent embryo culture medium used to culture a first embryo resulting in a confirmed positive outcome following transfer to a uterus of an individual relative to a second reference organoid contacted with a second spent embryo culture medium used to culture a second embryo resulting in a confirmed negative outcome following transfer to a uterus an individual. In some embodiments, an embryo can be in a stage selected from cleavage, morula, or blastocyst. In some embodiments, an embryo can be a human embryo. In some embodiments, the method can comprise preserving an embryo when an outcome can be a positive outcome. In some embodiments, a preserving can comprise freezing. In some embodiments, the method can comprise transferring an embryo into a uterus of recipient female when a outcome can be predicted as a positive outcome. In some embodiments, the method can comprise discarding an embryo when a outcome can be predicted as a negative outcome. In some embodiments, a method can comprise confirming a outcome. In some embodiments, a confirming comprises measuring a first amount of human chorionic gonadotrophin (hCG). In some embodiments, a measuring a first amount of hCG can occur from 1 day to 9 days after transfer of an embryo into an individual. In some embodiments, a positive outcome can be confirmed when a first amount of hCG can be greater than about 5 IU of hCG/ml of blood. In some embodiments, a confirming can comprise measuring a second amount of hCG. In some embodiments, a measuring a second amount of hCG can occur at least 2 hours, 5 hours, 10 hours, 15 hours, 24 hours or 48 hours after a measuring a first amount. In some embodiments, a positive outcome can be confirmed when a second amount of hCG has doubled from a first amount of hCG for each of 48 hours passed since a measuring of a first amount of hCG. In some embodiments, a confirming can comprise performing an ultrasound on an individual. In some embodiments, a positive outcome can be confirmed when a ultrasounds shows visual evidence of a positive outcome. In some embodiments, a organoid can be generated from a female individual. In some embodiments, a female individual can be a healthy female individual. In some embodiments, a healthy female individual can be selected from an individual who has not experienced a loss of a pregnancy, has not experienced a failure of an embryo to implant following in vitro fertilization, does not suffer from a reproductive system disorder or condition, or a combination thereof. In some embodiments, a reproductive system disorder or condition can be selected from endometriosis, uterine fibroids, polycystic ovary syndrome, premature ovarian failure, primary ovarian insufficiency, cancer of a reproductive organ, bacterial vaginosis, sexually transmitted disease, or a combination thereof. In some embodiments, a female individual can have a disease or condition. In some embodiments, a disease or condition can comprise endometriosis, uterine fibroids, polycystic ovary syndrome, premature ovarian failure, primary ovarian insufficiency, cancer of a reproductive organ, bacterial vaginosis, sexually transmitted disease, or a combination thereof. In some embodiments, a female individual can be a human. In some embodiments, an organoid can comprise a plurality of organoids. Further disclosed herein are compositions comprising an organoid wherein the organoid or a portion thereof was or is exposed to at least a portion of spent embryo culture medium.

[0006] Described herein, in certain embodiments, are arrays comprising an organoid described herein. In some embodiments, an organoid can comprise a plurality of organoids. Further described herein, in certain embodiments are kits comprising an array described herein. In some embodiments, a kit can comprise instructions for use. In some embodiments, a kit can comprise reagents for carrying out any of the methods described herein.

[0007] Described herein, in certain embodiments, are arrays comprising a nucleic acid probe for detecting a nucleic acid expressed by an organoid, wherein a nucleic acid can be differential expressed in: i. a first reference organoid contacted with first spent embryo culture medium used to culture a first embryo, wherein a first embryo resulted in a confirmed positive outcome in a uterus of a first individual; and ii. a second reference organoid contacted with second spent embryo culture medium used to culture a second embryo, wherein a second embryo resulted in a confirmed negative outcome following transfer to a uterus of a second individual. In some embodiments, a confirmed positive outcome can be selected from live birth or implantation. In some embodiments, a confirmed negative outcome can be no live birth or no implantation. In some embodiments, an organoid can be an endometrial organoid. In some embodiments, a nucleic acid can be RNA or DNA. In some embodiments, a RNA can be mRNA. In some embodiments, a nucleic acid probe comprises a plurality of nucleic acid probes. In some embodiments, a plurality of nucleic acid probes can comprise at least 5, at least 10, at least 20, at least 30, at least 40, at least 50, at least 100, or at least 500 nucleic acid probes. In some embodiments, a nucleic acid can comprise a plurality of nucleic acids. In some embodiments, a plurality of nucleic acids can comprise at least 5, at least 10, at least 20, at least 30, at least 40, at least 50, at least 100, or at least 500 nucleic acids. In some embodiments, a nucleic acid probe can be immobilized on a solid support. Described herein, in certain embodiments, are kits comprising any of the arrays described herein. In some embodiments, a kit further comprises instructions for use.

INCORPORATION BY REFERENCE

[0008] All publications, patents, and patent applications mentioned in this specification are herein incorporated by reference to the same extent as if each individual publication, patent, or patent application was specifically and individually indicated to be incorporated by reference.

BRIEF DESCRIPTION OF THE DRAWINGS [0009] Various features of the disclosure are set forth with particularity in the appended claims. A better understanding of the features and advantages of the present disclosure will be obtained by reference to the following detailed description that sets forth illustrative embodiments, in which the principles of the disclosure are utilized, and the accompanying drawings of which: [0010] FIG. 1 illustrates a method for determination of the outcome of a plurality of embryos using an array (EM-O-EM array). [0011] FIG. 2 illustrates endometrial organoid (EM-O) uptake of fluorescently Cy3-labelled miR-30c from the culture medium in concentration of 0, 0.5, 1.0. 5.0 and 10 ng/ml) over a period of 30, 60 or 120 minutes.

[0012] FIG. 3 illustrates a heat map showing change in the expression of 386 genes (fold-change >1.5, p-value <0.5) 24 h after the EM-Os were exposed to Cy3-labelled 1 ng/ml miR-30c for 120 min. Samples 2AA and 2AB were untreated control, whereas 2BA and 2BB were cultured in the presence of 1 ng/ml miR-30c for 120 min.

[0013] FIG. 4 illustrates a heat map showing change in the expression of 511 genes (fold-change >1.5, p-value <0.5) between EM-Os exposed to 1 and 10 ng/ml Cy3-labelled miR-30c for 120 min. Samples 1C A, 1CB and ICC were cultured in the presence of 1 ng/ml, whereas 1EA, 1EB and 1EC were cultured in the presence of 10 ng/ml miR-30c for 120 min.

[0014] FIG. 5 shows a computer control system that may be programmed or otherwise configured to implement methods provided herein.

DETAILED DESCRIPTION

[0015] Embryos created via in vitro fertilization have been shown to secrete microRNAs which can be detected in the spent embryo culture medium. Since microRNAs can be involved in post- transcriptional regulation of gene expression, altering gene expression of genes important in the implantation process by some of these miRNAs may play a contributing role in failure of implantation of an otherwise normal embryo. Described herein, in certain embodiments, are methods of predicting an outcome of at least one embryo following transplantation into a recipient, wherein the outcome is a positive outcome or a negative outcome. The outcome of the at least one embryo can be determined based on expression of at least one gene in at least one endometrial organoid following contact of the at least one endometrial organoid with a spent embryo culture medium used to culture the at least one embryo. The methods described herein can comprise contacting at last a portion of an organoid with at least a portion of spent embryo culture medium used to culture an embryo. The methods described herein can comprise determining an expression of a gene in the organoid. Further disclosed herein are compositions comprising an organoid wherein the organoid or a portion thereof was or is exposed to at least a portion of spent embryo culture medium.

[0016] The terminology used herein is for the purpose of describing particular cases only and is not intended to be limiting. The below terms are discussed to illustrate meanings of the terms as used in this specification, in addition to the understanding of these terms by those of skill in the art. As used herein and in the appended claims, the singular forms “a,” “an,” and, “the” include plural referents unless the context clearly dictates otherwise. It is further noted that the claims can be drafted to exclude any optional element. As such, this statement is intended to serve as antecedent basis for use of such exclusive terminology as “solely,” “only,” and the like in connection with the recitation of claim elements, or use of a “negative” limitation.

[0017] Certain ranges are presented herein with numerical values being preceded by the term “about.” The term “about” can be used herein to provide literal support for the exact number that it precedes, as well as a number that is near to or approximately the number that the term precedes. In determining whether a number is near to or approximately a specifically recited number, the near or approximating un-recited number may be a number which, in the context in which it is presented, provides the substantial equivalent of the specifically recited number. Where a range of values is provided, it is understood that each intervening value, to the tenth of the unit of the lower limit unless the context clearly dictates otherwise, between the upper and lower limit of that range and any other stated or intervening value in that stated range, is encompassed within the methods and compositions described herein. The upper and lower limits of these smaller ranges may independently be included in the smaller ranges and are also encompassed within the methods and compositions described herein, subject to any specifically excluded limit in the stated range. Where the stated range includes one or both of the limits, ranges excluding either or both of those included limits are also included in the methods and compositions described herein. In some embodiments, “about” or “approximately” can mean a range of up to 10% of a given value. “Similar” can refer to something that is done to a great extent or degree of identity. In some embodiments, “similar” can mean at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, 98%, 99%, identical. [0018] As used herein, the terms “subject” and “individual” can be used interchangeably. None of the terms are to be interpreted as requiring the supervision of a medical professional (e.g., a doctor, nurse, physician’s assistant, orderly, or hospice worker). As used herein, the subject can be any animal, including mammals (e.g., a human or non-human animal). In one embodiment of the methods and compositions provided herein, the mammal is a human. The subject can be a female or a male. The subject may be any animal or living organism. Animals can be mammals, such as humans, non-human primates, rodents such as mice and rats, dogs, cats, pigs, sheep, rabbits, and others. Animals can be fish, reptiles, or others. Animals can be neonatal, infant, adolescent, or adult animals. Humans can be more than about: 1, 2, 5, 10, 20, 30, 40, 50, 60, 65, 70, 75, or about 80 years of age. The subject may have or be suspected of having a condition or a disease. The subject may be a patient, such as a patient being treated for a condition or a disease. The subject may be predisposed to a risk of developing a condition or a disease. The subject may be in remission from a condition or a disease. The subject may be healthy.

[0019] Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which the methods and compositions described herein belong. Although any methods and materials similar or equivalent to those described herein can also be used in the practice or testing of the methods and compositions described herein, representative illustrative methods and materials are now described.

