Genetic and genealogical analysis for identification of birth location and surname information
A system identifies ancestral birth locations or surnames estimated to be associated with an individual's ancestors using an individual's genetic sample. The system identifies users who are genetic matches to the individual and determines whether and how often a birth location or surname appears in the pedigrees of those users. Birth locations or surnames that appear frequently throughout the pedigrees of genetically matching users may represent birth locations or surnames that are affiliated with the individual's ancestors. The system determines whether the frequency of appearance of a birth location or surname is statistically significant to eliminate biases for certain birth locations or surnames that appear more frequently than others. The birth location or surname may be provided to the individual based on an also-determined enrichment score.
1. A method comprising:
receiving, from an individual, at least one sequence of genetic data;
accessing pedigrees of a set of users, each pedigree comprising a genealogical graph of relatives for one of the users;
identifying a subset from the set of users, the subset having matching users, each matching user being a genetic match for the individual based on the at least one sequence of genetic data;
determining a match frequency for a target birth location amongst the subset of matching users, determining the match frequency comprising:
examining the pedigrees of the matching users in the subset;
examining, for each matching user, birth locations of relatives in the pedigree of the matching user to determine whether there is at least one of the relatives whose birth location matches the target birth location;
incrementing, for each matching user who has at least one of the relatives whose birth location matches the target birth location, a count of matching users; and
determining the match frequency as a ratio of the count of the matching users over a total number of the matching users in the subset;
determining a background frequency for the target birth location amongst the set of users determining the background frequency comprising:
examining the pedigrees of the users in the set;
examining, for each user, birth locations of relatives in the pedigree of the user to determine whether there is at least one of the relatives whose birth location matches the target birth location;
incrementing, for each user who has at least one of the relatives whose birth location matches the target birth location, a count of users; and
determining the background frequency as a ratio of the count of the users over a total number of the users in the set;
calculating a summary statistic based on the match frequency and the background frequency, the summary statistics increases in magnitude as the difference between the match frequency and the background frequency increases in magnitude;
determining an enrichment score for the birth location based on the summary statistic, the enrichment score representing a significance of the birth location to ancestors of the individual; and
providing the birth location to a computing device based on the determined enrichment score for the birth location.
2. The method of claim 1 wherein the at least one sequence of genetic data comprises a pair of haplotypes for the individual.
3. The method of claim 2 wherein the subset of the set of users are Identity-By-Descent matches based on the pair of haplotypes for the individual and haplotypes of the set of users.
4. The method of claim 1 wherein calculating the summary statistic comprises:
performing a maximum likelihood ratio test under the null hypothesis that the match frequency is equal to the background frequency.
5. The method of claim 1 wherein calculating the summary statistic comprises:
determining a first likelihood of observing the match frequency and the background frequency for the birth location in view of a null hypothesis;
determining a second likelihood of observing the match frequency and the background frequency for the birth location in view of an alternative hypothesis; and
calculating a test statistic based on a ratio between the first likelihood and the second likelihood.
6. The method of claim 1 wherein determining the enrichment score for the birth location based on the summary statistic further comprises:
determining whether the summary statistic is statistically significant relative to a statistical significance level; and
calculating the enrichment score based on the determination.
7. The method of claim 6 wherein the significance level varies based on a country of origin of the birth location.
8. The method of claim 6 wherein the calculated enrichment score is based on the match frequency and the background frequency.
9. A method comprising:
receiving, from an individual, at least one sequence of genetic data;
accessing pedigrees of a set of users, each pedigree comprising a genealogical graph of relatives for one of the users;
identifying a subset from the set of users, the subset having matching users, each matching user being a genetic match for the individual based on the at least one sequence of genetic data;
determining a match frequency for a target surname amongst the subset of matching users, determining the match frequency comprising:
examining the pedigrees of the matching users in the subset;
examining, for each matching user, surnames of relatives in the pedigree of the matching user to determine whether there is at least one of the relatives whose surname matches the target surname;
incrementing, for each matching user who has at least one of the relatives whose surname matches the target surname, a count of matching users; and
determining the match frequency as a ratio of the count of the matching users over a total number of the matching users in the subset;
determining a background frequency for the target surname amongst the set of users, determining the background frequency comprising:
examining the pedigrees of the users in the set;
examining, for each user, surnames of relatives in the pedigree of the user to determine whether there is at least one of the relatives whose surnames matches the target surname;
incrementing, for each user who has at least one of the relatives whose surname matches the target surname, a count of users; and
determining the background frequency as a ratio of the count of the users over a total number of the users in the set;
determining an enrichment score for the surname based on a ratio of the match frequency to the background frequency, the enrichment score representing a significance of the surname to ancestors of the individual wherein the enrichment score increases in magnitude as the difference between the match frequency and the background frequency increases in magnitude; and
providing the surname to a computing device based on the determined enrichment score for the surname.
