Systems and methods for sample preparation, sample sequencing, and sequencing data bias correction and quality control

Abstract

Described herein are various methods of collecting and processing of tumor and/or healthy tissue samples to extract nucleic acid and perform nucleic acid sequencing. Also described herein are various methods of processing nucleic acid sequencing data to remove bias from the nucleic acid sequencing data. Also described herein are various methods of evaluating the quality of nucleic acid sequence information. The identity and/or integrity of nucleic acid sequence data is evaluated prior to using the sequence information for subsequent analysis (for example for diagnostic, prognostic, or clinical purposes). The methods enable a subject, doctor, or user to characterize or classify various types of cancer precisely, and thereby determine a therapy or combination of therapies that may be effective to treat a cancer in a subject based on the precise characterization.

1 . A method, comprising:
 using at least one computer hardware processor to perform:
 obtaining nucleic acid data comprising:
 sequence data indicating a nucleotide sequence for at least 5 kilobases (kb) of DNA and/or RNA from a previously obtained biological sample of a subject having, suspected of having, or at risk of having a disease; and 
 asserted information indicating an asserted source and/or an asserted integrity of the sequence data; and 
 
 validating the nucleic acid data by:
 processing the sequence data to obtain determined information indicating a determined source and/or a determined integrity of the sequence data; and 
 determining whether the determined information matches the asserted information. 
 
   
     
     
         2 . The method of  claim 1 , further comprising:
 processing the sequence data to determine whether the sequence data is indicative of one or more disease features when it is determined that the asserted information matches the determined information.   
     
     
         3 . The method of  claim 1  or any other preceding claim, further comprising:
 determining that the determined information matches the asserted information; and 
 processing the sequence data to determine whether it is indicative of one or more disease features. 
 
     
     
         4 . The method of  claim 1  or any other preceding claim, further comprising:
 generating an indication:
 that the determined information does not match the asserted information, 
 to not process the sequence data in a subsequent analysis, and/or 
 to obtain additional sequence data and/or other information about the biological sample and/or the subject, 
 
 when it is determined that the asserted information does not match the determined information. 
 
     
     
         5 . The method of  claim 1  or any other preceding claim, further comprising:
 determining that the asserted information does not match the determined information; and 
 generating an indication:
 that the determined information does not match the asserted information, 
 to not process the sequence data in a subsequent analysis, and/or 
 to obtain additional sequence data and/or other information about the biological sample and/or the subject. 
 
 
     
     
         6 . The method of  claim 1  or any other preceding claim, wherein the asserted information indicates the asserted source of the sequence data, the method further comprising:
 processing the sequence data to obtain determined information indicative of a determined source for the sequence data; and 
 determining whether the determined source matches the asserted source for the sequence data. 
 
     
     
         7 . The method of  claim 6  or any other preceding claim, wherein the determined information indicative of the determined source for the sequence data is indicative of an MHC genotype of the subject; whether the nucleic acid data is RNA data or DNA data; a tissue type of the biological sample; a tumor type of the biological sample; a sequencing platform used to generate the sequence data; SNP concordance, and/or a whether an RNA sample is polyA enriched. 
     
     
         8 . The method of  claim 7  or any other preceding claim, wherein the determined information indicative of the determined source for the sequence data is indicative of at least two of an MHC genotype of the subject; whether the nucleic acid data is RNA data or DNA data; a tissue type of the biological sample; a tumor type of the biological sample; a sequencing platform used to generate the sequence data; SNP concordance, and a whether an RNA sample is polyA enriched. 
     
     
         9 . The method of  claim 8  or any other preceding claim, wherein the determined information indicative of the determined source for the sequence data is indicative of at least three of an MHC genotype of the subject; whether the nucleic acid data is RNA data or DNA data; a tissue type of the biological sample; a tumor type of the biological sample; a sequencing platform used to generate the sequence data; SNP concordance, and a whether an RNA sample is polyA enriched. 
     
     
         10 . The method of  claim 1  or any other preceding claim, wherein the asserted information
 indicates the asserted integrity of the sequence data, the method further comprising:
 processing the sequence data to obtain determined information indicative of a determined integrity of the sequence data; and 
 determining whether the determined integrity matches the asserted integrity for the sequence data. 
 