EVALUATION OF EMBRYOS OUTCOMES

[0020] The methods described herein can comprise: contacting at least one endometrial organoid with a spent embryo medium used to culture at least one embryo. The method can further comprise determining an expression of at least one gene in the endometrial organoid. The method can comprise predicting the outcome of the at least one embryo following transplantation into a recipient female based on the expression of the at least one gene. The outcome can be selected from the group consisting of a positive outcome or a negative outcome. The positive outcome can be live birth or implantation. The negative outcome can be no live birth or no implantation. An embryo predicted to have a positive outcome can be referred to as an implantation capable embryo.

[0021] In some embodiments, a method for predicting the outcome of at least one embryo can be seen in FIG. 1. In some embodiments, a method for predicting implantation potential of at least one embryo can be seen in FIG. 1. The method can comprise, in an organoid exposed to spent embryo culture medium, determine gene expression of a target gene previously determined to show differential gene expression in an endometrial organoid exposed to spent embryo media from embryo which resulted in a live birth or implantation compared to an endometrial organoid exposed to spent embryo media from an embryo that did not result in a live birth or implantation. [0022] Culture media can be used to allow an in vitro fertilized egg to develop into an embryo prior to transfer to a uterus or frozen for storage. As used herein, “embryo” can refer to a fertilized egg that has undergone cell division to a later developmental stage, such as a cleavage stage, a morula, or a blastocyst. The cleavage stage can refer to a fertilized egg undergoing cell division up to and including eight cells. Following the cleavage stage, a morula can be produced, which can comprise at least sixteen cells up to about 70 cells. Following the morula, a blastocyst can be produced, which can comprise from about 70 to about 100 cells. Example of culture medium can include Universal IVF Medium (Medicult, Denmark), ISM1™ (Medicult,

Denmark), ISM2™ (Medicult, Denmark), Sydney IVF Fertilization Medium (Cook Medical, Bloomington, Indiana), G-TL™ (Vitrolife, Gothenburg, Sweden), G-l PLUS™ (Vitrolife, Gothenburg, Sweden), G-l™ (Vitrolife, Gothenburg, Sweden) G-2 PLUS™ (Vitrolife, Gothenburg, Sweden), G-2™ (Vitrolife, Gothenburg, Sweden), and GL BLAST™ (Ingamed, Maringa, Brazil). In some cases, at least two culture media are used. For example, G-l™ (Vitrolife, Gothenburg, Sweden) can be used to culture a fertilized ova from fertilization to day 2 or day 3, while G-2™ (Vitrolife, Gothenburg, Sweden) can be used to culture the embryo from day 3 to the blastocyst stage. The fertilized egg, during its development into an embryo, can secrete nucleic acids, metabolites, proteins, and enzymes into the culture media. Following development of the embryo to a specific stage, removal of the embryo from the culture medium, or storage of the embryo, the culture media can be referred to herein as spent embryo culture medium. The specific stage can be a stage of the embryo for transfer to a uterus of a recipient female, a stage that the embryo will be transferred to a second culture media, a stage for which the media can be used to determine an outcome, or a stage of the embryo useful for determining the outcome of the embryo following transfer to the uterus of a recipient. The specific stage can be a cleavage stage, a morula, or a blastocyst. In some embodiments, an embryo can be removed from the spent embryo culture medium prior to the predicting of the outcome of the embryo. In some cases, a portion of the spent embryo culture medium can be removed for use in the predicting of the outcome of the embryo.

[0023] In some embodiments, a spent embryo culture medium can comprise nucleic acids, metabolites, protein, and enzymes secreted by the embryo. In some embodiments, nucleic acids can be DNA or RNA. In some embodiments, nucleic acids can be cell free. As used herein, the term “cell-free” or “cell free” refers to the condition of the nucleic acid sequence as it appeared in, for example, the body, before a sample is obtained from the body. For example, circulating cell-free nucleic acid sequences in a sample may have originated as cell-free nucleic acid sequences circulating in the bloodstream of the human body. In contrast, nucleic acid sequences that are extracted from a solid tissue, such as a biopsy, are generally not considered to be “cell- free.” In some embodiments, RNA can be microRNA (miRNA). In some embodiments, a microRNA found in spent embryo culture medium can be secreted during a specific embryo developmental stage (e.g. cleavage, morula, blastocyst). In some embodiments, a microRNA found in spent embryo culture medium can be secreted during more than one embryo development stage (e.g. cleavage, morula, blastocyst). Examples of microRNAs found in spent embryo culture medium can include but is not limited to miR-16, miR-19b, miR-20a, miR-24, miR-28-3p, miR-30b, miR-30c, miR-92a, miR-126, miR-136, miR-146a, miR-184, miR-191, miR-192, miR-193b, miR-195, miR-200c, miR-202, miR-203, miR-204, miR-212, miR-222, miR-223, miR-302b, miR-320, miR-331, miR-342, miR-345, miR-370, miR-371-3p, miR-373, miR-433, miR-454, miR-484, miR-486-3p, miR-512-3p, miR-517a, miR-517c, miR-518e, miR- 519a, miR-636, or miR-642.

[0024] In some embodiments, the least one endometrial organoid can be 1, 2, 3, 4, 5, 6, 7, 8, 9,

10, or more than 10 endometrial organoids. In some embodiments, at least one endometrial organoid can be generated from at least one individual. In some embodiments, the at least one individual can be female. In some embodiments, the at least one individual can be one individual. In some embodiments, the at least one individual can be 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more than 10 individuals. In some embodiments, the at least one individual can be human. In some embodiments, the at least one individual can be a non-human mammal. In some embodiments, the non-human mammal can be a non-human primate, cow, horse, pig, sheep, goat, llama, rabbit, camel, dog, cat, rat, mouse, hamster, or guinea pig.

[0025] In some embodiments, the at least one individual can be at least one healthy individual. In some embodiments, the at least one healthy individual can be at least one individual who has not experienced a loss of a pregnancy, has not experienced a failure of an embryo to implant following in vitro fertilization, does not suffer from a reproductive system disorder or condition, or a combination thereof. In some embodiments, the reproductive system disorder or condition can be endometriosis, uterine fibroids, polycystic ovary syndrome, premature ovarian failure, primary ovarian insufficiency, cancer of a reproductive organ, bacterial vaginosis, sexually transmitted disease, or a combination thereof.

[0026] In some embodiments, the at least one individual can be an unhealthy individual. In some embodiments, the at least one unhealthy individual can be at least one individual who has experienced a loss of a pregnancy, has experienced a failure of an embryo to implant following in vitro fertilization, suffers from a reproductive system disorder or condition, or a combination thereof. In some embodiments, the reproductive system disorder or condition can be endometriosis, uterine fibroids, polycystic ovary syndrome, premature ovarian failure, primary ovarian insufficiency, cancer of a reproductive organ, bacterial vaginosis, sexually transmitted disease, or a combination thereof. In one example, the endometrial organoid can be generated from a human female who will be receiving or plans to receive a transplantation of an embryo for which the array will be used to evaluate the outcome of, for example, wherein the human female previously experienced a negative outcome of a previously transferred embryo.

[0027] In some embodiments, a method disclosed herein can comprise contacting at least one endometrial organoid with a spent embryo medium used to culture an embryo. In some embodiments, the method can comprise contacting at least one endometrial organoid in each partition of an array comprising a plurality of partitions of endometrial organoids, with a spent embryo media used to culture an embryo. In some cases, each partition of at least one endometrial organoid can be contacted with spent embryo culture medium used to culture a single embryo. In some cases, each partition of at least one endometrial organoid can be contacted with a different spent embryo culture medium from a plurality of spent embryo culture media used to culture a plurality of embryos.

[0028] In some embodiments, the method can comprise contacting an array comprising one or a plurality of partitions, each partition comprising at least one endometrial organoid, with a spent embryo medium used to culture an embryo from the plurality of embryos. In some embodiments, the method can comprise predicting the outcomes of a plurality of embryos. In some embodiments, each partition of the plurality of partitions of endometrial organoids can be contacted with a different spent embryo medium from a plurality of spent embryo media, each spent embryo medium in the plurality of spent embryo media used to culture a different embryo from the plurality of embryos.

[0029] In some embodiments, the contacting can comprise contacting the at least one endometrial organoid with at least a portion of spent embryo culture medium. In some embodiments, the portion of spent embryo culture medium can comprise from about 1 pi to 1000 mL of the spent embryo culture medium. In some embodiments, the portion of spent embryo culture medium can comprise from about at least 1 mΐ to 1ml, from 1 mΐ to 500 mΐ, from 1 mΐ to 50 mΐ, from 1 mΐ to 10 mΐ, or from 1 mΐ to 5 mΐ of the spent embryo culture medium. In some embodiments, the at least one endometrial organoid can be at least one endometrial organoid in a partition of a plurality of partitions of endometrial organoids. In some embodiments, the contacting can occur from about 10, 20, 30, 40, 50, or 60 minutes to about at least 70, 100, 120, 130, 140, 150, 160, 170, or 180 minutes. In some embodiments, the contacting can occur for at least 60 minutes, 90 minutes, 120 minutes, 150 minutes, 180 minutes or more.

[0030] In some embodiments, expression of at least one gene expression can be determined. In some embodiments, the at least one gene can beat least 5, at least 10, at least 20, at least 30, at least 40, at least 50, or at least 100 genes. In some embodiments, the at least one gene can be at least one gene showing differential expression in an endometrial organoid contacted with spent embryo culture medium used to culture a first embryo resulting in confirmed positive outcome following transfer to an individual relative to at an endometrial organoid contacted with spent embryo culture medium from a second embryo resulting in confirmed negative outcome following transfer to a different individual. In some embodiments, the at least one gene can be a gene involved in implantation of an embryo.

[0031] In some embodiments, the determining can comprise determining the expression of at least one gene by the at least one endometrial organoids. In some embodiments, the determining can be carried out from a least about 2, 4, 6, 8 ,10 or 12 hours to at least about 30, 40, 50, 60 hours or more after the contacting. In some embodiments, the determining can be carried out at least 12 hours, 24 hours, 36 hours, 48 hours, or 60 hours or more after the contacting. In some embodiments, the expression can comprise an amount of at least one gene expressed, a ratio of expression of a gene to an expression of a different gene, a presence of expression of a gene, an absence of the expression of a gene, an overexpression of a gene relative to a reference amount, an under expression of a gene or a level of a gene expression relative to a reference amount. In some embodiments, a reference amount can be an amount of the at least one gene expressed in the endometrial organoid prior to the contacting. In some embodiments, a reference can be a control. In some embodiments, an overexpression or an under expression can be a fold change in the amount of expression of a gene relative to the reference amount. For example, the overexpression can be a 0.5-fold increase, 1-fold increase, 2-fold increase, 3-fold increase or more or the under expression can be a 0.5-fold decrease, 1-fold decrease, 2-fold decrease, 3-fold decrease or more.

