(12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT)
`(19) World Intellectual Property
`Organization
`International Bureau
`
`(10) International Publication Number
`
`(43) International Publication Date
`WO 2013/188846 A1
`WIPOI PCT
`I 9 December 2013 (19.12.2013)
`
`
`\2
`
`(51)
`
`International Patent Classification:
`CIZQ 1/68 (2006.01)
`C403 30/04 (2006.01)
`G01N 33/53 (2006.01)
`
`(21)
`
`International Application Number:
`
`PCT/US2013/046020
`
`(22)
`
`International Filing Date:
`
`(25)
`
`(26)
`
`(30)
`
`(72)
`(71)
`
`(74)
`
`(81)
`
`Filing Language:
`
`Publication Language:
`
`14 June 2013 (14.06.2013)
`
`English
`
`English
`
`Priority Data:
`61/660,427
`
`15 June 2012 (15.06.2012)
`
`US
`
`Inventor; and
`Applicant : STYLLI, Harry [GB/US]; 2452 Paseo Dor-
`ado, La Jolla, CA 92037 (US).
`
`Agents: HALEY, James, F. et 31.; Ropes & Gray LLP,
`1211 Avenue ofthe Americas, New York, NY 10036 (US).
`
`Designated States (unless otherwise indicated, for every
`kind of national protection available): AE, AG, AL, AM,
`AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BVV, BY,
`BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DK, DM,
`
`DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT,
`HN, HR, HU, ID, IL, IN, IS, JP, KE, KG, KN, KP, KR,
`KZ, LA, LC, LK, LR, LS, LT, LU, LY, MA, MD, ME,
`MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ,
`OM, PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SC,
`SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN,
`TR, TT, TZ, UA, UG, Us, UZ, VC, VN, ZA, ZM, ZW.
`
`(84)
`
`Designated States (unless otherwise indicated, for every
`kind of regional protection available): ARIPO (BW, GH,
`GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, SZ, TZ,
`UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, RU, TJ,
`TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, DK,
`EE, ES, FI, FR, GB, GR, HR, HU, IE, IS, IT, LT, LU, LV,
`MC, MK, MT, NL, NO, PL, PT, RO, RS, SE, SI, SK, SM,
`TR), OAPI (BF, BJ, CF, CG, CI, CM, GA, GN, GQ, GVV,
`KM, ML, MR, NE, SN, TD, TG).
`Published:
`
`with international search report (Art. 21(3))
`
`before the expiration of the time limit for amending the
`claims and to be republished in the event of receipt of
`amendments (Rule 48.2(h))
`
`(54) Title: METHODS OF DETECTING DISEASES OR CONDITIONS
`
`
`
` 1 Con Ik-ma ion
`
`W»£~~:--—-—-— ,,,,-,-—.-n-r,,,_..‘t -m,
`a...” n. M“,
`"““w ,,~*.~,'«,, ,
`
`a
`
`I
`
`a1 3
`
`
`
`Figure 2
`
`(57) Abstract: This invention provides methods olw using a sample with multiple analytical components in the diagnosis, prognosis,
`or monitoring of diseases or conditions. The invention also provides methods of identifying markers of diseases or conditions.
`
`
`
`W02013/188846A1I||||||||||||||||||||||||||||||||||||||||||||||||||\|||||||||||||||||||||||||||||||||||||||||||
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`

`

`WO 2013/188846
`
`PCT/U52013/046020
`
`METHODS OF DETECTING DISEASES OR CONDITIONS
`
`Priority Information
`
`[0001] This application claims priority from US. Provisional Application
`
`6l/660,427, filed June l5, 20l 2. The content and disclosure ofthat application is
`
`incorporated by reference herein in its entirety.
`
`Field of the Invention
`
`[0002] This invention relates generally to methods of using combinations of two or
`
`more different components selected from cell-free bodily fluids, phagocytic cells,
`
`circulating vesicles, and circulating diseased cells in the diagnosis, prognosis, or
`
`monitoring of a disease or condition. The invention also relates to methods of using
`
`the combinations to identify markers of diseases or conditions.
`
`Background of the Invention
`
`[0003] Leukocytes begin as pluripotent hematopoietic stem cells in the bone
`
`marrow and develop along either the myeloid lineage (monocytes, macrophages,
`
`neutrophils, eosinophils, and basophils) or the lymphoid lineage (T and B
`
`lymphocytes and natural killer cells). The major function of the myeloid lineage cells
`
`(e.g., neutrophils and macrophages) is the phagocytosis of infectious organisms, live
`
`unwanted damaged cells, senescent and dead cells (apoptotic and necrotic), as well as
`
`the clearing of cellular debris. Phagocytes from healthy animals do not replicate and
`
`are diploid, i.e., have a DNA content of 211. On average, each cell contains <10 ng
`
`

