Method of characterizing sequences from genetic material samples

Abstract

Among other aspects provided herein is a method describing the use of Single Nucleotide Polymorphism (SNP) genotyping microarrays to resolve whether genetic material (such as genomic DNA) derived from a particular individual is present in a genetic material mixture (such as a complex genomic DNA mixture) is disclosed. Furthermore, it is demonstrated that the identification of the presence of genetic material (such as genomic DNA) of specific individuals within a series of complex genomic mixtures is possible.

1 . A method for determining a likelihood that a subject contributed genetic material to a test genetic material sample, said method comprising:
 providing a test genetic material sample;   performing a single nucleotide polymorphism analysis on the test genetic material sample, whereby at least 50 different single nucleotide polymorphisms in said test genetic material sample are analyzed, thereby creating a sample SNP signature; and   comparing the sample SNP signature to a subject's SNP signature to determine a likelihood that the subject contributed genetic material to a test genetic material sample.   
     
     
         2 . The method of  claim 1 , wherein comparing the sample SNP signature to determine the likelihood that it matches a subject's SNP signature further comprises providing and employing a reference SNP signature. 
     
     
         3 . The method of  claim 2 , wherein the reference SNP signature has a similar ancestral make-up as that of the sample SNP signature. 
     
     
         4 . The method of  claim 1 , wherein the test genetic material sample is likely to be contaminated. 
     
     
         5 . The method of  claim 4 , wherein the contamination comprises bacterial genetic material. 
     
     
         6 . The method of  claim 4 , wherein the contamination comprises nonhuman genetic material. 
     
     
         7 . A method of characterizing a test genetic material sample, said method comprising:
 providing a first allele frequency for a SNP for a person of interest (POI);   providing a second allele frequency for the SNP from a reference population of genetic material;   providing a third allele frequency for the SNP for the test genetic material sample;   repeating the above processes for at least 10 different SNPs; and   analyzing the first, second, and third allele frequencies to characterize the test genetic material sample.   
     
     
         8 . The method of  claim 7 , wherein the processes are repeated for at least 50 different SNPs. 
     
     
         9 . The method of  claim 8 , wherein analyzing the first, second, and third allele frequencies is achieved by the following processes:
 a) determining the absolute value of the difference in the allele frequencies of the person of interest and the reference population;   b) determining the absolute value of the difference in the allele frequencies of the person of interest and the test genetic material sample; and   c) subtracting b) from a) to obtain a distance value for the SNP.   
     
     
         10 . The method of  claim 9 , wherein when the distance value for the SNP is positive, it is more likely that the POI contributed genetic material to the test genetic material sample, when the distance value is negative, the POI'S genetic material is more likely to be part of the reference sample, and when the distance value is 0, the POI'S genetic material is equally likely to be in the test genetic material sample and the reference sample. 
     
     
         11 . The method of  claim 10 , wherein the above processes are repeated for at least 50,000 SNPs 
     
     
         12 . The method of  claim 10 , wherein the frequencies are expressed as a numerical value. 
     
     
         13 . The method of  claim 10 , wherein the frequencies are expressed as fluorescence levels. 
     
     
         14 . The method of  claim 10 , wherein the frequencies are expressed as normalized values for the POI, reference population, and test genetic material sample. 
     
     
         15 . The method of  claim 8 , wherein the characterization allows one to determine if there is at least a 99% likelihood that the person of interest contributed to the sample. 
     
     
         16 . The method of  claim 8 , wherein the characterization determines that the test genetic material sample contains genetic material from a person other than the person of interest. 
     
     
         17 . The method of  claim 8 , wherein the characterization determines a likelihood that the test genetic material sample contains genetic material from the person of interest. 
     
     
         18 . The method of  claim 8 , wherein the test genetic material sample comprises degraded genetic material. 
     
     
         19 . The method of  claim 8 , wherein the test genetic material sample is collected from a crime scene and the characterization is performed to identify if the test genetic material sample includes DNA from the person of interest. 
     
     
         20 . The method of  claim 8 , further comprising the process of collecting a test genetic material sample, running the sample on a SNP detecting array, and monitoring what SNPs are present in the sample, thereby providing the third allele frequency for the SNP for the test genetic material sample. 
     
     
         21 . The method of  claim 8 , wherein providing a third allele frequency for the SNP for the test genetic material sample comprises having the frequency for the SNP for the test genetic material sample. 
     
