Noninvasive diagnosis of fetal aneuploidy by sequencing
First Claim
1. A method for performing prenatal diagnosis of a fetal chromosomal aneuploidy in a maternal sample obtained from a pregnant woman, wherein the maternal sample includes nucleic acid molecules, the method comprising:
- receiving the maternal sample;
sequencing at least a portion of a plurality of the nucleic acid molecules contained in the maternal sample, wherein the sequenced portions comprise a number of sequence tags of sufficient length of determined sequence to be assigned to a chromosome location within a genome;
based on the sequencing;
determining a length for each of the portion of nucleic acid molecules;
determining a first amount of a first chromosome by counting numbers of sequence tags mapping to portions of a first chromosome by using a number of windows of defined length; and
determining a second amount of one or more second chromosomes by counting numbers of sequence tags mapping to portions of one or more second chromosomes by using a number of windows of defined length,wherein said counting of sequence tags is within normally or abnormally distributed chromosome portions, and is based on the lengths of the corresponding nucleic acid molecules;
calculating a relationship between numbers of sequence tags and GC content associated with sequence tags in a given window and correcting for a higher or lower number of reads resulting from a change in GC content in said window;
determining a differential from the first amount and the second amount;
determining whether the differential is statistically significant; and
correlating a statistically significant result with the presence of a fetal chromosomal aneuploidy on the first chromosome.
2 Assignments
0 Petitions
Accused Products
Abstract
Disclosed is a method to achieve digital quantification of DNA (i.e., counting differences between identical sequences) using direct shotgun sequencing followed by mapping to the chromosome of origin and enumeration of fragments per chromosome. The preferred method uses massively parallel sequencing, which can produce tens of millions of short sequence tags in a single run and enabling a sampling that can be statistically evaluated. By counting the number of sequence tags mapped to a predefined window in each chromosome, the over- or under-representation of any chromosome in maternal plasma DNA contributed by an aneuploid fetus can be detected. This method does not require the differentiation of fetal versus maternal DNA. The median count of autosomal values is used as a normalization constant to account for differences in total number of sequence tags is used for comparison between samples and between chromosomes.
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Citations
23 Claims
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1. A method for performing prenatal diagnosis of a fetal chromosomal aneuploidy in a maternal sample obtained from a pregnant woman, wherein the maternal sample includes nucleic acid molecules, the method comprising:
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receiving the maternal sample; sequencing at least a portion of a plurality of the nucleic acid molecules contained in the maternal sample, wherein the sequenced portions comprise a number of sequence tags of sufficient length of determined sequence to be assigned to a chromosome location within a genome; based on the sequencing; determining a length for each of the portion of nucleic acid molecules; determining a first amount of a first chromosome by counting numbers of sequence tags mapping to portions of a first chromosome by using a number of windows of defined length; and determining a second amount of one or more second chromosomes by counting numbers of sequence tags mapping to portions of one or more second chromosomes by using a number of windows of defined length, wherein said counting of sequence tags is within normally or abnormally distributed chromosome portions, and is based on the lengths of the corresponding nucleic acid molecules; calculating a relationship between numbers of sequence tags and GC content associated with sequence tags in a given window and correcting for a higher or lower number of reads resulting from a change in GC content in said window; determining a differential from the first amount and the second amount; determining whether the differential is statistically significant; and correlating a statistically significant result with the presence of a fetal chromosomal aneuploidy on the first chromosome. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17)
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18. A computer program including instructions for performing prenatal diagnosis of a fetal chromosomal aneuploidy in a maternal sample obtained from a pregnant woman, wherein the maternal sample includes nucleic acid molecules, the operation comprising:
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receiving the maternal sample; sequencing at least a portion of a plurality of the nucleic acid molecules contained in the maternal sample, wherein the sequenced portions comprise a number of sequence tags of sufficient length of determined sequence to be assigned to a chromosome location within a genome; based on the sequencing; determining a length for each of the portion of nucleic acid molecules; determining a first amount of a first chromosome by counting numbers of sequence tags mapping to portions of a first chromosome by using a number of windows of defined length; and determining a second amount of one or more second chromosomes by counting numbers of sequence tags mapping to portions of one or more second chromosomes by using a number of windows of defined length, wherein said counting of sequence tags is within normally or abnormally distributed chromosome portions, and is based on the lengths of the corresponding nucleic acid molecules; calculating a relationship between numbers of sequence tags and GC content associated with sequence tags in a given window and correcting for a higher or lower number of reads resulting from a change in GC content in said window; determining a differential from the first amount and the second amount; determining whether the differential is statistically significant; and correlating a statistically significant result with the presence of a fetal chromosomal aneuploidy on the first chromosome.
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19. A method for performing prenatal diagnosis of a fetal chromosomal aneuploidy in a maternal sample obtained from a pregnant woman, wherein the maternal sample includes nucleic acid molecules, the method comprising:
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receiving the maternal sample; sequencing at least a portion of a plurality of the nucleic acid molecules contained in the maternal sample, wherein the nucleic acid molecules of the maternal sample comprise a number of sequence tags of sufficient length of determined sequence to be assigned to a chromosome location within a genome and have been selected for sequences less than a first predetermined number of nucleotides, wherein the first predetermined number is less than 330 nucleotides; based on the sequencing; determining a first amount of a first chromosome by counting numbers of sequence tags mapping to portions of a first chromosome by using a number of windows of defined length; and determining a second amount of one or more second chromosomes by counting numbers of sequence tags mapping to portions of one or more second chromosomes by using a number of windows of defined length, wherein said counting of sequence tags is within normally or abnormally distributed chromosome portions; calculating a relationship between numbers of sequence tags and GC content associated with sequence tags in a given window and correcting for a higher or lower number of reads resulting from a change in GC content in said window; determining a differential from the first amount and the second amount; determining whether the differential is statistically significant; and correlating a statistically significant result with the presence of a fetal chromosomal aneuploidy on the first chromosome. - View Dependent Claims (20, 21, 22, 23)
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Specification