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 with reduced bias genomic section levels for a test sample, comprising:
 (a) obtaining counts of sequence reads mapped to portions of a reference genome, which sequence reads are reads of circulating cell-free nucleic acid from a test sample;   (b) determining a guanine and cytosine (GC) bias coefficient for the test sample based on a fitted relation between (i) the counts of the sequence reads mapped to respective portions of the reference genome and (ii) GC content for the respective portions; and   (c) determining a genomic section level for respective portions of the reference genome based on the counts of (a), the GC bias coefficient of (b), and a fitted relation, for the respective portions of the reference genome, between (i) the GC bias coefficient for each of multiple samples and (ii) counts of sequence reads mapped to the respective portions of the reference genome for the multiple samples, thereby providing calculated genomic section levels, whereby bias in the counts of the sequence reads mapped to the respective portions of the reference genome is reduced in the calculated genomic section levels.   
     
     
         2 . The method of  claim 1 , wherein the GC bias coefficient in (b) is a slope for a linear fitted relation. 
     
     
         3 . The method of  claim 2 , wherein the fitted relation in (b) is fitted by a linear regression. 
     
     
         4 . The method of  claim 1 , wherein the fitted relation of (c) is linear. 
     
     
         5 . The method of  claim 4 , wherein the fitted relation of (c) is fitted by a linear regression. 
     
     
         6 . The method of  claim 5 , wherein the GC bias coefficient for each of the multiple samples in (c)(i) is the slope of a fitted linear relation, for each of the multiple samples, between (i′) the counts of the sequence reads mapped to the respective portions of the reference genome and (ii′) GC content for the respective portions. 
     
     
         7 . The method of  claim 6 , wherein a calculated genomic section level L is determined for the test sample for the respective portions of the reference genome according to Equation B:
     L =( M−GS )/ I   Equation B
   
       wherein M is the counts of the sequence reads mapped to the portion for the test sample obtained in (a), G is the GC bias coefficient for the test sample determined in (b), I is an intercept of the fitted linear relation of (c) for the portion, S is a slope of the fitted linear relation of (c) for the portion. 
     
     
         8 . The method of  claim 1 , further comprising filtering one or more portions and removing counts associated with the one or more filtered portions. 
     
     
         9 . The method of  claim 8 , wherein the one or more filtered portions are selected according to one or more criteria chosen from measure of error or mappability, or measure of error and mappability. 
     
     
         10 . The method of  claim 9 , wherein the one or more filtered portions are selected according to one or more criteria chosen from portions having no guanine and cytosine (GC) content, portions consistently receiving no counts, and repeat masking. 
     
     
         11 . The method of  claim 9 , wherein the measure of error is an R factor. 
     
     
         12 . The method of  claim 11 , wherein portions of the reference genome having an R factor of about 7% or greater are selected as filtered portions. 
     
     
         13 . The method of  claim 11 , wherein portions of the reference genome having an R factor of about 7% to about 10% are selected as filtered portions. 
     
     
         14 . The method of  claim 8 , wherein the filtering is performed prior to (b). 
     
     
         15 . The method of  claim 8 , wherein the filtering is performed after (c). 
     
     
         16 . The method of  claim 1 , wherein the sequence reads in (a) comprise thousands to millions of sequence reads. 
     
     
         17 . The method of  claim 1 , further comprising sequencing the circulating cell-free nucleic acid from the test sample by a massively parallel sequencing process. 
     
     
         18 . The method of  claim 17 , wherein the massively parallel sequencing process is performed with 1-fold coverage or fraction thereof. 
     
     
         19 . The method of  claim 17 , wherein millions of nucleic acid fragments are sequenced by the massively parallel sequencing process. 
     
     
         20 . The method of  claim 17 , wherein the massively parallel sequencing process generates thousands to millions of sequence reads.