Method for the detection of chromosomal aneuploidies

Abstract

The non-invasive detection of fetal chromosomal aneuploidies is demonstrated. Alleles of fetal RNA-SNPs present in a biological sample (e.g. maternal blood) containing fetal RNA are detected and quantified in order to determine the ratio of the alleles. This ratio is compared to a standard control consisting of euploid fetuses. Deviation of allele ratio indicates the presence of chromosomal aneuploidy.

1 . A method for detecting the presence of a chromosomal disorder in the fetus of a pregnant woman, comprising the steps of:
 (a) obtaining an RNA-containing biological sample from the pregnant woman, wherein the RNA-containing biological sample contains fetal RNA;   (b) discriminating alleles from RNA transcribed from at least one genetic locus from at least one chromosome of concern;   (c) determining the ratio of the alleles of the RNA transcripts; and   (d) comparing the ratio from step (c) to a standard control representing a ratio of alleles from comparable biological samples obtained from pregnant women each carrying a chromosomally normal fetus, wherein an increase or decrease in the ratio from the standard control indicates an increased risk of having a fetus with a chromosomal disorder.   
     
     
         2 . The method of  claim 1 , in which the chromosomal disorder is a member selected from the group consisting of trisomy 21, trisomy 18 and trisomy 13 . 
     
     
         3 . The method of  claim 2 , in which the chromosomal disorder is trisomy 21. 
     
     
         4 . The method of  claim 1 , in which the chromosomal disorder is on the X chromosome or the Y chromosome. 
     
     
         5 . The method of  claim 1 , in which the biological sample in step (a) is a member selected from the group consisting of maternal blood, maternal plasma or serum, amniotic fluid, a chorionic villus sample, biopsy material from a preimplantation embryo, fetal nucleated cells or fetal cellular remnants isolated from maternal blood, maternal urine, maternal saliva, washings of the female reproductive tract and a sample obtained by celocentesis. 
     
     
         6 . The method of  claim 1 , in which the biological sample in step (a) is maternal blood. 
     
     
         7 . The method of  claim 1 , in which the biological sample in step (a) contains cellular elements or cellular remnants in maternal blood, 
     
     
         8 . The method of  claim 1 , in which the fetal RNA in step (a) is derived from the placenta. 
     
     
         9 . The method of  claim 1 , in which step (b) is performed using reverse transcriptase polymerase chain reaction (RT-PCR). 
     
     
         10 . The method of  claim 1 , in which step (b) and/or step (c) is performed using a member selected from the group consisting of a primer extension reaction, mass spectrometry, hybridization using at least one probe, hybridization using at least one fluorescently labeled probe, direct sequencing, cloning and sequencing, and electrophoresis. 
     
     
         11 . The method of  claim 1 , in which the alleles in steps (b), (c) and (d) are differentiated by sequence variation. 
     
     
         12 . The method of  claim 11 , in which the sequence variation is a single nucleotide polymorphism (SNP). 
     
     
         13 . The method of  claim 11 , in which the sequence variation is an insertion/deletion polymorphism. 
     
     
         14 . The method of  claim 11 , in which the sequence variation is a simple tandem repeat polymorphism. 
     
     
         15 . The method of  claim 1 , in which the RNA is transcribed from a member selected from the group consisting of chromosome 21, chromosome 18, chromosome 13, chromosome X, and chromosome Y. 
     
     
         16 . The method of  claim 15 , in which the RNA is transcribed from chromosome 21. 
     
     
         17 . The method of  claim 1 , in which the RNA is mRNA. 
     
     
         18 . The method of  claim 1 , wherein the RNA is transcribed from at least one genetic locus selected from the group consisting of collagen VI alpha 1(COL6A1), superoxide dismutase 1 (SOD1), collagen VI alpha2 (COL6A2), mitochondrial ATP synthase O subunit (ATP5O), BTG family, member 3 (BTG 3), a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 1 (ADAMTS1), beta-site APP-cleaving enzyme 2 (BACE2), intersectin 1 (ITSN1), amyloid beta (A4) precursor protein (APP), ATP synthase, H+ transporting, mitochondrial F0 complex, subunit F6 (ATP5J), Down syndrome critical region gene 5 (DSCR5), placenta-specific 4 (PLAC4), hypothetical protein BC005107 (LOC90625), ribosomal protein L17 (RPL17), serpin peptidase inhibitor clade B (ovalbumin) member2(SERPINB2) and collagen type IV alpha 2(COL4A2). 
     
     
         19 . The method of  claim 18 , wherein the RNA contains at least one single nucleotide polymorphism (SNP) of the genetic locus. 
     
     
         20 . The method of  claim 19 , wherein the RNA is transcribed from at least one genetic locus selected from the group consisting of collagen VI alpha 1(COL6A1) and collagen VI alpha 2(COL6A2). 
     
     
         21 . The method of  claim 20 , wherein the SNP in the RNA transcribed from the genetic locus of the COL6A1 is  Arg 850 His , or  Ser 932 Ser . 
     
     
         22 . The method of  claim 20 , wherein the SNP in the RNA transcribed from the genetic locus of the COL6A2 is  Val 728 Val.    
     
     
         23 . The method of  claim 18 , wherein the RNA is transcribed from the genetic locus for placenta-specific 4 (PLAC4). 
     
     
         24 . The method of  claim 23 , wherein the RNA is any variant transcribed from the PLAC4 gene, such as AF269287, AK027868, AK092431, BC093685, BC101615, BC101617, L13197, NM — 182832 and LOC191585. 
     
     
         25 . The method of  claim 23 , wherein the RNA transcribed from the genetic locus of the PLAC4 gene contains a single nucleotide polymorphism or an insertion-deletion polymorphism selected from the group consisting of rs3804026, rs4818219, rs7844, rs9015, rs13643, rs9305729, rs9305730, rs5019195, rs5019194, rs5844069, rs1049904, rs16998089, rs12482116, rs11909439, rs7278659, rs12106409, rs12106395, rs12106401, rs12106434, rs2183584, rs3949725, rs8130833, rs10222145, rs9981478, rs8130833, rs9977003, PLAC4-41471145 and PLAC4-41476236. 
     
     
         26 . The method of  claim 1 , wherein the woman is during the first trimester of gestation. 
     
     
         27 . The method of  claim 1 , wherein the woman is during the second trimester of gestation. 
     
     
         28 . The method of  claim 1 , wherein the comparison in step (d) shows an increased risk of the fetus having a chromosomal disorder if the ratio in step (c) is higher or lower by 1 standard deviation from the standard control. 
     
     
         29 . The method of  claim 1 , wherein the comparison in step (d) shows an increased risk of the fetus having a chromosomal disorder if the ratio in step (c) is higher or lower by 2 standard deviations from the standard control. 
     
     
         30 . The method of  claim 1 , wherein the comparison in step (d) shows an increased risk of the fetus having a chromosomal disorder if the ratio in step (c) is higher or lower by 3 standard deviations from the standard control. 
     
     
         31 . A kit for detecting the presence of a fetus with a chromosomal disorder in a pregnant woman, the kit comprising:
 (a) primers for amplifying the region of interest; and   (b) a standard control representing a ratio of alleles from comparable biological samples obtained from pregnant women each carrying a chromosomally normal fetus.   
     
     
         32 . The kit of  claim 31 , further comprising:
 (c) hybridization probes for discriminating between the different alleles of each RNA species.