Ancestry painting with local ancestry inference

• US 10,296,847 B1
• Filed: 06/13/2016
• Issued: 05/21/2019
• Est. Priority Date: 03/19/2008
• Status: Active Grant

• Current Assignee: 23andme Incorporated (23andMe Holding Co.)
• Original Assignee: 23andme Incorporated (23andMe Holding Co.)
• Inventors: Do, Chuong, Durand, Eric, MacPherson, John Michael, Naughton, Brian Thomas, Mountain, Joanna Louise
• Primary Examiner(s): Holmes, Michael B
• Application Number:
  US15/181,083
• Time in Patent Office: 1,072 Days
• CPC Class Codes: G06F 11/0793 Remedial or corrective actions recovery from an exception in an instruction pipeline G06F9/3861; by retry G06F11/1402; for recovering from a failure of a protocol instance or entity H04L69/40
• CPC Class Codes: G06F 16/29 Geographical information databases
• CPC Class Codes: G06F 3/04812 Interaction techniques based on cursor appearance or behaviour, e.g. being affected by the presence of displayed objects
• CPC Class Codes: G06F 3/0484 for the control of specific functions or operations, e.g. selecting or manipulating an object, an image or a displayed text element, setting a parameter value or selecting a range
• CPC Class Codes: G06N 20/00 Machine learning
• CPC Class Codes: G06N 5/022 Knowledge engineering; Knowledge acquisition
• CPC Class Codes: G06N 5/04 Inference or reasoning models
• CPC Class Codes: G06N 7/01 Probabilistic graphical models, e.g. probabilistic networks
• CPC Class Codes: G16B 20/00 ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• CPC Class Codes: G16B 20/20 Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
• CPC Class Codes: G16B 20/40 Population genetics; Linkage disequilibrium
• CPC Class Codes: G16B 30/00 ICT specially adapted for sequence analysis involving nucleotides or amino acids
• CPC Class Codes: G16B 40/00 ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
• CPC Class Codes: G16B 40/20 Supervised data analysis
• CPC Class Codes: G16B 40/30 Unsupervised data analysis
• CPC Class Codes: G16B 45/00 ICT specially adapted for bioinformatics-related data visualisation, e.g. displaying of maps or networks
• CPC Class Codes: G16H 10/60 for patient-specific data, e.g. for electronic patient records

Abstract

Presenting ancestral origin information, comprising: receiving a request to display ancestry data of an individual; obtaining ancestry composition information of the individual, the ancestry composition information including information pertaining to a proportion of the individual'"'"'s genotype data that is deemed to correspond to a specific ancestry; and presenting the ancestry composition information to be displayed.

Claims

1. A system of presenting ancestry composition information, comprising:

one or more processors; and

one or more memories coupled to the one or more processors, wherein the one or more memories are configured to provide the one or more processors with instructions which when executed cause the one or more processors to;

receive a request to display ancestry composition information of an individual for whom genotype data is available;

obtain ancestry composition information of the individual, the ancestry composition information including information pertaining to a proportion of the individual'"'"'s genotype data that is deemed to correspond to a geographical or ethnic ancestry; and

cause the ancestry composition information of the individual to be displayed in an interactive user interface adapted to allow the individual to interact with the ancestry composition information of the individual.

2. The system of claim 1, wherein the geographical or ethnic ancestry is a geographical ancestry that corresponds to a geographical region, and wherein the one or more memories are further configured to provide the one or more processors with instructions which when executed cause the one or more processors to:

receive a request via the interactive user interface to display one or more subregions of the geographical region that correspond to the proportion of the individual'"'"'s genotype data that is deemed to correspond to the geographical ancestry; and

cause the one or more subregions to be displayed on the interactive user interface.

3. The system of claim 2, wherein the one or more processors are further configured to cause one or more proportions of the individual'"'"'s genotype data that are deemed to correspond to respective ones of the one or more subregions to be displayed on the interactive user interface as percentages.

4. The system of claim 1, wherein the genotype data includes single nucleotide polymorphism (SNP) based genotype data.

8. The method of claim 4, wherein the genotype data includes single nucleotide polymorphism (SNP) based genotype data.

9. The system of claim 1, wherein the individual'"'"'s genotype data comprises autosomal chromosome data.

10. The system of claim 9, wherein the geographical or ethnic ancestry is a geographical ancestry and the interactive user interface includes a graphical representation of the ancestry composition information of the individual to be displayed, the graphical representation comprising:

a portion of a world map showing a portion of the ancestry composition information of the individual; and

the proportion of the individual'"'"'s genotype data that is deemed to correspond to the geographical ancestry represented as a percentage.

11. The system of claim 10, wherein the proportion of the individual'"'"'s genotype data that is deemed to correspond to the geographical ancestry represented as the percentage is arranged in a tabular or list view in the graphical representation.

12. The system of claim 2, wherein the geographical region is a continental region.

13. The system of claim 12, wherein the one or more subregions are sub-continental regions.

14. The system of claim 1, wherein the geographical or ethnic ancestry is a geographical ancestry selected from Asian ancestry, European ancestry, and African ancestry.