[0032] In some embodiments, a gene expression can correlate with expression of a protein for which the gene encodes. In some embodiments, gene express can be correlated with expression of a protein encoded by the gene. In some embodiments, a gene expression can refer to the expression a gene as detected by a method disclosed herein.

[0033] In some embodiments, determining expression of a gene can include a method to detect and measure absorbance, fluorescence, phosphorescence, refractive index, polarization or light scattering. These include direct and/or indirect means to measure such parameters. Methods involving fluorescence include fluorescent tagging in immunological methods such as ELISA or sandwich assay. Methods involving refractive index include surface Plasmon resonance (SPR), grating coupled methods (e.g. sensors uniform grating couplers, wavelength-interrogated optical sensors (WIOS) and chirped grating couplers), resonant minor and interferometric techniques. Methods involving polarization can include ellipsometry. Light scattering methods may also be used. Other means for tagging and/or separating and/or detecting can also include magnetic means. Magnetic resonance imaging, gas phase ion spectrometry, MRI may all be used.

[0034] In some embodiments, the determining can comprise isolating nucleic acid from the at least one endometrial organoid. In some embodiments, the at least one endometrial organoid can be at least one endometrial organoid in a partition of a plurality of partitions of endometrial organoids. In some embodiments, the determining can comprise isolating nucleic acid from an endometrial organoid. In some embodiments, the nucleic acid can be DNA or RNA. In some embodiments, the RNA can be messenger RNA (mRNA). In some embodiments, the nucleic acid can be cell free nucleic acid. The cell free nucleic acid can be cell free DNA (cfDNA) or cell free RNA (cfRNA). In some embodiments, determining an expression of the at least one gene can comprise sequencing the isolated nucleic acid. In some embodiments, complementary DNA (cDNA) is reverse transcribed from the isolated mRNA. In some embodiments, determining an expression of the at least one gene can comprise sequencing. In some embodiments, the sequencing can be whole genome sequencing or exome sequencing. The term “sequencing” as used herein, may comprise, high-throughput sequencing, Maxam-Gilbert sequencing, massively parallel signature sequencing, Polony sequencing, 454 pyrosequencing, Sanger sequencing, Illumina sequencing, SOLiD sequencing, Ion Torrent semiconductor sequencing, DNA nanoball sequencing, Heliscope single molecule sequencing, single molecule real time (SMRT) sequencing, nanopore sequencing, shot gun sequencing, RNA sequencing, Enigma sequencing, or any combination thereof. In some embodiments, sequencing can comprise transcriptome sequencing, for example RNA-seq. In some embodiments, the method can comprise determining an expression of the at least one gene prior to the contacting. In some embodiments, the method can comprise comparing the expression of the at least one gene prior to the contacting to the expression of the at least one gene following the contacting.

[0035] In some embodiments, determining an expression of at least one gene can comprise contacting a nucleic acid probe or an array comprising at least one nucleic acid probe for detecting at least one gene with nucleic acid isolated from the at least one endometrial organoid after the contacting. In some embodiments, determining an expression of at least one gene can comprise contacting a nucleic acid probe array comprising the at least one nucleic acid probe for detecting the at least one gene with a test sample and or a reference sample. In some embodiments, the test sample can comprise nucleic acid isolated from the at least one endometrial organoid after the contacting. In some embodiments, the reference sample can comprise nucleic acid isolated from the at least one endometrial organoid before the contacting. In some embodiments, the reference sample can comprise nucleic acid isolated from at least one endometrial organoid not exposed to spent embryo culture media. In some embodiments, the reference sample can comprise nucleic acid isolated from at least one endometrial organoid contacted with spent embryo culture media from an embryo with a known outcome following transfer to a uterus, for example resulting in a live birth or not a live birth. In some embodiments, the test sample can be labeled with a first fluorescent probe and the reference sample can be labeled with a second fluorescent probe. In some embodiments, the first fluorescent probe and the second fluorescent probe can be different. In some embodiment, a test sample or a portion thereof can be labeled with a first tag. In some embodiment, a reference sample or a portion thereof can be labeled with a second tag. The first tag and the second tag can be different. The tag can be an optically detectable tag. The optically detectable tag can be a fluorescent probe.

The fluorescent probe can be a Cyanine dye. The Cyanine dye can be Cyanine 3 (Cy3) or Cyanine 5 (Cy5). In some embodiments, the tag is optically detectable upon further contact of the tag with a second compound. For example, the tag can be biotin and the second compound can be streptavidin.

[0036] In some embodiments, a tag may comprise a glutathione-S-transferase (GST), a maltose binding protein (MBP), a green fluorescent protein (GFP), an AviTag, a Calmodulin tag, a polyglutamate tag, a FLAG tag, an human influenza hemagglutinin (HA) tag, a polyhistidine (His) tag, a Myc-tag, an S-tag, an streptavi din-binding peptide (SBP) tag, a Softag 1, a Strep tag, a TC tag, a V5 tag, an Xpress tag, an Isopeptag, a SpyTag, a biotin carboxyl carrier protein (BCCP) tag, a chitin binding protein (CBP) tag, a HaloTag, a thioredoxin tag, a T7 tag, a protein kinase A (PKA) tag, a c-Myc tag, a Trx tag, a Hsv tag, a CBD tag, a Dsb tag, a pelB/ompT, a KSI, a VSV-G tag, a 3-Gal tag, or any combination thereof. A tag may be a fusion tag, a covalent peptide tag, a protein tag, a peptide tag, an affinity tag, an epitope tag, a solubilization tag, or any combination thereof. A tag may comprise a recombinant protein. A tag may associate with a protein or protein fragment. A FLAG-tag may comprise a sequence or a portion thereof comprising DYKDDDDK, where D may be aspartic acid, Y may be tyrosine, and K may be lysine.

[0037] In some embodiments, the predicting can comprise applying a classifier to the expression of at least one gene. In some embodiments, the classifier can be trained with training data. In some embodiments, the training data can comprise gene expression data of a plurality of genes from a plurality of endometrial organoids contacted with a plurality of spent embryo culture media, wherein each spent embryo culture medium from the plurality of spent embryo culture media can be produced by an in vitro fertilized embryo cultured in a culture media where the outcome of the embryo is known (i.e., confirmed outcome). In some embodiments, the outcome can be a confirmed positive outcome (e.g. live birth or implantation) or a confirmed negative outcome (e.g. no live birth or no implantation following transfer of the embryo into a recipient female). In some embodiments an outcome can be a percentage (5%, 10%, 15%, 20%, 25%,

30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100%) possibility of a live birth, implantation, no live birth, or no implantation. In some embodiments, the training data can comprise gene expression data from at least one reference. In some embodiments, a reference can be an endometrial organoid contacted with spent embryo culture medium used to culture an embryo resulting in a confirmed positive outcome following transfer to an individual. In some embodiments, a reference can be at least one reference endometrial organoid contacted with spent embryo culture medium used to culture an embryo resulting in a confirmed negative following transfer to an individual. [0038] In some embodiments, the classifier can predict the outcome of the embryo with an AUC (area under the ROC curve) of greater than 0.7, 0.8, 0.9, or 0.95. In some embodiments, the classifier can be a Naive Bayes classifier, decision tree classifier, logistic regression classifier, K- nearest neighbor classifier, neural network classifier, or a support vector machine classifier. In some embodiments, the outcome predicted by the classifier can be one of the known outcomes from the training data used to generate the classifier. In some embodiments, predicting the outcome of an embryo can comprise applying the classifier to the expression of a subset of genes from the at least one endometrial organoid following contacting of the at least one endometrial organoid with the spent embryo culture medium used to culture an embryo, wherein the subset of genes is the subset of genes used to generate the classifier. In some embodiments, an embryo predicted to have a positive outcome can have an expression of the at least one gene similar to expression of the at least one gene in embryos that resulted in the confirmed positive outcome, as determined by the classifier. In some embodiments, an embryo predicted to have a negative outcome can have an expression of the at least one gene similar to expression of the at least one gene in embryos that resulted in the confirmed negative outcome, as determined by the classifier. [0039] In some embodiments, the method can comprise preserving an embryo. In some embodiments, the embryo is predicted as having a positive outcome. In some embodiments, preserving the embryo can comprise freezing the embryo. In some embodiments, the embryo can be frozen using liquid nitrogen. In some embodiments, the embryo can be frozen to a temperature of 0°C or less, -50°C or less, -80°C or less, -100°C or less or -150°C or less. In some embodiments, the embryo can be frozen to a temperature of approximately -196°C. In some embodiments, the method can comprise transferring an embryo into a uterus or fallopian tube. In some embodiments, an embryo is transferred to a recipient female when the embryo is predicted as having a positive outcome, i.e. implantation capable. In some embodiments, the embryo can be transferred into a uterus of the recipient female or a fallopian tube of the recipient female. In some embodiments, the embryo transferred into the recipient female can be an embryo that was previously frozen or an embryo that was never previously frozen. In some embodiments, the embryo transferred into the recipient female can be an embryo in the cleavage stage, a morula, or a blastocyst. In some embodiments, the embryo can have been created from an egg from the recipient female. In some embodiments, the recipient female can be a surrogate, wherein the embryo was not created from an egg from the recipient female. In some embodiments, the recipient female can be a human female. In some embodiments, the recipient female can be a non-human mammal female. In some embodiments, the non-human mammal female can be a non-human primate, cow, horse, pig, sheep, goat, llama, rabbit, camel, dog, cat, rat, mouse, hamster, or guinea pig. In some embodiments, the embryo can be of the same species as the recipient female. In some embodiments, the embryo can have been created using an egg of the recipient female or a donor egg.