     
         22 . The method of  claim 8 , wherein the characterization comprises the following analysis:
     T ( Y   i )=(mean( D ( Y   i,j ))−μ 0 )/(sd( D ( Y   i,j )/sqrt( s )))   wherein μ 0  is the mean of D(Y k ) over individuals Y k  not in the mixture, sd(D(Y i,j )) is the standard deviation of D(Y i,j ) for all SNPs j and individual Y i , sqrt(s) is the square root of the number of SNPs, and D(Y i,j )=|Y i,j −Pop j |−|Y i,j −M j |, where Y i,j =allele frequency of individual for SNP j, Pop j =allele frequency of reference population for SNP j, and M j =allele frequency of mixture for SNP j.   
     
     
         23 . The method of  claim 22 , wherein μ 0  is zero. 
     
     
         24 . The method of  claim 8 , wherein the test genetic material sample comprises genetic material from at least two different organisms. 
     
     
         25 . The method of  claim 8 , wherein the test genetic material sample comprises genetic material from at least 10 different organisms. 
     
     
         26 . The method of  claim 8 , wherein the test genetic material sample comprises genetic material from at least two different humans. 
     
     
         27 . The method of  claim 8 , wherein the test genetic material sample comprises genetic material from at least 100 different organisms. 
     
     
         28 . The method of  claim 8 , wherein the characterization is achieved without knowing the number of individuals that contributed to the test genetic material sample. 
     
     
         29 . The method of  claim 8 , wherein the characterization is achieved without computationally considering the number of individuals that contributed to the test genetic material sample. 
     
     
         30 . The method of  claim 8 , wherein the method is performed on a computer and wherein the characterization is output to a user. 
     
     
         31 . The method of  claim 30 , wherein the computer comprises software for implementing the method. 
     
     
         32 . The method of  claim 31 , wherein the software comprises that attached in Appendix A or in the computer program listing appendix in electronic format. 
     
     
         33 . A method of characterizing a test genetic material sample to determine if a person of interest's (“POI's”) genetic material is within the test genetic material sample, said method comprising:
 providing a SNP analysis of the test genetic material sample;   providing a SNP analysis of a reference genetic material sample;   providing a SNP analysis of a POI's genetic material;   in a first comparison, comparing the SNP analysis of the test genetic material sample to the SNP analysis of the POI's genetic material;   in a second comparison, comparing the SNP analysis of the reference genetic material to the SNP analysis of the POI's genetic material; and   comparing the first and second comparisons, thereby determining if the POI'S genetic material is likely in the test genetic material sample.   
     
     
         34 . The method of  claim 33 , wherein, the SNP analysis of the POI's genetic material comprises the SNP identities of at least 100 SNPs. 
     
     
         35 . The method of  claim 33 , wherein genomic DNA from the POI is present in the test genetic material sample in an amount of less than 1% of total genomic DNA in the test genetic material sample. 
     
     
         36 . The method of  claim 33 , wherein DNA from the POI's is present in the test genetic material sample in an amount of less than 0.1% of the total genomic DNA in the test genetic material sample. 
     
     
         37 . The method of  claim 33 , wherein a probe is used to analyze the SNP of the test genetic material sample, and wherein the probe variance is less than 20%. 
     
     
         38 . The method of  claim 33 , wherein at least 1,000 SNPs are analyzed in the test genetic material sample. 
     
     
         39 . A kit for analyzing a test genetic material sample, said kit comprising:
 software on a computer readable format for implementing the method of  claim 33 ; and   a set of probes for binding to and detecting one or more SNPs.   
     
     
         40 . A method for determining if a person of interest contributed genetic material to a test genetic material sample, said method comprising determining a bias of an allele frequency within SNPs of the test genetic material sample relative to a reference and a subject's SNP signature. 
     
     
         41 . A system for determining if a subject contributed genetic material to a sample, the system comprising:
 an input module configured to allow the input of one or more of a sample SNP signature, a reference SNP signature, and a subject SNP signature;   a module configured to determine a bias of an allele frequency within SNPs of the sample SNP signature relative to the reference SNP signature and the subject SNP signature; and   a module configured to output the bias, wherein one or more of the modules is executed on a computing device.   
     
     
         42 . The system of  claim 41 , further comprising a module configured to provide a sample SNP signature; 
     
     
         43 . The system of  claim 41 , further comprising a module configured to provide a reference SNP signature; 
     
     
         44 . The system of  claim 41 , further comprising a module configured to provide a subject SNP signature;