NON-CODING RNA FOR DETECTION OF CANCER

1 . A method of diagnosing a subject with a benign, pre-malignant, or malignant hyperproliferative cell comprising:

detecting the presence, absence, and/or quantity of at least one non-coding RNA or functional fragment thereof in a sample.

2 . The method of claim 1 , wherein the subject is a human diagnosed with or suspected as having a breast cancer.

3 . The method of claim 1 , wherein the step of detecting comprises:

a) contacting the sample with one or a plurality of probes specific for the at least one non-coding RNA or functional fragment thereof, and normalizing the quantity in the sample with a measurement taken from a control sample;

b) contacting total RNA of the sample to at least one probe complementary to T3p;

c) contacting the total RNA of the sample to at least one probe complementary to one or a combination of nucleic acid sequences comprising any of the sequences in Tables 1, 2, and/or 3; and/or

d) using a chemiluminescent probe, fluorescent probe, and/or fluorescence microscopy.

4 . The method of claim 1 further comprising exposing a sample from a subject to at least one nucleic acid molecule complementary to one or a combination of non-coding RNAs chosen from: SEQ ID NO:1 through SEQ ID NO:201 or one or combination of non-coding nucleic acid sequences that comprise at least 70%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% sequence homology to any nucleic acid of Tables 1, 2, and/or

5 . The method of claim 1 , wherein the at least one non-coding RNA is T3p or a functional fragment thereof.

6 - 7 . (canceled)

8 . The method of claim 1 , further comprising correlating the amount of at least one non-coding RNA or homologous sequence thereof in the sample to the probability or likelihood the subject has a benign, pre-malignant, or malignant growth, relative to a measurement of the amount of at least one non-coding RNA or homologous sequence thereof in a control sample.

9 . The method of claim 1 , wherein the benign, pre-malignant, or malignant hyperproliferative cell is from breast tissue.

10 . The method of claim 1 , wherein the sample comprises:

a) blood or serum from a subject;

b) RNA taken from a culture of cells seeded or inoculated by at least one cell from a subject;

c) human tissue sample comprising a tissue or liquid sample from a plasma, serum or blood draw, brushing, biopsy, or surgical resection of a subject; or

d) a cell that is freshly obtained, formalin fixed, alcohol-fixed and/or paraffin embedded.

11 - 12 . (canceled)

13 . The method of claim 1 , further comprising culturing at least one biopsy from the subject with a culture medium under conditions and for a time period sufficient to grow at least one cell from a subject's breast tissue.

14 . The method of claim 1 , wherein the step of measuring the quantity of at least one non-coding RNA or a functional fragment thereof in a sample comprises one or a combination of: digitally imaging a sample; exposing a sample to a known amount of labeled antibody specific for an epitope of non-coding RNA or a functional fragment thereof, exposing a sample to one or a plurality of dyes of specific for non-coding RNA or a functional fragment thereof, exposing a sample to at least one labeled probe complementary to a sequence of the non-coding RNA or a functional fragment thereof, exposing a sample to chromatography, isolating total RNA of a sample and exposing the total RNA to sequencing analysis and/or exposing the sample to mass spectrometry, and, optionally, further comprising analyzing morphology of cells from the sample.

15 . The method of claim 1 , comprising:

a) contacting one or a plurality of probes specific for the at least one non-coding RNA or functional fragment thereof with the sample;

b) quantifying the presence, absence, or quantity of the at least one non-coding RNA or functional fragment thereof in the sample;

c) calculating one or more scores based upon the presence, absence, or quantity of the at least one non-coding RNA or functional fragment thereof;

d) correlating the one or more scores to the presence, absence, or quantity of the at least one non-coding RNA or functional fragment thereof, such that, if the amount of the at least one non-coding RNA or functional fragment thereof is greater than the quantity of the at least one non-coding RNA or functional fragment thereof in a control sample, the correlating step comprises diagnosing the subject with the benign, pre-malignant, or malignant hyperproliferative cell.

16 - 20 . (canceled)

21 . A method of detecting a cancer cell in a subject comprising:

detecting whether a non-coding RNA is present in a sample of the subject by contacting the sample with an amount of one or a combination of probes complementary to one or a combination of non-coding RNA sequences.

22 . The method of claim 21 , wherein the step of detecting is preceded by a step of obtaining RNA from the sample of the subject.

23 . The method of claim 21 , wherein the method further comprises:

calculating one or more scores based upon the presence, absence, or quantity of one non-coding RNA and/or a homologous sequence thereof; and

correlating the one or more scores to the presence, absence, or quantity of non-coding RNA and/or functional fragment thereof, such that, if the amount of non-coding RNA and/or functional fragment thereof is greater than the quantity of non-coding RNA and/or functional fragment thereof in a control sample; or, if the amount of non-coding RNA and/or functional fragment thereof is substantially equal to the quantity of non-coding RNA and/or functional fragment thereof in a sample taken from a subject known to have cancer then the subject is diagnosed as having cancer.

24 . The method of claim 21 , further comprising detecting a presence or quantifying two or more non-coding RNAs chosen from those nucleic acid sequences of Tables 1, 2, and/or 3 or one or combination of nucleic acids sequences that comprise at least 70%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% sequence homology to any of the sequences of Tables 1, 2 and/or 3.

25 . The method of claim 21 , wherein the sample:

a) is a human tissue sample comprising a tissue from a serum or plasma or blood draw, brushing, biopsy, or surgical resection of the subject;

b) comprises total RNA from a cell that is freshly obtained, formalin fixed, alcohol-fixed and/or paraffin embedded; or

c) is plasma, blood or serum.

26 - 27 . (canceled)

28 . The method of claim 21 , wherein the probe complementary to is an RNA sequence that is T3p.

29 - 38 . (canceled)

39 . A method of treating a subject in need thereof diagnosed with or suspected of having breast cancer, comprising:

(a) contacting one or a plurality of probes specific for one or a combination of non-coding RNA and/or a homologous sequence thereof with a sample;

(b) quantifying the presence, absence or amount of non-coding RNA and/or a homologous sequence thereof in the sample;

(c) calculating one or more scores based upon the presence, absence, or quantity of non-coding RNA and/or a homologous sequence thereof;

(d) correlating the one or more scores to the presence, absence, or quantity of non-coding RNA and/or a homologous sequence thereof, such that, if the amount of non-coding RNA and/or a homologous sequence thereof is greater than the quantity of non-coding RNA and/or a homologous sequence thereof in a control sample, the correlating step comprises diagnosing a subject with breast cancer; and

(e) administering to the subject a therapeutically effective amount of treatment for the breast cancer.

40 . (canceled)

41 . The method of claim 39 , wherein the probe is one or a plurality of nucleic acid sequences complementary to a nucleic acid sequence chosen from one or a combination of sequences of Table 1, Table 2 and/or Table 3.

42 . The method of claim 39 , wherein the one or plurality of probes comprise a fluorophore, a chemiluminescent agent, and/or a quenching agent.

43 - 48 . (canceled)