[0040] In some embodiments, the method can comprise confirming an outcome. In some embodiments, when the outcome is implantation, the confirming can comprise measuring a first amount of human chorionic gonadotrophin (hCG). In some embodiments, measuring the first amount of hCG can occurs at least 5 days, 6 days, 7 days, 8 days, or 9 days after transfer of the embryo into the individual. In some embodiments, measuring the first amount of hCG can occur from 5 days to 9 days after transfer of the embryo into the individual. In some embodiments, a positive outcome can be confirmed when a first amount of hCG is greater than 5 IU of hCG/ml of blood. In some embodiments, a confirming can comprise measuring a second amount of hCG. In some embodiments, measuring a second amount of hCG can occur at least 48 hours after measuring a first amount. In some embodiments, a positive outcome can be confirmed when a second amount of hCG has doubled from the first amount of hCG for each of 48 hours passed since the measuring of the first amount of hCG. In some embodiments, a positive outcome is implantation, and confirming can comprise performing an ultrasound on the individual. In some embodiments, implantation can be confirmed when ultrasounds shows visual evidence of the implantation. In some embodiments, ultrasound can be performed when measuring the first amount of hCG, measuring the second amount of hCG, or the combination thereof indicates implantation has occurred.

ENDOMETRIAL ORGANOID ARRAYS

[0041] Described herein, in certain embodiments, are arrays of endometrial organoids (EM-O).

In some embodiments, an array can comprises genes that are differentially expressed in a first reference organoid contacted with a first reference spent embryo culture medium used to culture a first embryo resulting in confirmed positive outcome following transfer to a uterus of a first subject relative to a second reference organoid contacted with a second spent embryo culture medium used to culture a second embryo resulting in confirmed negative following transfer to a uterus a second subject.

[0042] In some embodiments, endometrial organoid arrays can comprise a plurality of partitions, wherein each partition in the plurality of partitions comprises at least one endometrial organoid. [0043] In some embodiments, the plurality of endometrial organoids can be generated from at least one individual. In some embodiments, the at least one individual can be female. In some embodiments, the at least one individual can be one individual. In some embodiments, the at least one individual can comprise at least 2, at least 3, at least 4, at least 5, or more than 5 individuals. In some embodiments, the at least one individual can be human. In some embodiments, the at least one individual can be a non-human mammal. In some embodiments, the non-human mammal can be a non-human primate, cow, horse, pig, sheep, goat, llama, rabbit, camel, dog, cat, rat, mouse, hamster, or guinea pig.

[0044] In some embodiments, the at least one individual can be at least one healthy individual. In some embodiments, the at least one healthy individual can comprise at least one individual who has not experienced a loss of a pregnancy, has not experienced a failure of an embryo to implant following in vitro fertilization, does not suffer from a reproductive system disorder or condition, or a combination thereof. In some embodiments, the reproductive system disorder or condition can be endometriosis, uterine fibroids, polycystic ovary syndrome, premature ovarian failure, primary ovarian insufficiency, cancer of a reproductive organ, bacterial vaginosis, sexually transmitted disease, or a combination thereof.

[0045] In some embodiments, the at least one individual can be an unhealthy individual. In some embodiments, the at least one unhealthy individual can comprise at least one individual who has experienced a loss of a pregnancy, has experienced a failure of an embryo to implant following in vitro fertilization, suffers from a reproductive system disorder or condition, or a combination thereof. In some embodiments, a reproductive system disorder or condition can be endometriosis, uterine fibroids, polycystic ovary syndrome, premature ovarian failure, primary ovarian insufficiency, cancer of a reproductive organ, bacterial vaginosis, sexually transmitted disease, or a combination thereof. In one example, the endometrial organoids from an array can be generated from a human female who will be receiving a transplantation of at least one embryo for which the array will be used to predict the outcome.

[0046] In some embodiments, the plurality of partitions can comprise at least 2, at least 3, at least 4, at least 5, at least 10, at least 15, at least 20, at least 30, at least 40, at least 50, at least 75, or at least 100 partitions. The plurality of partitions can comprise a plurality of wells in a microplate microplate can comprise 6, 12, 24, 48, 96, 384, or 1536 wells. In some embodiments, each well in a microplate can be a partition.

[0047] In some embodiments, each partition in the plurality of partitions can comprise at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, or at least 10 endometrial organoids. In some embodiments, each partition in the plurality of partitions can comprise an identical number of endometrial organoids. Alternatively, in some embodiments, at least one partition in the plurality of partitions can comprise a different number of endometrial organoids than at least one other partition. In some embodiments, each endometrial organoid in each partition of the plurality of partitions can from different individuals. In some embodiments, each endometrial organoid in each partition of the plurality of partitions can from a same individual. In one example, each well of a 24-well microplate can comprise 3 endometrial organoids, with each of the 3 endometrial organoids created from different individuals. In another example, a 48-well microplate can comprise 3 endometrial organoids created from the same individual. In another example, a plurality of endometrial organoids is created from 10 individuals, pooled, and subdivided into a 96-well microplate, wherein a well of the microplate may comprise a different number of endometrial organoids from a different number of individuals compared to a different well.

[0048] Further disclosed herein, in certain embodiments, are kits comprising at least one array of endometrial organoids. The kit can comprise at least 1, at least 2, at least 3, at least 4, or at least 5 arrays of endometrial organoids. The kit can further comprise instructions for use of the at least one array endometrial organoids. In some embodiments, he instructions can be in the form of a label or separate insert. The instructions may inform the consumer how to contact a spent embryo culture medium with the at least one array, how to determine an expression of at least one gene in endometrial organoids of the array, how to predict the outcome of an embryo, or a combination thereof.

NUCLEIC ACID PROBE ARRAYS

[0049] Described herein, in certain embodiments, are arrays comprising at least one nucleic acid probe for detecting at least one nucleic acid expressed by an endometrial organoid, wherein said at least one nucleic acid shows differential expression in at least one first reference endometrial organoid contacted with spent embryo culture medium used to culture a first embryo resulting in a live birth following transfer to a uterus of a first individual relative to at least one second reference endometrial organoid. In some embodiments, the at least one second reference endometrial organoid can be an endometrial organoid contacted with spent embryo culture medium from a second embryo not resulting in a live birth following transfer to a uterus of a second individual. The at least one second reference endometrial organoid can be an endometrial organoid not contacted with a spent embryo culture medium.

[0050] The at least one nucleic acid expressed by said endometrial organoid can be RNA or DNA. The RNA can be mRNA. The at least one nucleic acid can be a cell free nucleic acid, for example a cell free RNA (cfRNA) or cell free DNA (cfDNA). In some embodiments, the at least one nucleic acid can encode a gene, or a fragment thereof, showing differential expression in an endometrial organoid contacted with spent embryo culture medium used to culture a first embryo resulting in a live birth following transfer to an individual relative to at an endometrial organoid contacted with spent embryo culture medium from a second embryo not resulting in a live birth following transfer to a different individual. [0051] In some embodiments, the at least one nucleic acid probe can comprise a plurality of nucleic acid probes. The at least one nucleic acid probe can be immobilized on a solid support. The array described herein can be a microarray. The plurality of nucleic acid probes can comprise at least at least 5, at least 10, at least 20, at least 30, at least 40, at least 50, at least 100, at least 500, at least 1000, or at least 5000 nucleic acid probes. Each nucleic acid probe from the plurality of nucleic acid probes can comprise a region of sequence complementarity with one of the at least one nucleic acid expressed by the endometrial organoid. In some embodiments, each probe on an array disclosed herein are different. In some embodiments, each probe on an array disclosed herein detects a different gene.

[0052] Described herein, in certain embodiments, are methods of detecting at least one nucleic acid showing differential expression in at least one first reference endometrial organoid contacted with spent embryo culture medium used to culture a first embryo resulting in a live birth following transfer to a uterus of a first individual relative to at least one second reference endometrial organoid. The at least one second reference endometrial organoid can be an endometrial organoid contacted with spent embryo culture medium from a second embryo not resulting in a live birth following transfer to a uterus of a second individual. The at least one second reference endometrial organoid can be an endometrial organoid not contacted with a spent embryo culture medium.

[0053] The method can comprise extracting nucleic acid from an endometrial organoid. The nucleic acid can be DNA or RNA. The RNA can be mRNA. The method can comprise reverse transcribing the mRNA into complementary DNA (cDNA). The method can comprise in vitro transcription of the cDNA to produce complementary RNA (cRNA). The method can comprise extracting nucleic acid from an endometrial organoid after contracting the endometrial organoid with a spent embryo culture medium used to culture an embryo. The extracting the nucleic acid can occur least 1 hour, 2 hours, 3 hours, 4 hours, 5 hours, 6 hours, 7 hours, 8 hours, 9 hours, 10 hours, 11 hours, 12 hours, 24 hours, 36 hours, 48 hours, or 60 hours or more after the contacting. The method can comprise extracting nucleic acid from a first endometrial organoid and a second endometrial organoid.

[0054] The nucleic acid extracted from a first endometrial organoid, or reverse transcribed or in vitro transcribed from the nucleic acid extracted from the first endometrial organoid, can be labeled with a first optically detectable tag. The nucleic acid extracted from a second endometrial organoid, or reverse transcribed or in vitro transcribed from the nucleic acid extracted from the second endometrial organoid, can be labeled with a second optically detectable tag. The first optically detectable tag and the second optically detectable tag can be different. The first optically detectable tag and the second optically detectable tag can be identical. [0055] The first endometrial organoid can be an endometrial organoid contacted with spent embryo culture from a first embryo not yet transferred into a uterus of an individual. The outcome of the embryo following transfer to a uterus can be desired to be determined. The second endometrial organoid can be an endometrial organoid contacted with spent embryo culture medium from a second embryo of known outcome following transfer to a uterus of a second individual. The known outcome can be no live birth or no implantation. The second endometrial organoid can be an endometrial organoid not contacted with a spent embryo culture medium.

[0056] In some cases, the methods described herein can comprise contacting an array with a sample comprising nucleic acids or nucleic acid extracted from the first endometrial organoid and a sample comprising a nucleic acid or nucleic acid extracted from the second endometrial organoid. An equal amount of nucleic acid extracted from the first endometrial organoid and the nucleic acid extracted from the second endometrial organoid can be contacted with the array. The method can comprise detecting the optical intensity of the first optically detectable tag, the second optically detectable tag, or a combination thereof. The optical intensity of a probe on the array can represent an expression of the gene represented by the probe.

SUPPORTS/SUBSTRATES

[0057] The present disclosure provides substrates and methods of making substrates. The nature and geometry of a support or substrate can depend upon a variety of factors, including the type of array (e.g., one-dimensional, two-dimensional or three- dimensional). Generally, a substrate can be composed of any material which will permit coupling of a probe, which will not melt or otherwise substantially degrade under the conditions used to hybridize and/or denature nucleic acids. A substrate can be composed of any material which will permit coupling of a probe, and/or other moiety at one or more discrete regions and/or discrete locations within the discrete regions. A substrate can be composed of any material which permit washing or physical or chemical manipulation without dislodging a probe from the solid support.