`

`WO 2013/188846
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`PCT/US2013/046020
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`-2-
`
`DNA, <20 ng RNA, and <300 ng of protein. Non-phagocytic cells are also diploid
`
`and are not involved in the internalization of dead cells or infectious organisms and
`
`also have a DNA content of Zn.
`
`[0004] The lifetime of various white blood cell subpopulations varies from a few
`
`days (e. g., neutrophils) to several months (e. g., macrophages). Like other cell types,
`
`leukocytes age and eventually die. During their aging process, human blood— and
`
`tissue-derived phagocytes (e.g., neutrophils) exhibit all the classic markers of
`
`programmed cell death (i.e., apoptosis), including caspase activation, pyknotic nuclei,
`
`and chromatin fragmentation. These cells also display a number of "eat-me" flags
`
`(e. g., phosphatidylserine, sugars) on the extracellular surfaces of their plasma
`
`membranes. Consequently, dying and dead cells and subcellular fragments thereof
`
`are cleared from tissues and blood by other phagocytie cells.
`
`[0005] Early diagnosis of a disease often increases the likelihood of successful
`
`treatment or cure of such disease. Current diagnostic methods, however, focus on
`
`either using whole blood or separating the blood into different components, of which
`
`a single component is chosen for testing. Although this approach may enrich the
`
`signal being detected, it also results in the loss of potentially important information.
`
`Personalized diagnostic methods are needed that enable the diagnosis, especially the
`
`early diagnosis, of the presence of a disease or a condition in individuals who are not
`
`known to have the disease or who have recurrent disease.
`
`[0006] One object of the present invention is to provide diagnostic methods that can
`
`facilitate the detection of a disease or condition-specific markers, e. g., nucleic acids,
`
`proteins, carbohydrates, and/or lipids and the like by using combinations of two or
`
`more different components selected from cell-free bodily fluids, phagocytic cells,
`
`circulating vesicles, and circulating diseased cells. Another object of this invention is
`
`to provide methods of identifying a disease or condition—specific markers and further
`
`use such markers alone or together with any known markers to diagnose diseases or
`
`conditions.
`
`

`

`WO 2013/188846
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`PCT/US2013/046020
`
`Summary of the Invention
`
`[0007]
`
`Some embodiments of the invention are:
`
`l.
`
`A method for diagnosing or aiding in the diagnosis of a disease or condition in
`
`a subject comprising:
`
`a)
`
`determining a first profile of one or more markers of the disease or
`
`condition from a sample comprising two or more different components selected from
`
`the group consisting of: a cell-free bodily fluid isolated from the subject, a population
`
`of phagocytic cells isolated from the subject, a population of phagocytic cells having a
`
`DNA content more than 2n (>2n phagocytic cells) isolated from the subject, a
`
`population of circulating vesicles isolated from the subject, and a population of
`
`circulating diseased cells isolated from the subject;
`
`b)
`
`determining a second profile of at least one of the one or more markers
`
`from a control comprising a component selected from the group consisting of: a
`
`population of phagocytic cells having a DNA content of Zn (:2n phagocytic cells)
`
`isolated from the subject, a population of non-phagocytic cells isolated from the
`
`subject, and a population of control cells isolated from the subject, wherein the
`
`control cells are substantially free of cells affected by the disease or condition, and
`
`0)
`
`identifying a difference between the first and second profiles, wherein
`
`the difference is indicative of the presence of said disease or condition in the subject.
`
`2.
`
`A method for assessing the risk of developing a disease or condition in a
`
`subject comprising:
`
`a)
`
`determining a first profile of one or more markers of the disease or
`
`condition from a sample comprising two or more different components selected from
`
`the group consisting of: a cell-free bodily fluid isolated from the subject, a population
`
`of phagocytic cells isolated from the subject, a population of phagocytic cells having a
`
`DNA content more than 2n (>2n phagocytic cells) isolated from the subject, a
`
`population of circulating vesicles isolated from the subject, and a population of
`
`circulating diseased cells isolated from the subject;
`
`

