Methods and processes for non-invasive assessment of genetic variations

Abstract

Provided herein are methods, processes and apparatuses for non-invasive assessment of genetic variations.

What is claimed is: 
     
         1 . A method for determining the presence or absence of a chromosome aneuploidy, comprising:
 (a) obtaining counts of sequence reads mapped to chromosomes 13, 18 and 21, or segments thereof, which sequence reads are reads of circulating cell-free nucleic acid from a pregnant female subject bearing a fetus;   (b) determining three ratios or ratio values, each of which three ratios is a ratio of (i) counts mapped to each of chromosomes 13, 18 and 21, or segments thereof, to (ii) counts mapped to each of the other chromosomes 13, 18 and 21, or segments thereof;   (c) comparing the three ratios or ratio values, thereby generating a comparison; and   (d) determining the presence or absence of a chromosome aneuploidy based on the comparison generated in (c), with the proviso that the comparison generated in (c) and the determination in (d) are not based on segments of the genome other than in chromosomes 13, 18 and 21; whereby the determination of the presence or absence of the chromosome aneuploidy is generated from the sequence reads.   
     
     
         2 . The method of  claim 1 , wherein the presence or absence of the chromosome aneuploidy is determined for the fetus. 
     
     
         3 . The method of  claim 1 , wherein the circulating cell-free nucleic acid is from a sample from the pregnant female subject, and the presence or absence of the chromosome aneuploidy is determined for the sample. 
     
     
         4 . The method of  claim 1 , wherein obtaining counts of sequence reads mapped to chromosomes 13, 18 and 21, or segments thereof, comprises filtering. 
     
     
         5 . The method of  claim 1 , wherein obtaining counts of sequence reads mapped to chromosomes 13, 18 and 21, or segments thereof, does not comprise filtering. 
     
     
         6 . The method of  claim 1 , wherein the chromosome aneuploidy is a deletion or addition of a chromosome. 
     
     
         7 . The method of  claim 6 , wherein the chromosome aneuploidy is a trisomy. 
     
     
         8 . The method of  claim 7 , wherein the trisomy is trisomy 21, trisomy 18, or trisomy 13. 
     
     
         9 . The method of  claim 1 , comprising obtaining counts of sequence reads mapped to chromosomes 13, 18 and 21, or segments thereof, for a subset of the genome, which subset comprises chromosomes 13, 18 and 21, or segments thereof. 
     
     
         10 . The method of  claim 1 , comprising obtaining counts of sequence reads mapped to an entire genome or to a genome excluding sex chromosomes. 
     
     
         11 . The method of  claim 1 , wherein the comparison is a Cartesian coordinate in three-dimensional space. 
     
     
         12 . The method of  claim 11 , wherein generating the comparison in (c) comprises plotting the three ratios or ratios or ratio values determined in (b) in three dimensions, which dimensions are the ratios or ratio values, thereby generating a point for the subject on a three dimensional plot. 
     
     
         13 . The method of  claim 1 , wherein determining in (d) comprises comparing the comparison determined in (c) to a comparison for one or more euploid samples. 
     
     
         14 . The method of  claim 13 , wherein the determination in (d) comprises determining the distance between the comparison for the subject to a comparison expected for a euploid fetus. 
     
     
         15 . The method of  claim 1 , wherein the determination in (d) is provided with a specificity equal to or greater than 90% and a sensitivity equal to or greater than 90%. 
     
     
         16 . The method of  claim 1 , wherein the three ratios consist of
 (i) a ratio between counts mapped to chromosome 13, or segments thereof, to counts mapped to chromosome 21, or segments thereof,   (ii) a ratio between counts mapped to chromosome 13, or segments thereof, to counts mapped to chromosome 18, or segments thereof, and   (iii) a ratio between counts mapped to chromosome 18, or segments thereof, to counts mapped to chromosome 21, or segments thereof.   
     
     
         17 . The method of  claim 1 , which comprises obtaining nucleic acid sequence reads. 
     
     
         18 . The method of  claim 17 , wherein obtaining nucleic acid sequencing reads comprises use of massively parallel shotgun sequencing (MPSS). 
     
     
         19 . The method of  claim 17 , wherein obtaining nucleic acid sequencing reads does not comprise use of a chromosome-selective sequencing technique. 
     
     
         20 . The method of  claim 17 , wherein obtaining nucleic acid sequencing reads comprises use of a chromosome-selective sequencing technique. 
     
     
         21 . The method of  claim 17 , which comprises mapping the nucleic acid sequence reads to chromosomes 13, 18, and 21 or segments thereof. 
     