[0058] Substrates can be fabricated by the transfer of probes onto the solid surface in an organized high-density format followed by coupling the probe thereto. The techniques for fabrication of a substrate of the invention include, but are not limited to, photolithography, inkjet and contact printing, liquid dispensing and piezoelectrics. The patterns and dimensions of arrays are to be determined by each specific application. The sizes of each probe spots may be easily controlled by the users.

[0059] A method of making a solid substrate can comprise contacting or coupling a probe to a discrete location. [0060] A substrate may take a variety of configurations ranging from simple to complex, depending on the intended use of the array. Thus, a substrate can have an overall slide or plate configuration, such as a rectangular or disc configuration. A standard microplate configuration can be used. In some embodiments, the surface may be smooth or substantially planar, or have irregularities, such as depressions or elevations. For example, the substrates of the presently disclosed subject matter can include at least one surface on which a pattern of recombinant virion microspots can be coupled or deposited. In some instances, a substrate may have a rectangular cross-sectional shape, having a length of from about 10-200 mm, 40-150 mm, or 75-125 mm; a width of from about 10-200 mm, 20-120 mm, or 25-80 mm, and a thickness of from about 0.01- 5.0 mm, 0.1-2 mm, or 0.2 to 1 mm.

[0061] A support may be organic or inorganic; may be metal ( e.g ., copper or silver) or non- metal; may be a polymer or nonpolymer; may be conducting, semiconducting or nonconducting (insulating); may be reflecting or nonreflecting; may be porous or nonporous; etc. A solid support as described above can be formed of any suitable material, including metals, metal oxides, semiconductors, polymers (particularly organic polymers in any suitable form including woven, nonwoven, molded, extruded, cast, etc.), silicon, silicon oxide, and composites thereof. [0062] A number of materials (e.g., polymers) suitable for use as substrates (e.g, solid substrates) in the instant invention have been described in the art. Suitable materials for use as substrates include, but are not limited to, polycarbonate, gold, silicon, silicon oxide, silicon oxynitride, indium, tantalum oxide, niobium oxide, titanium, titanium oxide, platinum, iridium, indium tin oxide, diamond or diamond-like film, acrylic, styrene-methyl methacrylate copolymers, ethyl ene/acrylic acid, acrylonitrile-butadiene-styrene (ABS), AB S/polycarbonate, ABS/polysulfone, ABS/polyvinyl chloride, ethylene propylene, ethylene vinyl acetate (EVA), nitrocellulose, nylons (including nylon 6, nylon 6/6, nylon 6/6-6, nylon 6/9, nylon 6/10, nylon 6/12, nylon 11 and nylon 12), polyacrylonitrile (PAN), polyacrylate, polycarbonate, polybutylene terephthalate (PBT), poly(ethylene) (PE) (including low density, linear low density, high density, cross-linked and ultra-high molecular weight grades), poly(propylene) (PP), cis and trans isomers of poly(butadiene) (PB), cis and trans isomers of poly(isoprene), polyethylene terephthalate) (PET), polypropylene homopolymer, polypropylene copolymers, polystyrene (PS) (including general purpose and high impact grades), polycarbonate (PC), poly(epsilon-caprolactone) (PECL or PCL), poly(methyl methacrylate) (PMMA) and its homologs, poly(methyl acrylate) and its homologs, poly(lactic acid) (PLA), poly(glycolic acid), polyorthoesters, poly(anhydrides), nylon, polyimides, polydimethylsiloxane (PDMS), polybutadiene (PB), polyvinylalcohol (PVA), polyacrylamide and its homologs such as poly(N-isopropyl acrylamide), fluorinated polyacrylate (PFOA), poly(ethylene-butylene) (PEB), poly(styrene-acrylonitrile) (SAN), polytetrafluoroethylene (PTFE) and its derivatives, polyolefin plastomers, fluorinated ethylene- propylene (FEP), ethylene-tetrafluoroethylene (ETFE), perfluoroalkoxyethylene (PFA), polyvinyl fluoride (PVF), polyvinylidene fluoride (PVDF), polychlorotrifluoroethylene (PCTFE), polyethylene-chlorotrifluoroethylene (ECTFE), styrene maleic anhydride (SMA), metal oxides, glass, silicon oxide or other inorganic or semiconductor material ( e.g ., silicon nitride), compound semiconductors (e.g., gallium arsenide, and indium gallium arsenide), and combinations thereof. [0063] Examples of well-known solid supports include polypropylene, polystyrene, polyethylene, dextran, nylon, amylases, glass, natural and modified celluloses (e.g, nitrocellulose), polyacrylamides, agaroses and magnetite. In some instances, the solid support can be silica or glass because of its great chemical resistance against solvents, its mechanical stability, its low intrinsic fluorescence properties, and its flexibility of being readily functionalized. In one embodiment, the substrate is glass, particularly glass coated with nitrocellulose, more particularly a nitrocellulose-coated slide (e.g, FAST slides).

[0064] A substrate may be modified with one or more different layers of compounds or coatings that serve to modify the properties of the surface in a desirable manner. For example, a substrate may further comprise a coating material on the whole or a portion of the surface of the substrate. In some embodiments, a coating material enhances the affinity of the probe or another moiety (e.g, a functional group) for the substrate. For example, the coating material can be nitrocellulose, silane, thiol, disulfide, or a polymer. When the material is a thiol, the substrate may comprise a gold-coated surface and/or the thiol comprises hydrophobic and hydrophilic moieties. When the coating material is a silane, the substrate comprises glass and the silane may present terminal moieties including, for example, hydroxyl, carboxyl, phosphate, glycidoxy, sulfonate, isocyanato, thiol, or amino groups. In an alternative embodiment, the coating material may be a derivatized monolayer or multilayer having covalently bonded linker moieties. For example, the monolayer coating may have thiol (e.g, a thioalkyl selected from the group consisting of a thioalkyl acid (e.g, 16-mercaptohexadecanoic acid), thioalkyl alcohol, thioalkyl amine, and halogen containing thioalkyl compound), disulfide or silane groups that produce a chemical or physicochemical bonding to the substrate. The attachment of the monolayer to the substrate may also be achieved by non-covalent interactions or by covalent reactions.

[0065] After attachment to the substrate, the coating may comprise at least one functional group. Examples of functional groups on the monolayer coating include, but are not limited to, carboxyl, isocyanate, halogen, amine or hydroxyl groups. In one embodiment, these reactive functional groups on the coating may be activated by standard chemical techniques to corresponding activated functional groups on the monolayer coating (e.g, conversion of carboxyl groups to anhydrides or acid halides, etc.). Exemplary activated functional groups of the coating on the substrate for covalent coupling to terminal amino groups include anhydrides, N- hydroxysuccinimide esters or other common activated esters or acid halides, Exemplary activated functional groups of the coating on the substrate include anhydride derivatives for coupling with a terminal hydroxyl group; hydrazine derivatives for coupling onto oxidized sugar residues of the linker compound; or maleimide derivatives for covalent attachment to thiol groups of the linker compound. To produce a derivatized coating, at least one terminal carboxyl group on the coating can be activated to an anhydride group and then reacted, for example, with a linker compound. Alternatively, the functional groups on the coating may be reacted with a linker having activated functional groups ( e.g ., N-hydroxysuccinimide esters, acid halides, anhydrides, and isocyanates) for covalent coupling to reactive amino groups on the coating.

[0066] A substrate can contain a linker (e.g., to indirectly couple a moiety to the substrate). In one embodiment, a linker has one terminal functional group, a spacer region and a probe adhering region. The terminal functional groups for reacting with functional groups on an activated coating include halogen, amino, hydroxyl, or thiol groups. In some instances, a terminal functional group is selected from the group consisting of a carboxylic acid, halogen, amine, thiol, alkene, acrylate, anhydride, ester, acid halide, isocyanate, hydrazine, maleimide and hydroxyl group. The spacer region may include, but is not limited to, polyethers, polypeptides, polyamides, polyamines, polyesters, polysaccharides, polyols, multiple charged species or any other combinations thereof. Exemplary spacer regions include polymers of ethylene glycols, peptides, glycerol, ethanolamine, serine, inositol, etc. The spacer region may be hydrophilic in nature. The spacer region may be hydrophobic in nature. In some instances, the spacer has n oxyethylene groups, where n is between 2 and 25. In some instances, a region of a linker that adheres to a probe, or other moiety is hydrophobic or amphiphilic with straight or branched chain alkyl, alkynyl, alkenyl, aryl, arylalkyl, heteroalkyl, heteroalkynyl, heteroalkenyl, heteroaryl, or heteroarylalkyl. In some instances, a region of a linker that adheres to a probe, or other moiety comprises a C10-C25 straight or branched chain alkyl or heteroalkyl hydrophobic tail. In some instances, a linker comprises a terminal functional group on one end, a spacer, a probe adhering region, and a hydrophilic group on another end. The hydrophilic group at one end of the linker may be a single group or a straight or branched chain of multiple hydrophilic groups (e.g, a single hydroxyl group or a chain of multiple ethylene glycol units).

[0067] In some embodiments, the support can be planar. In some instances, the support can be spherical. In some instances, the support can be a bead. In some instances, a support can be magnetic. In some instances, a magnetic solid support can comprise magnetite, maghemitite,

FePt, SrFe, iron, cobalt, nickel, chromium dioxide, ferrites, or mixtures thereof. In some instances, a support can be nonmagnetic. In some embodiments, the nonmagnetic solid support can comprise a polymer, metal, glass, alloy, mineral, or mixture thereof. In some instances, a nonmagnetic material can be a coating around a magnetic solid support. In some instances, a magnetic material may be distributed in the continuous phase of a magnetic material. In some embodiments, the solid support comprises magnetic and nonmagnetic materials. In some instances, a solid support can comprise a combination of a magnetic material and a nonmagnetic material. In some embodiments, the magnetic material is at least about 5, 10, 20, 30, 40, 50, 60, 70, or about 80 % by weight of the total composition of the solid support. In some embodiments, the bead size can be quite large, on the order of 100-900 microns or in some cases even up to a diameter of 3 mm. In other embodiments, the bead size can be on the order of 1-150 microns.