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`PCT/US2013/046020
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`-4-
`
`b)
`
`determining a second profile of at least one of the one or more markers
`
`from a control comprising a component selected from the group consisting of: a
`
`population of phagocytic cells having a DNA content of Zn (=2n phagocytic cells)
`
`isolated from the subject, a population of non-phagocytic cells isolated from the
`
`subject, and a population of control cells isolated from the subject, wherein the
`
`control cells are substantially free of cells affected by the disease or condition; and
`
`c)
`
`identifying a difference between the first and second profiles, wherein
`
`the difference is indicative of the risk of developing said disease or condition in the
`
`subject.
`
`3.
`
`A method for prognosing or aiding in the prognosis of a disease or condition
`
`in a subject comprising:
`
`a)
`
`determining a first profile of one or more markers of the disease or
`
`condition from a sample comprising two or more different components selected from
`
`the group consisting of: a cell-free bodily fluid isolated from the subject, a population
`
`of phagocytic cells isolated from the subject, a population of phagocytic cells having a
`
`DNA content more than 2n (>2n phagocytic cells) isolated from the subject, a
`
`population of circulating vesicles isolated from the subject, and a population of
`
`circulating diseased cells isolated from the subject;
`
`b)
`
`determining a second profile of at least one of the one or more markers
`
`from a control comprising a component selected from the group consisting of: a
`
`population of phagocytic cells having a DNA content of Zn (=2n phagocytic cells)
`
`isolated from the subject, a population of non-phagocytic cells isolated from the
`
`subject, and a population of control cells isolated from the subject, wherein the
`
`control cells are substantially free of cells affected by the disease or condition; and
`
`c)
`
`identifying a difference between the first and second profiles, wherein
`
`the difference is indicative of the prognosis of said disease or condition in the subject.
`
`4.
`
`A method for assessing the efficacy of a treatment for a disease or condition in
`
`a subject comprising:
`
`

`

`WO 2013/188846
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`PCT/US2013/046020
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`-5-
`
`a)
`
`determining a first profile of one or more markers of the disease or
`
`condition from a first sample comprising two or more different components selected
`
`from the group consisting of: a cell—free bodily fluid isolated from the subject before
`
`the treatment, a population of phagocytic cells isolated from the subject before the
`
`treatment, a population of phagocytic cells having a DNA content more than 2n (>2n
`
`phagocytic cells) isolated from the subject before the treatment, a population of
`
`circulating vesicles isolated from the subject before the treatment, and a population of
`
`circulating diseased cells isolated from the subject before the treatment;
`
`determining a second profile of at least one of the one or more markers
`
`from a first control comprising a component selected from the group consisting of: a
`
`population of phagocytic cells having a DNA content of Zn (=2n phagocytic cells)
`
`isolated from the subject before the treatment, a population of non-phagocytic cells
`
`isolated from the subject before the treatment, and a population of control cells
`
`isolated from the subject, wherein the control cells are substantially free of cells
`
`affected by the disease or condition, before the treatment;
`
`identifying a difference between the first and second profiles;
`
`b)
`
`determining a third profile of one or more markers of the disease or
`
`condition from a second sample comprising two or more different components
`
`selected from the group consisting of: a cell-free bodily fluid isolated from the subject
`
`after the treatment, a population of phagocytic cells isolated from the subject after the
`
`treatment, a population of phagocytic cells having a DNA content more than 2n (>2n
`
`phagocytic cells) isolated from the subject after the treatment, a population of
`
`Circulating vesicles isolated from the subject after the treatment, and a population of
`
`circulating diseased cells isolated from the subject after the treatment;
`
`determining a fourth profile of at least one of the one or more markers
`
`from a second control comprising a component selected from the group consisting of:
`
`a population of phagocytic cells having a DNA content of Zn (=2n phagocytic cells)
`
`isolated from the subject after the treatment, a population of non—phagocytic cells
`
`isolated from the subject after the treatment, and a population of control cells isolated
`
`

