IP Library › Granted Patent US 12,229,141
Granted Patent B2
US 12,229,141 · App. 17/868,775 · Granted Feb 18, 2025

Linking individual datasets to a database

Inventors: Shiya Song (San Mateo, CA); Jingwen Pei (San Mateo, CA); Brett Frederick Jorgensen (Draper, UT); Aaron James Stern (Berkeley, CA); Ross E. Curtis (Cedar Hills, UT)
Assignee: Ancestry.com DNA, LLC
G06F16/24558G06F16/2246G06F16/24578G16B10/00
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Quick Facts
Patent No.
US 12,229,141
App. No.
17/868,775
Granted
Feb 18, 2025
Kind
B2
Abstract

The disclosed system links an individual dataset to a database. The system receives a target individual dataset associated with a target individual and identifies candidate individual datasets that are potentially related to the target individual dataset. The system identifies a related individual dataset that has data bits that match some data bits in the target individual dataset. The system then identifies a parent node that is a common parent node to both the target individual dataset and the related individual dataset. The system retrieves a data tree that the parent node belongs to with the data tree containing information describing inter-relationships among datasets in the data tree. A node in the data tree is identified to assign the target individual dataset based on strings of matched data bits and number of the matched strings between the target individual dataset and the datasets in the data tree.

Claims (95)

1. A computer-implemented method comprising:

receiving a target individual dataset associated with a target individual;

identifying a plurality of candidate individual datasets that are potentially related to the target individual dataset;

identifying a related individual dataset from the plurality of candidate individual datasets, wherein the related individual dataset has data bits that match at least a portion of data bits in the target individual dataset, wherein identifying the related individual dataset comprises:

phasing a genotype corresponding to the target individual and a genotype corresponding to the related individual;

identifying identity by descent (IBD) segments shared between the phased genotype of the target individual dataset and the phased genotype of the related individual dataset;

determining a total length of the IBD segments shared between the phased genotype of the target individual dataset and the phased genotype of the related individual dataset; and

determining that the total length of shared IBD segments exceeds a threshold;

identifying a parent node that is a common parent node for both the related individual dataset and the target individual dataset;

retrieving a data tree to which the parent node belongs, the data tree describing inter-relationships among datasets in the data tree;

identifying, based on strings of matched data bits and number of the strings of matched data bits between the target individual dataset and the datasets in the data tree, a descendant position to the common parent node in the data tree to which the target individual dataset is assigned, wherein identifying the descendant position to the common parent node in the data tree comprises: generating a plurality of candidate data trees that have the individual dataset assigned to different candidate descendant positions to the common parent node, wherein generating the plurality of candidate data trees comprises:

generating a first candidate data tree that is based on the data tree to which the parent node belongs, the first candidate data tree being the data tree with a first new descendant position, the first candidate data tree adding the individual dataset to the first new descendant position, and

generating a second candidate data tree that is based on the data tree to which the parent node belongs, the second candidate data tree being the data tree with a second new descendant position, the second candidate data tree adding the individual dataset to the second new descendant position,

calculating, for each of the candidate data trees with new descendant positions added for the individual dataset to the common parent node, a plurality of pairwise relationship likelihoods, each pairwise relationship likelihood measuring a likelihood between a candidate descendant position and another dataset that also represents a descendant of the common parent node, and

selecting a candidate data tree as the data tree based on the plurality of pairwise relationship likelihoods; and

outputting the data tree with the target individual dataset located in the descendant position.

2. The method of claim 1 , wherein identifying a parent node further comprises:

identifying a plurality of candidate parent nodes, wherein a candidate parent node represents a candidate common ancestor for both the target individual dataset and one of the candidate individual datasets;

calculating confidence scores for the candidate parent nodes; and

selecting one of the candidate parent nodes as the parent node based on a ranking of the candidate parent nodes by the confidence scores.

3. The method of claim 2 , wherein identifying the parent node further comprises a pruning process, the pruning process comprising:

retrieving a meiosis separation between the related individual represented by the related individual dataset and the target individual;

determining a generation value between the related individual and one of the candidate parent nodes;

determining a range for the generation value based on the meiosis; and

removing the one of the candidate parent nodes as a candidate in response to the generation value out of the range.

4. The method of claim 1 , wherein generating the plurality of candidate data trees that have the individual dataset assigned to different candidate descendant positions to the common parent node comprises one or more of the following:

(i) assigning the target individual dataset at an existing node in the data tree as the one of the new descendant positions, the one of the new descendant positions replacing the existing node;

(ii) adding a child node that descends from a leaf node in the data tree as the one of the new descendant positions of the target individual dataset; and/or

(iii) adding a child node that descends from an inner node in the data tree wherein the child node is in a new branch descending from the inner node, the child node being the one of the new descendant positions of the target individual dataset.