     
         22 . The method of  claim 21 , which comprises mapping the nucleic acid sequence reads to chromosomes other than chromosomes 13, 18, and 21, or segments thereof. 
     
     
         23 . The method of  claim 21 , which comprises not mapping the nucleic acid sequence reads to chromosomes other than chromosomes 13, 18, and 21. 
     
     
         24 . The method of  claim 1 , wherein the counts of sequence reads mapped to chromosomes 13, 18, and 21 or segments thereof are normalized. 
     
     
         25 . The method of  claim 24 , wherein the counts of sequence reads mapped to chromosomes 13, 18, and 21 or segments thereof are normalized by GC content, bin-wise normalization, GC LOESS, PERUN, GCRM, or combinations thereof. 
     
     
         26 . The method of  claim 1 , wherein obtaining counts of sequence reads mapped to chromosomes 13, 18 and 21 comprises:
 (a) obtaining counts of sequence reads mapped to genomic sections of a reference genome;   (b) determining a guanine and cytosine (GC) bias for each of the genomic sections of the reference genome for multiple samples from a fitted relation for each sample between (i) the counts of the sequence reads mapped to each of the genomic sections of the reference genome, and (ii) GC content for each of the genomic sections; and   (c) calculating a genomic section level for each of the genomic sections of the reference genome from a fitted relation between (i) the GC bias and (ii) the counts of the sequence reads mapped to each of the genomic sections of the reference genome, thereby providing calculated genomic section levels, whereby bias in the counts of the sequence reads mapped to each of the genomic sections of the reference genome is reduced in the calculated genomic section levels.   
     
     
         27 . A system comprising one or more processors and memory,
 which memory comprises instructions executable by the one or more processors and which memory comprises counts of nucleic acid sequence reads mapped to genomic sections of three selected autosomes, or segments thereof, which sequence reads are reads of circulating cell-free nucleic acid from a pregnant female; and   which instructions executable by the one or more processors are configured to:   (a) determine three ratios or ratio values, each of which ratios is a ratio of (i) counts mapped to each of chromosomes 13, 18 and 21, or segments thereof, to (ii) counts mapped to each of the other chromosomes 13, 18 and 21, or segments thereof;   (b) compare the ratios or ratio values, thereby generating a comparison; and   (c) determine the presence or absence of a chromosome aneuploidy based on the comparison generated in (b), with the proviso that the comparison generated in (b) and the determination in (c) are not based on segments of the genome other than in chromosomes 13, 18 and 21; whereby the determination of the presence or absence of the chromosome aneuploidy is generated from the sequence reads.   
     
     
         28 . An apparatus comprising one or more processors and memory,
 which memory comprises instructions executable by the one or more processors and which memory comprises counts of nucleic acid sequence reads mapped to genomic sections of three selected autosomes, or segments thereof, which sequence reads are reads of circulating cell-free nucleic acid from a pregnant female; and   which instructions executable by the one or more processors are configured to:   (a) determine three ratios or ratio values, each of which ratios is a ratio of (i) counts mapped to each of chromosomes 13, 18 and 21, or segments thereof, to (ii) counts mapped to each of the other chromosomes 13, 18 and 21, or segments thereof;   (b) compare the ratios or ratio values, thereby generating a comparison; and   (c) determine the presence or absence of a chromosome aneuploidy based on the comparison generated in (b), with the proviso that the comparison generated in (b) and the determination in (c) are not based on segments of the genome other than in chromosomes 13, 18 and 21; whereby the determination of the presence or absence of the chromosome aneuploidy is generated from the sequence reads.   
     
     
         29 . A computer program product tangibly embodied on a computer-readable medium, comprising instructions that when executed by one or more processors are configured to:
 (a) access counts of nucleic acid sequence reads mapped to genomic sections of chromosomes 13, 18 and 21, or segments thereof, which sequence reads are reads of circulating cell-free nucleic acid from a pregnant female;   (b) determine three ratios or ratio values, each of which ratios is a ratio of (i) counts mapped to each of chromosomes 13, 18 and 21, or segments thereof, to (ii) counts mapped to each of the other chromosomes 13, 18 and 21, or segments thereof;   (c) compare the three ratios or ratio values or ratio values, thereby generating a comparison; and   (d) determine the presence or absence of a chromosome aneuploidy based on the comparison generated in (c), with the proviso that the comparison generated in (c) and the determination in (d) are not based on segments of the genome other than in chromosomes 13, 18 and 21; whereby the determination of the presence or absence of the chromosome aneuploidy is generated from the sequence reads.