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`WO 2013/188846
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`PCT/US2013/046020
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`—6—
`
`from the subject, wherein the control cells are substantially free of cells affected by
`
`the disease or condition, after the treatment;
`
`identifying a difference between the third and fourth profiles; and
`
`c)
`
`identifying a difference between the difference identified in a) and the
`
`difference identified in b) wherein the identified difference in c) is indicative of the
`
`efficacy of the treatment for said disease or condition in the subject.
`
`5.
`
`A method for monitoring the progression or regression of a disease or
`
`condition in a subject comprising:
`
`a)
`
`determining a first profile of one or more markers of the disease or
`
`condition fiom a first sample comprising two or more different components selected
`
`from the group consisting of: a cell-free bodily fluid isolated from the subject at a first
`
`time point, a population of phagocytic cells isolated from the subject at a first time
`
`point, a population of phagocytic cells having a DNA content more than 2n (>2n
`
`phagocytic cells) isolated from the subject at a first time point; a population of
`
`circulating vesicles isolated from the subject at a first time point, and a population of
`
`circulating diseased cells isolated from the subject at a first time point;
`
`determining a second profile of at least one of the one or more markers
`
`from a first control comprising a component selected from the group consisting of: a
`
`population of phagocytic cells having a DNA content of Zn (:2n phagocytic cells)
`
`isolated from the subject at a first time point, a population of non-phagocytic cells
`
`isolated from the subject at a first time point, and a population of control cells isolated
`
`from the subject, wherein the control cells are substantially free of cells affected by
`
`the disease or condition, at a first time point;
`
`identifying a difference between the first and second profiles;
`
`b)
`
`determining a third profile of one or more markers of the disease or
`
`condition from a second sample comprising two or more different components
`
`selected from the group consisting of: a cell-free bodily fluid isolated from the subject
`
`at a second time point, a population of phagocytic cells isolated from the subject at a
`
`

`

`WO 2013/188846
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`PCT/US2013/046020
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`-7-
`
`second time point, a population of phagocytic cells having a DNA content more than
`
`2n (>2n phagocytic cells) isolated from the subject at a second time point, a
`
`population of circulating vesicles isolated from the subject at a second time point, and
`
`a population of circulating diseased cells isolated from the subject at a second time
`
`point;
`
`determining a fourth profile of at least one of the one or more markers
`
`from a second control comprising a component selected from the group consisting of:
`
`a population of phagocytic cells having a DNA content of Zn (:2n phagocytic cells)
`
`isolated from the subject at a second time point, a population of non-phagocytic cells
`
`isolated from the subject at a second time point, and a population of control cells
`
`isolated from the subject, wherein the control cells are substantially free of cells
`
`affected by the disease or condition, at a second time point;
`
`identifying a difference between the third and fourth profiles; and
`
`C)
`
`identifying a difference between the difference identified in a) and the
`
`difference identified in b) wherein the identified difference in c) is indicative of the
`
`progression or regression of said disease or condition in the subject.
`
`6.
`
`A method for identifying a compound capable of ameliorating or treating a
`
`disease or condition in a subject comprising:
`
`a)
`
`determining a first profile of one or more markers of the disease or
`
`condition from a first sample comprising two or more different components selected
`
`from the group consisting of: a cell-free bodily fluid isolated from the subject before
`
`administering the compound to the subject, a population of phagocytic cells isolated
`
`from the subject before administering the compound to the subject, a population of
`
`phagocytic cells having a DNA content more than 2n (>2n phagocytic cells) isolated
`
`from the subject before administering the compound to the subject, a population of
`
`circulating vesicles isolated from the subject before administering the compound to
`
`the subject, and a population of circulating diseased cells isolated from the subject
`
`before administering the compound to the subject;
`
`

