Systems and methods for genetic identification and analysis

Patent metadata

Field	Value
Publication number	US-12065696-B2
Application number	US-202318104727-A
Country	US
Kind code	B2
Filing date	Feb 1, 2023
Priority date	Jul 7, 2017
Publication date	Aug 20, 2024
Grant date	Aug 20, 2024

Abstract

The disclosure provides various systems and methods for identifying individuals from one or more samples. In particular, improved systems and methods of analysis are provided for handling multiple contributors, as well as systems and methods that model not only individual error rates per locus but factor in amplification of errors induced through PCR cycles. In some embodiments, modeling of error rates can be applied in multi-contributor settings to more accurately establish real alleles from artifacts. Other aspects involve application of sequencing in error modeling. Further, methods are provided for determining the presence of common individual DNA profiles in one or more complex DNA mixtures and for deconvolution of multiple complex DNA mixtures into shared individual components. The methods of the disclosure do not require any prior knowledge of individual DNA profiles or contributors to the complex DNA mixtures. Moreover, the methods of the disclosure may use any SNP panel, including those panels already existing and those panels specifically designed to maximize performance characteristics of the methods described herein.

First claim

What is claimed is:

1. A SNP panel comprising one, two, or more loci of a single-nucleotide polymorphism (SNP) having at least one of:
(a) a low fixation index (FST);
(b) a low minor allele frequency (mAF) value or a low average heterozygosity value; and
wherein a low mAF indicates that the minor allele is rare in a population.

2. The panel of claim 1 , wherein a low FST indicates that the minor allele of the SNP has no statistically significant correlation with ancestry.

3. The panel of claim 1 , wherein the FST is less than 0.06.

4. The panel of claim 1 , wherein the mAF is a value between 0.01 and 0.3, inclusive of the endpoints.

5. The panel of claim 1 , wherein the mAF is a value between 0.03 and 0.07, inclusive of the endpoints.

6. The panel of claim 1 , wherein a low average heterozygosity value indicates that the minor allele of the SNP is rare in a population.

7. The panel of claim 1 , wherein the value of average heterozygosity is calculated or derived from information present in public databases (e.g. dbSNP).

8. The panel of claim 1 , wherein the value of average heterozygosity is between 0.058 and 0.13, inclusive of the endpoints.

9. The panel of claim 5 , wherein the population is a plurality of individuals or a database.

10. A method for resolving a DNA profile for a major and/or a minor contributor from a complex DNA mixture comprising the steps of:
(a) amplifying a sequence containing at least one minor SNP allele from the SNP panel of claim 1 in the complex DNA mixture using a quantitative amplification method;
(b) contacting the resultant amplification product with a detectable label, wherein each sequence containing a distinct minor SNP allele contacts a distinct detectable label;
(c) detecting a signal from each of the resultant amplification products;
(d) comparing the signal amplitude between amplification products, wherein the signal amplitude of a sequence provided by a major contributor is greater than the signal amplitude of a sequence provided by a minor contributor, and
(e) assembling the sequences having a low signal amplitude into a DNA profile to identify a minor contributor to the complex DNA mixture, and/or
(f) assembling the sequences having a high signal amplitude into a DNA profile to identify a major contributor to the complex DNA mixture,
thereby resolving from a DNA profile for a major and/or a minor contributor from a complex DNA mixture.

11. The method of claim 10 , wherein the complex DNA mixture is obtained from a forensic laboratory.

12. The method of claim 11 , wherein the major or minor contributor is a victim of a crime.

13. The method of claim 11 , wherein the major or minor contributor is a perpetrator of a crime.

14. The method of claim 10 , wherein the complex DNA mixture is obtained from a biopsy, a medical examination or a medical laboratory.

15. The method of claim 14 , wherein the major contributor is a benign cell or tissue.

16. The method of claim 14 , wherein the minor contributor is a cancerous cell or tissue.

17. The method of claim 10 , wherein a percentage of DNA in the complex DNA mixture provided by the minor contributor is between 0 and 49.9 percent of total DNA.

18. The method of claim 10 , wherein a percentage of DNA in the complex DNA mixture provided by the minor contributor is between 0.001 and 49 percent of total DNA.

19. The method of claim 10 , wherein accuracy or efficacy of the method increases as
(a) an amount of total DNA contained in the complex DNA mixture increases, and/or
(b) a greater number of loci from the SNP panel of any one of claims 1-13 are analyzed.

20. A method for building an individual DNA profile from one, two, or more complex DNA mixtures comprising the steps of:
(a) determining the presence of at least one minor SNP allele from the SNP panel of claim 1 in a first complex DNA mixture;
(b) determining the presence of at least one minor SNP allele in a second complex DNA mixture;
(c) identifying a common set of minor alleles present in the first and second complex mixtures, wherein the occurrence of a common set of minor alleles indicates the presence of a common individual contributor to each of the first and the second complex mixtures; and
(d) assembling all common minor alleles identified in (c) to generate an individual DNA profile,
thereby building an individual DNA profile from one, two, or more complex DNA mixtures.

21. The method of claim 20 , comprising at least five complex DNA mixtures.

22. The method of claim 21 , comprising at least ten complex DNA mixtures.

23. The method of claim 20 , wherein the accuracy and/or specificity of the individual DNA profile increases as the number of complex mixtures increases.

24. The method of claim 20 , wherein the one, two, or more complex DNA mixtures are obtained from a forensic investigation.

25. The method of claim 20 , wherein the one, two, or more complex DNA mixtures are obtained from a medical or biological sample.

Assignees

• Massachusetts Inst Technology

Inventors

• Ricke Darrell Orlyn
• Harper James
• Helfer Brian S
• Isaacson Joseph
• Michaleas Adam M
• Petrovick Martha S
• Schwoebel Eric
• Shcherbina Anna
• Fremont-Smith Philip
• Watkins James G
• Wack Edward C

Classifications

• G16B20/00

  ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations · CPC title

• C12Q2600/156

  Polymorphic or mutational markers · CPC title

• C12Q1/6886 Primary

  for cancer (immunoassay for cancer G01N33/575) · CPC title

• C12Q1/6869

  Methods for sequencing · CPC title

• G16B40/10

  Signal processing, e.g. from mass spectrometry [MS] or from PCR · CPC title