The average particle diameters of beads of the invention can be in the range of about 2 pm to several millimeters, e.g., diameters in ranges having lower limits of 2 pm, 4 pm, 6 pm, 8 pm, 10 pm, 20 pm, 30 pm, 40 pm, 50 pm, 60 pm, 70 pm, 80 pm, 90 pm, 100 pm, 150 pm, 200 pm, 300 pm, or 500 pm, and upper limits of 20 pm, 30 pm, 40 pm, 50 pm, 60 pm, 70 pm, 80 pm, 90 pm, 100 pm, 150 pm, 200 pm, 300 pm, 500 pm, 750pm, 1 mm, 2 mm, or 3 mm.

[0068] A support or substrate can be an array. The array can be a nucleic acid probe array described herein. In some embodiment a solid support comprises an array. An array of the invention can comprise an ordered spatial arrangement of two or more discrete regions. Address, spot, microspot, and discrete region are terms used interchangeably and refer to a particular position, such as on an array. An array can comprise probes located at known or unknown discrete regions.

[0069] Row and column arrangements of arrays can be selected due to the relative simplicity in making such arrangements. The spatial arrangement can, however, be essentially any form selected by the user, and optionally, in a pattern. Microspots of an array may be any convenient shape, including circular, ellipsoid, oval, annular, or some other analogously curved shape, where the shape may, in certain embodiments, be a result of the particular method employed to produce the array. The microspots may be arranged in any convenient pattern across or over the surface of the array, such as in rows and columns so as to form a grid, in a circular pattern, and the like, where generally the pattern of spots will be present in the form of a grid across the surface of the substrate.

[0070] An array can comprise an ordered spatial arrangement of two or more probes, on a solid surface. For example, an array can comprise at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 30, 40, 50,

60, 70, 80, 90, 100, 200, 500, 1,000, 2,000, 3,000, 4,000, 5,000, 6,000, 7,000, 8,000, 9,000, 10,000, 11,000, 12,000, 13,000, 14,000, 15,000, 16,000, 17,000, 18,000, 19,000, 20,000, 25,000 or 30,000 probes. An array can comprise at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 200, 500, 1,000, 2,0 _^ 00, 3,000, 4,000, 5,000, 6,000, 7,000, 8,000, 9,000, 10,000 11,000, 12,000, 13,000, 14,000, 15,000, 16,000, 17,000, 18,000, 19,000, 20,000, 25,000, or

30,000 probes for one or more genes.

[0071] An array can comprise an ordered spatial arrangement of two or more same or different probes, on a solid surface. For example, an array can comprise at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 15,

20, 30, 40, 50, 60, 70, 80, 90, 100, 200, 500, 1,000, 2,000, 3,000, 4,000, 5,000, 6,000, 7,000, 8,000, 9,000, 10,000, 11,000, 12,000, 13,000, 14,000, 15,000, 16,000, 17,000, 18,000, 19,000,

20,000, 25,000, or 30,000 same or probes. For example, an array can comprise at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 200, 500, 1,000, 2,000, 3,000, 4,000, 5,000, 6,000, 7,000, 8,000, 9,000, 10,000, 11,000, 12,000, 13,000, 14,000, 15,000, 16,000, 17,000,

18,000, 19,000, 20,000, 25,000, or 30,000 same or different probes.

An array can be a high-density array. A high-density array can comprise tens, hundreds, thousands, tens-of-thousands or hundreds-of-thousands of probes. The density of microspots of an array may be at least about 1/cm² or at least about 10/cm², up to about 1,000/cm² or up to about 500/cm². In certain embodiments, the density of all the microspots on the surface of the substrate may be up to about 400/cm², up to about 300/cm², up to about 200/cm², up to about 100/cm², up to about 90/cm², up to about 80/cm², up to about 70/cm², up to about 60/cm², or up to about 50/cm². For example, an array can comprise at least 50, 60, 70, 80, 90, 100, 150, 200, 250, 300, 350, 400, 450, 500, 600, 700, 800, 900, or 1,000 distinct antibodies per a surface area of less than about 1 cm². For example, an array can comprise 50, 60, 70, 80, 90, 100, 150, 200, 250, 300, 350 or 400 discrete regions in an area of about 16 mm², or 2,500 discrete regions/cm². In some embodiments, probes, linkers, or another moiety in each discrete region are present in a defined amount ( e.g ., between about 0.1 femtomoles and 100 nanomoles). For example, an array can comprise at least about 2 probes per cm². For example, an array can comprise at least about

2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 40, 50, 60, 70, 80, 90, 100 200, 300, 400, 500, 600, 700, 800, 900, 1,000, 2,000, 3,000, 4,000, 5,000, 6,000, 7,000, 8,000 9,000, 10,000, 11,000, 12,000, 13,000, 14,000, 15,000, 16,000, 17,000, 18,000, 19,000, 20,000

21,000, 22,000, 23,000, 24,000, 25,000, or more probes. For example, an array can be a high- density protein array comprising at least about 10 probes per cm². For example, an array can comprise at least about 20, 30, 40, 50, 60, 70, 80, 90, 100, 200, 300, 400, 500, 600, 700, 800, 900, 1,000, 2,000, 3,000, 4,000, 5,000, 6,000, 7,000, 8,000, 9,000, 10,000, 11,000, 12,000, 13,000, 14,000, 15,000, 16,000, 17,000, 18,000, 19,000, 20,000, 21,000, 22,000, 23,000, 24,000,

25,000, or more probes

COMPUTER CONTROL SYSTEMS [0072] The present disclosure provides computer control systems that are programmed to implement methods of the disclosure. FIG. 5 shows a computer system 101 that is programmed or otherwise configured to interface with a sequence library, a sequencer, a PCR machine, an apparatus that is configured to sequence, amplify or analyze an oligonucleotide, a substrate, or any combination thereof. The computer system 101 can regulate various aspects of the present disclosure. The computer system 101 can regulate amplification conditions, associating conditions, sequencing conditions, such as buffer types, temperatures, or time periods of incubation. The computer system 101 can be an electronic device of a user or a computer system that is remotely located with respect to the electronic device. The electronic device can be a mobile electronic device.

[0073] The computer system 101 can include a central processing unit (CPU, also “processor” and “computer processor” herein) 105, which can be a single core or multi core processor, or a plurality of processors for parallel processing. The computer system 101 also includes memory or memory location 110 (e.g., random-access memory, read-only memory, flash memory), electronic storage unit 115 (e.g., hard disk), communication interface 120 (e.g., network adapter) for communicating with one or more other systems, and peripheral devices 125, such as cache, other memory, data storage and/or electronic display adapters. The memory 110, storage unit 115, interface 120 and peripheral devices 125 can be in communication with the CPU 105 through a communication bus (solid lines), such as a motherboard. The storage unit 115 can be a data storage unit (or data repository) for storing data. The computer system 101 can be operatively coupled to a computer network (“network”) 130 with the aid of the communication interface 120. The network 130 can be the Internet, an internet and/or extranet, or an intranet and/or extranet that is in communication with the Internet. The network 130 in some cases can be a telecommunication and/or data network. The network 130 can include one or more computer servers, which can enable distributed computing, such as cloud computing. The network 130, in some cases with the aid of the computer system 101, can implement a peer-to- peer network, which may enable devices coupled to the computer system 101 to behave as a client or a server.

[0074] The CPU 105 can execute a sequence of machine-readable instructions, which can be embodied in a program or software. The instructions may be stored in a memory location, such as the memory 110. The instructions can be directed to the CPU 105, which can subsequently program or otherwise configure the CPU 105 to implement methods of the present disclosure. Examples of operations performed by the CPU 105 can include fetch, decode, execute, and writeback. [0075] The CPU 105 can be part of a circuit, such as an integrated circuit. One or more other components of the system 101 can be included in the circuit. In some cases, the circuit is an application specific integrated circuit (ASIC).

[0076] The storage unit 115 can store files, such as drivers, libraries and saved programs. The storage unit 115 can store user data, e.g., user preferences and user programs. The computer system 101 in some cases can include one or more additional data storage units that are external to the computer system 101, such as located on a remote server that is in communication with the computer system 101 through an intranet or the Internet.

[0077] The computer system 101 can communicate with one or more remote computer systems through the network 130. For instance, the computer system 101 can communicate with a remote computer system of a user. Examples of remote computer systems include personal computers (e.g., portable PC), slate or tablet PC’s (e.g., Apple® iPad, Samsung® Galaxy Tab), telephones, Smart phones (e.g., Apple® iPhone, Android-enabled device, Blackberry®), or personal digital assistants. The user can access the computer system 1101 via the network 130.

[0078] Methods as described herein can be implemented by way of machine (e.g., computer processor) executable code stored on an electronic storage location of the computer system 101, such as, for example, on the memory 110 or electronic storage unit 115. The machine executable or machine readable code can be provided in the form of software. During use, the code can be executed by the processor 105. In some cases, the code can be retrieved from the storage unit 115 and stored on the memory 110 for ready access by the processor 105. In some situations, the electronic storage unit 115 can be precluded, and machine-executable instructions are stored on memory 110.

[0079] The code can be pre-compiled and configured for use with a machine having a processer adapted to execute the code, or can be compiled during runtime. The code can be supplied in a programming language that can be selected to enable the code to execute in a pre-compiled or as- compiled fashion.

[0080] Aspects of the systems and methods provided herein, such as the computer system 101, can be embodied in programming. Various aspects of the technology may be thought of as “products” or “articles of manufacture” typically in the form of machine (or processor) executable code and/or associated data that is carried on or embodied in a type of machine readable medium. Machine-executable code can be stored on an electronic storage unit, such as memory (e.g., read-only memory, random-access memory, flash memory) or a hard disk. “Storage” type media can include any or all of the tangible memory of the computers, processors or the like, or associated modules thereof, such as various semiconductor memories, tape drives, disk drives and the like, which may provide non-transitory storage at any time for the software programming. All or portions of the software may at times be communicated through the Internet or various other telecommunication networks. Such communications, for example, may enable loading of the software from one computer or processor into another, for example, from a management server or host computer into the computer platform of an application server. Thus, another type of media that may bear the software elements includes optical, electrical and electromagnetic waves, such as used across physical interfaces between local devices, through wired and optical landline networks and over various air-links. The physical elements that carry such waves, such as wired or wireless links, optical links or the like, also may be considered as media bearing the software. As used herein, unless restricted to non-transitory, tangible “storage” media, terms such as computer or machine “readable medium” refer to any medium that participates in providing instructions to a processor for execution.