`

`WO 2013/188846
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`PCT/US2013/046020
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`—8—
`
`determining a second profile of at least one of the one or more markers
`
`from a first control comprising a component selected from the group consisting of: a
`
`population of phagocytic cells having a DNA content of Zn (=2n phagocytic cells)
`
`isolated from the subject before administering the compound to the subject, a
`
`population of non—phagocytic cells isolated from the subject before administering the
`
`compound to the subject, and a population of control cells isolated from the subject,
`
`wherein the control cells are substantially free of cells affected by the disease or
`
`condition, before administering the compound to the subject;
`
`identifying a difference between the first and second profiles;
`
`b)
`
`determining a third profile of one or more markers of the disease or
`
`condition from a second sample comprising two or more different components
`
`selected from the group consisting of: a cell—free bodily fluid isolated from the subject
`
`after administering the compound to the subject, a population of phagocytic cells
`
`isolated from the subject after administering the compound to the subject, a
`
`population of phagocytic cells having a DNA content more than 2n (>2n phagocytic
`
`cells) isolated from the subject after administering the compound to the subject, a
`
`population of circulating vesicles isolated from the subject after administering the
`
`compound to the subject, and a population of circulating diseased cells isolated from
`
`the subject after administering the compound to the subject;
`
`determining a fourth profile of at least one of the one or more markers
`
`from a second control comprising a component selected from the group consisting of:
`
`a population of phagocytic cells having a DNA content of Zn (=2n phagocytic cells)
`
`isolated from the subject after administering the compound to the subject, a
`
`population of non—phagocytic cells isolated from the subject after administering the
`
`compound to the subject, and a population of control cells isolated from the subject,
`
`wherein the control cells are substantially free of cells affected by the disease or
`
`condition, after administering the compound to the subject;
`
`identifying a difference between the third and fourth profiles; and
`
`

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`-9-
`
`C)
`
`identifying a difference between the difference identified in a) and the
`
`difference identified in b) wherein the identified difference in c) indicates that the
`
`compound is capable of ameliorating or treating said disease or condition in the
`
`subject.
`
`7.
`
`A method for assessing the efficacy ofa treatment for a disease or condition in
`
`a subject comprising:
`
`a)
`
`determining a first profile of one or more markers of the disease or
`
`condition from a first sample comprising two or more different components selected
`
`from the group consisting of: a cell-free bodily fiuid isolated from the subject before
`
`the treatment, a population of phagocytic cells isolated from the subject before the
`
`treatment, a population of phagocytic cells having a DNA content more than 2n (>2n
`
`phagocytic cells) isolated from the subject before the treatment, a population of
`
`circulating vesicles isolated from the subject before the treatment, and a population of
`
`circulating diseased cells isolated from the subject before the treatment;
`
`b)
`
`determining a second profile of one or more markers of the disease or
`
`condition from a second sample comprising two or more different components
`
`selected from the group consisting of: a cell-free bodily fluid isolated from the subject
`
`after the treatment, a population of phagocytic cells isolated from the subject after the
`
`treatment, a population of phagocytic cells having a DNA content more than 2n (>2n
`
`phagocytic cells) isolated from the subject after the treatment, a population of
`
`Circulating vesicles isolated from the subject after the treatment, and a population of
`
`circulating diseased cells isolated from the subject; and
`
`0)
`
`identifying a difference between the first profile and the second profile,
`
`wherein the identified difference is indicative of the efficacy of the treatment for said
`
`disease or condition in the subject.
`
`8.
`
`A method for monitoring the progression or regression of a disease or
`
`condition in a subject comprising:
`
`a)
`
`determining a first profile of one or more markers of the disease or
`
`condition from a first sample comprising two or more different components selected
`
`

`

`WO 2013/188846
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`PCT/US2013/046020
`
`-10-
`
`from the group consisting of: a cell-free bodily fluid isolated from the subject at a first
`
`time point, a population of phagocytic cells isolated from the subject at a first time
`
`point, a population of phagocytic cells having a DNA content more than 2n (>2n
`
`phagocytic cells) isolated from the subject at a first time point, a population of
`
`circulating vesicles isolated from the subject at a first time point, and a population of
`
`circulating diseased cells isolated from the subject at a first time point;
`
`b)
`
`determining a second profile of one or more markers of the disease or
`
`condition from a second sample comprising two or more different components
`
`selected from the group consisting of: a cell-free bodily fluid isolated from the subject
`
`at a second time point, a population of phagocytic cells isolated from the subject at a
`
`second time point, a population of phagocytic cells having a DNA content more than
`
`2n (>2n phagocytic cells) isolated from the subject at a second time point, a
`
`population of circulating vesicles isolated from the subject at a second time point, and
`
`a population of circulating diseased cells isolated from the subject at a second time
`
`point; and
`
`c)
`
`identifying a difference between the first profile and the second profile,
`
`wherein the identified difference is indicative of the progression or regression of said
`
`disease or condition in the subject.
`
`9.
`
`A method for identifying a compound capable of ameliorating or treating a
`
`disease or condition in a subject comprising:
`
`a)
`
`determining a first profile of one or more markers of thc discasc or
`
`condition from a first sample comprising two or more different components selected
`
`from the group consisting of: a cell—free bodily fluid isolated from the subject before
`
`administering the compound to the subject, a population of phagocytic cells isolated
`
`from the subject before administering the compound to the subject, a population of
`
`phagocytic cells having a DNA content more than 2n (>2n phagocytic cells) isolated
`
`from the subject before administering the compound to the subject, a population of
`
`circulating vesicles isolated from the subject before administering the compound to
`
`the subject, and a population of circulating diseased cells isolated from the subject
`
`before administering the compound to the subject;
`
`