10. The method of claim 9 wherein the at least one sequence of genetic data comprises a pair of haplotypes for the individual.
11. The method of claim 10 wherein the subset of the set of users are Identity-By-Descent matches based on the pair of haplotypes for the individual and haplotypes of the set of users.
12. The method of claim 9 further comprising:
determining a likelihood of observing the match frequency and the background frequency for the surname in view of a null hypothesis; and
calculating a summary statistic based on the determined likelihood.
13. The method of claim 12 wherein calculating the summary statistic comprises:
performing a maximum likelihood ratio test under the null hypothesis that the match frequency is equal to the background frequency.
14. The method of claim 12 wherein calculating the summary statistic comprises:
determining a first likelihood of observing the match frequency and the background frequency for the surname in view of a null hypothesis;
determining a second likelihood of observing the match frequency and the background frequency for the surname in view of an alternative hypothesis; and
calculating a test statistic based on a ratio between the first likelihood and the second likelihood.
15. The method of claim 14 wherein determining an enrichment score for the surname based on a ratio of the match frequency to the background frequency further comprises:
multiplying the match frequency by a logarithmic ratio between the match frequency and the background frequency.
16. The method of claim 9 wherein determining an enrichment score for the surname based on a ratio of the match frequency to the background frequency further comprises:
determining whether the summary statistic is statistically significant relative to a statistical significance level; and
calculating the enrichment score based on the determination.
17. A non-transitory computer-readable medium comprising computer program code, the computer program code when executed by a processor causing the processor to perform steps comprising:
receiving, from an individual, at least one sequence of genetic data;
accessing pedigrees of a set of users, each pedigree comprising a genealogical graph of relatives for one of the users;
identifying a subset from the set of users, the subset having matching users, each matching user being a genetic match for the individual based on the at least one sequence of genetic data;
determining a match frequency for a target birth location amongst the subset of matching users, determining the match frequency comprising:
examining the pedigrees of the matching users in the subset;
examining, for each matching user, birth locations of relatives in the pedigree of the matching user to determine whether there is at least one of the relatives whose birth location matches the target birth location;
incrementing, for each matching user who has at least one of the relatives whose birth location matches the target birth location, a count of matching users; and
determining the match frequency as a ratio of the count of the matching users over a total number of the matching users in the subset;
determining a background frequency for the target birth location amongst the set of users determining the background frequency comprising:
examining the pedigrees of the users in the set;
examining, for each user, birth locations of relatives in the pedigree of the user to determine whether there is at least one of the relatives whose birth location matches the target birth location;
incrementing, for each user who has at least one of the relatives whose birth location matches the target birth location, a count of users; and
determining the background frequency as a ratio of the count of the users over a total number of the users in the set;
calculating a summary statistic based on the match frequency and the background frequency, the summary statistics increases in magnitude as the difference between the match frequency and the background frequency increases in magnitude;
determining an enrichment score for the birth location based on the summary statistic, the enrichment score representing a significance of the birth location to ancestors of the individual; and
providing the birth location to a computing device based on the determined enrichment score for the birth location.
18. A non-transitory computer-readable medium comprising computer program code, the computer program code when executed by a processor causing the processor to perform steps comprising:
receiving, from an individual, at least one sequence of genetic data;
accessing pedigrees of a set of users, each pedigree comprising a genealogical graph of relatives for one of the users;
identifying a subset from the set of users, the subset having matching users, each matching user being a genetic match for the individual based on the at least one sequence of genetic data;
determining a match frequency for a target surname amongst the subset of matching users, determining the match frequency comprising:
examining the pedigrees of the matching users in the subset;
examining, for each matching user, surnames of relatives in the pedigree of the matching user to determine whether there is at least one of the relatives whose surname matches the target surname;
incrementing, for each matching user who has at least one of the relatives whose surname matches the target surname, a count of matching users; and
determining the match frequency as a ratio of the count of the matching users over a total number of the matching users in the subset;
determining a background frequency for the target surname amongst the set of users, determining the background frequency comprising:
examining the pedigrees of the users in the set;
examining, for each user, surnames of relatives in the pedigree of the user to determine whether there is at least one of the relatives whose surnames matches the target surname;
incrementing, for each user who has at least one of the relatives whose surname matches the target surname, a count of users; and
determining the background frequency as a ratio of the count of the users over a total number of the users in the set;
determining an enrichment score for the surname based on a ratio of the match frequency to the background frequency, the enrichment score representing a significance of the surname to ancestors of the individual wherein the enrichment score increases in magnitude as the difference between the match frequency and the background frequency increases in magnitude; and
providing the surname to a computing device based on the determined enrichment score for the surname.