Methods and systems for spatial mapping of genetic variants

Abstract

The present disclosure provides methods and systems for determining the location and identity of variant sequences. The present disclosure also provides methods of treating diseases and of using spatial information of variant sequences in a biological sample to guide treatment selection in a corresponding subject.

1 .- 78 . (canceled) 
     
     
         79 . A method of analyzing a spatial distribution of a human leukocyte antigen (HLA) variant sequence in a biological sample from a subject comprising:
 (a) obtaining a genetic profile of the subject and detecting the HLA variant sequence in the subject by analyzing the genetic profile;   (b) hybridizing a first probe comprising an HLA targeting sequence to a first nucleic acid in the biological sample corresponding to the HLA variant sequence;   (c) identifying at least a portion of the first probe; and   (d) determining a location of the HLA variant sequence within the biological sample by determining a location of the first probe, wherein the first probe preferentially hybridizes to the first nucleic acid corresponding to the HLA variant sequence detected in the genetic profile.   
     
     
         80 . The method of  claim 79 , wherein the genetic profile is generated via ribonucleic acid (RNA) sequencing or exome sequencing. 
     
     
         81 . The method of  claim 79 , wherein the biological sample comprises a second nucleic acid and the method further comprises:
 (A) hybridizing a second probe comprising another nucleic acid targeting sequence to the second nucleic acid;   (B) identifying at least a portion of the second probe; and   (C) determining a location of the second nucleic acid within the biological sample by determining a location of the second probe.   
     
     
         82 . The method of  claim 81 , wherein the second nucleic acid corresponds to an additional HLA variant sequence. 
     
     
         83 . The method of  claim 81 , wherein the second nucleic acid comprises a mutation. 
     
     
         84 . The method of  claim 81 , wherein the second nucleic acid is associated with a tumor antigen or a marker of inflammation. 
     
     
         85 . The method of  claim 81 , wherein the second nucleic acid is associated with a marker for cell typing. 
     
     
         86 . The method of  claim 81 , further comprising generating a visual representation of the location of the HLA variant sequence and the location of the second nucleic acid for display on a graphical user interface (GUI). 
     
     
         87 . The method of  claim 81 , further comprising predicting the presentation of a peptide on a major histocompatibility complex (MHC) protein expressed in the biological sample, wherein the peptide is at least partially encoded by the second nucleic acid and the MHC protein is at least partially encoded by the HLA variant sequence. 
     
     
         88 . The method of  claim 79 , further comprising, prior to identifying the at least a portion of the first probe, subjecting the first probe to an amplification reaction to generate an amplified nucleic acid molecule that corresponds to the HLA variant sequence. 
     
     
         89 . The method of  claim 79 , further comprising contacting the biological sample with a plurality of fluorescently label oligonucleotides directly or indirectly to identify at least a portion of the first probe. 
     
     
         90 . A method of analyzing a biological sample from a subject, comprising:
 (a) obtaining the biological sample comprising a first nucleic acid and a second nucleic acid, wherein the first nucleic acid corresponds to an HLA variant sequence;   (b) hybridizing a first probe comprising an HLA targeting sequence to the first nucleic acid corresponding to the HLA variant sequence and hybridizing a second probe comprising another nucleic acid targeting sequence to the second nucleic acid;   (c) identifying at least a portion of the first probe and at least a portion of the second probe; and   (d) determining a location of the HLA variant sequence and a location of the second nucleic acid within the biological sample.   
     
     
         91 . The method of  claim 90 , wherein the second nucleic acid corresponds to an additional HLA variant sequence. 
     
     
         92 . The method of  claim 90 , wherein the second nucleic acid comprises a mutation. 
     
     
         93 . The method of  claim 90 , wherein the second nucleic acid is associated with a tumor antigen or a marker of inflammation. 
     
     
         94 . The method of  claim 90 , wherein the second nucleic acid is associated with a marker for cell typing. 
     
     
         95 . The method of  claim 90 , further comprising generating a visual representation of the location of the HLA variant sequence and the location of the second nucleic acid for display on a graphical user interface (GUI). 
     
     
         96 . The method of  claim 90 , further comprising predicting the presentation of a peptide on a major histocompatibility complex (MHC) protein expressed in the biological sample, wherein the peptide is at least partially encoded by the second nucleic acid and the MHC protein is at least partially encoded by the HLA variant sequence. 
     
     
         97 . The method of  claim 90 , further comprising, prior to identifying the at least a portion of the first probe, subjecting the first probe to an amplification reaction to generate an amplified nucleic acid molecule that corresponds to the HLA variant sequence. 
     
     
         98 . The method of  claim 90 , further comprising contacting the biological sample with a plurality of fluorescently label oligonucleotides directly or indirectly to identify at least a portion of the first probe.