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`
`b)
`
`determining a second profile of one or more markers of the disease or
`
`condition from a second sample comprising two or more different components
`
`selected from the group consisting of: a cell—free bodily fluid isolated from the subject
`
`after administering the compound to the subject, a population of phagocytic cells
`
`isolated from the subject after administering the compound to the subject, a
`
`population of phagocytic cells having a DNA content more than 2n (>2n phagocytic
`
`cells) isolated from the subject after administering the compound to the subject, a
`
`population of circulating vesicles isolated from the subject after administering the
`
`compound to the subject, and a population of circulating diseased cells isolated from
`
`the subject after administering the compound to the subject; and
`
`c)
`
`identifying a difference between the first profile and the second profile,
`
`wherein the identified difference indicates that the compound is capable of
`
`ameliorating or treating said disease or condition in the subject.
`
`10.
`
`A method for diagnosing or aiding in the diagnosis of a disease or condition in
`
`a subject comprising:
`
`a)
`
`determining a first profile of one or more markers of the disease or
`
`condition from a sample comprising components selected from the group consisting
`
`of: an analyte isolated from a cell-free bodily fluid isolated from the subject, an
`
`analyte isolated from a population of phagocytic cells isolated from the subject, an
`
`analyte isolated from a population of phagocytic cells having a DNA content more
`
`than 2n (>2n phagocytic cells) isolated from the subject, an analyte isolated from a
`
`population of circulating vesicles isolated from the subject, and an analyte isolated
`
`from a population of circulating diseased cells isolated from the subject;
`
`b)
`
`determining a second profile of at least one of the one or more markers
`
`from a control comprising a component selected from the group consisting of: an
`
`analyte isolated from a population of phagocytic cells having a DNA content of Zn
`
`(=2n phagocytic cells) isolated from the subject, an analyte isolated from a population
`
`of non—phagocytic cells isolated from the subject, and an analyte isolated from a
`
`population of control cells isolated from the subject, wherein the control cells are
`
`substantially free of cells affected by the disease or condition; and
`
`

`

`WO 2013/188846
`
`PCT/US2013/046020
`
`-12-
`
`c)
`
`identifying a difference between the first and second profiles, wherein
`
`the difference is indicative of the presence of said disease or condition in the subject.
`
`1 l.
`
`A method for assessing the risk of developing a disease or condition in a
`
`subject comprising:
`
`a)
`
`determining a first profile of one or more markers of the disease or
`
`condition fi‘OIIl a sample comprising two or more different components selected from
`
`the group consisting of: an analyte isolated from a cell-free bodily fiuid isolated from
`
`the subject, an analyte isolated from a population of phagocytic cells isolated from the
`
`subject, an analyte isolated from a population of phagocytic cells having a DNA
`
`content more than 2n (>2n phagocytic cells) isolated from the subject, an analyte
`
`isolated from a population of circulating vesicles isolated from the subject, and an
`
`analyte isolated from a population of circulating diseased cells isolated from the
`
`subject;
`
`b)
`
`determining a second profile of at least one of the one or more markers
`
`from a control comprising a component selected from the group consisting of: an
`
`analyte isolated from a population of phagocytic cells having a DNA content of 2n
`
`(=2n phagocytic cells) isolated from the subject, an analyte isolated from a population
`
`of non-phagocytic cells isolated from the subject, and an analyte isolated from a
`
`population of control cells isolated from the subject, wherein the control cells are
`
`substantially free of cells affected by the disease or condition; and
`
`c)
`
`identifying a difference between the first and second profiles, wherein
`
`the difference is indicative of the risk of developing said disease or condition in the
`
`subject.
`
`12.
`
`A method for prognosing or aiding in the prognosis of a disease or condition
`
`in a subject comprising:
`
`a)
`
`determining a first profile of one or more markers of the disease or
`
`condition from a sample comprising two or more different components selected from
`
`the group consisting of: an analyte isolated from a cell-free bodily fluid isolated from
`
`the subject, an analyte isolated from a population of phagocytic cells isolated from the
`
`