5. The method of claim 1 , wherein each candidate data is associated with a likelihood score determined from the pairwise relationship likelihoods, the likelihood score for each candidate data tree is a composite likelihood calculated based on individual datasets in each candidate data tree, wherein the individual datasets contain DNA information.

6. The method of claim 5 , wherein the composite likelihood for each candidate data tree is determined based on steps comprising:

determining a likelihood for each pairwise individual datasets between the target individual and other individuals in the candidate data tree, the pairwise individual datasets containing DNA information in the candidate data tree, the likelihood calculated based on matched DNA information and positions of the pair of individual datasets in the candidate data tree; and

generating the composite likelihood based on a product of the likelihood of each pair of individual datasets.

7. The method of claim 1 , wherein identifying the descendant position to the common parent node in the data tree to which the target individual dataset is assigned is further based on a relationship between the target individual dataset and the related individual dataset determined based on matched DNA information.

8. The method of claim 1 , wherein:

the data bits contain information associated with DNA;

the strings of matched data bits contain information associated with matched DNA segments; and

the number of the strings contain information associated with number of matched DNA segments.

9. The computer-implemented method of claim 1 , wherein identifying a parent node that is a common parent node for both the related individual dataset and the target individual dataset comprises:

identifying a data tree corresponding to the target individual dataset and a data tree corresponding to the related individual dataset in a large-scale network comprising concatenated data trees corresponding to a plurality of individuals, the concatenated data trees having been linked in the large-scale network by identifying common individuals in different data trees, and

identifying a parent node by defining a path connecting the target individual dataset and the related individual dataset in the large-scale network.

10. A system comprising:

a computing server comprising one or more processors and memory for storing computer code comprising instructions, wherein the instructions, when executed by one or more computer processors, cause the one or more computer processors to perform steps comprising:

receiving a target individual dataset associated with a target individual;

identifying a plurality of candidate individual datasets that are potentially related to the target individual dataset;

identifying a related individual dataset from the plurality of candidate individual datasets, wherein the related individual dataset has data bits that match at least a portion of data bits in the target individual dataset, wherein identifying the related individual dataset comprises:

phasing a genotype corresponding to the target individual and a genotype corresponding to the related individual;

identifying identity by descent (IBD) segments shared between the phased genotype of the target individual dataset and the phased genotype of the related individual dataset;

determining a total length of the IBD segments shared between the phased genotype of the target individual dataset and the phased genotype of the related individual dataset; and

determining that the total length of shared IBD segments exceeds a threshold;

identifying a parent node that is a common parent node for both the related individual dataset and the target individual dataset;

retrieving a data tree to which the parent node belongs, the data tree describing inter-relationships among datasets in the data tree;

identifying, based on strings of matched data bits and number of the strings of matched data bits between the target individual dataset and the datasets in the data tree, a descendant position to the common parent node in the data tree to which the target individual dataset is assigned, wherein identifying the descendant position to the common parent node in the data tree comprises:

generating a plurality of candidate data trees that have the individual dataset assigned to different candidate descendant positions to the common parent node, wherein generating the plurality of candidate data trees comprises:

generating a first candidate data tree that is based on the data tree to which the parent node belongs, the first candidate data tree being the data tree with a first new descendant position, the first candidate data tree adding the individual dataset to the first new descendant position, and generating a second candidate data tree that is based on the data tree to which the parent node belongs, the second candidate data tree being the data tree with a second new descendant position, the second candidate data tree adding the individual dataset to the second new descendant position,

calculating, for each of the candidate data trees with new descendant positions added for the individual dataset to the common parent node, a plurality of pairwise relationship likelihoods, each pairwise relationship likelihood measuring a likelihood between a candidate descendant position and another dataset that also represents a descendant of the common parent node, and

selecting a candidate data tree as the data tree based on the plurality of pairwise relationship likelihoods; and

outputting the data tree with the target individual dataset located in the descendant position; and

a graphical user interface in communication with the computing server, the graphical user interface configured to display the data tree with the target individual dataset located in the descendant position.

11. The system of claim 10 , wherein identifying a parent node further comprises:

identifying a plurality of candidate parent nodes, wherein a candidate parent node represents a candidate common ancestor for both the target individual dataset and one of the candidate individual datasets;

calculating confidence scores for the candidate parent nodes; and

selecting one of the candidate parent nodes as the parent node based on a ranking of the candidate parent nodes by the confidence scores.