 
     
     
         11 . The method of  claim 10  or any other preceding claim, wherein the determined information indicative of the determined integrity is indicative of total sequence coverage; exon coverage; chromosomal coverage; a ratio of nucleic acids encoding two or more subunits of a multimeric protein; species contamination; single nucleotide polymorphisms (SNPs); complexity; and/or guanine (G) and cytosine (C) percentage (%) of the sequence data. 
     
     
         12 . The method of  claim 11  or any other preceding claim, wherein the determined information indicative of the determined integrity is indicative of at least two of total sequence coverage; exon coverage; chromosomal coverage; a ratio of nucleic acids encoding two or more subunits of a multimeric protein; species contamination; single nucleotide polymorphisms (SNPs); complexity; and guanine (G) and cytosine (C) percentage (%) of the sequence data. 
     
     
         13 . The method of  claim 12  or any other preceding claim, wherein the determined information indicative of the determined integrity is indicative of at least three of total sequence coverage; exon coverage; chromosomal coverage; a ratio of nucleic acids encoding two or more subunits of a multimeric protein; species contamination; single nucleotide polymorphisms (SNPs); complexity; and guanine (G) and cytosine (C) percentage (%) of the sequence data. 
     
     
         14 . The method of  claim 1  or any other preceding claim, wherein the asserted information for the sequence data comprises MHC allele information for the subject. 
     
     
         15 . The method of  claim 14  or any other preceding claim, further comprising:
 determining one or more MHC allele sequences from the sequence data and determining whether the one or more MHC alleles sequences match the asserted MHC allele information for the subject. 
 
     
     
         16 . The method of  claim 15  or any other preceding claim, wherein determining the one or more MHC allele sequences comprises determining MHC allele sequences for six MHC loci from the sequence data. 
     
     
         17 . The method of  claim 1  or any other preceding claim, wherein the sequence data indicates the nucleotide sequence for RNA, the asserted information indicates whether the RNA is polyA enriched. 
     
     
         18 . The method of  claim 1  or any other preceding claim, further comprising:
 determining, using the sequence data, a therapy for the subject when it is determined that the asserted information matches the determined information. 
 
     
     
         19 . The method of  claim 18  or any other preceding claim, wherein determining the therapy comprises:
 determining a plurality of gene group expression levels, the plurality of gene group expression levels comprising a gene group expression level for each gene group in a set of gene groups, wherein the set of gene groups comprises at least one gene group associated with cancer malignancy, and at least one gene group associated with cancer microenvironment; 
 identifying the therapy using the determined gene group expression levels. 
 
     
     
         20 . The method of  claim 19  or any other preceding claim, further comprising administering the therapy to the subject. 
     
     
         21 - 28 . (canceled) 
     
     
         29 . A system comprising:
 at least one computer hardware processor;   at least one non-transitory computer-readable storage medium storing processor executable instructions that, when executed by the at least one computer hardware processor, cause the at least one computer hardware processor to perform a method, comprising:   obtaining nucleic acid data comprising:
 sequence data indicating a nucleotide sequence for at least 5 kilobases (kb) of DNA and/or RNA from a previously obtained biological sample of a subject having, suspected of having, or at risk of having a disease; and 
 asserted information indicating an asserted source and/or an asserted integrity of the sequence data; and 
   validating the nucleic acid data by:
 processing the sequence data to obtain determined information indicating a determined source and/or a determined integrity of the sequence data; and 
 determining whether the determined information matches the asserted information. 
   
     
     
         30 . At least one non-transitory computer-readable storage medium storing processor executable instructions that, when executed by at least one computer hardware processor, cause the at least one computer hardware processor to perform a method, comprising:
 obtaining nucleic acid data comprising:
 sequence data indicating a nucleotide sequence for at least 5 kilobases (kb) of DNA and/or RNA from a previously obtained biological sample of a subject having, suspected of having, or at risk of having a disease; and 
 asserted information indicating an asserted source and/or an asserted integrity of the sequence data; and 
   validating the nucleic acid data by:
 processing the sequence data to obtain determined information indicating a determined source and/or a determined integrity of the sequence data; and 
 determining whether the determined information matches the asserted information. 
   
     
     
         31 - 56 . (canceled)