`

`WO 2013/188846
`
`PCT/US2013/046020
`
`-13-
`
`subject, an analyte isolated from a population of phagocytic cells having a DNA
`
`content more than 2n (>2n phagocytic cells) isolated from the subject, an analyte
`
`isolated from a population of circulating vesicles isolated from the subject, and an
`
`analyte isolated from a population of circulating diseased cells isolated from the
`
`subject;
`
`b)
`
`determining a second profile of at least one of the one or more markers
`
`from a control comprising a component selected from the group consisting of: an
`
`analyte isolated from a population of phagocytic cells having a DNA content of 2n
`
`(=2n phagocytic cells) isolated from the subject, an analyte isolated from a population
`
`ofnon-phagocytic cells isolated from the subject, and an analyte isolated from a
`
`population of control cells isolated from the subject, wherein the control cells are
`
`substantially free of cells affected by the disease or condition; and
`
`c)
`
`identifying a difference between the first and second profiles, wherein
`
`the difference is indicative of the prognosis of said disease or condition in the subject.
`
`13.
`
`A method for assessing the efficacy of a treatment for a disease or condition in
`
`a subject comprising:
`
`a)
`
`determining a first profile of one or more markers of the disease or
`
`condition from a first sample comprising two or more different components selected
`
`from the group consisting of: an analyte isolated from a cell-free bodily fluid isolated
`
`from the subject before the treatment, an analyte isolated from a population of
`
`phagocytic cells isolated from the subject before the treatment, an analyte isolated
`
`from a population of phagocytic cells having a DNA content more than 2n (>2n
`
`phagocytic cells) isolated from the subject before the treatment, an analyte isolated
`
`from a population of circulating vesicles isolated from the subject before the
`
`treatment, and an analyte isolated from a population of circulating diseased cells
`
`isolated from the subject before the treatment;
`
`determining a second profile of at least one of the one or more markers
`
`from a first control comprising a component selected from the group consisting of: an
`
`analyte isolated from a population of phagocytic cells having a DNA content of Zn
`
`

`

`WO 2013/188846
`
`PCT/US2013/046020
`
`-14-
`
`(:2n phagocytic cells) isolated from the subject before the treatment, an analyte
`
`isolated from a population of non-phagocytic cells isolated from the subject before the
`
`treatment, and an analyte isolated from a population of control cells isolated from the
`
`subject, wherein the control cells are substantially free of cells affected by the disease
`
`or condition, before the treatment;
`
`identifying a difference between the first and second profiles;
`
`b)
`
`determining a third profile of one or more markers of the disease or
`
`condition from a second sample comprising two or more different components
`
`selected from the group consisting of: an analyte isolated from a cell-free bodily fluid
`
`isolated from the subject after the treatment, an analyte isolated from a population of
`
`phagocytic cells isolated from the subject after the treatment, an analyte isolated from
`
`a population of phagocytic cells having a DNA content more than 2n (>2n phagocytic
`
`cells) isolated from the subject after the treatment, an analyte isolated from a
`
`population of circulating vesicles isolated from the subject after the treatment, and an
`
`analyte isolated from a population of circulating diseased cells isolated from the
`
`subject after the treatment;
`
`determining a fourth profile of at least one of the one or more markers
`
`from a second control comprising a component selected from the group consisting of:
`
`an analyte isolated from a population of phagocytic cells having a DNA content of Zn
`
`(=2n phagocytic cells) isolated from the subject after the treatment, an analyte isolated
`
`fro