System for determining a health status of a tissue of interest

Abstract

The invention generally relates to methods for assessing the health of a tissue by characterizing circulating nucleic acids in a biological sample. According to certain embodiments, methods for assessing the health of a tissue include the steps of detecting a sample level of RNA in a biological sample, comparing the sample level of RNA to a reference level of RNA specific to the tissue, determining whether a difference exists between the sample level and the reference level, and characterizing the tissue as abnormal if a difference is detected.

What is claimed is: 
     
         1 . A method for providing a clinical intervention for a pregnant subject, comprising:
 (a) obtaining a cell-free blood sample from said pregnant subject;   (b) sequencing nucleic acid molecules derived from said cell-free blood sample to determine levels of a set of ribonucleic acid (RNA) transcripts;   (c) comparing said levels of said set of RNA transcripts determined in (b) to reference levels of said set of RNA transcripts;   (d) determining that said pregnant subject has or is at an elevated risk of having pre-eclampsia, based at least in part on said comparing in (c); and   (e) providing said clinical intervention for said pregnant subject for said preeclampsia or said elevated risk of having said pre-eclampsia, based on said determining in (d).   
     
     
         2 . The method of  claim 1 , wherein said cell-free blood sample comprises a serum sample or a plasma sample. 
     
     
         3 . The method of  claim 2 , wherein said cell-free blood sample comprises said plasma sample. 
     
     
         4 . The method of  claim 1 , wherein sequencing said nucleic acid molecules comprises reverse transcribing RNA molecules derived from said cell-free blood sample to produce complementary deoxyribonucleic acid (cDNA) molecules, and sequencing said cDNA molecules or derivatives thereof to determine said levels of said set of RNA transcripts. 
     
     
         5 . The method of  claim 4 , further comprising amplifying said cDNA molecules to produce amplified products, and sequencing said amplified products or derivatives thereof to determine said levels of said set of RNA transcripts. 
     
     
         6 . The method of  claim 1 , wherein said set of RNA transcripts comprises tissue-specific differentially expressed transcripts. 
     
     
         7 . The method of  claim 6 , wherein said tissue-specific differentially expressed transcripts comprise placental-specific transcripts. 
     
     
         8 . The method of  claim 6 , wherein said tissue-specific differentially expressed transcripts comprise fetal-specific transcripts. 
     
     
         9 . The method of  claim 1 , wherein said clinical intervention comprises a drug treatment. 
     
     
         10 . The method of  claim 1 , wherein said set of RNA transcripts comprises pregnancy-associated differentially expressed transcripts. 
     
     
         11 . The method of  claim 1 , wherein said pregnant subject is in a first trimester of pregnancy. 
     
     
         12 . The method of  claim 1 , wherein said pregnant subject is in a second trimester of pregnancy. 
     
     
         13 . The method of  claim 1 , wherein said pregnant subject is in a third trimester of pregnancy. 
     
     
         14 . The method of  claim 1 , wherein said reference levels correspond to a set of RNA transcripts from non-pregnant subjects. 
     
     
         15 . The method of  claim 1 , wherein said reference levels correspond to a set of RNA transcripts from pregnant subjects. 
     
     
         16 . The method of  claim 1 , wherein said nucleic acid molecules sequenced in (b) comprise fetal-derived or placenta-derived nucleic acid molecules enriched from a mixture comprising maternal nucleic acid molecules and said fetal-derived or placenta-derived nucleic acid molecules of said cell-free blood sample, at least in part by use of gel electrophoresis, centrifugation, an enzyme inhibitor, nucleic acid amplification, nuclease treatment, DNase treatment, or flow cytometry. 
     
     
         17 . The method of  claim 1 , wherein said nucleic acid molecules sequenced in (b) are enriched from among a maternally-derived portion of said cell-free blood sample at least in part by use of gel electrophoresis, centrifugation, an enzyme inhibitor, nucleic acid amplification, nuclease treatment, DNase treatment, or flow cytometry. 
     
     
         18 . The method of  claim 1 , further comprising identifying a fetal-specific or placental-specific RNA transcript among said set of RNA transcripts, and determining that said pregnant subject has or is at said elevated risk of having said pre-eclampsia, based at least in part on said fetal-specific or placental-specific RNA transcript. 
     
     
         19 . The method of  claim 1 , further comprising determining a response of said subject to said clinical intervention. 
     
     
         20 . The method of  claim 1 , wherein (b) comprises performing single molecule sequencing. 
     
     
         21 . The method of  claim 1 , wherein (b) comprises performing whole transcriptome sequencing. 
     
     
         22 . The method of  claim 1 , wherein comparing said levels of said set of RNA transcripts to said reference levels comprises determining a difference between said levels of said set of RNA transcripts and said reference levels. 
     
     
         23 . The method of  claim 22 , further comprising using said difference to determine that said pregnant subject has or is at said elevated risk of having said pre-eclampsia. 
     
     
         24 . The method of  claim 22 , wherein determining said difference further comprises determining a level of fold change in quantitative polymerase chain reaction (qPCR) measurements based at least in part on data corresponding to said levels of said set of RNA transcripts and said reference levels. 
     
     
         25 . The method of  claim 1 , further comprising comparing levels of said sets of RNA transcripts in cell-free blood samples obtained at two or more different time points to said reference levels. 
     
     
         26 . The method of  claim 1 , further comprising monitoring said pregnant subject for said pre-eclampsia or said elevated risk of having said pre-eclampsia.