METHODS OF FETAL ABNORMALITY DETECTION
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.