Ancestry painting with local ancestry inference

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, wherein the proportion of the individual's genotype data that is deemed to correspond to the geographical or ethnic ancestry is at least partially determined by clustering, based on a geographical hierarchy, a plurality of probabilities, wherein each probability is a probability that the proportion of the individual's genotype data corresponds to one of a plurality of predicted geographical or ethnic ancestries; 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 corresponds to a geographical region, and the one or more processors are further configured to:

receive a request to display subregions that correspond to the geographical or ethnic ancestry and the individual's genotype data; and

cause the subregions to be displayed, wherein at least one subregion corresponds to one of the clustered probabilities.

3. The system of claim 2 , wherein the one or more processors are further configured to cause proportions of the individual's genotype data that are deemed to correspond to the subregions to be displayed.

4. The system of claim 1 , wherein the genotype data includes genomic data.

5. The system of claim 1 , wherein the genotype data includes data of a specific chromosome.

6. The system of claim 5 , wherein the one or more processors are further configured to:

receive a request to display ancestry composition information pertaining to the specific chromosome; and

cause ancestry composition information pertaining to the specific chromosome to be displayed.

7. The system of claim 1 , wherein the ancestry composition information is determined by:

obtaining unphased genotype data of the individual;

phasing the unphased genotype data to generate phased haplotype data;

using a learning machine to classify portions of the phased haplotype data as corresponding to geographical or ethnic ancestries respectively and generate initial classification results;

correcting errors in the initial classification results to generate modified classification results, and

recalibrating the modified classification results to generate the plurality of predicted geographical or ethnic ancestries.

8. 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 corresponds to one of a plurality of predicted geographical or ethnic ancestries

clustering, based on a geographical hierarchy, a plurality of probabilities to determine a geographical or ethnic ancestry for a proportion of the individual's genotype data, wherein each probability is a probability that the proportion of the individual's genotype data corresponds to one of the plurality of predicted geographical or ethnic ancestries; 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, wherein the ancestry composition information includes the geographical or ethnic ancestry for the proportion of the individual's genotype data.

9. The method of claim 8 , wherein the geographical or ethnic ancestry corresponds to a geographical region, and the method further comprises:

receiving a request to display subregions that correspond to the geographical or ethnic ancestry and the individual's genotype data; and

causing the subregions to be displayed, wherein at least one subregion corresponds to one of the clustered probabilities.

10. The method of claim 9 , further comprising causing proportions of the individual's genotype data that are deemed to correspond to the subregions to be displayed.

11. The method of claim 8 , wherein the genotype data includes genomic data.

12. The method of claim 8 , wherein the genotype data includes data of a specific chromosome.

13. The method of claim 12 , further comprising:

receiving a request to display ancestry composition information pertaining to the specific chromosome; and

causing ancestry composition information pertaining to the specific chromosome to be displayed.

14. The method of claim 8 , wherein the ancestry composition information is determined by:

obtaining unphased genotype data of the individual;

phasing the unphased genotype data to generate phased haplotype data;

using a learning machine to classify portions of the phased haplotype data as corresponding to specific ancestries respectively and generate initial classification results; and

correcting errors in the initial classification results to generate modified classification results, wherein the modified classification results are the plurality of probabilities.

15. A computer program product for presenting ancestry composition information, the computer program product being embodied in a tangible computer readable storage medium and comprising computer instructions for:

receiving a request to display ancestry composition information 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 geographical or ethnic ancestry, wherein the proportion of the individual's genotype data that is deemed to correspond to a geographical or ethnic ancestry is at least partially determined by clustering, based on a geographical hierarchy, a plurality of probabilities, wherein each probability is a probability that the proportion of the individual's genotype data corresponds to one of a plurality of predicted geographical or ethnic ancestries; and

presenting the ancestry composition information to be displayed.

16. The system of claim 1 , wherein the geographical hierarchy comprises subregions within a region, each predicted geographical or ethnic ancestry corresponds with a subregion, and clustering is performed by adding the probabilities for each subregion within at least one region.

17. The system of claim 1 , wherein the geographical or ethnic ancestry corresponds to the clustered predicted geographical or ethnic ancestries.

18. The system of claim 1 , wherein clustering is performed until a clustered probability meets or exceeds a threshold value.

19. The system of claim 1 , wherein the geographical hierarchy comprises a first region and a second region, each region comprises a plurality of subregions, each predicted geographical or ethnic ancestry corresponds with a subregion, and the one or more processors are configured to cluster the plurality of probabilities by:

determining a subregion within the first region and corresponding to a predicted geographical or ethnic ancestry has the highest probability of the plurality of probabilities, and

adding the probabilities corresponding with each subregion of the first region.

20. The system of claim 19 , wherein a probability of the first region is a summation of the probabilities corresponding with each subregion of the first region, and the one or more processors are further configured to cluster the plurality of probabilities by:

determining the probability of the first region is less than a threshold value, and

adding the probability of the first region with a probability of the second region, the probability of the second region being a summation of the probabilities corresponding with each subregion of the second region.

21. The system of claim 1 , wherein the genotype data includes a full DNA sequence set for the individual.

22. The system of claim 1 , wherein the interactive user interface is displayed via a mobile device, smart phone, or tablet device.

23. The method of claim 8 , wherein the geographical hierarchy comprises subregions within a region, each predicted geographical or ethnic ancestry corresponds with a subregion, and clustering is performed by adding the probabilities for each subregion within at least one region.

24. The method of claim 8 , wherein the geographical or ethnic ancestry corresponds to the clustered predicted geographical or ethnic ancestries.

25. The method of claim 8 , wherein clustering is performed until a clustered probability meets or exceeds a threshold value.

26. The method of claim 8 , wherein the geographical hierarchy comprises a first region and a second region, each region comprises a plurality of subregions, each predicted geographical or ethnic ancestry corresponds with a subregion, and clustering further comprises:

determining a subregion within the first region and corresponding to a predicted geographical or ethnic ancestry has the highest probability of the plurality of probabilities, and

adding the probabilities corresponding with each subregion of the first region.

27. The method of claim 26 , wherein a probability of the first region is a summation of the probabilities corresponding with each subregion of the first region, and clustering further comprises:

determining the probability of the first region is less than a threshold value, and

adding the probability of the first region with a probability of the second region, the probability of the second region being a summation of the probabilities corresponding with each subregion of the second region.

28. The method of claim 8 , wherein the genotype data includes a full DNA sequence set for the individual.

29. The method of claim 8 , wherein the interactive user interface is displayed via a mobile device, smart phone, or tablet device.