15. The system of claim 1, wherein the geographical or ethnic ancestry is a geographical ancestry selected from one of African ancestry, Native American ancestry, Eastern Asian ancestry, Southern Asian ancestry, Eastern European ancestry, Western European ancestry, Middle Eastern ancestry, and Scandinavian ancestry.

16. The system of claim 1, wherein the geographical or ethnic ancestry is a geographical ancestry corresponding to a geographical region selected from Greece, Italy, Ireland, France, Germany, Finland, and United Kingdom.

17. The method of claim 4, wherein the proportion of the individual'"'"'s genotype data comprises autosomal chromosome data.

18. The method of claim 17, wherein the interactive user interface includes a graphical representation of the ancestry composition information of the individual to be displayed, the graphical representation comprising:

a portion of a world map showing a portion of the ancestry composition information of the individual; and

the proportion of the individual'"'"'s genotype data that is deemed to correspond to the geographical or ethnic ancestry represented as a percentage.

19. The method of claim 18, wherein the proportion of the individual'"'"'s genotype data that is deemed to correspond to the geographical or ethnic ancestry represented as the percentage is arranged in a tabular or list view in the graphical representation.

20. The method of claim 17, further comprising:

obtaining unphased genotype data of the individual;

phasing the unphased genotype data to generate phased haplotype data; and

comparing the phased haplotype data to a plurality of reference populations to generate estimates for the most probable geographical or ethnic ancestries for the ancestry composition information of the individual.

5. A method of presenting ancestry composition information, comprising:

receiving a request to display ancestry composition information of an individual for whom genotype data is available;

obtaining ancestry composition information of the individual, the ancestry composition information including information pertaining to a proportion of the individual'"'"'s genotype data that is deemed to correspond to a geographical or ethnic ancestry; and

causing the ancestry composition information of the individual to be displayed in an interactive user interface adapted to allow the individual to interact with the ancestry composition information of the individual.

6. The method of claim 5, wherein the geographical or ethnic ancestry is a geographical ancestry that corresponds to a geographical region, and the method further comprises:

receiving a request from the interactive user interface to display one or more subregions of the geographical region that correspond to the proportion of the individual'"'"'s genotype data that is deemed to correspond to the geographical ancestry; and

causing the one or more subregions to be displayed on the interactive user interface.

7. The method of claim 6, further comprising causing one or more proportions of the individual'"'"'s genotype data that are deemed to correspond to respective ones of the one or more subregions to be displayed on the interactive user interface as percentages.

21. A system of presenting ancestry composition information, comprising:

one or more processors; and

one or more memories coupled to the one or more processors, wherein the one or more memories are configured to provide the one or more processors with instructions which when executed cause the one or more processors to;

receive a request to display ancestry composition information of an individual for whom genotype data is available;

obtain ancestry composition information of the individual, the ancestry composition information including information pertaining to a proportion of the individual'"'"'s genotype data that is deemed to correspond to a geographical ancestry; and

cause the ancestry composition information of the individual to be displayed in an interactive user interface adapted to allow the individual to interact with the ancestry composition information of the individual, wherein the interactive user interface includes a graphical representation of the ancestry composition information of the individual to be displayed, the graphical representation comprising;

a portion of a world map showing a geographical region that corresponds to the geographical ancestry; and

the proportion of the individual'"'"'s genotype data that is deemed to correspond to the geographical ancestry represented as a percentage.

22. The system of claim 21, wherein the proportion of the individual'"'"'s genotype data that is deemed to correspond to the geographical ancestry represented as the percentage is arranged in a tabular or list view in the graphical representation.

23. The system of claim 21, wherein the graphical representation includes a plurality of geographical ancestries and a plurality of colors, with a unique color of the plurality of colors selected for each of the geographical ancestries.

24. The system of claim 21, wherein the proportion of the individual'"'"'s genotype data comprises autosomal chromosome data.

25. The system of claim 21, wherein the geographical region is one of:

Asia, Europe, and Africa.

26. The system of claim 21, wherein the geographical region is selected from African, Native American, Eastern Asian, Southern Asian, Eastern European, Western European, Middle Eastern, and Scandinavian regions.

27. The system of claim 21, wherein the geographical region is one of:

Greece, Italy, Ireland, France, Germany, Finland, and United Kingdom.

28. The system of claim 21, wherein the ancestry composition information is determined by:

obtaining unphased genotype data of the individual; and

phasing the unphased genotype data to generate phased haplotype data.

29. The system of claim 28, wherein the ancestry composition information is determined by:

classifying a plurality of portions of the phased haplotype data as likely corresponding to one or more specific ancestries by comparing the plurality of portions of the phased haplotype data to a plurality of reference populations.

30. The system of claim 29, further comprising:

summing up the one or more specific ancestries of the plurality of portions of the phased haplotype data to generate the geographical ancestry represented as the percentage.

31. The system of claim 21, wherein the genotype data includes single nucleotide polymorphism (SNP) based genotype data.

32. The system of claim 21, wherein the ancestry composition information includes information pertaining to a plurality of proportions of the individual'"'"'s genotype data each of which is deemed to correspond to a respective one of a plurality of geographical ancestries and wherein the portion of the world map shows a plurality of geographical regions each of which corresponds to a respective one of the plurality of geographical ancestries.