Noninvasive Diagnosis of Fetal Aneuploidy by Sequencing

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.

1 . A method of testing for an abnormal distribution of a specified chromosome portion in a mixed sample of normally and abnormally distributed chromosome portions obtained from a subject, comprising:
 (a) obtaining sequences from multiple chromosome portions of the mixed sample to obtain a number of sequence tags of sufficient length of determined sequence to be assigned to a chromosome location within a genome;   (b) assigning the sequence tags to corresponding chromosome portions including at least the specified chromosome by comparing the sequence to a reference genomic sequence;   (c) determining values for numbers of sequence tags mapping to chromosome portions by using a number of windows of defined length within normally and abnormally distributed chromosome portions to obtain a first value and a second value therefrom; and   (d) using the values from step (c) to determine a differential, between the first value and the second value, which is determinative of whether or not the abnormal distribution exists.   
     
     
         2 . The method of  claim 1  wherein to determine a differential includes the step of comparing a normalized sequence tag density of the specified DNA chromosome portion to a normalized sequence tag density of another DNA chromosome portion in said mixed sample, wherein all autosomes are used to calculate the normalized sequence tag density. 
     
     
         3 . The method of  claim 1  wherein the mixed sample is a mixture of maternal and fetal DNA. 
     
     
         4 . The method of  claim 1  wherein the mixed sample is a mixture of normal and genetically altered DNA from a tumor. 
     
     
         5 . The method of  claim 1  wherein the sequencing is massively parallel sequencing. 
     
     
         6 . The method of  claim 1  wherein the abnormal distribution is an aneuploidy of at least one of chromosome 13, 18 and 21. 
     
     
         7 . The method of  claim 1  wherein the step of assigning sequence tags to corresponding chromosome portions allows one mismatch. 
     
     
         8 . The method of  claim 1  wherein the sequence tags are about 25-100 by in length. 
     
     
         9 . The method of  claim 8  wherein at least about 1 million sequence tags are obtained. 
     
     
         10 . The method of  claim 8  further comprising the steps of calculating a normalized sequence tag density of the specified DNA chromosome portion to a normalized sequence tag density of another DNA chromosome portion in said mixed sample. 
     
     
         11 . The method of  claim 10  wherein the step of calculating a differential includes the step of comparing a normalized sequence tag density of the specified DNA chromosome portion to a normalized sequence tag density of another DNA chromosome portion in said mixed sample, wherein all autosomes are used to calculate the normalized sequence tag density. 
     
     
         12 . The method of  claim 11  further comprising the step of measuring over- and under-representation of a chromosome by determining a sequence tag density for each chromosome in the sample, namely chromosomes 1-22, X and also chromosome Y if present. 
     
     
         13 . A method for measuring a fetal DNA fraction in a sample of mixed maternal and fetal DNA, wherein a chromosome having trisomy is measured by being (1+ε/2) of that of a corresponding disomy, where ε represents the fetal DNA fraction. 
     
     
         14 . A noninvasive method for enumerating an abnormally distributed specified chromosome or portion thereof in a mixed sample of DNA from the plasma of a pregnant subject, comprising:
 (a) sequencing multiple portions of the mixed sample of DNA to obtain at least one million sequence tags of sufficient length of determined sequence to be assigned to a chromosome location within a genome;   (b) determining a number representing a number of sequence tags within a number of discrete windows each of which is a subsequence of a chromosome and is between about 10 Kb and 100 Kb in length; and   (c) calculating a differential between a number on a normal chromosome and a number on the abnormally distributed chromosome which is determinative of whether or not the abnormally distributed chromosome is present or not.   
     
     
         15 . The method of  claim 14  wherein the chromosome is any one of X, Y, 18, 21, 17 or 13. 
     
     
         16 . The method of  claim 14  wherein said calculating a differential comprises obtaining a sequence density of the abnormally distributed chromosome and comparing it to a value of a disomic chromosome. 
     
     
         17 . The method of  claim 14  wherein said number of discrete windows are comprised of sliding non overlapping windows of 10-100 kb extending along substantially an entire chromosome. 
     
     
         18 . The method of  claim 14  further comprising the step of measuring a number of sequence tags within transcriptional start sites. 
     
     
         19 . A method of determining an abnormally distributed chromosome portion of interest in a mixed sample of normally and abnormally distributed DNA molecules, comprising:
 (a) sequencing DNA in said sample by massively parallel sequencing to obtain a number of sequence tags   (b) mapping said sequence tags to specific chromosome portions, each chromosomal portion being comprised in a sliding window of a predetermined length;   (c) determining numbers of sequence tags mapped to each sliding window on at least each autosome;   (d) determining a mean of said numbers for each autosome and a second mean for at least all autosomes;   (e) calculating a normalized value from all autosomes, using said second mean; and   (f) comparing normalized values among autosomes to determine any abnormally distributed autosomal chromosome portion of interest.   
     
     
         20 . The method of  claim 19  further comprising the step of calculating a relationship between numbers of sequence tags and GC content associated with sequence tags in a given sliding window and correcting for a higher number of reads resulting from a change in GC content. 
     
     
         21 . The method of  claim 19  further comprising the step of calculating at statistic for each chromosome relative to other chromosomes in the mixed sample, whereby each t statistic indicates a value of a chromosome relative to other chromosomes in a sample, said value being indicative of disomy. 
     
     
         22 . The method of  claim 19  further comprising the step of calculating a normalized value for chromosome X and, if present, Y. 
     
     
         23 . The method of  claim 19  wherein said mapping includes mapping sequences with one mismatch. 
     
     
         24 . A method for correcting for GC bias of sequence reads from massively parallel sequencing of a genome, comprising the steps of:
 (a) dividing the genome into a number of windows within each chromosome and calculating the GC content of each window;   (b) calculating the relationship between sequence coverage and GC content of each window by determining a number of reads per a given window and a GC content of that window; and   (c) assigning a weight to said number of reads per a given window based on GC content, where the weight has a relationship to GC content such that increasing numbers of reads with increasing GC content results in decreasing weight per increasing GC content.