[0081] Hence, a machine readable medium, such as computer-executable code, may take many forms, including but not limited to, a tangible storage medium, a carrier wave medium or physical transmission medium. Non-volatile storage media include, for example, optical or magnetic disks, such as any of the storage devices in any computer(s) or the like, such as may be used to implement the databases, etc. shown in the drawings. Volatile storage media include dynamic memory, such as main memory of such a computer platform. Tangible transmission media include coaxial cables; copper wire and fiber optics, including the wires that comprise a bus within a computer system. Carrier-wave transmission media may take the form of electric or electromagnetic signals, or acoustic or light waves such as those generated during radio frequency (RF) and infrared (IR) data communications. Common forms of computer-readable media therefore include for example: a floppy disk, a flexible disk, hard disk, magnetic tape, any other magnetic medium, a CD-ROM, DVD or DVD-ROM, any other optical medium, punch cards paper tape, any other physical storage medium with patterns of holes, a RAM, a ROM, a PROM and EPROM, a FLASH-EPROM, any other memory chip or cartridge, a carrier wave transporting data or instructions, cables or links transporting such a carrier wave, or any other medium from which a computer may read programming code and/or data. Many of these forms of computer readable media may be involved in carrying one or more sequences of one or more instructions to a processor for execution.

[0082] The computer system 101 can include or be in communication with an electronic display 135 that comprises a user interface (UI) 140 for providing, for example, one or more results (immediate results or archived results from a previous experiment), one or more user inputs, reference values from a library or database, or a combination thereof. Examples of UFs include, without limitation, a graphical user interface (GUI) and web-based user interface. [0083] Methods and systems of the present disclosure can be implemented by way of one or more algorithms. An algorithm can be implemented by way of software upon execution by the central processing unit 105. The algorithm can, for example, determine optimized conditions via supervised learning to optimize conditions such as a buffer type, a buffer concentration, a temperature, an incubation period. Conditions may be optimized for an oligonucleotide fragment, such as an oligonucleotide fragment having a particular number of epigenetic modifications or a particular length of sequence.

COMMUNICATING A RESULT

[0084] Additional embodiments relate to the communication of results and or outcomes to technicians, physicians or subjects, for example. In certain embodiments, computers will be used to communicate results or outcomes to interested parties, e.g., physicians and their subjects. In some embodiments, analysis or results can be analyzed in a country or jurisdiction which differs from the country or jurisdiction to which the results are communicated. In some embodiments, an outcome identified by a method disclosed herein may be communicated to the subject as soon as possible after the outcome is obtained. The outcome may be communicated to the subject by the subject's treating physician. Alternatively, the outcome may be sent to a test subject by email or communicated to the subject by phone. A computer may be used to communicate the diagnosis by email or phone. In certain embodiments, the message containing results of an analysis maybe generated and delivered automatically to the subject using a combination of computer hardware and software which will be familiar to artisans skilled in telecommunications.

EXAMPLES

EXAMPLE 1 - miRNAs secreted from embryos into culture medium can be internalized into endometrial organoids

[0085] Endometrial organoids (EM-Os) were cultured in chemically defined HVK medium and matured by oestradiol (E2) and progesterone treatment. miR-30c, labelled with fluorescent dye Cy3 (Sigma-Aldrich), was dissolved in SAGE-HSA, a single step medium for uninterrupted embryo culture (Cooper Surgical), at a concentration 1 pg/mL. Then, it was diluted in HVK medium to final concentrations of 0 (ctl), 0.5, 1.0, 5.0 and 10.0 ng/pL EM-0 were exposed to different concentrations of Cy3 -labelled miR-30c for 30, 60, or 120 min.

[0086] Uptake was detectable already after 30 min, whereas maximum fluorescence was observed after 120 min (FIG. 2) These data demonstrated that miRNAs secreted from embryos into culture medium can be internalized into EM-Os. EXAMPLE 2 - miRNAs secreted from embryos into culture medium can regulate gene expression when internalized into endometrial organoids

[0087] EM-Os from two healthy donors, cultured in chemically defined HVK medium and matured by oestradiol (E2) and progesterone treatment, were exposed either to 0 and 1.0 ng/ml (donor #2; n=2 for each concentration) or 1.0 and 10 ng/ml (donor #1; n=3 for each concentration) of Cy3-labelled miR-30c. After 120 min, medium containing Cy3-labelled miR- 30c was removed and EM-Os were washed with prewarmed HEPES-containing DMEM/F12 and then cultured in HVK medium for the next 24 h. The next day, EM-Os were washed and spun down in cold HEPES-containing DMEM/F12 at 200g for 5 min. Supernatant was removed and pelleted EM-Os were snap-frozen for RNAseq analyses.

[0088] It was found that 120 min exposure to 1.0 ng/ml Cy3-labelled miR-30c correlated with change in the expression of 386 genes (fold-change >1.5, p-value <0.5) 24 h post exposure (FIG.3). Increasing concentration from 1.0 ng/ml to 10 ng/ml was followed with change in the expression of 511 genes (fold-change >1.5, p-value <0.5) 24 h post exposure (FIG. 4). In conclusion, these data suggested that miRNAs secreted from embryos into culture medium and internalized into EM-Os can regulate gene expression in the cells of EM-Os.

EXAMPLE 3 - Identification of genes expressed in endometrial organoids indicative of embryo outcome following contact of the endometrial organoids with spent embryo culture medium

[0089] Spent embryo culture media is collected from human embryos that resulted in either a live birth or no live birth following transfer into a uterus. Each spent embryo culture media is contacted to a different endometrial organoid. Hours following the contacting of the endometrial organoids to the spent embryo culture media, gene expression in the endometrial organoid is determined. The gene expression is differentially expressed in endometrial organoids exposed to spent embryo culture media from embryos resulting in a live birth compared to endometrial organoids exposed to spent embryo culture media from embryos not resulting in a live birth. The expression of the differentially expressed gene or genes are indicative of embryo outcome. Based on the expression of the differentially expressed gene or genes, an outcome is predicted. Based on the predicted outcome, an embryo is transplanted into a female, stored or discarded.

[0090] While preferred embodiments of the present disclosure have been shown and described herein, such embodiments are provided by way of example only. Numerous variations, changes, and substitutions will now occur to those skilled in the art without departing from the disclosure. It should be understood that various alternatives to the embodiments of the disclosure described herein may be employed in practicing the disclosure.

Claims

CLAIMS WHAT IS CLAIMED IS:

1. A method comprising contacting an organoid with at least a portion of spent embryo culture medium used to culture an embryo.

2. The method of claim 1, wherein said contacting occurs for at least about 60 minutes, at least about 90 minutes, at least about 120 minutes, at least about 150 minutes, or at least about 180 minutes.

3. The method of claim 1 or claim 2, wherein said organoid is an endometrial organoid.

4. The method of any one of claims 1-3, wherein said organoid is generated from a female individual.

5. The method of claim 4, wherein said female individual is a healthy female individual, wherein said healthy female individual is selected from the group consisting of: an individual who has not experienced a loss of a pregnancy, has not experienced a failure of an embryo to implant following in vitro fertilization, does not suffer from a reproductive system disorder or condition, and a combination thereof.

6. The method of claim 5, wherein said healthy female individual is said individual who does not suffer from a reproductive system disorder or condition.

7. The method of claim 6, wherein said reproductive system disorder or condition is selected from the group consisting of: endometriosis, uterine fibroids, polycystic ovary syndrome, premature ovarian failure, primary ovarian insufficiency, cancer of a reproductive organ, bacterial vaginosis, sexually transmitted disease, and a combination thereof.

8. The method of claim 4, wherein said female individual has a disease or condition.

9. The method of claim 8, wherein said disease or condition is selected from the group consisting of: endometriosis, uterine fibroids, polycystic ovary syndrome, premature ovarian failure, primary ovarian insufficiency, cancer of a reproductive organ, bacterial vaginosis, sexually transmitted disease, and a combination thereof.

10. The method of any one of claims 4-9, wherein said female individual is a human.

11. The method of any one of claims 1-10, wherein said organoid comprises a plurality of organoids.

12. The method of any one of claims 1-11, wherein said spent embryo culture medium comprises a molecule secreted by said embryo.

13. The method of claim 12, wherein said molecule secreted by said embryo comprises at least one MicroRNA (miRNA).

14. The method of any one of claims 1-13, wherein said embryo is in a stage selected from the group consisting of cleavage, morula, and blastocyst.

15. The method of any one of claims 1-14, wherein said embryo is a human embryo.

16. The method of any one of claims 1-15, further comprising determining an expression of a gene in said organoid.

17. The method of claim 16, wherein said gene is differentially expressed in a first reference organoid contacted with a first reference spent embryo culture medium used to culture a first embryo resulting in confirmed positive outcome following transfer to a uterus of a first subject relative to a second reference organoid contacted with a second spent embryo culture medium used to culture a second embryo resulting in confirmed negative outcome following transfer to a uterus a second subject.

18. The method of claim 16 or claim 17, wherein said determining is carried out at least about 12 hours, at least about 24 hours, at least about 36 hours, at least about 48 hours, or at least about 60 hours after said contacting.

19. The method of any one of claims 16-18, wherein said expression indicates an outcome of an embryo following transfer of said embryo to a uterus of an individual.

20. The method of claim 19, wherein said outcome is a positive outcome or a negative outcome.

21. The method of claim 20, wherein said positive outcome is selected from the group consisting of live birth, implantation and any combination thereof.

22. The method of claim 20, wherein said negative outcome is selected from the group consisting of: no live birth, no implantation and any combination thereof.

23. The method of any one of claims 19-22, further comprising predicting said outcome.

24. The method of claim 23, wherein said predicting comprises comparing said expression to a reference.

25. The method of claim 24, wherein said reference comprises a reference expression of said gene in a first reference organoid contacted with a first reference spent embryo culture medium used to culture a first reference embryo, wherein said first reference embryo resulted in a confirmed positive outcome following transfer to a uterus of a test subject.

26. The method of claim 25, wherein said outcome is predicted as said positive outcome if said expression is similar to said reference expression.

27. The method of claim 25, wherein said outcome is predicted as said negative outcome if said expression is different compared to said reference expression.

28. The method of claim 24, wherein said reference comprises a reference expression of said gene in a second reference organoid contacted with a second reference spent embryo culture medium used to culture a second reference embryo, wherein said second reference embryo resulted in a confirmed negative outcome following transfer to a uterus of a test subject.

29. The method of claim 28, wherein said outcome is predicted as said negative if said expression is similar to said reference expression.

30. The method of claim 28, wherein said outcome is predicted as said positive outcome if said expression is different compared to said reference expression.