12. The system of claim 11 , wherein identifying the parent node further comprises a pruning process, the pruning process comprising:

retrieving a meiosis separation between the related individual represented by the related individual dataset and the target individual;

determining a generation value between the related individual and one of the candidate parent nodes;

determining a range for the generation value based on the meiosis; and

removing the one of the candidate parent nodes as a candidate in response to the generation value out of the range.

13. The system of claim 10 , wherein generating one or more candidate data trees that have the individual dataset assigned to different candidate descendant positions to the common parent node comprises one or more of the following:

(i) assigning the target individual dataset at an existing node in the data tree as the one of the new descendant positions, the new descendant positions replacing the existing node;

(ii) adding a child node that descends from a leaf node in the data tree as the one of the new descendant positions of the target individual dataset; and/or

(iii) adding a child node that descends from an inner node in the data tree wherein the child node is in a new branch descending from the inner node, the child node being the one of the new descendant positions of the target individual dataset.

14. The system of claim 10 , wherein each candidate data is associated with a likelihood score determined from the pairwise relationship likelihoods, the likelihood score for each candidate data tree is a composite likelihood calculated based on individual datasets in each candidate data tree, wherein the individual datasets contain DNA information.

15. The system of claim 14 , wherein the composite likelihood for each candidate data tree is determined based on steps comprising:

determining a likelihood for each pairwise individual datasets between the target individual and other individuals in the candidate data tree, the pairwise individual datasets containing DNA information in the candidate data tree, the likelihood calculated based on matched DNA information and positions of the pair of individual datasets in the candidate data tree; and

generating the composite likelihood based on a product of the likelihood of each pair of individual datasets.

16. The system of claim 10 , wherein identifying the descendant position to the common parent node in the data tree to which the target individual dataset is assigned is further based on metadata associated with the datasets.

17. The system of claim 10 , wherein identifying the descendant position to the common parent node in the data tree to which the target individual dataset is assigned is further based on a relationship between the target individual dataset and the related individual dataset determined based on matched DNA information.

18. A non-transitory computer readable medium for storing computer code comprising instructions for linking an individual dataset to a database, the instructions, when executed by one or more computer processors, cause the one or more computer processors to perform steps comprising:

receiving a target individual dataset associated with a target individual;

identifying a plurality of candidate individual datasets that are potentially related to the target individual dataset;

identifying a related individual dataset from the plurality of candidate individual datasets, wherein the related individual dataset has data bits that match at least a portion of data bits in the target individual dataset, wherein identifying the related individual dataset comprises:

phasing a genotype corresponding to the target individual and a genotype corresponding to the related individual;

identifying identity by descent (IBD) segments shared between the phased genotype of the target individual dataset and the phased genotype of the related individual dataset;

determining a total length of the IBD segments shared between the phased genotype of the target individual dataset and the phased genotype of the related individual dataset; and

determining that the total length of shared IBD segments exceeds a threshold;

identifying a parent node that is a common parent node for both the related individual dataset and the target individual dataset;

retrieving a data tree to which the parent node belongs, the data tree describing inter-relationships among datasets in the data tree;

identifying, based on strings of matched data bits and number of the strings of matched data bits between the target individual dataset and the datasets in the data tree, a descendant position to the common parent node in the data tree to which the target individual dataset is assigned, wherein identifying the descendant position to the common parent node in the data tree comprises:

generating a plurality of candidate data trees that have the individual dataset assigned to different candidate descendant positions to the common parent node, wherein generating the plurality of candidate data trees comprises:

generating a first candidate data tree that is based on the data tree to which the parent node belongs, the first candidate data tree being the data tree with a first new descendant position, the first candidate data tree adding the individual dataset to the first new descendant position, and

generating a second candidate data tree that is based on the data tree to which the parent node belongs, the second candidate data tree being the data tree with a second new descendant position, the second candidate data tree adding the individual dataset to the second new descendant position,

calculating, for each of the candidate data trees with new descendant positions added for the individual dataset to the common parent node, a plurality of pairwise relationship likelihoods, each pairwise relationship likelihood measuring a likelihood between a candidate descendant position and another dataset that also represents a descendant of the common parent node, and

selecting a candidate data tree as the data tree based on the plurality of pairwise relationship likelihoods; and

outputting the data tree with the target individual dataset located in the descendant position.

Assignments (1)
ASSIGNMENT OF ASSIGNOR'S INTEREST Recorded Nov 14, 2022
From: SONG, SHIYA; PEI, JINGWEN; JORGENSEN, BRETT FREDERICK; STERN, AARON JAMES; CURTIS, ROSS E.
To: ANCESTRY.COM DNA, LLC
Reel/Frame 061748/0881 →
Continuity (3)
Continuation 17128009 · Dec 19, 2020
Provisional Application 62951646 · Dec 20, 2019
Related Publication 20220365934A1 · Nov 17, 2022
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