Methods and systems for determining a pregnancy-related state of a subject

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 comprising:
 (a) sequencing nucleic acid molecules derived from a cell-free blood sample of a pregnant subject to determine at least one ribonucleic acid (RNA) level of at least one genomic locus that is differentially expressed in a first population of subjects having pre-term birth as compared to a second population of subjects not having pre-term birth;   (b) computer processing said at least one RNA level of said at least one genomic locus determined in (a) (i) against at least one reference RNA level of said at least one genomic locus or (ii) with a trained machine learning algorithm; and   (c) determining, based at least in part on said computer processing in (b), that said pregnant subject has an elevated risk of having a pre-term birth, based at least in part on said computer processing in (c).   
     
     
         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 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 to determine said at least one RNA level of said at least one genomic locus. 
     
     
         4 . The method of  claim 1 , wherein said at least one genomic locus comprises a tissue-specific differentially expressed genomic locus. 
     
     
         5 . The method of  claim 1 , wherein said pregnant subject is in a first trimester of pregnancy a second trimester of pregnancy, or a third trimester of pregnancy. 
     
     
         6 . The method of  claim 1 , wherein said at least one reference RNA level is determined from pregnant subjects or non-pregnant subjects. 
     
     
         7 . The method of  claim 1 , wherein processing said at least one RNA level of said at least one genomic locus against said at least one reference RNA level further comprises determining a difference between said at least one RNA level of said at least one genomic locus and said at least one reference RNA level. 
     
     
         8 . The method of  claim 7 , further comprising 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 to determine said difference. 
     
     
         9 . The method of  claim 7 , further comprising performing principle component analysis on data corresponding to said levels of said set of RNA transcripts and said reference levels to determine said difference. 
     
     
         10 . The method of  claim 1 , wherein said at least one genomic locus comprises at least two genomic loci selected from the group of genes consisting of B3GNT2, PPBPL2, PTGS2, U2AF1, CSH1, CAPN6, CYP19A1, SVEP1, PAPPA, and PSG1. 
     
     
         11 . A system comprising:
 one or more computer processors; and   a memory comprising instructions stored thereon that, when executed by said one or more computer processors, cause said one or more computer processors to perform:   (a) sequencing nucleic acid molecules derived from a cell-free blood sample of a pregnant subject to determine at least one ribonucleic acid (RNA) level of at least one genomic locus that is differentially expressed in a first population of subjects having pre-term birth as compared to a second population of subjects not having pre-term birth;   (b) computer processing said at least one RNA level of said at least one genomic locus determined in (a) (i) against at least one reference RNA level of said at least one genomic locus or (ii) with a trained machine learning algorithm; and   (c) determining, based at least in part on said computer processing in (b), that said pregnant subject has an elevated risk of having a pre-term birth, based at least in part on said computer processing in (c).   
     
     
         12 . The system of  claim 11 , wherein said cell-free blood sample comprises a serum sample or a plasma sample. 
     
     
         13 . The system of  claim 11 , 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 to determine said at least one RNA level of said at least one genomic locus. 
     
     
         14 . The system of  claim 11 , wherein said at least one genomic locus comprises a tissue-specific differentially expressed genomic locus. 
     
     
         15 . The system of  claim 11 , wherein said pregnant subject is in a first trimester of pregnancy a second trimester of pregnancy, or a third trimester of pregnancy. 
     
     
         16 . The system of  claim 11 , wherein said at least one reference RNA level is determined from pregnant subjects or non-pregnant subjects. 
     
     
         17 . The system of  claim 11 , wherein processing said at least one RNA level of said at least one genomic locus against said at least one reference RNA level further comprises determining a difference between said at least one RNA level of said at least one genomic locus and said at least one reference RNA level. 
     
     
         18 . The system of  claim 17 , 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. 
     
     
         19 . The system of  claim 17 , wherein determining said difference further comprises performing principle component analysis on data corresponding to said levels of said set of RNA transcripts and said reference levels. 
     
     
         20 . The system of  claim 11 , wherein said at least one genomic locus comprises at least two genomic loci selected from the group of genes consisting of B3GNT2, PPBPL2, PTGS2, U2AF1, CSH1, CAPN6, CYP19A1, SVEP1, PAPPA, and PSG1.