Methods of fetal abnormality detection

Abstract

Methods and kits for selectively enriching non-random polynucleotide sequences are provided. Methods and kits for generating libraries of sequences are provided. Methods of using selectively enriched non-random polynucleotide sequences for detection of fetal aneuploidy are provided.

1 . A method for determining the presence or absence of fetal aneuploidy comprising:
 a. selectively enriching non-random polynucleotide sequences of genomic DNA from a cell-free DNA sample;   b. sequencing said enriched polynucleotide sequences;   c. enumerating sequence reads from said sequencing step; and   d. determining the presence or absence of fetal aneuploidy based on said enumerating.   
     
     
         2 . The method of  claim 1 , wherein said selectively enriching comprises performing PCR. 
     
     
         3 . The method of  claim 1 , wherein said selectively enriching comprises linear amplification. 
     
     
         4 . The method of  claim 1 , wherein said selectively enriching comprises enriching at least 1, 5, 10, 50, 100, or 1000 non-random polynucleotide sequences from a first chromosome. 
     
     
         5 . The method of  claim 1 , wherein said selectively enriching comprises enriching at least 1, 10, or 100 polynucleotide sequences from one or more regions of a first chromosome, wherein each region is up to 50 kb. 
     
     
         6 . The method of  claim 1 , wherein said non-random polynucleotide sequences comprise sequences that are sequenced at a rate of greater than 5-fold than other sequences on the same chromosome. 
     
     
         7 . The method of  claim 1 , wherein said non-random polynucleotide sequences each comprise about 50-1000 bases. 
     
     
         8 . The method of  claim 1 , wherein said cell-free DNA sample is a maternal sample. 
     
     
         9 . The method of  claim 8 , wherein said maternal sample is a maternal blood sample. 
     
     
         10 . The method of  claim 9 , wherein said maternal sample comprises fetal and maternal cell-free DNA. 
     
     
         11 . The method of  claim 1 , wherein said cell-free DNA is from a plurality of different individuals. 
     
     
         12 . The method of  claim 1 , wherein said sequencing comprises Sanger sequencing, sequencing-by-synthesis, or massively parallel sequencing. 
     
     
         13 . The method of  claim 1 , wherein said aneuploidy is trisomy 21, trisomy 18, or trisomy 13. 
     
     
         14 . The method of  claim 1 , wherein said aneuploidy is suspected or determined when the number of enumerated sequences is greater than a predetermined amount. 
     
     
         15 . The method of  claim 14 , wherein said predetermined amount is based on estimated amount of DNA in said cell-free DNA sample. 
     
     
         16 . The method of  claim 14 , wherein said predetermined amount is based on the amount of enumerated sequences from a control region. 
     
     
         17 . A method comprising:
 a. providing oligonucleotides that specifically hybridize to one or more polynucleotide sequences from a polynucleotide template, wherein said one or more polynucleotide sequences comprise sequences that are sequenced at rate greater than 5-fold than other sequences from the polynucleotide template;   b. selectively enriching said one or more polynucleotide sequences; and   c. optionally sequencing said enriched one or more polynucleotide sequences.   
     
     
         18 . The method of  claim 17 , wherein each of said oligonucleotides has a substantially similar thermal profile. 
     
     
         19 . The method of  claim 17 , wherein said polynucleotide sequences each comprise about 50-1000 bases. 
     
     
         20 . The method of  claim 17 , wherein said polynucleotide sequences are from a cell-free DNA sample. 
     
     
         21 . The method of  claim 17 , wherein said polynucleotide sequences are from a maternal sample. 
     
     
         22 . The method of  claim 21 , wherein said maternal sample is a maternal blood sample. 
     
     
         23 . The method of  claim 22 , wherein said maternal sample comprises fetal and maternal cell-free DNA. 
     
     
         24 . The method of  claim 17 , wherein said polynucleotide template is a chromosome suspected of being aneuploid. 
     
     
         25 . The method of  claim 17 , wherein said polynucleotide template is chromosome 21.