Methods for assessing a genomic region of a subject

Abstract

The invention generally relates to method for assessing a genomic region of a subject. In certain embodiments, methods of the invention involve obtaining a sample including nucleic acid from a subject. The nucleic acid includes a target sequence from a target genomic region and a paralogous sequence from a non-target genomic region. The target sequence and the paralogous sequence are isolated from the sample. The target sequence and the paralogous sequence are sequenced to obtain sequence reads that include target sequence reads and paralogous sequence reads. The paralogous sequence reads are excluded, and the genomic region of the subject are assessed based on the target sequence reads.

1 . A method for assessing a genomic region of a subject, the method comprising:
 obtaining a sample comprising nucleic acid from a subject, the nucleic acid comprising a target sequence from a target genomic region and a paralogous sequence from a non-target genomic region;   isolating the target sequence and the paralogous sequence from the sample, wherein isolating comprises conducting an assay that uses molecular inversion probes;   sequencing the target sequence and the paralogous sequence to obtain sequence reads that comprise target sequence reads and paralogous sequence reads;   excluding the paralogous sequence reads; and   assessing the genomic region of the subject based on the target sequence reads.   
     
     
         2 . The method according to  claim 1 , wherein excluding comprises:
 creating a training set of target sequence reads;   identifying one or more common variants present in the training set of target sequence reads, wherein common variants observed in the sequence reads that are not present in the training set of target sequence reads are of paralogous origin;   calculating a frequency of sequence reads containing variants paralogous sequence reads;   defining variant paralogous sequence reads to be excluded based on their frequency; and   excluding paralogous sequence reads based the defining step.   
     
     
         3 . (canceled) 
     
     
         4 . The method according to  claim 3 , wherein the assay comprises:
 hybridizing molecular inversion probes to the target sequence the paralogous sequence;   circularizing the hybridized probes;   isolating the circularized probes; and   linearizing the circularized probes.   
     
     
         5 . The method according to  claim 1 , wherein sequencing is sequencing by synthesis. 
     
     
         6 . The method according to  claim 4 , wherein sequencing by synthesis is single molecule sequencing by synthesis. 
     
     
         7 . The method according to  claim 1 , wherein the sample is a human body fluid sample. 
     
     
         8 . The method according to  claim 7 , wherein the sample is a maternal blood sample. 
     
     
         9 . The method according to  claim 8 , wherein the maternal blood sample comprises cell free circulating nucleic acid. 
     
     
         10 . The method according to  claim 9 , wherein at least a portion of the cell free circulating nucleic acid is from a fetus being carried the subject. 
     
     
         11 . A method for assessing a genomic region of a subject, the method comprising:
 obtaining sequence reads that comprise target sequence reads and paralogous sequence reads by conducting an assay that uses molecular inversion probes;   excluding the paralogous sequence reads; and   assessing a genomic region of a subject based on the target sequence reads.   
     
     
         12 . The method according to  claim 11 , wherein excluding comprises:
 creating a training set of target sequence reads;   identifying one or more common variants present in the training set of target sequence reads, wherein common variants observed in the sequence reads that are not present in the training set of target sequence reads are of paralogous origin;   calculating a frequency of sequence reads containing variants paralogous sequence reads;   defining variant paralogous sequence reads to be excluded based on their frequency; and   excluding paralogous sequence reads based the defining step.   
     
     
         13 . The method according to  claim 11 , wherein the sequence reads are generated by sequencing nucleic acid from a sample from the subject using a sequencing instrument. 
     
     
         14 . The method according to  claim 13 , wherein sequencing by is sequencing by synthesis. 
     
     
         15 . The method according to  claim 14 , wherein sequencing by synthesis is single molecule sequencing by synthesis. 
     
     
         16 . The method according to  claim 13 , wherein the sample is a human body fluid sample. 
     
     
         17 . The method according to  claim 16 , wherein the body fluid sample comprises cell free circulating nucleic acid. 
     
     
         18 . The method according to  claim 16 , wherein the sample is a maternal blood sample. 
     
     
         19 . The method according to  claim 18 , wherein the maternal blood sample comprises cell free circulating nucleic acid. 
     
     
         20 . The method according to  claim 19 , wherein at least a portion of the cell free circulating nucleic acid is from a fetus being carried the subject.