Systems and methods for genetic identification and analysis

Patent metadata

Field	Value
Publication number	US-11655498-B2
Application number	US-201816629081-A
Country	US
Kind code	B2
Filing date	Jul 6, 2018
Priority date	Jul 7, 2017
Publication date	May 23, 2023
Grant date	May 23, 2023

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.

First claim

What is claimed is:

1. A DNA analysis system, the system comprising:
at least one processor operatively connected to a memory;
a comparison component configured to generate a first error profile for a first DNA locus by comparing read data for the first DNA locus to known reference sequences for the first DNA locus;
a receiver component configured to receive DNA analysis information including locus and allele read information generated from PCR amplification of DNA in a DNA sample;
an analysis component, executed by the at least one processor, configured to:

evaluate the locus and allele read information against the first error profile to determine an adjusted read threshold;
confirm presence of the first locus and allele in the DNA sample;
responsive to the confirmed presence of the first locus and allele information adjust error analysis of at least a second allele or at least a second locus to account for amplification error reads of the confirmed first locus and allele in the DNA sample; and
determine for each respective locus and allele associated with read data obtained from the DNA sample whether a total number of reads from the DNA sample exceeds an error profile adjusted threshold, and for each confirmation or exclusion of read data adjust the threshold based on the confirmation or exclusion.

2. The system of claim 1 , wherein the analysis component is further configured to generate, by the least one processor, an identification profile for at least one individual within the DNA sample comprising each confirmed locus and allele for the at least one individual.

3. The system of claim 1 , wherein the receiver component further comprises a physical DNA sample receiver and PCR analysis element for generating read information for respective loci and alleles.

4. The system of claim 1 , wherein the error profile for the first locus and allele includes calculations of different threshold adjustments according to PCR amplification cycles executed on the sample.

5. The system of claim 4 , wherein the error profile includes calculations for a number of reads associated with at least −1 stutter allele, a +1 stutter allele, and a −2 stutter allele, wherein the calculations are adjusted by the analysis component to a number of PCR amplification cycles.

6. The system of claim 1 , wherein the analysis component is further configured to determine whether the total number of reads from the sample exceeds the error profile adjusted threshold based on a combined error read count derived from stutter alleles from at least a first and second allele.

7. The system of claim 1 , wherein the analysis component is further configured to determine the total number of reads from the sample exceeds the error profile adjusted threshold based on a combined error read count derived from stutter alleles from at least a first, second, and third allele.

8. The system of claim 1 , wherein the analysis component is further configured to identify PCR products from the sample for sequencing.

9. The system of claim 8 , wherein the analysis component is further configured to evaluate confirmed alleles to determine information on a respective dominant −1 stutter allele and identify PCR products from the sample from sequencing based on the properties of the respective dominant −1 stutter allele.

10. The system of claim 9 , wherein the analysis component is further configured to update confirmed allele information responsive to reducing reads counts for each dominant −1 stutter allele identified based on sequencing.

11. A method for analyzing DNA comprising:
generating a first error profile for a first DNA locus by comparing read data for the first DNA locus to known reference sequences for the first DNA locus;
receiving DNA analysis information including locus and allele read information generated from PCR amplification of DNA in a DNA sample;
evaluating the locus and allele read information against the first error profile to determine an adjusted read threshold;
confirming presence of the first locus and allele in the DNA sample;
responsive to the confirmed presence of the first locus and allele information, adjusting error analysis of at least a second allele or at least a second locus to account for amplification error reads of the confirmed first locus and allele in the DNA sample; and
determining for each respective locus and allele associated with read data obtained from the DNA sample whether a total number of reads from the DNA sample exceeds an error profile adjusted threshold, and for each confirmation or exclusion of read data adjust the threshold based on the confirmation or exclusion.

12. The method of claim 11 , further comprising generating an identification profile for at least one individual within the DNA sample comprising each confirmed locus and allele for the at least one individual.

13. The method of claim 11 , wherein the act of receiving further comprises controlling a physical DNA sample receiver and PCR analysis element for generating read information for respective loci and alleles.

14. The method of claim 11 , wherein the error profile for the first locus and allele includes calculations of different threshold adjustments according to PCR amplification cycles executed on the sample.

15. The method of claim 14 , wherein the error profile includes calculations for a number of reads associated with at least −1 stutter allele, a +1 stutter allele, and a −2 stutter allele, wherein the method comprises adjusting the calculations by the analysis component to a number of PCR amplification cycles.

16. The method of claim 11 , further comprising determining whether the total number of reads from the sample exceeds the error profile adjusted threshold based on a combined error read count derived from stutter alleles from at least a first and second allele.

17. The method of claim 11 , further comprising determining the total number of reads from the sample exceeds the error profile adjusted threshold based on a combined error read count derived from stutter alleles from at least a first, second, and third allele.

18. The method of claim 11 , further comprising identifying PCR products from the sample for sequencing.

19. The method of claim 18 , further comprising evaluating confirmed alleles to determine information on a respective dominant −1 stutter allele and identify PCR products from the sample from sequencing based on the properties of the respective dominant −1 stutter allele.

20. The method of claim 19 , further comprising updating confirmed allele information responsive to reducing reads counts for each dominant −1 stutter allele identified based on sequencing.

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

• C12Q1/68

  involving nucleic acids · CPC title

• C12Q1/6886 Primary

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

• C12Q1/6858 Primary

  Allele-specific amplification · CPC title

• G16B40/10

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

• C12Q2600/156

  Polymorphic or mutational markers · CPC title