Sequencing methods and compositions for prenatal diagnoses
The invention provides methods for determining aneuploidy and/or fetal fraction in maternal samples comprising fetal and maternal cfDNA by massively parallel sequencing. The method comprises a novel protocol for preparing sequencing libraries that unexpectedly improves the quality of library DNA while expediting the process of analysis of samples for prenatal diagnoses.
1. A method for determining a fetal chromosomal aneuploidy in a maternal sample comprising a mixture of fetal and maternal nucleic acids molecules, said method comprising:
preparing a sequencing library from said mixture of fetal and maternal nucleic acid molecules; wherein preparing said library comprises the consecutive steps of end-repairing, dA-tailing and adaptor ligating said nucleic acids;
sequencing at least a portion of said nucleic acid molecules, thereby obtaining sequence information for a plurality of fetal and maternal nucleic acid molecules of a maternal sample;
using the sequence information to obtain a chromosome dose for an aneuploid chromosome;
comparing said chromosome dose to at least one threshold value, and thereby identifying the presence or absence of fetal aneuploidy; and
using the sequence information to identify a number of mapped sequence tags for at least one normalizing chromosome and for an aneuploid chromosome.
2. The method of claim 1 , further comprising:
using the number of mapped sequence tags identified for said aneuploid chromosome and the number of mapped sequence tags identified for the at least one normalizing chromosome to calculate a chromosome dose for said aneuploid chromosome as a ratio of the number of mapped sequence tags identified for said aneuploid chromosome and the number of mapped sequence tags identified for the at least one normalizing chromosome.
3. The method of claim 2 , wherein calculating a chromosome dose for said aneuploid chromosome comprises:
calculating a sequence tag density ratio for said aneuploid chromosome, by relating the number of mapped sequence tags identified for said aneuploid chromosome in step (a) to the length of said aneuploid chromosome;
(ii) calculating a sequence tag density ratio for said at least one normalizing chromosome, by relating the number of mapped sequence tags identified for said at least one normalizing chromosome to the length of said at least one normalizing chromosome; and
(iii) using the sequence tag density ratios calculated in steps (i) and (ii) to calculate a chromosome dose for said aneuploid chromosome, wherein the chromosome dose is calculated as the ratio of the sequence tag density ratio for said aneuploid chromosome and the sequence tag density ratio for said at least one normalizing chromosome.
4. The method of claim 1 , wherein said at least one normalizing chromosome is a chromosome having the smallest variability and/or the greatest differentiability.
5. The method of claim 1 , wherein said aneuploid chromosome is chromosome 21, and said at least one normalizing chromosome is selected from chromosome 9, chromosome 1, chromosome 2, chromosome 11, chromosome 12, and chromosome 14.
6. The method of claim 1 , wherein said aneuploid chromosome is chromosome 21, and said at least one normalizing chromosome is a group of chromosomes selected from chromosome 9, chromosome 1, chromosome 2, chromosome 11, chromosome 12, and chromosome 14.