31. The method of claim 23, wherein said predicting comprises applying a classifier to said expression.

32. The method of claim 31, wherein said classifier is trained with gene expression data from a first reference organoid contacted with a first reference spent embryo culture medium used to culture a first reference embryo resulting in confirmed positive outcome following transfer to a uterus of a first test subject and a second reference organoid contacted with a second reference spent embryo culture medium used to culture a second reference embryo resulting in confirmed negative outcome following transfer to a uterus of a second test subject.

33. The method of claim 31 or claim 32, wherein said classifier is selected from the group consisting of: a Naive Bayes classifier, a decision tree classifier, a logistic regression classifier, a K-nearest neighbor classifier, a neural network classifier, a support vector machine classifier and a combination thereof.

34. The method of any one of claims 15-33, further comprising preserving said embryo when said outcome is predicted as said positive outcome.

35. The method of claim 34, wherein said preserving comprises freezing.

36. The method of any one of claims 23-35, further comprise transferring said embryo into a uterus of recipient female when said outcome is predicted as said positive outcome.

37. The method of any one of claims 23-35, further comprising discarding said embryo when said outcome is predicted as said negative outcome.

38. The method of any one of claims 23-36, further comprising confirming said outcome.

39. The method of claim 38, wherein said confirming comprises measuring a first amount of human chorionic gonadotrophin (hCG).

40. The method of claim 39, wherein said first amount of hCG is from a recipient female to whom said embryo was transferred.

41. The method of claim 39, wherein said measuring said first amount of hCG occurs from about 5 days to about 9 days after transfer of said embryo into said individual.

42. The method of any one of claims 39 - 41, wherein said positive outcome is confirmed when said first amount of hCG is greater than 5 IU of hCG/ml of blood.

43. The method of any one of claims 39-42, wherein said confirming comprises measuring a second amount of hCG.

44. The method of claim 43, wherein said measuring said second amount of hCG occurs at least about 48 hours after said measuring said first amount.

45. The method of claim 44, wherein said positive outcome is confirmed when said second amount of hCG has doubled from said first amount of hCG for each of about 48 hours passed since said measuring of said first amount of hCG.

46. The method of any one of claims 38-45, wherein said confirming comprises performing an ultrasound on said individual.

47. The method of claim 46, wherein said positive outcome is confirmed when said ultrasounds shows visual evidence of said positive outcome.

48. A method comprising determining an expression of a gene in an organoid, wherein said expression indicates an outcome of an embryo following transfer of said embryo to a uterus of an individual.

49. The method of claim 48, wherein said embryo is cultured in a culture medium.

50. The method of claim 48, wherein said culture medium is spent culture medium following contact with said embryo.

51. The method of claim 50, wherein said organoid is contacted with at least a portion of said spent culture medium prior to said determining.

52. The method of any one of claims 48-51, wherein said organoid is an endometrial organoid.

53. The method of any one of claims 48-52, wherein said outcome is a positive outcome or a negative outcome.

54. The method of claim 53, wherein said positive outcome is selected from the group consisting of: live birth, implantation and a combination thereof.

55. The method of claim 53, wherein said negative outcome is selected from the group consisting of: no live birth, no implantation and a combination thereof.

56. The method of any one of claims 53-55, wherein said outcome is determined by comparing said expression to a reference.

57. The method of claim 56, wherein said reference comprises a reference expression of said gene in a first reference organoid contacted with a first reference spent embryo culture medium used to culture a first reference embryo, wherein said first reference embryo resulted in a confirmed positive outcome following transfer to a uterus of an individual.

58. The method of claim 57, wherein said outcome is said positive outcome if said expression is similar to said reference expression.

59. The method of claim 57, wherein said outcome is said negative outcome if said expression is different compared to said reference expression.

60. The method of claim 56, wherein said reference comprises a reference expression of said gene in a second reference organoid contacted with a second reference spent embryo culture medium used to culture a second reference embryo, wherein said second reference embryo resulted in a negative outcome following transfer to a uterus to an individual.

61. The method of claim 60, wherein said outcome is said negative outcome if said expression is similar to said reference expression.

62. The method of claim 60, wherein said outcome is said positive outcome if said expression is different compared to said reference expression.

63. The method of any one of claims 53-55, wherein said outcome is determined by applying a classifier to said expression.

64. The method of claim 63, wherein said classifier is trained with gene expression data from a first reference organoid contacted with a first reference spent embryo culture medium used to culture a first reference embryo resulting in a confirmed positive outcome following transfer to a uterus of an individual and a second reference organoid contacted with a second reference spent embryo culture medium used to culture a second reference embryo resulting in a confirmed negative outcome following transfer to a uterus of an individual.

65. The method of claim 63 or claim 64, wherein said classifier is selected from the group consisting of: a Naive Bayes classifier, a decision tree classifier, a logistic regression classifier, a K-nearest neighbor classifier, a neural network classifier, a support vector machine classifier and a combination thereof.

66. The method of any one of claims 48-65, wherein said gene is differentially expressed in a first reference organoid contacted with a first reference spent embryo culture medium used to culture a first embryo resulting in a confirmed positive outcome following transfer to a uterus of an individual relative to a second reference organoid contacted with a second spent embryo culture medium used to culture a second embryo resulting in a confirmed negative outcome following transfer to a uterus an individual.

67. The method of any one of claims 48-66, wherein said embryo is in a stage selected from the group consisting of cleavage, morula, and blastocyst.

68. The method of any one of claims 48-67, wherein said embryo is a human embryo.

69. The method of any one of claims 53-68, further comprising preserving said embryo when said outcome is said positive outcome.

70. The method of claim 69, wherein said preserving comprises freezing.

71. The method of any one of claims 53-70, further comprise transferring said embryo into a uterus of recipient female when said outcome is predicted as said positive outcome.

72. The method of any one of claims 53-71, further comprising discarding said embryo when said outcome is predicted as said negative outcome.

73. The method of any one of claims 53-71, further comprising confirming said outcome.

74. The method of claim 73, wherein said confirming comprises measuring a first amount of hCG.

75. The method of claim 74, wherein said first amount of hCG is from said recipient female.

76. The method of claim 74, wherein said measuring said first amount of hCG occurs from about 5 days to about 9 days after transfer of said embryo into said individual.

77. The method of claim 74 or claim 76, wherein said positive outcome is confirmed when said first amount of hCG is greater than 5 IU of hCG/ml of blood.

78. The method of any one of claims 74-75, wherein said confirming comprises measuring a second amount of hCG.

79. The method of claim 78, wherein said measuring said second amount of hCG occurs at least 48 hours after said measuring said first amount.

80. The method of claim 79, wherein said positive outcome is confirmed when said second amount of hCG has doubled from said first amount of hCG for each of about 48 hours passed since said measuring of said first amount of hCG.

81. The method of any one of claims 73-80, wherein said confirming comprises performing an ultrasound on said individual.

82. The method of claim 81, wherein said positive outcome is confirmed when said ultrasounds shows visual evidence of said positive outcome.

83. The method of any one of claims 48-82, wherein said organoid is generated from a female individual.

84. The method of claim 83, wherein said female individual is a healthy female individual, wherein said healthy female individual is selected from the group consisting of an individual who has not experienced a loss of a pregnancy, has not experienced a failure of an embryo to implant following in vitro fertilization, does not suffer from a reproductive system disorder or condition, and a combination thereof.

85. The method of claim 84, wherein said healthy female individual is said individual who des not suffer from a reproduction system disorder or condition.

86. The method of claim 85, wherein said reproductive system disorder or condition is selected from the group consisting of: endometriosis, uterine fibroids, polycystic ovary syndrome, premature ovarian failure, primary ovarian insufficiency, cancer of a reproductive organ, bacterial vaginosis, sexually transmitted disease, and a combination thereof.

87. The method of claim 83, wherein said female individual has a disease or condition.

88. The method of claim 87, wherein said disease or condition is selected from the group consisting of: endometriosis, uterine fibroids, polycystic ovary syndrome, premature ovarian failure, primary ovarian insufficiency, cancer of a reproductive organ, bacterial vaginosis, sexually transmitted disease, and a combination thereof.

89. The method of any one of claims 83-88, wherein said female individual is a human.

90. The method of any one of claims 48-89, wherein said organoid comprises a plurality of organoids.

91. An array comprising said organoid of any one of claims 1-90.

92. The array of claim 91, wherein said organoid comprises a plurality of organoids.

93. A kit comprising said array of any one of claims 91-92.

94. The kit of claim 93, further comprising instructions for use.

95. The kit of any one of claims 93-94, further comprising reagents for carrying out the method of any one of claims 1-90.

96. An array comprising a nucleic acid probe for detecting a nucleic acid expressed by an organoid, wherein said nucleic acid is differentially expressed in: i. a first reference organoid contacted with first spent embryo culture medium used to culture a first embryo, wherein said first embryo resulted in a confirmed positive outcome in a uterus of a first individual; and ii. a second reference organoid contacted with second spent embryo culture medium used to culture a second embryo, wherein said second embryo resulted in a confirmed negative outcome following transfer to a uterus of a second individual.

97. The array of claim 96, wherein said confirmed positive outcome is selected from the group consisting of live birth, implantation and a combination thereof.

98. The array of claim 96, wherein said confirmed negative outcome is selected from the group consisting of no live birth, no implantation and a combination thereof.

99. The array of any one of claims 96-98, wherein said organoid is an endometrial organoid.

100. The array of any one of claims 96-99, wherein said nucleic acid is RNA.

101. The array of claim 100, wherein said RNA is mRNA.

102. The array of any one of claims 96-101, wherein said nucleic acid probe comprises a plurality of nucleic acid probes.

103. The array of claim 102, wherein said plurality of nucleic acid probes comprise at least about 5, at least about 10, at least about 20, at least about 30, at least about 40, at least about 50, at least about 100, or at least about 500 nucleic acid probes.

104. The array of any one of claims 96-103, wherein said nucleic acid comprises a plurality of nucleic acids.

105. The array of claim 104, wherein said plurality of nucleic acids comprise at least about 5, at least about 10, at least about 20, at least about 30, at least about 40, at least about 50, at least about 100, or at least about 500 nucleic acids.

106. The array of any one of claims 96-105, wherein said nucleic acid probe is immobilized on a solid support.

107. A kit comprising an array of any one of claims 96-106.

108. The kit of claim 107, further comprising instructions for use.

109. A composition comprising an organoid, wherein said organoid or at least a portion thereof was exposed to spent embryo culture medium.

110. The composition of claim 109, wherein said spent embryo culture medium was used to culture an embryo.